<?xml version="1.0"?>
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xml:base="http://purl.obolibrary.org/obo/stato/stato.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:terms="http://purl.org/dc/terms/"
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<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/stato.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/stato/releases/2025-02-23/stato.owl"/>
<dc:contributor>Brian Alper (https://orcid.org/000-0003-4300-4928)</dc:contributor>
<dc:contributor>Camille Maumet (http://orcid.org/0000-0002-6290-553X)</dc:contributor>
<dc:contributor>Chris Mungall (http://orcid.org/0000-0002-6601-2165)</dc:contributor>
<dc:contributor>Gavin Lloyd</dc:contributor>
<dc:contributor>Guillaume Bauchet</dc:contributor>
<dc:contributor>Hanna Cwiek (https://orcid.org/0000-0001-9113-567X)</dc:contributor>
<dc:contributor>Harold Lehmann (https://orcid.org/0000-0002-7698-219X)</dc:contributor>
<dc:contributor>Joanne Dehnbostel (https://orcid.org/0000-0002-9896-9842)</dc:contributor>
<dc:contributor>Kenneth Wilkins (https://orcid.org/0000-0003-0531-7165)</dc:contributor>
<dc:contributor>Khalid Shahin (https://orcid.org/0000-0002-3526-7667)</dc:contributor>
<dc:contributor>Nolan Nichols (http://orcid.org/0000-0003-1099-3328)</dc:contributor>
<dc:contributor>Ralf Weber (https://orcid.org/0000-0002-8796-4771)</dc:contributor>
<dc:contributor>Thomas Nichols (http://orcid.org/0000-0002-4516-5103)</dc:contributor>
<dc:creator>Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262)</dc:creator>
<dc:creator>Orlaith Burke</dc:creator>
<dc:creator>Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668)</dc:creator>
<dc:description>STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.</dc:description>
<dc:rights rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">This Ontology is distributed under a Creative Commons Attribution License</dc:rights>
<dc:subject xml:lang="en">Statistical Method, Design of Experiment, Plots, Statistical Model</dc:subject>
<dc:title>STATO: the statistical methods ontology</dc:title>
<terms:license rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://creativecommons.org/licenses/by/3.0/</terms:license>
<doap:bug-database>https://github.com/ISA-tools/stato/issues</doap:bug-database>
<doap:homepage>http://stato-ontology.org/</doap:homepage>
<doap:mailing-list xml:lang="en">stat-ontology@googlegroups.com</doap:mailing-list>
<owl:versionInfo>2025-02-23</owl:versionInfo>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://protege.stanford.edu/plugins/owl/protege#defaultLanguage -->
<owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000179 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000179">
<obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.</obo:IAO_0000115>
<obo:IAO_0000232 xml:lang="en">Really of interest to developers only</obo:IAO_0000232>
<rdfs:label xml:lang="en">BFO OWL specification label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000180 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000180">
<obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2</obo:IAO_0000115>
<obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">Really of interest to developers only</obo:IAO_0000232>
<rdfs:label xml:lang="en">BFO CLIF specification label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<obo:IAO_0000111>editor preferred label</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">editor preferred label</obo:IAO_0000111>
<obo:IAO_0000111>editor preferred term</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
<obo:IAO_0000111>editor preferred term~editor preferred label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor preferred label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
<obo:IAO_0000111 xml:lang="en">example</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">example of usage</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
<obo:IAO_0000111 xml:lang="en">has curation status</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000281</obo:IAO_0000119>
<rdfs:label xml:lang="en">has curation status</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">textual definition</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. </obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
<obo:IAO_0000111 xml:lang="en">editor note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obfoundry.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">term editor</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
<obo:IAO_0000111 xml:lang="en">alternative term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">alternative term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
<obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">definition source</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
<obo:IAO_0000111 xml:lang="en">curator note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note of use for a curator but of no use for a user</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">curator note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000233 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000233">
<obo:IAO_0000111>term tracker item</obo:IAO_0000111>
<obo:IAO_0000112>the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>An IRI or similar locator for a request or discussion of an ontology term.</obo:IAO_0000115>
<obo:IAO_0000117>Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119>Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg</obo:IAO_0000119>
<rdfs:comment>The 'tracker item' can associate a tracker with a specific ontology term.</rdfs:comment>
<rdfs:label xml:lang="en">term tracker item</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
<obo:IAO_0000111 xml:lang="en">imported from</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">For external terms/classes, the ontology from which the term was imported</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">imported from</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000589 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000589">
<obo:IAO_0000111 xml:lang="en">OBO foundry unique label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An alternative name for a class or property which is unique across the OBO Foundry.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBO Foundry <http://obofoundry.org/></obo:IAO_0000119>
<rdfs:label xml:lang="en">OBO foundry unique label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000600 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
<obo:IAO_0000111 xml:lang="en">elucidation</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Barry Smith</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">elucidation</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000601 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000601">
<obo:IAO_0000111 xml:lang="en">has associated axiom(nl)</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">An axiom associated with a term expressed using natural language</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has associated axiom(nl)</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000602 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000602">
<obo:IAO_0000111 xml:lang="en">has associated axiom(fol)</obo:IAO_0000111>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000600 xml:lang="en">An axiom expressed in first order logic using CLIF syntax</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">has associated axiom(fol)</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001847 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001847">
<obo:IAO_0000111 xml:lang="en">ISA alternative term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>An alternative term used by the ISA tools project (http://isa-tools.org).</obo:IAO_0000115>
<obo:IAO_0000116>Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178</obo:IAO_0000116>
<obo:IAO_0000117>Person: Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Person: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>ISA tools project (http://isa-tools.org)</obo:IAO_0000119>
<rdfs:label xml:lang="en">ISA alternative term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/OBI_9991118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OBI_9991118">
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB alternative term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An alternative term used by the IEDB.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB alternative term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001900 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
<rdfs:label xml:lang="en">temporal interpretation</rdfs:label>
<foaf:page rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROAndTime</foaf:page>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000032 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000032">
<obo:IAO_0000115 xml:lang="en">an alternative term used for STATO statistical ontology and ISA team</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">STATO alternative term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000041 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000041">
<obo:IAO_0000115 xml:lang="en">a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">R command</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000391 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000391">
<obo:IAO_0000115 xml:lang="en">an annotation property to provide a canonical command to invoke a method implementation using Python programming language</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">Python command</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000404 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000404">
<obo:IAO_0000115 xml:lang="en">the most common series or system of written mathematical symbols used to represent the entity</obo:IAO_0000115>
<obo:IAO_0000119>AGB</obo:IAO_0000119>
<rdfs:label xml:lang="en">preferred mathematical notation</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor">
<dc:description xml:lang="en-us">Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.</dc:description>
<rdfs:comment xml:lang="en-us">An entity responsible for making contributions to the
content of the resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Contributor</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator">
<dc:description xml:lang="en-us">Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.</dc:description>
<rdfs:comment xml:lang="en-us">An entity primarily responsible for making the content
of the resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Creator</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/date -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date">
<dc:description xml:lang="en-us">Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.</dc:description>
<rdfs:comment xml:lang="en-us">A date associated with an event in the life cycle of the
resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Date</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description">
<dc:description xml:lang="en-us">Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.</dc:description>
<rdfs:comment xml:lang="en-us">An account of the content of the resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Description</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/format -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/format">
<dc:description xml:lang="en-us">Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).</dc:description>
<rdfs:comment xml:lang="en-us">The physical or digital manifestation of the resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Format</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/rights -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/rights"/>
<!-- http://purl.org/dc/elements/1.1/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/source">
<dc:description xml:lang="en-us">The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.</dc:description>
<rdfs:comment xml:lang="en-us">A reference to a resource from which the present resource
is derived.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Source</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/subject -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/subject">
<dc:description xml:lang="en-us">Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.</dc:description>
<rdfs:comment xml:lang="en-us">The topic of the content of the resource.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.org/dc/elements/1.1/"/>
<rdfs:label>Subject and Keywords</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license">
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mark Miller</obo:IAO_0000117>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-05-11T13:47:29Z</dc:date>
<rdfs:label xml:lang="en">license</rdfs:label>
</owl:AnnotationProperty>
<!-- http://usefulinc.com/ns/doap#bug-database -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#bug-database"/>
<!-- http://usefulinc.com/ns/doap#homepage -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#homepage"/>
<!-- http://usefulinc.com/ns/doap#mailing-list -->
<owl:AnnotationProperty rdf:about="http://usefulinc.com/ns/doap#mailing-list"/>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#label">
<obo:IAO_0000111>label</obo:IAO_0000111>
<rdfs:label xml:lang="en">label</rdfs:label>
</rdf:Description>
<!-- http://xmlns.com/foaf/0.1/page -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/page"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Datatypes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.w3.org/2001/XMLSchema#date -->
<rdfs:Datatype rdf:about="http://www.w3.org/2001/XMLSchema#date"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">is part of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is part of my body (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this day is part of this year (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a part and its whole</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
</rdf:Description>
</owl:equivalentProperty>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my body has part my brain (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this year has part this day (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000054 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000054">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000111 xml:lang="en">realized in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this disease is realized in this disease course</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this fragility is realized in this shattering</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator role is realized in this investigation</obo:IAO_0000112>
<obo:IAO_0000118 xml:lang="en">is realized by</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">realized_in</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
<rdfs:comment>Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">realized in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:IAO_0000111 xml:lang="en">realizes</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this disease course realizes this disease</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigation realizes this investigator role</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this shattering realizes this fragility</obo:IAO_0000112>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])</obo:IAO_0000600>
<rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">realizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000062">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">preceded by</obo:IAO_0000111>
<obo:IAO_0000116 xml:lang="en">An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is preceded by</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">preceded_by</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:preceded_by</dc:source>
<rdfs:label xml:lang="en">preceded by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002222"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">precedes</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000039 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000039">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has measurement unit label</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000112 xml:lang="en">This document is about information artifacts and their representations</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">is_about is a (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000 years of philosophy</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000219 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000219">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<obo:IAO_0000112 xml:lang="en">A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment xml:lang="en"></rdfs:comment>
<rdfs:label xml:lang="en">denotes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000221 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000221">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000417"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000417"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000115 xml:lang="en">m is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is quality measurement of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000407 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000407">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/UO_0000001"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment xml:lang="en">relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point</rdfs:comment>
<rdfs:label xml:lang="en">has coordinate unit label</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000413 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000413">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">relates a process to a time-measurement-datum that represents the duration of the process</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is duration of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000417 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000417">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000221"/>
</rdf:Description>
</owl:equivalentProperty>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">inverse of the relation of is quality measurement of</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is quality measured as</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000581 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000581">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has time stamp</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000583 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000583">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
<rdfs:range>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
<owl:Class>
<owl:complementOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">relates a time stamped measurement datum to the measurement datum that was measured</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has measurement datum</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000124 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000124">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001909"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_supported_by_data</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process</obo:IAO_0000115>
<obo:IAO_0000117>OBI</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philly 2011 workshop</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_supported_by_data</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000293 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 xml:lang="en">has_specified_input</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_specified_input</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">see is_input_of example_of_usage</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Coutot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has_specified_input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000295 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000295">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_specified_input_of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is_specified_input_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 xml:lang="en">has_specified_output</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_specified_output</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has_specified_output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 xml:lang="en">is_specified_output_of</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_specified_output_of</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a continuant participating in a planned process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000314 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000314">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_proxy_for</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples:
A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality.
Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
level of radioactivity is_proxy_for level of toxicity</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A relation between continuant instances c1 and c2 where within a protocol
application, measurement of c1 is related to a what would be the
measurement of c2.
(another definition)</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is_proxy_for</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000417 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000417">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000833"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">achieves_planned_objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell sorting process achieves the objective specification 'material separation objective'</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BP, AR, PPPB branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch derived</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">modified according to email thread from 1/23/09 in accordince with DT and PPPB branch</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">achieves_planned_objective</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000643 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000643">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has grain</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has grain</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000833 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000833">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">objective_achieved_by</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.</obo:IAO_0000115>
<obo:IAO_0000117>OBI</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">objective_achieved_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000846 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000846">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000114"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001688"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000245"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is member of organization</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Helen Parkinson</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is member of organization</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001688 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001688">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000245"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000245"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000111 xml:lang="en">has organization member</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Relating an organization to a legal person or organization.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">See tracker:
https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person: Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has organization member</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001927 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001927">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000110"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000111>specifies value of</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>A relation between a value specification and an entity which the specification is about.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>specifies value of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001938 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001938">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000111>has value specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>A relation between an information content entity and a value specification that specifies its value.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: James A. Overton</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>has value specification</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000052 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000052">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<obo:IAO_0000111 xml:lang="en">inheres in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this fragility inheres in this vase</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this red color inheres in this apple</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A dependent inheres in its bearer at all times for which the dependent exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">inheres_in</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">inheres in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000111 xml:lang="en">bearer of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this apple is bearer of this red color</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this vase is bearer of this fragility</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">bearer_of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">is bearer of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">bearer of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">participates in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood clot participates in this blood coagulation</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this input material (or this output material) participates in this process</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator participates in this investigation</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">participates_in</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000057"/>
</owl:propertyChainAxiom>
<obo:IAO_0000111 xml:lang="en">has participant</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood coagulation has participant this blood clot</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigation has participant this investigator</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this process has participant this input material (or this output material)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_participant</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</dc:source>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000058 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">is concretized as</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000059 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000058"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000112 xml:lang="en">A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">concretizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000079 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000079">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000112 xml:lang="en">this catalysis function is a function of this enzyme</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">function_of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">is function of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">function of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000080 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000080">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<obo:IAO_0000112 xml:lang="en">this red color is a quality of this apple</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A quality inheres in its bearer at all times for which the quality exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is quality of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">quality_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">quality of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000081 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000081">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<obo:IAO_0000112 xml:lang="en">this investigator role is a role of this person</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">is role of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">role_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">role of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000085">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000079"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000112 xml:lang="en">this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_function</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has function</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000086 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000086">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000112 xml:lang="en">this apple has quality this red color</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_quality</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has quality</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000087 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000087">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000112 xml:lang="en">this person has role this investigator role (more colloquially: this person has this role of investigator)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_role</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has role</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001000 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001001"/>
</rdf:Description>
</owl:equivalentProperty>
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001001"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">derives from</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this cell derives from this parent cell (cell division)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this nucleus derives from this parent nucleus (nuclear division)</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">derives_from</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">derives from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001001 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001001">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
</rdf:Description>
</owl:equivalentProperty>
<obo:IAO_0000112 xml:lang="en">this parent cell derives into this cell (cell division)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this parent nucleus derives into this nucleus (nuclear division)</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">derives_into</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">derives into</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001015 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001015">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
</rdf:Description>
</owl:equivalentProperty>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">is location of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my head is the location of my brain</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this cage is the location of this rat</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between two independent continuants, the location and the target, in which the target is entirely within the location</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">location_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<rdfs:label xml:lang="en">location of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0001025 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001025">
<owl:equivalentProperty>
<rdf:Description>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0001015"/>
</rdf:Description>
</owl:equivalentProperty>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">located in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is located in my head</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this rat is located in this cage</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between two independent continuants, the target and the location, in which the target is entirely within the location</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">located_in</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</dc:source>
<rdfs:label xml:lang="en">located in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002222 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000116>move to BFO?</obo:IAO_0000116>
<obo:IAO_0000119>Allen</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment>A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.</rdfs:comment>
<rdfs:label xml:lang="en">temporal relation</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000001 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000001">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000004"/>
<obo:IAO_0000115 xml:lang="en">property to indicate that a design declares a variable; the inverse property is 'is declared by'</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">declares</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000004 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000004">
<obo:IAO_0000115 xml:lang="en">property to indicate the variables declared by a design; the inverse property is 'declares'</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">is declared by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000101 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000101">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AsymmetricProperty"/>
<obo:IAO_0000115 xml:lang="en">the relationship between a fraction and the number above the line</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB</obo:IAO_0000119>
<rdfs:label>has numerator</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000102 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000102">
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000055"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0000059"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115 xml:lang="en">relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>AGB</obo:IAO_0000119>
<rdfs:label>executes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000110 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000110">
<obo:IAO_0000112>This is the inverse of 'specifies value of' and it is intended to say things such as 'compound' 'assumes values specified by' 'independent variable specification'</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A relation between an entity and a value specification, where the value specification is about the entity.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>AGB</obo:IAO_0000119>
<rdfs:label xml:lang="en">assumes values specified by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000114 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000114">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000115"/>
<obo:IAO_0000115 xml:lang="en">relationship between an element and a set it belongs to</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB</obo:IAO_0000119>
<rdfs:label xml:lang="en">is member of</rdfs:label>
<rdfs:seeAlso>http://purl.obolibrary.org/obo/RO_0002350</rdfs:seeAlso>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000115 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000115">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000115 xml:lang="en">relationship between a set and one of its elements</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>AGB</obo:IAO_0000119>
<rdfs:label xml:lang="en">has member</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000205 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000205">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<obo:IAO_0000115 xml:lang="en">Inverse relation of 'denotes', where denotation is what happens when someone creates an information content entity E in order to specifically refer to something (from 'denotes' definition).</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">is denoted by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000259 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000259">
<obo:IAO_0000115 xml:lang="en">the relationship between a fraction and the number below the line (or divisor)</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>AGB</obo:IAO_0000119>
<rdfs:label>has denominator</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000341 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000341">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000476"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000751"/>
<obo:IAO_0000115 xml:lang="en">This property is the inverse relationship of 'is model by' and represents the relationship between a dependent variable and an statistical model.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">is model for</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000344 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000344">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/STATO_0000258"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/STATO_0000258"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">'has effect on' is a special case of the 'is about' relationship to be used for mixed effect models</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75
Thus the definition is temporary.
The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed.
Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has effect on</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000345 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000345">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000344"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">'has fixed effect on' is a special case of the 'is about' relationship to be used with fixed effect models</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75
Thus the definition is temporary.
The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed.
Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has fixed effect on</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000380 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000380">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000344"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">'has interaction effect on' is a special case of the 'is about' relationship to be used for mixed effect models</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75
Thus the definition is temporary.
The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed.
Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has interaction effect on</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000381 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000381">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000344"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">'has random effect on' is a special case of the 'is about' relationship to be used for random effect models</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75
Thus the definition is temporary.
The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed.
Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has random effect on</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000382 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000382">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000467"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000468"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000469"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000470"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000115 xml:lang="en">'has order in sequence' is a special case of the 'is about' relation being used to be able to enumerate the different terms within a linear mixed model formula (thus assinging and order to random effect terms, fixed effect terms, interaction effect terms and error terms).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Ćwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has order in sequence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000403 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000403">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/STATO_0000034"/>
<obo:IAO_0000115 xml:lang="en">Relationship between a parameter of a model and the estimate produced by estimation process as used in statistical modeling.</obo:IAO_0000115>
<rdfs:label xml:lang="en">estimate of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000476 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000476">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<obo:IAO_0000115 xml:lang="en">This property is a specialization of the 'is about' property to represent the relationship between a dependent variable and an statistical model.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">is modeled by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000557 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000557">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115 xml:lang="en">computed_from is a relation between 2 information content entity denoting how one is derived from another on through the application of a data transformation or computation process.</obo:IAO_0000115>
<rdfs:label>computed from</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000004 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000004">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topDataProperty"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has measurement value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000404 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000404">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topDataProperty"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has x coordinate value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000406 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000406">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topDataProperty"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has y coordinate value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0001937 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0001937">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002135"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<rdfs:range rdf:resource="http://www.w3.org/2002/07/owl#real"/>
<obo:IAO_0000111>has specified numeric value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>A relation between a value specification and a number that quantifies it.</obo:IAO_0000115>
<obo:IAO_0000116>A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON: James A. Overton</obo:IAO_0000117>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>has specified numeric value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0002135 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0002135">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000111 xml:lang="en">has specified value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>A relation between a value specification and a literal.</obo:IAO_0000115>
<obo:IAO_0000116>This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.</obo:IAO_0000116>
<obo:IAO_0000119>OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has specified value</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.obolibrary.org/obo/STATO_0000129 -->
<owl:DatatypeProperty rdf:about="http://purl.obolibrary.org/obo/STATO_0000129">
<obo:IAO_0000115 xml:lang="en">A relationship (data property) between an entity and its value.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">has value</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<obo:BFO_0000179>entity</obo:BFO_0000179>
<obo:BFO_0000180>Entity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Julius Caesar</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">Verdi’s Requiem</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the Second World War</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your body mass index</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])</obo:IAO_0000600>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:BFO_0000179>continuant</obo:BFO_0000179>
<obo:BFO_0000180>Continuant</obo:BFO_0000180>
<obo:IAO_0000115 xml:lang="en">An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240]</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:BFO_0000179>occurrent</obo:BFO_0000179>
<obo:BFO_0000180>Occurrent</obo:BFO_0000180>
<obo:IAO_0000115 xml:lang="en">An entity that has temporal parts and that happens, unfolds or develops through time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.</obo:IAO_0000116>
<obo:IAO_0000116>Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">occurrent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>ic</obo:BFO_0000179>
<obo:BFO_0000180>IndependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a chair</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a leg</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a molecule</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a spatial region</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an atom</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an orchestra.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the bottom right portion of a human torso</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the interior of your mouth</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000601 xml:lang="en">For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]</obo:IAO_0000602>
<obo:IAO_0000602>(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">independent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
<obo:BFO_0000179>s-region</obo:BFO_0000179>
<obo:BFO_0000180>SpatialRegion</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Spatial regions do not participate in processes.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">spatial region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
<obo:BFO_0000179>2d-s-region</obo:BFO_0000179>
<obo:BFO_0000180>TwoDimensionalSpatialRegion</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">an infinitely thin plane in space.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the surface of a sphere-shaped part of space</obo:IAO_0000112>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">two-dimensional spatial region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:BFO_0000179>process</obo:BFO_0000179>
<obo:BFO_0000180>Process</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a process of cell-division, \ a beating of the heart</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of meiosis</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a process of sleeping</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the course of a disease</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the flight of a bird</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the life of an organism</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">your process of aging.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000602>(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:BFO_0000179>disposition</obo:BFO_0000179>
<obo:BFO_0000180>Disposition</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">an atom of element X has the disposition to decay to an atom of element Y</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">certain people have a predisposition to colon cancer</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">children are innately disposed to categorize objects in certain ways.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the cell wall is disposed to filter chemicals in endocytosis and exocytosis</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">disposition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:BFO_0000179>realizable</obo:BFO_0000179>
<obo:BFO_0000180>RealizableEntity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the disposition of this piece of metal to conduct electricity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of your blood to coagulate</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of your reproductive organs</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of this boundary to delineate where Utah and Colorado meet</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]</obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">realizable entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
<obo:BFO_0000179>0d-s-region</obo:BFO_0000179>
<obo:BFO_0000180>ZeroDimensionalSpatialRegion</obo:BFO_0000180>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">zero-dimensional spatial region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:BFO_0000179>quality</obo:BFO_0000179>
<obo:BFO_0000180>Quality</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the ambient temperature of this portion of air</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the color of a tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the length of the circumference of your waist</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mass of this piece of gold.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nose</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of your nostril</obo:IAO_0000112>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">quality</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>sdc</obo:BFO_0000179>
<obo:BFO_0000180>SpecificallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of one-sided specifically dependent continuants: the mass of this tomato</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the disposition of this fish to decay</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of this heart: to pump blood</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of proton donors and acceptors in chemical reactions [79</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pink color of a medium rare piece of grilled filet mignon at its center</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of being a doctor</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the shape of this hole.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the smell of this portion of mozzarella</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000602>(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]</obo:IAO_0000602>
<obo:IAO_0000602>(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]</obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:isDefinedBy xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<obo:BFO_0000179>role</obo:BFO_0000179>
<obo:BFO_0000180>Role</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the priest role</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a boundary to demarcate two neighboring administrative territories</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a building in serving as a military target</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of a stone in marking a property boundary</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the role of subject in a clinical trial</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the student role</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
<obo:BFO_0000179>1d-s-region</obo:BFO_0000179>
<obo:BFO_0000180>OneDimensionalSpatialRegion</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">an edge of a cube-shaped portion of space.</obo:IAO_0000112>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">one-dimensional spatial region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000028">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
<obo:BFO_0000179>3d-s-region</obo:BFO_0000179>
<obo:BFO_0000180>ThreeDimensionalSpatialRegion</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a cube-shaped region of space</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a sphere-shaped region of space,</obo:IAO_0000112>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">three-dimensional spatial region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:BFO_0000179>gdc</obo:BFO_0000179>
<obo:BFO_0000180>GenericallyDependentContinuant</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000602>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:BFO_0000179>function</obo:BFO_0000179>
<obo:BFO_0000180>Function</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">the function of a hammer to drive in nails</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of a heart pacemaker to regulate the beating of a heart through electricity</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the function of amylase in saliva to break down starch into sugar</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])</obo:IAO_0000600>
<obo:IAO_0000602>(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:BFO_0000179>material</obo:BFO_0000179>
<obo:BFO_0000180>MaterialEntity</obo:BFO_0000180>
<obo:IAO_0000112 xml:lang="en">a flame</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a forest fire</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a human being</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a hurricane</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a photon</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a puff of smoke</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a sea wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a tornado</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an aggregate of human beings.</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an energy wave</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">an epidemic</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">the undetached arm of a human being</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000600 xml:lang="en">A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])</obo:IAO_0000600>
<obo:IAO_0000601 xml:lang="en">Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])</obo:IAO_0000601>
<obo:IAO_0000601 xml:lang="en">every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])</obo:IAO_0000601>
<obo:IAO_0000602>(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] </obo:IAO_0000602>
<obo:IAO_0000602>(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] </obo:IAO_0000602>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">material entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000141">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<obo:BFO_0000179>immaterial</obo:BFO_0000179>
<obo:BFO_0000180>ImmaterialEntity</obo:BFO_0000180>
<obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<rdfs:label xml:lang="en">immaterial entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_16670 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_16670">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33839"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">peptide</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">peptide</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_16991 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_16991">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">deoxyribonucleic acid</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">deoxyribonucleic acid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_23367 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular entity</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33250 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33250">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">atom</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A chemical entity constituting the smallest component of an element having the chemical properties of the element.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">atom</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33696 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33696">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33839"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33697 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33697">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ribonucleic acid</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ribonucleic acid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33839 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33839">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">macromolecule</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">polymer</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/chebi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">macromolecule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">cell</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/cl.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000578"/>
<rdfs:subClassOf>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600036"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600036"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cultured cell</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell in vitro that is or has been maintained or propagated as part of a cell culture.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/cl.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cultured cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CL_0000578 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000578">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">experimentally modified cell in vitro</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/cl.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">experimentally modified cell in vitro</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0003674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003674">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular_function</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:molecular_function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0003824 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0003824">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0003674"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalytic activity</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">catalytic activity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0008150 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0008150">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">biological_process</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">biological_process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0010467 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0010467">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0008150"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gene expression</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gene expression</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/GO_0043234 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0043234">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PR_000000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein complex</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A ribosome is a protein complex</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/go.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein complex</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000111 xml:lang="en">conditional specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a directive information entity that specifies what should happen if the trigger condition is fulfilled</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">OBI_0000349</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">conditional specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000009"/>
<obo:IAO_0000111 xml:lang="en">measurement unit label</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of measurement unit labels are liters, inches, weight per volume.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">measurement unit label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000111 xml:lang="en">objective specification</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Answers the question, why did you do this experiment?</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">goal specification</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process/Roles Branch</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">OBI_0000217</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">objective specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000112 xml:lang="en">Pour the contents of flask 1 into flask 2</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a directive information entity that describes an action the bearer will take</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">action specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">datum label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">GROUP: IAO</obo:IAO_0000117>
<obo:IAO_0000232>9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">datum label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000015">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000390"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">information carrier</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A quality of an information bearer that imparts the information content</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.</obo:IAO_0000116>
<obo:IAO_0000116>2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000 years of philosophy</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">information carrier</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">data item</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Data items include counts of things, analyte concentrations, and statistical summaries.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.</obo:IAO_0000116>
<obo:IAO_0000116>2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Jonathan Rees</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">data</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data item</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000028">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">symbol</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">a serial number such as "12324X"</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a stop sign</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">a written proper name such as "OBI"</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">20091104, MC: this needs work and will most probably change</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: James A. Overton</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Jonathan Rees</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">based on Oxford English Dictionary</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">symbol</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">information content entity</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of information content entites include journal articles, data, graphical layouts, and graphs.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A generically dependent continuant that is about some thing.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000142</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">information content entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001938"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001931"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000004"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">10 feet. 3 ml.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">scalar measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An information content entity whose concretizations indicate to their bearer how to realize them in a process.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">directive information entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000037">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000111 xml:lang="en">dot plot</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Dot plot of SSC-H and FSC-H.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
<obo:IAO_0000115 xml:lang="en">A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Allyson Lister</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000123</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">dot plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000038 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000038">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000309"/>
<obo:IAO_0000111 xml:lang="en">graph</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Allyson Lister</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000240</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">graph</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000055 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000055">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000001"/>
<obo:IAO_0000111 xml:lang="en">rule</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">example to be added</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">a rule is an executable which guides, defines, restricts actions</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PRS</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0500021</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PRS</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">rule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000064 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000064">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
<obo:IAO_0000111 xml:lang="en">algorithm</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000270</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">algorithm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000078">
<owl:equivalentClass>
<owl:Class>
<owl:oneOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000002"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000120"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000121"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000122"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000123"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000124"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000423"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000428"/>
</owl:oneOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
<obo:IAO_0000111 xml:lang="en">curation status specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">OBI_0000266</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">curation status specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000100 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000100">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">data set</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type</obo:IAO_0000116>
<obo:IAO_0000116>2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Allyson Lister</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000042</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000101 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000101">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000308"/>
<obo:IAO_0000111 xml:lang="en">image</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Allyson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000030</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">image</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000102 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000115 xml:lang="en">data about an ontology part is a data item about a part of an ontology, for example a term</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data about an ontology part</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000104">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000007"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">plan specification</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2014-03-31: A plan specification can have other parts, such as conditional specifications.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process branch</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">OBI_0000344</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment xml:lang="en">2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them</rdfs:comment>
<rdfs:label xml:lang="en">plan specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000109 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000109">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001938"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">measurement datum</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 is_specified_output of some assay?</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI_0000305</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000129 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000129">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
<obo:IAO_0000111 xml:lang="en">version number</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">GROUP: IAO</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">version number</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000144 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000144">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000300"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001909"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000124"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000338"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">conclusion textual entity</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009/10/23 Alan Ruttenberg: We need to work on the definition still</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">conclusion textual entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000184 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000184">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000111 xml:lang="en">scatter plot</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Comparison of gene expression values in two samples can be displayed in a scatter plot</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">scattergraph</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Scatterplot</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">scatter plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000300 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000300">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">textual entity</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">text</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">textual entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000306 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000306">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000300"/>
<obo:IAO_0000111 xml:lang="en">table</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">| T F
--+-----
T | T F
F | F F</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000308 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000308">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">figure</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Any picture, diagram or table</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">figure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000309 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000309">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000308"/>
<obo:IAO_0000111 xml:lang="en">diagram</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A figure that expresses one or more propositions</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">diagram</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000310 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000310">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">document</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A journal article, patent application, laboratory notebook, or a book</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A collection of information content entities intended to be understood together as a whole</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Lawrence Hunter</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">document</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000400 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000400">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000407"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000232>AR notes: We need to discuss whether it should include site.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cartesian spatial coordinate datum</rdfs:label>
<rdfs:seeAlso xml:lang="en">http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000401 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000401">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000026"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000404"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">one dimensional cartesian spatial coordinate datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000402 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000402">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000009"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000404"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000406"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">two dimensional cartesian spatial coordinate datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000414 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000414">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UO_0000002"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000221"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000125"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A scalar measurement datum that is the result of measurement of mass quality</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">mass measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000416 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000416">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UO_0000003"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000413"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A scalar measurement datum that is the result of measuring a temporal interval</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">time measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000572 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000572">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a planned process in which a document is created or added to by including the specified input in it.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">wikipedia http://en.wikipedia.org/wiki/Documenting</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">documenting</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000573 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000573">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000656"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000657"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">line graph</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A line graph is a type of graph created by connecting a series of data
points together with a line.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">line chart</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Line_chart</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">line graph</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000577 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000577">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000578"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bill Hogan</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000118>CRID symbol</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Original proposal from Bjoern, discussions at IAO calls</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">centrally registered identifier symbol</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000578 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000578">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bill Hogan</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000118>CRID</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Original proposal from Bjoern, discussions at IAO calls</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">centrally registered identifier</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000579 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000579">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000112 xml:lang="en">PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bill Hogan</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000118>CRID registry</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Original proposal from Bjoern, discussions at IAO calls</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">centrally registered identifier registry</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000582 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000582">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000581"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000583"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">time stamped measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000584 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000584">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">pmid:20604925 - time-lapse live cell microscopy</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">experimental time series</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">time sampled measurement data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Viruses</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Viruses</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_117571 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_117571">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7742"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Euteleostomi</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bony vertebrates</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Euteleostomi</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_2 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacteria</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">eubacteria</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bacteria</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_2157 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2157">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Archaea</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Archaea</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_2759 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2759">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eukaryota</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">eucaryotes</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">eukaryotes</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Eukaryota</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_314146 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_314146">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_40674"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Euarchontoglires</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Euarchontoglires</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_32523 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_32523">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_117571"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tetrapoda</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tetrapods</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tetrapoda</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_32524 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_32524">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_32523"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Amniota</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">amniotes</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Amniota</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_33154 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33154">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Opisthokonta</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Opisthokonta</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_33213 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_33213">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33154"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bilateria</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bilateria</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_40674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_40674">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_32524"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mammalia</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mammals</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mammalia</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_7742 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_7742">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33213"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vertebrata <Metazoa></obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vertebrata</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">vertebrates</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Vertebrata <Metazoa></rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_314146"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homo sapiens</obo:IAO_0000111>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human being</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">man</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ncbitaxon.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Homo sapiens</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<obo:IAO_0000111 xml:lang="en">fluorescent reporter intensity</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">fluorescent reporter intensity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000111 xml:lang="en">planned process</obo:IAO_0000111>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">planned process</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Injecting mice with a vaccine in order to test its efficacy</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A processual entity that realizes a plan which is the concretization of a plan specification.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">branch derived</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6/11/9: Edited at workshop. Used to include: is initiated by an agent</obo:IAO_0000232>
<obo:IAO_0000232 xml:lang="en">This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">planned process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 xml:lang="en">biological feature identification objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">biological feature identification objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000047 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000047">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">processed material</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Is a material entity that is created or changed during material processing.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">processed material</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000066 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000066">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000572"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000338"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000471"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000339"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">investigation</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Could add specific objective specification</obo:IAO_0000232>
<obo:IAO_0000232 xml:lang="en">Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core
editor = PRS</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study</obo:OBI_0001847>
<rdfs:label xml:lang="en">investigation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000067 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000067">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">evaluant role</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">evaluant role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000070 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000070">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">assay</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.</obo:IAO_0000115>
<obo:IAO_0000116>12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. </obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">measuring</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">scientific observation</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study assay</obo:OBI_0001847>
<obo:OBI_9991118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">any method</obo:OBI_9991118>
<rdfs:label xml:lang="en">assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000071 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000071">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000609"/>
<obo:IAO_0000111 xml:lang="en">quantitative confidence value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data item which is used to indicate the degree of uncertainty about a measurement.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">quantitative confidence value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000079 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000079">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">culture medium</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178
Modification made by JZ.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person: Jennifer Fostel, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">culture medium</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000086 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000086">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">reagent role</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Buffer, dye, a catalyst, a solvating agent.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">reagent</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Matthew Brush</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment>(copied from ReO)
Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.
Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.
In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).</rdfs:comment>
<rdfs:label xml:lang="en">reagent role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000094 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000094">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000456"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material processing</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell lysis, production of a cloning vector, creating a buffer.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A planned process which results in physical changes in a specified input material</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Philippe Rocca Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">material transformation</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">material processing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000097 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000097">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000471"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">study subject role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.</obo:IAO_0000115>
<obo:IAO_0000116>A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">GROUP: Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">Following OBI call November 2012,26th:
1. it was decided there was no need for moving the children class and making them siblings of study subject role.
2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study
This note closes the issue and validates the class definition to be part of the OBI core
editor = PRS
</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">participant under investigation role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000112 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000112">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000659"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specimen role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">specimen role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000113 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000113">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000015"/>
<obo:IAO_0000111 xml:lang="en">sequence feature identification objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">sequence feature identification objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000115 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000115">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0500000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000931"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/OBI_0300311"/>
<obo:IAO_0000111 xml:lang="en">intervention design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philppe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">intervention design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000118 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000118">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000111 xml:lang="en">gene list</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">gene list</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000131 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000131">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000015"/>
<obo:IAO_0000111 xml:lang="en">molecular feature identification objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">molecular feature identification objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000164 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000164">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000731"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600064"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000731"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">cDNA library</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID:6110205. collection of cDNA derived from mouse splenocytes.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Luisa Montecchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP: PSI</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cDNA library</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000181">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">population</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area</obo:IAO_0000115>
<obo:IAO_0000116>1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms:
http://code.google.com/p/popcomm-ontology/</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Oxford English Dictionnary</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">rem1: collection somehow always involve a selection process</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000185 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000185">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000101"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">imaging assay</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">imaging assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000245 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000245">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">organization</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Susanna Sansone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">organization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000250 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000250">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/REO_0000171"/>
<obo:IAO_0000111 xml:lang="en">dye role</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. </obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dye</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A substance used to color materials www.answers.com/topic/dye 19feb09</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">dye role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000272 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000272">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
<obo:IAO_0000111 xml:lang="en">protocol</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study protocol</obo:OBI_0001847>
<rdfs:label xml:lang="en">protocol</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000274 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000274">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000434"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000652"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000319"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000444"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000319"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001025"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000444"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adding a material entity into a target</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BP</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">adding a material entity into a target</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000275 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000275">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002444"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_33250"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000443"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">analyte role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glucose in blood (measured in an assay to determine the concentration of glucose).</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">qualities such as weight, color are not assayed but measured, so they do not fall into this category.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">analyte role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000319 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000319">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material to be added role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">drug added to a buffer contained in a tube; substance injected into an animal;</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">9 March 09 from discussion with PA branch</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">material to be added role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000338 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000338">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001909"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">interpreting data</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">drawing a conclusion based on data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000339 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000339">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">planning</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a process of creating or modifying a plan specification</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. </obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Plans and Planned Processes Branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">planning</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000367 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000367">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000374"/>
<obo:IAO_0000111 xml:lang="en">light emission function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">light emission function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000370 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000370">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">contain function</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A syringe, a beaker</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A contain function is a function to constrain a material entities location in space</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">contain function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000371 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000371">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">heat function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A heat function is a function that increases the internal kinetic energy of a material</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">heat function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000372 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000372">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">material separation function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">material separation function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000374 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000374">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">excitation function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">excitation function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000378 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000378">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000372"/>
<obo:IAO_0000111 xml:lang="en">filter function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">filter function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000387 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000387">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">cool function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cool function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000399 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000399">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">solid support function</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Taped, glued, pinned, dried or molecularly bonded to a solid support</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">solid support function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000401 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000401">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<obo:IAO_0000111 xml:lang="en">environment control function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bill Bug</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">environment control function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000403 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000403">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000372"/>
<obo:IAO_0000111 xml:lang="en">sort function</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">sort function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000411 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000411">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000319"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600064"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cloning vector role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">pBluescript plays the role of a cloning vector</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.</obo:IAO_0000115>
<obo:IAO_0000116>JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cloning vector role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000416 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000416">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cloning insert role</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
<obo:IAO_0000115 xml:lang="en">cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: Role branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBII and Wikipedia</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cloning insert role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000423 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000423">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0302884"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">extract</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">an extract is a material entity which results from an extraction process</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">extracted material</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI Biomatrial Branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">extract</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000424 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000424">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001331"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000443"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000275"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0010467"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transcription profiling assay</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">gene expression profiling</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transcription profiling</obo:OBI_0001847>
<rdfs:label xml:lang="en">transcription profiling assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000425 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000425">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">averaging objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">averaging objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000427 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000427">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_33697"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0043234"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PR_000000001"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0043234"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PR_000000001"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0003824"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">enzyme</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">person: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP:OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">enzyme</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000434 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000434">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000686"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adding material objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">creating a mouse infected with LCM virus</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BP</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">adding material objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000435 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000435">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001305"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000443"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000275"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16991"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16991"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001305"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000113"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">genotyping assay</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">an assay which generates data about a genotype from a specimen of genomic DNA. A variety of
techniques and instruments can be used to produce information about sequence variation at particular genomic positions.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">genotype profiling, SNP genotyping</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI Biomaterial</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SNP analysis</obo:OBI_0001847>
<rdfs:label xml:lang="en">genotyping assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000437 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000437">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">analyte measurement objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to measure the concentration of glucose in a blood sample</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an assay objective to determine the presence or concentration of an analyte in the evaluant</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">analyte measurement objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000441 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000441">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">assay objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">the objective to determine the weight of a mouse.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">assay objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000443 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000443">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000437"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000275"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">analyte assay</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.</obo:IAO_0000115>
<obo:IAO_0000116>2013-09-23: simplify equivalent axiom</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum
and
('has measurement unit label' some 'measurement unit label') and
('is quality measurement of' some 'molecular concentration'))</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">analyte assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000444 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000444">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000274"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">target of material addition role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">target of material addition role is a role realized by an entity into which a material is added in a material addition process</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: Role Branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">target of material addition role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000451 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000451">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200169"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">normalized data set</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data set that is produced as the output of a normalization data transformation.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">normalized data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000453 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000453">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000079"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:allValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
</owl:Restriction>
</owl:allValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">measure function</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A glucometer measures blood glucose concentration, the glucometer has a measure function.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">measure function</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000456 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000456">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material transformation objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an objective specifiction that creates an specific output object from input materials.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Jennifer Fostel</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">artifact creation objective</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI PlanAndPlannedProcess Branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">material transformation objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000471 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000471">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design execution</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process that carries out a study design</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.</obo:IAO_0000116>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">branch derived</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design execution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000626 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000626">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_16991"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001573"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA sequencing</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI Branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleotide sequencing</obo:OBI_0001847>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA sequencing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000639 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000639">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000678"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000681"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000456"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material separation objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is an objective to transform a material entity into spatially separated components.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material separation objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000648 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000648">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200175"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">clustered data set</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A clustered data set is the output of a K means clustering data transformation</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">data set with assigned discovered class labels</obo:IAO_0000118>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AR thinks could be a data item instead</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">clustered data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000649 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000649">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200184"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">data set of features</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data set of features</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000650 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000650">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200031"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">differential expression analysis data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB:</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">differential expression analysis data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000652 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000652">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000686"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material combination</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is a material processing with the objective to combine two or more material entities as input into a single material entity as output.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bp</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bp</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material combination</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000659 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000659">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000684"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specimen collection process</obo:IAO_0000111>
<obo:IAO_0000112>drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A planned process with the objective of collecting a specimen.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.</obo:IAO_0000116>
<obo:IAO_0000116>Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.</obo:IAO_0000116>
<obo:IAO_0000116>Philly2013: The specimen_role for the specimen is created during the specimen collection process.</obo:IAO_0000116>
<obo:IAO_0000116>label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000118>specimen collection</obo:IAO_0000118>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession</obo:IAO_0000232>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6/9/09: used at workshop</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specimen collection process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000662 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000662">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000668"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">error corrected data set</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">error corrected data set</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000668 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000668">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200186"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">error correction data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EDITORS</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">error correction data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000671 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000671">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600005"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000740"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000747"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001479"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sample from organism</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a material obtained from an organism in order to be a representative of the whole</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">5/29: This is a helper class for now</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sample from organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000673 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000673">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001834"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000116"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000207"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000472"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000585"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">statistical hypothesis test</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119>http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032>NHST</obo:STATO_0000032>
<obo:STATO_0000032>Null Hypothesis Statistical Testing</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">statistical hypothesis testing</obo:STATO_0000032>
<rdfs:label xml:lang="en">statistical test hypothesis</rdfs:label>
<rdfs:seeAlso>https://www.wikidata.org/wiki/Q210832</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000674">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000574"/>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200181"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000152"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">center value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">median</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">center value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000675 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000675">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000288"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">statistical hypothesis test objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation </obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hypothesis test objective</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">statistical hypothesis test objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000678 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000678">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000639"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">portioning objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to obtain multiple aliquots of an enzyme preparation.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">portioning objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000679 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000679">
<owl:equivalentClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000573"/>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200170"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">average value</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">arithmetic mean</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">average value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000681 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000681">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000639"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">separation into different composition objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to obtain cells contained in a sample of blood.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives</obo:IAO_0000116>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">separation into different composition objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000684 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000684">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specimen collection objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A objective specification to obtain a material entity for potential use as an input during an investigation.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">specimen collection objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000686 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000686">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000456"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material combination objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is an objective to obtain an output material that contains several input materials.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PPPB branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bp</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material combination objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000722 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000722">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paired-end library</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mate-paired library</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paired-end tag (PET) library</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adapted from information provided by Solid web site</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paired-end library</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000727 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000727">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200171"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200175"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000648"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200178"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200172"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">k-nearest neighbors</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">k-NN</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">k-nearest neighbors</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000731 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000731">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600064"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">recombinant vector</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">recombinant vector</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000736 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000736">
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">single fragment library</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fragment library</obo:IAO_0000118>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">single fragment library</rdfs:label>
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cloning vector</obo:IAO_0000111>
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<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.</obo:IAO_0000115>
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Student's t-test</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>t-test</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WEB: http://en.wikipedia.org/wiki/T-test</obo:IAO_0000119>
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<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Student's t-test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0000740 -->
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material sample role</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.</obo:IAO_0000116>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material sample role</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0000744 -->
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material sampling process</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity</obo:IAO_0000115>
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<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material sampling process</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0000747 -->
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<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material entity that has the material sample role</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI: workshop</obo:IAO_0000117>
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<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sample</obo:OBI_0001847>
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<!-- http://purl.obolibrary.org/obo/OBI_0000750 -->
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">independent variable specification</obo:IAO_0000111>
<obo:IAO_0000112>In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.</obo:IAO_0000116>
<obo:IAO_0000116>In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling</obo:IAO_0000116>
<obo:IAO_0000116>an independent variable is a variable which assumes only values set by the operator according to a plan and which are expected to (or are being tested for) influence the ranges of values assumed by one or more dependent variables (also known as 'response variables').</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000118>experimental factor</obo:IAO_0000118>
<obo:IAO_0000118>independent variable</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.</obo:IAO_0000232>
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<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study factor</obo:OBI_0001847>
<obo:STATO_0000032 xml:lang="en">explanatory variable</obo:STATO_0000032>
<obo:STATO_0000032>factor</obo:STATO_0000032>
<rdfs:label xml:lang="en">study design independent variable</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0000751 -->
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dependent variable specification</obo:IAO_0000111>
<obo:IAO_0000112>In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.</obo:IAO_0000116>
<obo:IAO_0000116>In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000118>dependent variable</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en">response variable</obo:STATO_0000032>
<rdfs:label xml:lang="en">study design dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000789 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000789">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000047"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000047"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">survival rate</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A rate that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Oliver He</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adapted from wikipedia
http://en.wikipedia.org/wiki/Survival_rate</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">survival rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000791 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000791">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200186"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">multiple testing correction objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Application of the Bonferroni correction</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">multiple comparison correction objective</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Multiple_Testing_Correction</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">multiple testing correction objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000806 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000806">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material maintenance objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An objective specification maintains some or all of the qualities of a material over time.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material maintenance objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000811 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000811">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000058"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16991"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primary structure of DNA macromolecule</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">placeholder for SO</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BP et al</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primary structure of DNA macromolecule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000832 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000832">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000968"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000453"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">measurement device</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A ruler, a microarray scanner, a Geiger counter.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A device in which a measure function inheres.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP:OBI Philly workshop</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">measurement device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000838 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000838">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000806"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material maintenance</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a process with that achieves the objective to maintain some or all of the characteristics of an input material over time</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material maintenance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000848 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000848">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0666666"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">polyA RNA extraction</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person: Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UPenn Group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">polyA RNA extraction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000861 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000861">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000140"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Likelihood-ratio test</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">date: March 2013
AGB and PRS provide formal definition expressed the test in terms of output and input, specifying the nature of the variables, the purpose of the test and the distribution used.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzales-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tina Boussard</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000041 xml:lang="en">lrtest()
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/lrtest.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Likelihood-ratio test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000889 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000889">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000789"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000789"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200194"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">survival curve</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: http://www.graphpad.com/www/book/survive.htm</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">survival curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000916 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000916">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001977"/>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000034"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400044"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400044"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001501"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001977"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flow cytometry assay</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flow cytometry assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000924 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000924">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/REO_0000280"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600038"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000953"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001936"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled specimen</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A specimen that has been modified in order to be able to detect it in future experiments</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">added during call 3/1/2010</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI group</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled specimen</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000931 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000931">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000471"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000115"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study intervention</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">the part of the execution of an intervention design study which is varied between two or more subjects in the study</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study intervention</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000932 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000932">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000372"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material separation device</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flow cytometer</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A device with a separation function realized in a planed process</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material separation device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000938 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000938">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001938"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001930"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">categorical measurement datum</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A measurement datum that is reported on a categorical scale</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nominal mesurement datum</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters
</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">categorical measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000953 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000953">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">processed specimen</obo:IAO_0000111>
<obo:IAO_0000112>A tissue sample that has been sliced and stained for a histology study.
A blood specimen that has been centrifuged to obtain the white blood cells.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A specimen that has been intentionally physically modified.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment>A tissue sample that has been sliced and stained for a histology study.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">processed specimen</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000963 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000963">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000009"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">categorical label</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">categorical label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000964 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000964">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in live cell assay</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An assay in which a measurement is made by observing entities located in a live cell.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">in live cell assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000967 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000967">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000370"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">container</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A device that can be used to restrict the location of material entities over time</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">container</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000968 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000968">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000034"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">device</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A voltmeter is a measurement device which is intended to perform some measure function.</obo:IAO_0000112>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform.
2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:
(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.
(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.
(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.
In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. </obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">instrument</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI development call 2012-12-17.</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000973 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000973">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence data</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">sequence data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000984 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000984">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dose</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An organism has been injected 1ml of vaccine</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dose</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000423"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000953"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0666667"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid extract</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UPenn Group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid extract</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001032">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000367"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">light emission device</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a device which has a function to emit light.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">light emission device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001034">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000371"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000387"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000401"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">environmental control device</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A growth chamber is an environmental control device.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">environmental control device</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001143 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000924"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0600038"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001010"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled nucleic acid extract</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person: Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled extract</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MO_221 labeledExtract</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled extract</obo:OBI_0001847>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeled nucleic acid extract</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001172 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001172">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000984"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000751"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dose response curve</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. </obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Bjoern Peters; Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra, Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">dose response curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001225 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001225">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001404"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001305"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">genetic population background information</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a genetic characteristics information which is a part of genotype information that identifies the population of organisms</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">proposed and discussed on San Diego OBI workshop, March 2011</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Group: OBI group</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Group: OBI group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">genetic population background information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001265 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001265">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000662"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200066"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FWER adjusted p-value</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Addition of restriction 'output of null hypothesis testing' and specified output by AGB and PRS while working on STATO</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERS:Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) </obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032>Family-wise type I error rate</obo:STATO_0000032>
<rdfs:label xml:lang="en">FWER adjusted p-value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001271 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001271">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000424"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000848"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000275"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000973"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0010467"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001331"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">RNA-seq assay</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">transcription profiling by high throughput sequencing</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">EFO_0002770 transcription profiling by high throughput sequencing</obo:IAO_0000119>
<obo:IAO_0000232>JZ: should be inferred as 'DNA sequencing'. Will check in the future.</obo:IAO_0000232>
<obo:IAO_0000232 xml:lang="en">an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
WEB: http://en.wikipedia.org/wiki/RNA-Seq</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">RNA-seq assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001305 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001305">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001404"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001225"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001364"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">genotype information</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">discussed on San Diego OBI workshop, March 2011</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Group: OBI group</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Group: OBI group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">genotype information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001331 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001331">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000131"/>
<obo:IAO_0000111 xml:lang="en">transcription profiling identification objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A molecular feature identification objective that aims to characterize the abundance of transcripts</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person: Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Group: Penn Group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">transcription profiling identification objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001352 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001352">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001364"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001305"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SO_0000001"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">allele information</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">discussed on San Diego OBI workshop, March 2011</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Person: Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MO_58 Allele</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">allele information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001364 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001364">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001404"/>
<obo:IAO_0000111 xml:lang="en">genetic alteration information</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">proposed and discussed on San Diego OBI workshop, March 2011</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Group: OBI group</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Group: OBI group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">genetic alteration information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001404 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001404">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SO_0000001"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000058"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_33696"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">genetic characteristics information</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person: Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO_66 IndividualGeneticCharacteristics</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">MO definition:
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
examples in ArrayExpress
wild_type
MutaMouse (CD2F1 mice with lambda-gt10LacZ integration)
AlfpCre; SNF5 flox/knockout
p53 knock out
C57Bl/6 gp130lox/lox MLC2vCRE/+
fer-15; fem-1
df/df
pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">genetic characteristics information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001442 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001442">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000662"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200036"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200049"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">q-value</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines.
"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant.
To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERS:Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FDR adjusted p-value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Adapted from several sources, including
http://.en/wikipedia.org/wiki/False_discovery_rate
http://svitsrv25.epfl.ch/R-doc/library/qvalue.html</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000404>q</obo:STATO_0000404>
<rdfs:label xml:lang="en">q-value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001444 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001444">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000113"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000058"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000435"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000090"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001305"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">genotyping design</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person: Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO_560 genotyping_design</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">genotyping design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001479 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001479">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000477"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
<obo:IAO_0000111 xml:lang="en">specimen from organism</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">tissue specimen</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MO_954 organism_part</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">specimen from organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001501 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001501">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000018"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000018"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fluorescence detection assay</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An assay in which a material's fluorescence is determined.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fluorescence detection assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001554 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001554">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rate measurement datum</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A scalar measurement datum that represents the number of events occuring over a time interval</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern Peters, Randi Vita</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rate measurement datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001573 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001573">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000973"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000811"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA sequence data</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The part of a FASTA file that contains the letters ACTGGGAA </obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence data item that is about the primary structure of DNA</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI call; Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI call; Melanie Courtout</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. </obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DNA sequence data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001755 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001755">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000111 xml:lang="en">selection criterion</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">rats should be aged between 6 and 8 weeks and weight between 180-250grams</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A directive information entity which defines and states a principle of standard by which selection process may take place.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">selection rule</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">selection criterion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001834 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001834">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000144"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>drawing a conclusion</obo:IAO_0000111>
<obo:IAO_0000112>Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle.
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting.
</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>A planned process in which new information is inferred from existing information.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>drawing a conclusion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001865 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001865">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000968"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000399"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">assay array</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119>Penn Group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">assay array</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001909 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001909">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000124"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000338"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>conclusion based on data</obo:IAO_0000111>
<obo:IAO_0000112>The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting.
The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>An information content entity that is inferred from data.</obo:IAO_0000115>
<obo:IAO_0000116>In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. </obo:IAO_0000116>
<obo:IAO_0000117>Group:2013 Philly Workshop group</obo:IAO_0000117>
<obo:IAO_0000119>Group:2013 Philly Workshop group</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>conclusion based on data</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001912 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001912">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell freezing medium</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. </obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cell freezing medium</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001930 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001930">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<obo:IAO_0000111>categorical value specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>A value specification that is specifies one category out of a fixed number of nominal categories</obo:IAO_0000115>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>categorical value specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001931 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001931">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001933"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001937"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>scalar value specification</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>A value specification that consists of two parts: a numeral and a unit label</obo:IAO_0000115>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>scalar value specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001933 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001933">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111>value specification</obo:IAO_0000111>
<obo:IAO_0000112>The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>An information content entity that specifies a value within a classification scheme or on a quantitative scale.</obo:IAO_0000115>
<obo:IAO_0000116>This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label>value specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001936 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001936">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/REO_0000280"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600038"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular-labeled material</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000119>OBI developer call, 3-12-12</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular-labeled material</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001977 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001977">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000067"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytometry assay</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An assay that measures properties of cells.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cytometry assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0002089 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002089">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000401"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000967"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001034"/>
<obo:IAO_0000111 xml:lang="en">physical store</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">a freezer. a humidity controlled box.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A container with an environmental control function.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Duke Biobank, OBIB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<dc:source xml:lang="en">Biobank</dc:source>
<rdfs:label xml:lang="en">physical store</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0002444 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002444">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">measurand role</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.</obo:IAO_0000115>
<obo:IAO_0000117>Person: Alan Ruttenberg, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wiktionary.org/wiki/measurand</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/778</obo:IAO_0000233>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">measurand role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">organism</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">animal</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">fungus</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">plant</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">virus</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: OBI Biomaterial Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Organism</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100051">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000112"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 xml:lang="en">specimen</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A material entity that has the specimen role.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP: OBI Biomaterial Branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">specimen</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100060">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600024"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CL_0000010"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CL_0000010"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cultured cell population</obo:IAO_0000111>
<obo:IAO_0000112>A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000118>cell culture sample</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Matthew Brush</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.</rdfs:comment>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cultured cell population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100064 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100064">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<obo:IAO_0000111 xml:lang="en">screening library</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application
change biomaterial to material in definition</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP: IEDB</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7/13/09: Need to clarify if this meets reagent role definition</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">screening library</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200000">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000064"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">data transformation</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A planned process that produces output data from input data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Richard Scheuermann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Ryan Brinkman</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tina Hernandez-Boussard</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">data analysis</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">data processing</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Branch editors</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">differential expression analysis objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">differential expression analysis objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200163"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000662"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001442"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000791"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">Benjamini and Hochberg false discovery rate correction method</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2011-03-31: [PRS].
specified input and output of dt which were missing</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">Benjamini and Hochberg false discovery rate correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200041 -->
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200172"/>
</owl:Restriction>
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<obo:IAO_0000111 xml:lang="en">k-means clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/K-means</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">k-means clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200042 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200042">
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<owl:Restriction>
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</owl:Restriction>
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</owl:Class>
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<obo:IAO_0000111 xml:lang="en">hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200043 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200043">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200154"/>
<obo:IAO_0000111 xml:lang="en">average linkage hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">average linkage hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200044 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200044">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200154"/>
<obo:IAO_0000111 xml:lang="en">complete linkage hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">complete linkage hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200045 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200045">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200154"/>
<obo:IAO_0000111 xml:lang="en">single linkage hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">single linkage hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200163"/>
<rdfs:subClassOf>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001442"/>
</owl:Restriction>
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<obo:IAO_0000111 xml:lang="en">Benjamini and Yekutieli false discovery rate correction method</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2011-03-31: [PRS].
specified input and output of dt which were missing</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">Benjamini and Yekutieli false discovery rate correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200050 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200050">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200175"/>
<rdfs:subClassOf>
<owl:Class>
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</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200178"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
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<obo:IAO_0000111 xml:lang="en">dimensionality reduction</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">data projection</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">dimensionality reduction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200050"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000556"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
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<rdfs:subClassOf>
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</owl:Restriction>
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<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">principal components analysis dimensionality reduction</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">pca data reduction</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">principal components analysis dimensionality reduction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200066 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200066">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200073"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001265"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000791"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">Holm-Bonferroni family-wise error rate correction method</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition
Also added restriction to specify the output to be a FWER adjusted p-value
The 'editor preferred term' should be removed</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032>Bonferroni adjustment method</obo:STATO_0000032>
<rdfs:label xml:lang="en">Holm-Bonferroni family-wise error rate correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200073 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200073">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001265"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200089"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000791"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">family wise error rate correction method</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2011-03-31: [PRS].
creating a defined class by specifying the necessary output of dt
allows correct classification of FWER dt</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FWER correction</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">family wise error rate correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200078">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">descriptive statistical calculation objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Monnie McGee</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">descriptive statistical calculation objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200083 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200083">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">survival analysis objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Kaplan meier data transformation</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Tina Boussard</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">survival analysis</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Survival_analysis</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">survival analysis objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200089 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200089">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000791"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000668"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">multiple testing correction method</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">multiple testing procedure</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">multiple testing correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200094 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200094">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200169"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200167"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">logarithmic transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: http://en.wikipedia.org/wiki/Logarithm</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">logarithmic transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200102 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200102">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Class>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000119"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000218"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000107"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000751"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">regression analysis method</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Date:2013-11-15
Person: AGB,PRS
Adding restrictions, specifying model + parameter estimation process
change of label from 'regression analysis method' to 'regression analysis'</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tina Hernandez-Boussard</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en">regression analysis</obo:STATO_0000032>
<rdfs:label xml:lang="en">regression analysis method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200104">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200175"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000648"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200178"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">principal component regression</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Tina Hernandez-Boussard</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">principal component regression</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200111 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200111">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000101"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:allValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000101"/>
</owl:unionOf>
</owl:Class>
</owl:allValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">data visualization</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Generation of a heatmap from a microarray dataset</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An planned process that creates images, diagrams or animations from the input data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tina Boussard</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">data encoding as image</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">visualization</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Tina Boussard</obo:IAO_0000119>
<obo:IAO_0000232 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Possible future hierarchy might include this:
information_encoding
>data_encoding
>>image_encoding</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data visualization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200117 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200117">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200181"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200184"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000674"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200177"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000033"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200078"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">mode calculation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Monnie McGee</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">mode calculation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200119 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200119">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200181"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200184"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000674"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200177"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000574"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200078"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">median calculation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: Monnie McGee</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">median calculation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200154 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200154">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200042"/>
<obo:IAO_0000111 xml:lang="en">agglomerative hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">bottom-up hierarchical clustering</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">agglomerative hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200155 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200155">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200042"/>
<obo:IAO_0000111 xml:lang="en">divisive hierarchical clustering</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">top-down hierarchical clustering</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">divisive hierarchical clustering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200163 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200163">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001442"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200089"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000791"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">false discovery rate correction method</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">2011-03-31: [PRS].
creating a defined class by specifying the necessary output of dt
allows correct classification of FDR dt</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Monnie McGee</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FDR correction method</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">false discovery rate correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200166 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200166">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
<obo:IAO_0000111 xml:lang="en">data transformation objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">normalize objective</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An objective specification to transformation input data into output data</obo:IAO_0000115>
<obo:IAO_0000116>Modified definition in 2013 Philly OBI workshop</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data transformation objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200167 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200167">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">data normalization objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Helen Parkinson</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">data normalization objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200168 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200168">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">correction objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Type I error correction</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie Courtot</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">correction objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200169 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200169">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000451"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200167"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">normalization data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A normalization data transformation is a data transformation that has objective normalization.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">normalization data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200170 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200170">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000679"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000425"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">averaging data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">An averaging data transformation is a data transformation that has objective averaging.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">averaging data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200171 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200171">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200172"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">partitioning data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A partitioning data transformation is a data transformation that has objective partitioning.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">partitioning data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200172 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200172">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">partitioning objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Elisabetta Manduchi</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">partitioning objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200175">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000648"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200178"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">class discovery data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">clustering data transformation</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">unsupervised classification data transformation</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">class discovery data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200177 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200177">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">center calculation objective</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">center calculation objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200178 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200178">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200166"/>
<obo:IAO_0000111 xml:lang="en">class discovery objective</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">clustering objective</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">discriminant analysis objective</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">unsupervised classification objective</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Elisabetta Manduchi</obo:IAO_0000119>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">class discovery objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200181">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000674"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200177"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">center calculation data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A center calculation data transformation is a data transformation that has objective of center calculation.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">center calculation data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200184 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200184">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000649"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200078"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 xml:lang="en">descriptive statistical calculation data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">descriptive statistical calculation data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200186 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200186">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200168"/>
<obo:IAO_0000111 xml:lang="en">error correction objective</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Application of a multiple testing correction method</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">James Malone, Helen Parkinson</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">error correction objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200191 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200191">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000306"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000118"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gene list visualization</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">gene list visualization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200194 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200194">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200083"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">survival analysis data transformation</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data transformation which has the objective of performing survival analysis.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">survival analysis data transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200200 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200200">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">chi square test</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">negociation with OBI hence definition and definition source are missing from this class</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: James Malone</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Tina Boussard</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">chi square test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0200201 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200201">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000086"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
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<owl:Class>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
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</owl:Class>
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ANOVA</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB and PRS augmented the class with formal definitions as part of STATO extension</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James Malone</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>Analysis of Variance</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">stat.anova()</obo:STATO_0000041>
<rdfs:label xml:lang="en">ANOVA</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0300311 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0300311">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000111 xml:lang="en">observation design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">observation design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0302884 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302884">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600014"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000681"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">extraction</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid extraction using phenol chloroform</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material separation in which a desired component of an input material is separated from the remainder</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity.
'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">extraction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0302900 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302900">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600015"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group randomization</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">group randomization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0302903 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302903">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
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<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000034"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400110"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
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<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleic acid hybridization</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:OBI_0001847 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hybridization assay</obo:OBI_0001847>
<rdfs:label xml:lang="en">nucleic acid hybridization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400043 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400043">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000967"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000370"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flow cell</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Biofilm Flow Cell</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Person:John Quinn</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">flow_cell</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">flow cell</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400044 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400044">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400137"/>
<rdfs:subClassOf>
<owl:Class>
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</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400065"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400079"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400082"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400078"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0400153"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">flow cytometer</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">FACS Calibur</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">John Quinn</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Flow_cytometer</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">flow cytometer</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400065 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400065">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001032"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000367"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">light source</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Elizabeth M. Goralczyk</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">John Quinn</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Olga Tchuvatkina</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">light source</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400078">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000932"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000378"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">obscuration bar</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">obscuration bar in a flow cytometer</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">John Quinn</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">obscuration bar</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400079 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400079">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000932"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000378"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">optical filter</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">720 LP filter, 580/30 BP filter</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">John Quinn</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Optical_filter</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">optical filter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400082 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400082">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000832"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000453"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">photodetector</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">A photomultiplier tube, a photo diode</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">John Quinn</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://einstein.stanford.edu/content/glossary/glossary.html</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">photodetector</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0400103 -->
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<obo:IAO_0000111 xml:lang="en">DNA sequencer</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">ABI 377 DNA Sequencer, ABI 310 DNA Sequencer</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Trish Whetzel</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO</obo:IAO_0000119>
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<rdfs:label xml:lang="en">DNA sequencer</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0400110 -->
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<obo:IAO_0000111 xml:lang="en">hybridization chamber</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Glass Array Hybridization Cassette</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Trish Whetzel</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO_563 hybridization_chamber</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">hybridization chamber</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0400137 -->
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<obo:IAO_0000111 xml:lang="en">cytometer</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A cytometer is an instrument for counting and measuring cells.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://medical.merriam-webster.com/medical/cytometer</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">cytometer</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400147 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400147">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001865"/>
<obo:IAO_0000111 xml:lang="en">microarray</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris Stoeckert</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">microarray</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400148 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400148">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400147"/>
<obo:IAO_0000111 xml:lang="en">DNA microarray</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Frank Gibson</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">DNA Chip</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">DNA-array</obo:IAO_0000118>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">DNA microarray</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0400153 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400153">
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<obo:IAO_0000111 xml:lang="en">droplet sorter</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original
sample for particles of interest based on qualities determined by gating) or disposal.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI Instrument branch</obo:IAO_0000117>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI Instrument branch</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">droplet sorter</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0500000 -->
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<owl:equivalentClass>
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</owl:Restriction>
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<obo:IAO_0000111 xml:lang="en">study design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris Stoeckert</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">experimental design</obo:IAO_0000118>
<obo:IAO_0000232 xml:lang="en">rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">study design</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0500002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000115"/>
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</owl:Restriction>
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<obo:IAO_0000111 xml:lang="en">repeated measure design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.holah.karoo.net/experimentaldesigns.htm</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">repeated measure design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0500003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000115"/>
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500020"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000046"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000248"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
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<obo:IAO_0000111 xml:lang="en">cross over design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">cross over design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0500005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500005">
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<obo:IAO_0000111 xml:lang="en">matched pairs design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.</obo:IAO_0000112>
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<obo:IAO_0000115 xml:lang="en">A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.holah.karoo.net/experimentaldesigns.htm</obo:IAO_0000119>
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<obo:IAO_0000111 xml:lang="en">parallel group design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.</obo:IAO_0000112>
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<obo:IAO_0000115 xml:lang="en">A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">independent measure design</obo:IAO_0000118>
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<obo:IAO_0000111 xml:lang="en">randomized complete block design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))</obo:IAO_0000112>
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<obo:IAO_0000115 xml:lang="en">A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.tufts.edu/~gdallal/ranblock.htm</obo:IAO_0000119>
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<obo:IAO_0000111 xml:lang="en">latin square design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and</obo:IAO_0000119>
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<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">latin square design</rdfs:label>
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<obo:IAO_0000111 xml:lang="en">graeco latin square design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Greco-Latin square design is a study design which relates to Latin square design</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">only 2 articles in pubmed ->probably irrelevant</obo:IAO_0000232>
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<obo:STATO_0000032 xml:lang="en">Euler square design</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">orthogonal latin squares design</obo:STATO_0000032>
<rdfs:label xml:lang="en">graeco latin square design</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0500013 -->
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<obo:IAO_0000111 xml:lang="en">hyper graeco latin square design</obo:IAO_0000111>
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<obo:IAO_0000115 xml:lang="en">PRS to do</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">no example found in pubmed->not in use in the community</obo:IAO_0000232>
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<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">hyper graeco latin square design</rdfs:label>
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<obo:IAO_0000111 xml:lang="en">factorial design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)</obo:IAO_0000119>
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<rdfs:label xml:lang="en">factorial design</rdfs:label>
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<obo:IAO_0000111 xml:lang="en">2x2 factorial design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PMID: 17561240</obo:IAO_0000119>
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<rdfs:label xml:lang="en">2x2 factorial design</rdfs:label>
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<obo:IAO_0000111 xml:lang="en">fractional factorial design</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control</obo:IAO_0000119>
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<rdfs:label xml:lang="en">fractional factorial design</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/OBI_0500017 -->
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<obo:IAO_0000111 xml:lang="en">dye swap design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra on behalf of MO</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO_858</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">dye swap design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0500020 -->
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<obo:IAO_0000111 xml:lang="en">time series design</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Groups of assays that are related as part of a time series.</obo:IAO_0000115>
<obo:IAO_0000116>PRS-AGB adding formal restriction on independent variable specification about time (march 2013) and making time series design class a defined class.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra on behalf of MO</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">MO_887</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">time series design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600005">
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000684"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">collecting specimen from organism</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">collecting specimen from organism</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600014">
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000639"/>
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</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
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<rdfs:subClassOf>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">material component separation</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a material processing in which components of an input material become segregated in space</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">material component separation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
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</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">group assignment</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">group assignment is a process which has an organism as specified input and during which a role is assigned</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cohort assignment</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study assignment</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI Plan</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">group assignment</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000838"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100060"/>
</owl:Restriction>
</rdfs:subClassOf>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001912"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000806"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">maintaining cell culture</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">maintaining cell culture</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CL_0000000"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000079"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000456"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>'establishing cell culture'</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).</obo:IAO_0000115>
<obo:IAO_0000117>PERSON:Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000119>PERSON:Matthew Brush</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:comment>A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.</rdfs:comment>
<rdfs:label>establishing cell culture</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600038 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600038">
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_1110109"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/REO_0000280"/>
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</rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">addition of molecular label</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Matthew Brush</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">labeling</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI developer call, 3-12-12</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">addition of molecular label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600047 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600047">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000973"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000441"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
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<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_16991"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_33697"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/PR_000000001"/>
</owl:unionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">sequencing assay</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">the use of a chemical or biochemical means to infer the sequence of a biomaterial</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">has_output should be sequence of input; we don't have sequence well defined yet</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0600064 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600064">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000094"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000411"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000737"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000416"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000731"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000456"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">recombinant vector cloning</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">pa_branch (Alan, Randi, Kevin, Jay, Bjoern)</obo:IAO_0000117>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">molecular cloning</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">recombinant vector cloning</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0666666 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0666666">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0666667"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33697"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">RNA extraction</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A RNA extraction is a nucleic acid extraction where the desired output material is RNA</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">requested by Helen Parkinson for MO</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">RNA extraction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0666667 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0666667">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302884"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000671"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100060"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">nucleic acid extraction</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a material separation to recover the nucleic acid fraction of an input material</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess Branch</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">requested by Helen Parkinson for MO. Could be defined class</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">nucleic acid extraction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_1000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000731"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600064"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000643"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000731"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111 xml:lang="en">phage display library</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">display library</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">WEB: http://www.immuneepitope.org/home.do</obo:IAO_0000119>
<obo:IAO_0000232 xml:lang="en">PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction</obo:IAO_0000232>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">phage display library</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_1110108 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1110108">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000319"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material to be added</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A mixture of peptides that is being added into a cell culture.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a material that is added to another one in a material combination process</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export</obo:IAO_0000116>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes</obo:IAO_0000116>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material to be added</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_1110109 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1110109">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000444"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">target of material addition</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A cell culture into which a mixture of peptides is being added.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A material entity into which another is being added in a material combinatino process</obo:IAO_0000115>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.</obo:IAO_0000116>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IEDB</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">target of material addition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OGMS_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000111>phenotype</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
<rdfs:label>phenotype</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fluorescence</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fluorescence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PATO_0000125 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/PR_000000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PR_000000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_16670"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein</obo:IAO_0000111>
<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">antithrombin III is a protein</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pr.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">protein</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/REO_0000171 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/REO_0000171">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000111 xml:lang="en">molecular label role</obo:IAO_0000111>
<obo:IAO_0000115>a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.</obo:IAO_0000115>
<obo:IAO_0000116>MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)</obo:IAO_0000116>
<obo:IAO_0000118>molecular tracer role</obo:IAO_0000118>
<obo:IAO_0000119>OBI developer call, 3-12-12</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/reo.owl"/>
<rdfs:label xml:lang="en">molecular label role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/REO_0000280 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/REO_0000280">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/REO_0000171"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_23367"/>
<obo:IAO_0000111>molecular label</obo:IAO_0000111>
<obo:IAO_0000115>a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay</obo:IAO_0000115>
<obo:IAO_0000118>molecular tracer</obo:IAO_0000118>
<obo:IAO_0000119>OBI developer call, 3-12-12</obo:IAO_0000119>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/reo.owl"/>
<rdfs:label>molecular label</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/SO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">region</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">primary structure of sequence macromolecule</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">sequence</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">region</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000112 xml:lang="en">digital images may be stored as electronic file in TIFF format on mass memory storage devices</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">digital file</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a balanced design is a an experimental design where all experimental group have the an equal number of subject observations</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">balanced design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000005">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000750"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a single factor design is a study design which declares exactly 1 independent variable</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">single factor design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000011"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">x-axis is a cartesian coordinate axis which is orthogonal to the y-axis and the z-axis</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">x-axis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an axis is a line graph used as reference line for the measurement of coordinates.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.oxforddictionaries.com/definition/english/axis</obo:IAO_0000119>
<rdfs:label xml:lang="en">axis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000008 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">y-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the z-axis</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">y-axis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000009 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Cartesian_coordinate_system</obo:IAO_0000119>
<rdfs:label xml:lang="en">cartesian coordinate system</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000010 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Coordinate_system</obo:IAO_0000119>
<rdfs:label xml:lang="en">coordinate system</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000011 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a cartesian axis is one of 3 the axis in a cartesian coordinate system defining a referential in 3 dimensions. each of the axis is orthogonal to the other 2</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">rectangular coordinate axis</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from Wolfram Alpha:
https://www.wolframalpha.com/input/?i=cartesian+coordinates&lk=4&num=6&lk=4&num=6</obo:IAO_0000119>
<rdfs:label xml:lang="en">cartesian coordinate axis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000012 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000011"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">z-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the y-axis</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">z-axis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000009"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">two dimensional cartesian coordinate system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000014">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000226"/>
<obo:IAO_0000115 xml:lang="en">In mathematics, a spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Spherical_coordinate_system</obo:IAO_0000119>
<rdfs:label xml:lang="en">spherical coordinate system</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000010"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Cylindrical_coordinate_system</obo:IAO_0000119>
<rdfs:label xml:lang="en">cylindrical coordinate system</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000010"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Polar_coordinate_system</obo:IAO_0000119>
<rdfs:label xml:lang="en">polar coordinate system</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Wilks' lambda distribution (named for Samuel S. Wilks), is a probability distribution used in multivariate hypothesis testing, especially with regard to the likelihood-ratio test and Multivariate analysis of variance. It is a multivariate generalization of the univariate F-distribution, and generalizes the F-distribution in the same way that the Hotelling's T-squared distribution generalizes Student's t-distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">wikipedia:
last accessed: 2013-09-11
http://en.wikipedia.org/wiki/Wilks%27_lambda_distribution</obo:IAO_0000119>
<rdfs:label xml:lang="en">Wilk's lambda distribution</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000018 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum chosen as a fixed point of reference in a three dimensional spatial region.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">three dimensional cartesian spatial coordinate origin</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000058"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">normal distribution hypothesis is a goodness of fit hypothesis stating that the distribution computed from the sample population fits a normal distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">normal distribution hypothesis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000020 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum chosen as a fixed point of reference in a two dimensional spatial region.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">two dimensional cartesian spatial coordinate origin</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000021">
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0002135"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">90</owl:hasValue>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a confidence interval which covers 90% of the sampling distribution, meaning that there is a 90% risk of false positive (type I error)</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">90% confidence interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000009"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000006"/>
</owl:Restriction>
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</owl:Restriction>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A one dimensional cartesian coordinate system is a cartesian coordinate system which defines a one dimensional axis and which may be used to describe a one dimensional spatial region, i.e. a straight line. It is defined by a point O, the origin, a unit of length and the orientation for the one dimensional space.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">one dimensional cartesian coordinate system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<obo:IAO_0000112 xml:lang="en">http://www.stat.duke.edu/courses/Spring98/sta110c/qtable.html</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The studentized range (q) distribution is a probability distribution used by the Tukey Honestly Significant Difference test.
The distribution of the statistic
[x̄(k)- x̄(1)]/(s/√n)
where random samples of size n have been taken from k independent and identically distributed normal populations, with x̄(1) and x̄(k) being, respectively, the smallest and largest of the k sample means, and s2 being the pooled estimate of the common variance. This statistic is particularly used in multiple comparison tests.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">q distribution</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">A Dictionary of Statistics (2 rev ed.), OUP. ISBN-13: 9780199541454
http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1588</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Tukey.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">studentized range distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000009"/>
<rdfs:subClassOf>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000012"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">three dimensional cartesian coordinate system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000025 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000025">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000026"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum chosen as a fixed point of reference in a one dimensional spatial region.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">one dimensional cartesian spatial coordinate origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum chosen as a fixed point of reference in a spatial region.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">placeholder, more work needed</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">cartesian spatial coordinate origin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000027">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000121"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">linkage between 2 categorical variable test is a statistical test which evaluates if there is an association between a predictor variable assuming discrete values and a response variable also assuming discrete values</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">test of association</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">test of independence</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">test of independence between variables</obo:STATO_0000032>
<rdfs:label xml:lang="en">test of association between categorical variables</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000028">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032>measure of variation</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">measure of variation</obo:STATO_0000032>
<rdfs:label xml:lang="en">measure of dispersion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a measure of central tendency is a data item which attempts to describe a set of data by identifying the value of its centre.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032>measure of central tendency</obo:STATO_0000032>
<rdfs:label xml:lang="en">measure of central tendency</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000609"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000148"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">Chi-Squared statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">binary classification (or binomial classification) is a data transformation which aims to cast members of a set into 2 disjoint groups depending on whether the element have a given property/feature or not.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Binary_classifier
last accessed: 2013-11-21</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">binomial classification</obo:STATO_0000032>
<rdfs:label xml:lang="en">binary classification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000033">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200117"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000649"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000674"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000574"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The mode is a data item which corresponds to the most frequently occurring number in a set of numbers.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.sagepub.com/upm-data/47775_ch_3.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">mode</obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">scipy.stats.mode(a, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mode.html#scipy.stats.mode
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L586</obo:STATO_0000391>
<rdfs:label xml:lang="en">mode</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000466"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000265"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a model parameter is a data item which is part of a model and which is meant to characterize an theoritecal or unknown population. a model parameter may be estimated by considering the properties of samples presumably taken from the theoritecal population</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">model parameter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the range is a measure of variation which describes the difference between the lowest score and the highest score in a set of numbers (a data set)</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.sagepub.com/upm-data/47775_ch_3.pdf</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">range(..., na.rm = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/base/html/range.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">range</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Outliers are deviant scores that have been legitimately gathered and are not due to equipment failures.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.sagepub.com/upm-data/47775_ch_3.pdf</obo:IAO_0000119>
<rdfs:label xml:lang="en">outlier</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000037">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000562"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000401"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000403"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://stats.stackexchange.com/questions/50623/r-calculating-mean-and-standard-error-of-mean-for-factors-with-lm-vs-direct</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The standard error of the mean (SEM) is data item denoting the standard deviation of the sample-mean's estimate of a population mean.
It is calculated by dividing the sample standard deviation (i.e., the sample-based estimate of the standard deviation of the population) by the square root of n , the size (number of observations) of the sample.
A measure of dispersion applied to means across hypothetical repeated random samples.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Muhammad Afzal, Xing Song, Kenneth Wilkins, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SEM</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia (https://en.wikipedia.org/wiki/Standard_error)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">SEM</obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">scipy.stats.sem(a, axis=0, ddof=1)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.sem.html#scipy.stats.sem
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1928</obo:STATO_0000391>
<rdfs:label xml:lang="en">standard error of the mean</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000037</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000038 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000038">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000139"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a set of 2 subjects which result from a pairing process which assigns subject to a set based on a pairing rule/criteria</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">possibly submit to 'Population and Community Ontology'</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">matched pair of subjects</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000039 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">statistic</obo:STATO_0000032>
<rdfs:label xml:lang="en">statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000184"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000188"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000105"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000210"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200094"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200191"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000650"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an MA plot is a scatter plot of the log intensity ratios M = log_2(T/R) versus the average log intensities A = log_2(T*T)/2, where T and R represent the signal intensities in the test and reference channels respectively.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">M vs A plot</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.stat.berkeley.edu/users/terry/zarray/Software/SMAcode/html/plot.mva.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">MA plot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">plot.mva()</obo:STATO_0000041>
<rdfs:label xml:lang="en">MA plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000042 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000042">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">The Anderson–Darling test is a statistical test of whether a given sample of data is drawn from a given probability distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
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http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.anderson.html#scipy.stats.anderson
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<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
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<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Multi-way anova is an analysis of variance where the difference groups being compared are associated to the factor levels of more than 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">multiway ANOVA</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000058"/>
<obo:IAO_0000112>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581961/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hardy-Weinberg equilibrium hypothesis is a good of fit hypothesis which states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences (non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive).</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label>Hardy-Weinberg equilibrium hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000050 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000050">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
last accessed: 2013-10-18</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">S/N</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">SNR</obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.signaltonoise.html#scipy.stats.signaltonoise</obo:STATO_0000391>
<rdfs:label xml:lang="en">signal to noise ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000117"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function.
The expected value of a Poisson-distributed random variable is equal to λ and so is its variance.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dpois(x, lambda, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.poisson.html#scipy.stats.poisson</obo:STATO_0000391>
<dc:source xml:lang="en">NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm</dc:source>
<rdfs:label xml:lang="en">Poisson distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000052 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000052">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<rdfs:subClassOf>
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<owl:someValuesFrom>
<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000019"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000376"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Z-test is a statistical test which evaluate the null hypothesis that the means of 2 populations are equal and returns a p-value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://reference.wolfram.com/mathematica/ref/ZTest.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">simple.z.test(x, sigma, conf.level=0.95)
http://www.inside-r.org/packages/cran/UsingR/docs/simple.z.test</obo:STATO_0000041>
<rdfs:label xml:lang="en">Z-test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000053 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000053">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PRS,AGB adapted from wikipedia and wolfram alpha</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">significance level</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">type I error rate</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">α</obo:STATO_0000032>
<rdfs:label xml:lang="en">false positive rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000054 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000054">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000226"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">homoskedasticity states that all variances under consideration are homogenous.</obo:IAO_0000115>
<obo:IAO_0000116>definition edited according to the discussion documented in:
https://github.com/ISA-tools/stato/issues/39</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">equality of variance</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">homoskedasticity hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000055 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000055">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000197"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000129"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/assembly/model/
chrX:35,000,000-36,000,000.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">chromosome coordinate system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000056 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000056">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000121"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a null hypothesis which states that no linkage exists between 2 categorical variables</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">no relationship between the variables</obo:STATO_0000032>
<obo:STATO_0000032>variables are independent</obo:STATO_0000032>
<rdfs:label xml:lang="en">absence of association hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000057 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000057">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/STATO_0000208"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A null hypothesis is a statistical hypothesis that is tested for possible rejection under the assumption that it is true (usually that observations are the result of chance). The concept was introduced by R. A. Fisher.
The hypothesis contrary to the null hypothesis, usually that the observations are the result of a real effect, is known as the alternative hypothesis.[wolfram alpha]</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/NullHypothesis.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">null hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000058 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000058">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">goodness of fit hypothesis is a null hypothesis stating that the distribution computed from the sample population fits a theoretical distribution or that a dataset can be correctly explained by a model</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">goodness of fit hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000059 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000059">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000329"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000435"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000500"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000068"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Student's t distribution is a continuous probability distribution which arises when estimating the mean of a normally distributed population in situations where the sample size is small and population standard deviation is unknown.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Student's_t-distribution)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">t distribution</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dt(x, df, ncp, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TDist.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.t.html#scipy.stats.t</obo:STATO_0000391>
<rdfs:label xml:lang="en">Student's t distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000060">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000117"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">hypergeometric distribution is a probability distribution that describes the probability of k successes in n draws from a finite population of size N containing K successes without replacement</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Hypergeometric_distribution</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dhyper(x, m, n, k, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.hypergeom.html#scipy.stats.hypergeom</obo:STATO_0000391>
<rdfs:label xml:lang="en">hypergeometric distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000061 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000061">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">It is a null hypothesis stating that there are no differences observed between group of subjects.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">absence of between group difference hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000062 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000253"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">is a null hypothesis stating that there are no difference observed across a series of measurements made one same subject.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">absence of within subject difference hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000063 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000063">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">genomic coordinate datum is a data item which denotes a genomic position expressed using a genomic coordinate system</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">genomic coordinate datum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000064 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000064">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000811"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000626"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>http://left.subtree.org/2012/04/13/counting-the-number-of-reads-in-a-bam-file/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>sequence read count is a data item determining how many sequence reads have been generated by a DNA sequencing assay for a given stretch of DNA</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>AGB-PRS, STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">sequence read count</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000065 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000065">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">In statistics, a statement that can be tested.[wolfram alpha]</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/Hypothesis.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000066 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000066">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000037"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Cleveland dot plot is a dot plot which plots points that each belong to one of several categories. They are an alternative to bar charts or pie charts, and look somewhat like a horizontal bar chart where the bars are replaced by a dots at the values associated with each category. Compared to (vertical) bar charts and pie charts, Cleveland argues that dot plots allow more accurate interpretation of the graph by readers by making the labels easier to read, reducing non-data ink (or graph clutter) and supporting table look-up.which</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
http://en.wikipedia.org/wiki/Dot_plot_(statistics)
and
Cleveland, William S. (1993). Visualizing Data. Hobart Press. ISBN 0-9634884-0-6. hdl:2027/mdp.39015026891187.</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/dotchart.html
dotchart(x, labels = NULL, groups = NULL, gdata = NULL,
cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"),
color = par("fg"), gcolor = par("fg"), lcolor = "gray",
xlim = range(x[is.finite(x)]),
main = NULL, xlab = NULL, ylab = NULL, ...)</obo:STATO_0000041>
<rdfs:label>Cleveland dot plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000067 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000067">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a continuous probability distribution is a probability distribution which is defined by a probability density function</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution
last accessed:
14/01/2014</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">continuous probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000068 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000068">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Skewness is a data item indicating of the degree of asymmetry of a distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/Skewness.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">skewness(x, na.rm = FALSE, type = 3)
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/e1071/html/skewness.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.skew.html#scipy.stats.skew</obo:STATO_0000391>
<rdfs:label xml:lang="en">skewness</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000069 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000069">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">AGB: Addressing issue https://github.com/ISA-tools/stato/issues/77, removed 'number of degrees of freedom' subClassOf 'count' and added 'number of degrees of freedom' subClassOf 'measurement datum' instead.
For more details, see https://stats.stackexchange.com/questions/116511/explanation-for-non-integer-degrees-of-freedom-in-t-test-with-unequal-variances</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Ćwiek</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://stats.stackexchange.com/questions/16921/how-to-understand-degrees-of-freedom</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.optique-ingenieur.org/en/courses/OPI_ang_M07_C01/co/Contenu_07.html</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">the rank of the quadratic form (mathematical definition)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">degrees of freedom</obo:STATO_0000032>
<rdfs:label xml:lang="en">number of degrees of freedom</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000070 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000070">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000081"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000138"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000229"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000121"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Yate's corrected Chi-Squared test is a statistical test which is used to test the association/linkage/independence of 2 dichotomous variables while introducing a correction for using the continous Chi-squared distribution for the test.
To reduce the error in approximation, Frank Yates, an English statistician, suggested a correction for continuity that adjusts the formula for Pearson's chi-squared test by subtracting 0.5 from the difference between each observed value and its expected value in a 2 × 2 contingency table. This reduces the chi-squared value obtained and thus increases its p-value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Yates's_correction_for_continuity) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Yate's correction for continuity</obo:STATO_0000032>
<obo:STATO_0000041>chisq.test(x, y = NULL, correct = TRUE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Yate's corrected Chi-Squared test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000071 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000071">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">reaction rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000072 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000072">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000704"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">substrate concentration is a scalar measurement datum which denotes the amount of molecular entity involved in an enzymatic reaction (or catalytic chemical reaction) and whose role in that reaction is as substrate.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">substrate concentration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000073 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000073">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000207"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000060"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000121"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000140"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000193"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000088"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:maxInclusive rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">5</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/FishersExactTest.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">fisher.test(x) function, where x is a matrix</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.fisher_exact(table, alternative='two-sided')
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html#scipy.stats.fisher_exact
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2485</obo:STATO_0000391>
<rdfs:label xml:lang="en">Fisher's exact test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000074 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000074">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Cochran-Mantel-Haenzel test for repeated tests of independence is a statitiscal test which allows the comparison of two groups on a dichotomous/categorical response. It is used when the effect of the explanatory variable on the response variable is influenced by covariates that can be controlled. It is often used in observational studies where random assignment of subjects to different treatments cannot be controlled, but influencing covariates can.
The null hypothesis is that the two nominal variables that are tested within each repetition are independent of each other. So there are 3 variables to consider: two categorical variables to be tested for independence of each other, and the third variable identifies the repeats.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO adapted from wikipedia (http://en.wikipedia.org/wiki/Cochran–Mantel–Haenszel_statistics) and from the Handbook of Biological Statistics (http://udel.edu/~mcdonald/statcmh.html)</obo:IAO_0000119>
<obo:STATO_0000032>CHM test</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">Mantel–Haenszel test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">cmh.test(x,y,z)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Cochran-Mantel-Haenzel test for repeated tests of independence</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000075 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a rarefaction curve is a graph used for estimating species richness in ecology studies</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">>library(vegan)
>rarefaction(x, subsample=5, plot=TRUE, color=TRUE, error=FALSE, legend=TRUE, symbol)
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vegan/html/vegan-package.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">rarefaction curve</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000076 -->
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<owl:Class>
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<owl:Class>
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<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Mann-Whitney U-test is a null hypothesis statistical testing procedure which allows two groups (or conditions or treatments) to be compared without making the assumption that values are normally distributed.
The Mann-Whitney test is the non-parametric equivalent of the t-test for independent samples</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>U test</obo:IAO_0000118>
<obo:IAO_0000118>Wilcoxon rank-sum test</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">rank-sum test for the comparison of two samples</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from http://udel.edu/~mcdonald/statkruskalwallis.html
and from http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U
last accessed [2014-03-04]</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Wilcoxon Rank-Sum test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">wilcox.test(dependent variable ~ independant variable, data = dataset)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/wilcox.test.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.mannwhitneyu(x, y, use_continuity=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mannwhitneyu.html#scipy.stats.mannwhitneyu
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4049</obo:STATO_0000391>
<obo:STATO_0000391 xml:lang="en">scipy.stats.ranksums(x, y)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ranksums.html#scipy.stats.ranksums
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103</obo:STATO_0000391>
<rdfs:label xml:lang="en">Mann-Whitney U-test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000077 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000077">
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</owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
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</owl:intersectionOf>
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</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Shapiro-Wilk test is a goodness of fit test which evaluates the null hypothesis that the sample is drawn from a population following a normal distribution</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>S-W test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Shapiro–Wilk_test)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041>shapiro.test(x) function, where x is a numeric vector
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/shapiro.test.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.shapiro(x, a=None, reta=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.shapiro.html#scipy.stats.shapiro
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L944</obo:STATO_0000391>
<rdfs:label xml:lang="en">Shapiro-Wilk test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000078">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000137"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000226"/>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Levene's test is a null hypothesis statistical test which evaluates the null hypothesis of equality of variance in several populations.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Levene_test</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">levene.test(x) function, where x is a numeric vector</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.levene(*args, **kwds)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.levene.html#scipy.stats.levene
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1496</obo:STATO_0000391>
<rdfs:label xml:lang="en">Levene's test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000079 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000079">
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000137"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
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</owl:Restriction>
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</owl:Restriction>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Bartlett's test (see Snedecor and Cochran, 1989) is used to test if k samples are from populations with equal variances. Equal variances across samples is called homoscedasticity or homogeneity of variances. Some statistical tests, for example the analysis of variance, assume that variances are equal across groups or samples. The Bartlett test can be used to verify that assumption.
Bartlett's test is sensitive to departures from normality. That is, if the samples come from non-normal distributions, then Bartlett's test may simply be testing for non-normality. Levene's test and the Brown–Forsythe test are alternatives to the Bartlett test that are less sensitive to departures from normality.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Bartlett_test</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">bartlett.test(x) function, where x is a numeric vector</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.bartlett(*args)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.bartlett.html#scipy.stats.bartlett
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1450</obo:STATO_0000391>
<rdfs:label xml:lang="en">Barlett's test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000080 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000080">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Brown Forsythe test is a statistical test which evaluates if the variance of different groups are equal. It relies on computing the median rather than the mean, as used in the Levene's test for homoschedacity.
This test maybe used to, for instance, ensure that the conditions of applications of ANOVA are met.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia and Brown, M. B., and A. B. Forsythe. 1974a. The small sample behavior of some statistics which test the equality of several means. Technometrics, 16, 129-132.</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://www.statmethods.net/stats/anovaAssumptions.html
The hovPlot( ) function in the HH package provides a graphic test of homogeneity of variances based on Brown-Forsyth. In the following example, y is numeric and G is a grouping factor. Note that G must be of type factor.
# Homogeneity of Variance Plot
library(HH)
hov(y~G, data=mydata)
hovPlot(y~G,data=mydata)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Brown Forsythe test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000081 -->
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</owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000121"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Pearson's Chi-Squared test is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution or used to test independence of 2 categorical variables (ie absence of association between those variables).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Chi2 test for independence</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
and
http://en.wikipedia.org/wiki/Pearson's_chi-squared_test</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
chisq.test(x, y = NULL, correct = TRUE,
p = rep(1/length(x), length(x)), rescale.p = FALSE,
simulate.p.value = FALSE, B = 2000)</obo:STATO_0000041>
<obo:STATO_0000041>http://www.inside-r.org/packages/cran/nortest/docs/pearson.test
pearson.test(x) function, where x is a numeric vector</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2_contingency.html#scipy.stats.chi2_contingency</obo:STATO_0000391>
<rdfs:label xml:lang="en">Pearson's Chi square test of independence between categorical variables</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000082 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000082">
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<rdfs:subClassOf>
<owl:Class>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000470"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
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</owl:Restriction>
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<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
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<owl:Class>
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<owl:Restriction>
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</owl:unionOf>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a fixed effect model is a statistical model which represents the observed quantities in terms of explanatory variables that are treated as if the quantities were non-random.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS: this is a stub and more work is needed to reconcile conflicting definitions</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Fixed_effects_model</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">fixed effect model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000083 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000083">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Kolmogorov-Smirnov test is a goodness of fit test which evaluates the null hypothesis that a sample is drawn from a population that follows a specific continuous probability distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>K-S test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test)</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.itl.nist.gov/div898/handbook/eda/section3/eda35g.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041>ks.test(dataset, distribution)</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.kstwobign = <scipy.stats._continuous_distns.kstwobign_gen object at 0x7f6169f842d0>
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kstwobign.html#scipy.stats.kstwobign
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/_continuous_distns.py</obo:STATO_0000391>
<obo:STATO_0000391>scipy.stats.mstats.ks_twosamp(data1, data2,alternative='two-sided')
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.ks_twosamp.html
source code:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L821</obo:STATO_0000391>
<rdfs:label xml:lang="en">Kolmogorov-Smirnov test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000084 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000084">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000087"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is probit function.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_probit) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf</obo:STATO_0000041>
<rdfs:label xml:lang="en">multinomial probit regression for analysis of polychotomous dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000085 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000085">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB,PRS</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">effect size</obo:STATO_0000032>
<rdfs:label xml:lang="en">effect size estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000086 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000086">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000204"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000282"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an F-test is a statistical test which evaluates that the computed test statistics follows an F-distribution under the null hypothesis. The F-test is sensitive to departure from normality. F-test arise when decomposing the variability in a data set in terms of sum of squares.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">F-test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000087 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000087">
<owl:equivalentClass>
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<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statvartypes.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">polychotomous variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000088 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000088">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">statistical sample size is a count evaluating the number of individual experimental units</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB-PRS</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">statistical sample size</obo:STATO_0000032>
<rdfs:label xml:lang="en">study group population size</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000089 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000089">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500006"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a case-control study design is a observation study design which assess the risk of particular outcome (a trait or a disease) associated with an event (either an exposure or endogenous factor). A case-control study design therefore declares an exposure variable which is dichotomous in nature (exposed/non-exposed) and an outcome variable, which is also dichotomous (case or control), thus giving the name to the design. During the execution of the design, a case control study defines a population and counts the events to determine their frequency.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from:
http://www.drcath.net/toolkit/casecontrol.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">case-control study design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000090 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000090">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000087"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB-PRS</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statvartypes.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:comment>'has part' exactly 1 ('categorical measurement datum'
and ('has category label' exactly 2 'categorical label'))</rdfs:comment>
<rdfs:label xml:lang="en">dichotomous variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000091 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000091">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000235"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000254"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000182"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000196"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000245"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000700"/>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000247"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000027"/>
</owl:Restriction>
</owl:unionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000102"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001444"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000089"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB, PRS</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">GWAS study</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">whole genome association study</obo:STATO_0000032>
<rdfs:label xml:lang="en">genome-wide association study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000092 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000092">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000202"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000251"/>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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</owl:intersectionOf>
</owl:Class>
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</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000253"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000654"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Wilcoxon signed rank test is a statistical test which tests the null hypothesis that the median difference between pairs of observations is zero. This is the non-parametric analogue to the paired t-test, and should be used if the distribution of differences between pairs may be non-normally distributed.
The procedure involves a ranking, hence the name. The absolute value of the differences between observations are ranked from smallest to largest, with the smallest difference getting a rank of 1, then next larger difference getting a rank of 2, etc. Ties are given average ranks. The ranks of all differences in one direction are summed, and the ranks of all differences in the other direction are summed. The smaller of these two sums is the test statistic, W (sometimes symbolized Ts). Unlike most test statistics, smaller values of W are less likely under the null hypothesis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statsignedrank.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">signrank()</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.wilcoxon(x, y=None, zero_method='wilcox', correction=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.wilcoxon.html#scipy.stats.wilcoxon
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103</obo:STATO_0000391>
<rdfs:label xml:lang="en">Wilcoxon signed rank test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000093 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000093">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Information about a calendar date or timestamp indicating day, month, year and time of an event.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">date</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000094 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000094">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000198"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000118"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
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</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000087"/>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">The Kruskal–Wallis test is a null hypothesis statistical testing objective which allows multiple (n>=2) groups (or conditions or treatments) to be compared, without making the assumption that values are normally distributed. The Kruskal–Wallis test is the non-parametric equivalent of the independent samples ANOVA.
The Kruskal–Wallis test is most commonly used when there is one nominal variable and one measurement variable, and the measurement variable does not meet the normality assumption of an anova.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>H test</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">rank-sum test for the comparison of multiple (more than 2) samples.</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statkruskalwallis.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">kruskal.test()
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/kruskal.test.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.mstats.kruskalwallis(*args)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.kruskalwallis.html
source code:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L800</obo:STATO_0000391>
<rdfs:label xml:lang="en">Kruskal Wallis test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000095 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000095">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000739"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000202"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000139"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">paired t-test is a statistical test which is specifically designed to analysis differences between paired observations in the case of studies realizing repeated measures design with only 2 repeated measurements per subject (before and after treatment for example)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statpaired.html</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statsignedrank.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">t-test for dependent means</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">t-test for repeated measures</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE, paired= TRUE)</obo:STATO_0000041>
<obo:STATO_0000391>scipy.stats.ttest_rel(a, b, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_rel.html#scipy.stats.ttest_rel
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3389</obo:STATO_0000391>
<rdfs:label xml:lang="en">paired t-test</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">PRS+AGB adapted from wikipedia:
http://en.wikipedia.org/wiki/Stratified_sampling
polled on June 7th,2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">stratifying population</obo:STATO_0000032>
<rdfs:label>population stratification prior to sampling</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A stastical test power analysis is a data transformation which aims to determine the size of a statistical sample required to reach a desired significance level given a particular statistical test</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.statmethods.net/stats/power.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://www.statmethods.net/stats/power.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">statistical test power analysis</rdfs:label>
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<obo:IAO_0000112 xml:lang="en">http://arxiv.org/pdf/1007.1094.pdf</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">two sample Hotelling T2 test</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">a random effect(s) model, also called a variance components model, is a kind of hierarchical linear model. It assumes that the dataset being analysed consists of a hierarchy of different populations whose differences relate to that hierarchy.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS: this is a stub and more work is needed to reconcile conflicting definitions</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">variance components model</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Random_effects_model#Qualitative_description</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">random effect model</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000100 -->
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<obo:IAO_0000115 xml:lang="en">standardized mean difference is statistic computed by forming the difference between two means, divided by an estimate of the within-group standard deviation.
It is used to provide an estimation of the effect size between two treatments when the predictor (independent variable) is categorical and the response(dependent) variable is continuous.
A standardized mean difference is a statistic that is a difference between two means, divided by a statistical measure of dispersion.
The term Standardized Mean Difference is a description of the concept without an explicit type of statistical measure of dispersion. If the statistical measure of dispersion is specified, then a type (child term) of Standardized Mean Difference is preferred.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Brian S. Alper, Kenneth Wilkins, Harold Lehmann, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SMD</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000119 xml:lang="en">adapted from "Effect size, confidence interval and statistical significance: a practical guide for biologists" Nakagawa and Cuthill
DOI: 10.1111/j.1469-185X.2007.00027.x</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from http://htaglossary.net/standardised+mean+difference+(SMD)
revised during alignment and collaboration with the COKA/SEVCO group</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Cohen's d statistic</obo:STATO_0000032>
<rdfs:label xml:lang="en">standardized mean difference</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000103 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the multinomial distribution is a probability distribution which gives the probability of any particular combination of numbers of successes for various categories defined in the context of n independent trials each of which leads to a success for exactly one of k categories, with each category having a given fixed success probability.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from
http://mathworld.wolfram.com/MultinomialDistribution.html
and
http://en.wikipedia.org/wiki/Multinomial_distribution</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">dmultinom(x, size = NULL, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Multinom.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">multinomial distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000104">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000609"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000037"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000237"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">normal score</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">standard score</obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">scipy.stats.zscore(a, axis=0, ddof=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.zscore.html#scipy.stats.zscore
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1977</obo:STATO_0000391>
<rdfs:label xml:lang="en">z-score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000105 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000105">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/MA_plot
last accessed: 2014-03-13</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">M-value</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">log signal intensity ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000106 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000106">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000107"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000087"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">probit regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the probit function aka the quantile function, i.e., the inverse cumulative distribution function (CDF), associated with the standard normal distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">probit regression for analysis of polychotomous dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000107 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000107">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000034"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000218"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000289"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000341"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000751"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
http://en.wikipedia.org/wiki/Statistical_model
last accessed: 14/01/2014</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">statistical model</obo:STATO_0000032>
<rdfs:label xml:lang="en">statistical model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000108 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000108">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000107"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000251"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">linear regression model is a model which attempts to explain data distribution associated with response/dependent variable in terms of values assumed by the independent variable uses a linear function or linear combination of the regression parameters and the predictor/independent variable(s).
linear regression modeling makes a number of assumptions, which includes homoskedasticity (constance of variance)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Linear_regression) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">linear regression for analysis of continuous dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000109 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000109">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000107"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_logistic_regression) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf</obo:STATO_0000041>
<rdfs:label xml:lang="en">multinomial logistic regression for analysis of dichotomous dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000111 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000111">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001573"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000626"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">a sequence read is a DNA sequence data which is generated by a DNA sequencer</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">sequence read</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000112 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000112">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000184"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000155"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a Funnel plot is a scatter plot of treatment effect versus a measure of study size and aims to provide a visual aid to detecting bias or systematic heterogeneity. A symmetric inverted funnel shape arises from a ‘well-behaved’ data set, in which publication bias is unlikely. An asymmetric funnel indicates a relationship between treatment effect and study size.
Known caveats: If high precision studies really are different from low precision studies with respect to effect size (e.g., due to different populations examined) a funnel plot may give a wrong impression of publication bias. The appearance of the funnel plot can change quite dramatically depending on the scale on the y-axis — whether it is the inverse square error or the trial size.
Funnel plot was introduced by Light and Palmer in 1984.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
http://en.wikipedia.org/wiki/Funnel_plot</obo:IAO_0000119>
<rdfs:label xml:lang="en">Funnel plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000113 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000113">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">variance is a data item about a random variable or probability distribution. it is equivalent to the square of the standard deviation. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean (expected value).The variance is the second moment of a distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Belran</obo:IAO_0000117>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">σ2</obo:IAO_0000118>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">var(x, y = NULL, na.rm = FALSE, use)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000116 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000116">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">the process of using statistical analysis for interpreting and communicating "what the data say".</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">From "The strenght of statistical evidence" by Richard Royall.
https://www.stat.fi/isi99/proceedings/arkisto/varasto/roya0578.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">assess stastistical evidence</obo:STATO_0000032>
<rdfs:label xml:lang="en">assess statistical evidence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000117 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000117">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution
last accessed:
14/01/2014</obo:IAO_0000119>
<rdfs:label xml:lang="en">discrete probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000118 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000118">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000228"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">ranking is a data transformation which turns a non-ordinal variable into a Ordinal variable by sorting the values of the input variable and replacing their value by their position in the sorting result</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">ranking</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000119 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000119">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000144"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000144"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">textual definition modified following contributiong by Thomas Nichols:
https://github.com/ISA-tools/stato/issues/18</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<rdfs:label xml:lang="en">model parameter estimation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000120 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000120">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000112 xml:lang="en">http://www.r-bloggers.com/boxplots-beyond-iv-beanplots/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">beanplot is a plot in which (one or) multiple batches ("beans") are shown. Each bean consists of a density trace, which is mirrored to
form a polygon shape. Next to that, a one-dimensional scatter plot shows all the individual measurements, like in a stripchart.
The name beanplot stems from green beans. The density shape can be seen as the pod of a green bean, while the scatter plot shows the seeds inside the pod.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.jstatsoft.org/v28/c01/paper</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://cran.r-project.org/web/packages/beanplot/index.html</obo:STATO_0000041>
<rdfs:label>bean plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000121 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000121">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the objective of a data transformation to evaluate a null hypothesis of absence of linkage between variables.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">association between categorical variables testing objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000122 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000122">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000257"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a pedigree chart is a graph which plots parent child relations</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO adapted from wikipedia (https://en.wikipedia.org/wiki/Pedigree_chart)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">family tree</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">plot.pedigree {kinship}
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/kinship/html/plot.pedigree.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">pedigree chart</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000123 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000123">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<rdfs:subClassOf>
<owl:Class>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000147"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
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</owl:intersectionOf>
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<rdfs:subClassOf>
<owl:Restriction>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>R squared measure of LD</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580747/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">r2 measure of LD</obo:STATO_0000032>
<rdfs:label xml:lang="en">r2 measure of linkage desequilibrium</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000124 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000124">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000055"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Stratified_sampling
polled on June 7th,2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">stratification rule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000125 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000125">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000037"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The dot plot as a representation of a distribution consists of group of data points plotted on a simple scale. Dot plots are used for continuous, quantitative, univariate data. Data points may be labelled if there are few of them.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
Wilkinson, Leland (1999). "Dot plots". The American Statistician (American Statistical Association) 53 (3): 276–281. doi:10.2307/2686111</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label>Wilkinson dot plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000126 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000126">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000184"/>
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<owl:someValuesFrom>
<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000169"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200094"/>
</owl:Restriction>
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<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001265"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001442"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:unionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200094"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0010467"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200191"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000650"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis.
It is a popular method for visualizing differential occurence of variables between 2 conditions.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Volcano_plot_(statistics)</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...)
http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">volcano plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000127 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000127">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000561"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0002135"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">99</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a confidence interval which covers 99% of the sampling distribution, meaning that there is a 1% risk of false positive (type I error)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">confidence interval at 1% of type I error rate</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">99% confidence interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000128 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000128">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000243"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Altman Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Altman to create the 'whisker' of the plot.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Altman, D.G. Practical Statistics for Medical Research (Chapman and Hall, 1991).</obo:IAO_0000119>
<rdfs:label>Altman box and whisker plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000130 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000130">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000247"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000697"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000173"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000138"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000182"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.biomedcentral.com/1471-2288/11/58#B9</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Breslow-Day test is a statistical test which evaluates if the odds ratios are homogenous across N 2x2 contingency tables, for instance several 2x2 contingency tables associated with different strata of a stratified population when evaluating the relationship between exposure and outcome or associated with the different samples coming from several centres in a multicentric study in clinical trial context.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Odds_ratio#Statistical_inference
polled on June 8th,2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Breslow-Day test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://www.math.montana.edu/~jimrc/classes/stat524/Rcode/breslowday.test.r</obo:STATO_0000041>
<rdfs:label xml:lang="en">Breslow-Day test for homogeneity of odds ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000131 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000131">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000183"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a sphericity test is a null hypothesis statistical testing procedure which posits a null hypothesis of equality of the variances of the differences between levels of the repeated measures factor</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Sphericity#Sphericity_in_statistics)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">test of data sphericity</obo:STATO_0000032>
<rdfs:label xml:lang="en">sphericity test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000132 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000132">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hotelling T squared distribution is a probability distribution used in multivariate hypothesis testing, which is a univariate distribution proportional to the F-distribution and arises importantly as the distribution of a set of statistics which are natural generalizations of the statistics underlying Student's t-distribution.
In particular, the distribution arises in multivariate statistics in undertaking tests of the differences between the (multivariate) means of different populations, where tests for univariate problems would make use of a t-test.
The distribution is named for Harold Hotelling, who developed it[1] as a generalization of Student's t-distribution.
This distribution is commonly used to describe the sample Mahalanobis distance between two populations.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia
"http://en.wikipedia.org/wiki/Hotelling's_T-squared_distribution"
last polled: 2013-11-09</obo:IAO_0000119>
<rdfs:label xml:lang="en">Hotelling T2 distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000133 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000133">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A post-hoc analysis is a statistical test carried out following an analysis of variance which ruled out the null hypothesis of absence of difference between group which allows identifying which groups differ.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">a posteriori test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia: http://en.wikipedia.org/wiki/Post-hoc_analysis
last accessed: 2013-11-15</obo:IAO_0000119>
<rdfs:label xml:lang="en">post-hoc analysis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000134 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000134">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">specificity</obo:IAO_0000118>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">true negative rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000135 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000135">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000277"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">strictly standardized mean difference (SSMS) is a standardized mean difference which corresponds to the ratio of mean to the standard deviation of the difference between two groups.
SSMD directly measures the magnitude of difference between two groups.
SSMD is widely used in High Content Screen for hit selection and quality control.
When the data is preprocessed using log-transformation as normally done in HTS experiments, SSMD is the mean of log fold change divided by the standard deviation of log fold change with respect to a negative reference.
In other words, SSMD is the average fold change (on the log scale) penalized by the variability of fold change (on the log scale).
For quality control, one index for the quality of an HTS assay is the magnitude of difference between a positive control and a negative reference in an assay plate. For hit selection, the size of effects of a compound (i.e., a small molecule or an siRNA) is represented by the magnitude of difference between the compound and a negative reference. SSMD directly measures the magnitude of difference between two groups. Therefore, SSMD can be used for both quality control and hit selection in HTS experiments.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/SSMD</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">SSMD</obo:STATO_0000032>
<rdfs:label xml:lang="en">strictly standardized mean difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000136 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000136">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000247"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000697"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000229"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000173"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000182"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Tarone's test for homogeneity of odds ratio is a statistical test which evaluates the null hypothesis that odds ratio are homogeneous</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Tarone, R. E. ‘On heterogeneity tests based on efficient scores’, Biometrika, 72, 91-95 (1985).</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">> library("metafor")
> calcTaronesTest <- function(mylist,referencerow=2)
http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/en/latest/src/biomedicalstats.html#calculating-the-mantel-haenszel-odds-ratio-when-there-is-a-stratifying-variable</obo:STATO_0000041>
<rdfs:label xml:lang="en">Tarone's test for homogeneity of odds ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000137 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000137">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000226"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an homoskedasticity test is a statistical test aiming at evaluate if the variances from several random samples are similar</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">equivariance test</obo:STATO_0000032>
<rdfs:label xml:lang="en">homoskedasticity test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000138 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000138">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000140"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001927"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a 2x2 contingency table is a contingency table build for 2 dichotomous variables (i.e. 2 categorical variables, each with only 2 possible outcomes). It is the simplest of contingency tables</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">2x2 contingency table</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">2 by 2 contingency table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000139 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000139">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600015"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000038"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000102"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000278"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">pairing patients by age, pairing animals by body weight range</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">subject pairing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000140 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000140">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a contigency table is a data item which displays the (multivariate) frequency distribution of the possible values of categorical variables.
The first row of the table corresponds to categories of one categorical variable, the first column of the table corresponds to categories of the other categorical variable, the cells corresponding to each combination of categories is filled with the observed occurences in the sample being considered.
The table also contains marginal total (marginal sums) and grand total of the occurences
The term contingency table was first used by Karl Pearson in "On the Theory of Contingency and Its Relation to Association and Normal Correlation", part of the Drapers' Company Research Memoirs Biometric Series I published in 1904.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Contingency_table)</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">contingency table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000141 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000141">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001442"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000700"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000279"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000102"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0500006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0500014"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">acute toxicity study is an investigation which use interventions organized according to a factorial design and a parallel group design to observe the effect of use of high dose xenobiotics in animal models or cellular models</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en">acute toxicity study</obo:STATO_0000032>
<rdfs:label xml:lang="en">acute toxicity study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000142 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000142">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000611"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000301"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000237"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000258"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:someValuesFrom>
<rdfs:Datatype>
<owl:intersectionOf rdf:parseType="Collection">
<rdfs:Datatype>
<owl:onDatatype rdf:resource="http://www.w3.org/2002/07/owl#real"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:minInclusive rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">-1</xsd:minInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
<rdfs:Datatype>
<owl:onDatatype rdf:resource="http://www.w3.org/2002/07/owl#real"/>
<owl:withRestrictions rdf:parseType="Collection">
<rdf:Description>
<xsd:maxInclusive rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</xsd:maxInclusive>
</rdf:Description>
</owl:withRestrictions>
</rdfs:Datatype>
</owl:intersectionOf>
</rdfs:Datatype>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032>r</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">r statistic</obo:STATO_0000032>
<rdfs:label xml:lang="en">correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000143 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000328"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000266"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A Bayesian model selection is a data transformation which is based on Bayesian statistics to compute Bayes factor in order to evaluate which model best explains data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia</obo:IAO_0000119>
<rdfs:label xml:lang="en">Bayesian model selection</rdfs:label>
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<obo:IAO_0000112 xml:lang="en">for example , model parameter estimates could be produced using regression analysis (used in a model estimation process) , which attempts to express the response variable in terms of function of predictor variable and model parameters.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a model parameter estimate is a data item which results from a model parameter estimation process and which provides a numerical value about a model parameter.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">textual definition modified following contributiong by Thomas Nichols:
https://github.com/ISA-tools/stato/issues/18</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">model parameter estimate</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000145 -->
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<obo:IAO_0000115 xml:lang="en">the geometric distribution is a negative binomial distribution where r is 1.
It is useful for modeling the runs of consecutive successes (or failures) in repeated independent trials of a system.
The geometric distribution models the number of successes before one failure in an independent succession of tests where each test results in success or failure.
The geometric distribution with prob = p has density
p(x) = p (1-p)^x
for x = 0, 1, 2, …, 0 < p ≤ 1.
If an element of x is not integer, the result of dgeom is zero, with a warning.
The quantile is defined as the smallest value x such that F(x) ≥ p, where F is the distribution function.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.mathworks.co.uk/help/stats/geometric-distribution.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dgeom(x, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.geom.html#scipy.stats.geom</obo:STATO_0000391>
<rdfs:label xml:lang="en">geometric distribution</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000146 -->
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<obo:IAO_0000115 xml:lang="en">a null hypothesis stating that there are differences observed between group of subjects</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">presence of between group difference hypothesis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000147 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from R documentation (http://cran.r-project.org/web/packages/LDheatmap/index.html)</obo:IAO_0000119>
<obo:STATO_0000032>LD plot</obo:STATO_0000032>
<obo:STATO_0000032>Linkage Disequilibrium plot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">LD plot</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000148 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Cochran-Armitage test is a statistical test used in categorical data analysis when the aim is to assess for the presence of an association between a dichotomous variable (variable with two categories) and a polychotomous variable (a variable with k categories).
The two-level variable represents the response, and the other represents an explanatory variable with ordered levels. The null hypothesis is the hypothesis of no trend, which means that the binomial proportion is the same for all levels of the explanatory variable
For example, doses of a treatment can be ordered as 'low', 'medium', and 'high', and we may suspect that the treatment benefit cannot become smaller as the dose increases. The trend test is often used as a genotype-based test for case-control genetic association studies.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">CATT</obo:IAO_0000118>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Cochran%E2%80%93Armitage_test_for_trend</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">Cochran-Armitage test for trend</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000149 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">binomial logistic regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Logistic_regression) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">binomial logistic regression for analysis of dichotomous dependent variable</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000150 -->
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<obo:IAO_0000115 xml:lang="en">a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>COKA group</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">minimum value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label>minimum observed value</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000151 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>COKA group</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">maximum value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label>maximum observed value</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000152 -->
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<obo:IAO_0000115 xml:lang="en">a quartile is a quantile which splits data into sections accrued of 25% of data, so the first quartile delineates 25% of the data, the second quartile delineates 50% of the data and the third quartile, 75 % of the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Quartile)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">quartile</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000153 -->
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
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<obo:IAO_0000112 xml:lang="en">http://arxiv.org/pdf/1007.1094.pdf</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The one-sample Hotelling’s T2 is the multivariate extension of the common one-sample or paired Student’s t-test. In a one-sample t-test, the mean response is compared against a specific value. Hotelling’s one-sample T2 is used when the number of response variables is two or more, although it can be used when there is only one response variable. T2 makes the usual assumption that the data are approximately multivariate normal. Randomization tests are provided that do not rely on this assumption. These randomization tests should be used whenever you want exact results that do not rely on several assumptions.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
https://ncss-wpengine.netdna-ssl.com/wp-content/themes/ncss/pdf/Procedures/NCSS/Hotellings_One-Sample_T2.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">one sample Hotelling T2 test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000154 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a violin plot is a plot combining the features of box plot and kernel density plot. The violin plot is therefore similar to box plot but it incorporated in the display the probability density of the data at different values.
Typically violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Violin_plot
and
Hintze, J. L. and R. D. Nelson (1998). Violin plots: a box plot-density trace synergism. The American Statistician, 52(2):181-4.</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/vioplot/docs/vioplot
vioplot( x, ..., range=1.5, h, ylim, names, horizontal=FALSE,
col="magenta", border="black", lty=1, lwd=1, rectCol="black",
colMed="white", pchMed=19, at, add=FALSE, wex=1,
drawRect=TRUE)</obo:STATO_0000041>
<rdfs:label>violin plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000155 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">meta-analysis is a data transformation which uses the effect size estimates from several independent quantitative scientific studies addressing the same question in order to assess finding consistency.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Metaanalysis
last accessed: 2013-11-15</obo:IAO_0000119>
<rdfs:label xml:lang="en">meta analysis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000156 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000156">
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</owl:Restriction>
</rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Scheffe test is a data transformation which evaluates all possible contrasts and adjusting the levels significance by accounting for multiple comparison. The test is therefore conservative. Confidence intervals can be constructed for the corresponding linear regression. It was developped by American statistician Henry Scheffe in 1959.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Scheffé's_method)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041>http://www.inside-r.org/packages/cran/agricolae/docs/scheffe.test</obo:STATO_0000041>
<rdfs:label xml:lang="en">Scheffe test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000157 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000157">
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000133"/>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the LSD test is a statistical test for multiple comparisons of treatments by means of least significant difference following an ANOVA analysis</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>R</obo:IAO_0000119>
<obo:STATO_0000032>LSD test</obo:STATO_0000032>
<obo:STATO_0000041>http://rss.acs.unt.edu/Rdoc/library/agricolae/html/LSD.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Least significance different test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000158 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000158">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a null hypothesis which states that a linkage exists between 2 categorical variables</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">presence of association hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000159 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000159">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000166"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapter from
http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts
and
http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/
[last accessed: 2014-03-04]</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">barplot(height....)
set argument " beside = FALSE "
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html</obo:STATO_0000041>
<rdfs:label>stacked bar chart</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000160 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000160">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">2</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The exponential distribution (a.k.a. negative exponential distribution) is the probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. It is the continuous analogue of the geometric distribution, and it has the key property of being memoryless.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Exponential.html
dexp(x, rate = 1, log = FALSE)
pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE)
qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE)
rexp(n, rate = 1)</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.expon.html#scipy.stats.expon</obo:STATO_0000391>
<rdfs:label xml:lang="en">exponential distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000161 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000161">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">variable distribution is data item which denotes the spatial resolution of data point making up a variable. variable distribution may be compared to a known probability distribution using goodness of fit test or plotting a quantile-quantile plot for visual assessment of the fit.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">data distribution</obo:STATO_0000032>
<rdfs:label xml:lang="en">data distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000162 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000162">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">the role played by an entity part of study group as defined by an experimental design and realized in a data analysis and data interpretation</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">experimental unit role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000163 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000163">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">trimmed mean or truncated mean is a measure of central tendency which involves the calculation of the mean after discarding given parts of a probability distribution or sample at the high and low end, and typically discarding an equal amount of both</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia [last accessed 2014-03-04]
http://en.wikipedia.org/wiki/Truncated_mean</obo:IAO_0000119>
<obo:STATO_0000032>truncated mean</obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">scipy.stats.tmean(a, limits=None, inclusive=(True, True))
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.tmean.html#scipy.stats.tmean
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L684</obo:STATO_0000391>
<rdfs:label xml:lang="en">trimmed mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000164 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000164">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The interquartile range is a data item which corresponds to the difference between the upper quartile (3rd quartile) and lower quartile (1st quartile).
The interquartile range contains the second quartile or median.
The interquartile range is a data item providing a measure of data dispersion.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO. adapted from wikipedia, wolfram alpha and oxford dictionary of statistics</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">IQR(x, na.rm = FALSE, type = 7)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/IQR.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">inter quartile range</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000165 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000165">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a pie chart is a graph in which a circular graph is divided into sector illustrating numerical proportion, meaning that the arc length of each sector (and consequently its central angle and area), is proportional to the quantity it represents.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia, last accessed [2014-03-05]
http://en.wikipedia.org/wiki/Pie_chart</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">pie(x, labels = names(x), edges = 200, radius = 0.8,
clockwise = FALSE, init.angle = if(clockwise) 90 else 0,
density = NULL, angle = 45, col = NULL, border = NULL,
lty = NULL, main = NULL, ...)
https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/pie.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">pie chart</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000166 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000166">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
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<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000963"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>A bar chart is appropriate to represent counts of data.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia (http://en.wikipedia.org/wiki/Bar_chart) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">bar plot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">barplot(height, ...)
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">bar chart</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000167 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000167">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000152"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the first quartile is a quartile which splits the lower 25 % of the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">first quartile</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000168 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000168">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a real time quantitative pcr plot is a line graph which plots the signal fluorescence intensity as a function of the number of PCR cycle</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">real time quantitative pcr plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000169 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000169">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000300"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition</obo:IAO_0000115>
<obo:IAO_0000116>30/04/2014
- removed restriction:
'is about' exactly 2 'study group population'
- need more discussion for the relationship of fold change to study group populations for particular examples.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Fold_change</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">fold change</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000170 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000170">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000152"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the first quartile is a quartile which splits the 75 % of the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">third quartile</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000171 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000171">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000243"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Spear Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Spear to create the 'whisker' of the plot.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Spear, M.E. Charting Statistics (McGraw-Hill, 1952)</obo:IAO_0000119>
<rdfs:label>Spear box and whisker plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000172 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000172">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<rdfs:subClassOf>
<owl:Class>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0010467"/>
</owl:Restriction>
<owl:Restriction>
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</owl:someValuesFrom>
</owl:Restriction>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">FPKM, which is the expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software.
Recommended use:
-FPKM measure may be used for gene count comparisons within a sample.
-FPKM measure is NOT suited for between sample comparisons.
-FPKM measure is NOT suited for Differential Expression analysis.</obo:IAO_0000115>
<obo:IAO_0000116>The definition of FPKM has been modified in October 2019 to reflect the possible uses as detailed in https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html
and distinguish more clearly FPKM from measures such as TPM</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FPKM</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://seqanswers.com/forums/showthread.php?t=3254
and from
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
and from
https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">FPKM-fragments per kilobase of transcript per million fragments mapped</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000173 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000173">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">homogeneity testing objective is the objective of a data transformation to test a null hypothesis that two or more sub-groups of a population share the same distribution of a single categorical variable.
For example, do people of different countries have the same proportion of smokers to non-smokers</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">homogeneity test objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000174 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000174">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:someValuesFrom>
<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000155"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Forest_plot</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">metaplot(mn, se, nn=NULL, labels=NULL, conf.level=0.95,
xlab="Odds ratio", ylab="Study Reference",xlim=NULL,
summn=NULL, sumse=NULL, sumnn=NULL, summlabel="Summary",
logeffect=FALSE, lwd=2, boxsize=1,
zero=as.numeric(logeffect), colors=meta.colors(),
xaxt="s", logticks=TRUE, ...)
http://rss.acs.unt.edu/Rdoc/library/rmeta/html/metaplot.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Forest plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000175 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000175">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/confint.html</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">confidence interval calculation is a data transformation which determines a confidence interval for a given statistical parameter</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">confidence interval calculation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000176 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000176">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000739"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000404>T</obo:STATO_0000404>
<rdfs:label xml:lang="en">t-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000177 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000177">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000436"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the beta distribution is a continuous probability distributions defined on the interval [0, 1] parametrized by two positive shape parameters, denoted by α and β, that appear as exponents of the random variable and control the shape of the distribution</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
http://en.wikipedia.org/wiki/Beta_distribution</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Beta.html
dbeta(x, shape1, shape2, ncp = 0, log = FALSE)
pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)
qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)
rbeta(n, shape1, shape2, ncp = 0)</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.beta.html#scipy.stats.beta</obo:STATO_0000391>
<rdfs:label>beta distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000178 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000178">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Kurtosis is a data item which denotes the degree of peakedness of a distribution. It is defined as a normalized form of the fourth central moment of a distribution.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/Kurtosis.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kurtosis.html#scipy.stats.kurtosis</obo:STATO_0000391>
<rdfs:label xml:lang="en">kurtosis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000179 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000179">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000251"/>
</owl:intersectionOf>
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<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">ANCOVA or analysis of covariance is a data transformation which evaluates if population means of a dependent variable are equal across levels of a categorical independent variables while controlling for the effects of other continuous variable s, known as covariates. Therefore, when performing ANCOVA, we are adjusting the dependent variable means to what they would be if all groups were equal on the covariates.
It augments the ANOVA model with one or more additional quantitative variables, called covariates, which are related to the response variable. The covariates are included to reduce the variance in the error terms and provide more precise measurement of the treatment effects. ANCOVA is used to test the main and interaction effects of the factors, while controlling for the effects of the covariate</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label>ANCOVA</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000180 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000180">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000227"/>
<rdfs:subClassOf>
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<owl:someValuesFrom>
<owl:Class>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</owl:hasValue>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000230"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">standard normal distribution is a normal distribution with variance = 1 and mean=0</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">we need to formally set value for mean and variance</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dnorm(x, mean = 0, sd = 1, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Normal.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">standard normal distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000181 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000181">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000861"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000073"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000081"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hardy-Weinberg equilibrium test is a statistical test which aims to evaluate if a population's proportion of allele is stable or not. It is used as means of quality control to evaluate possibility of genotyping error or population structure.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO: adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">> library(HardyWeinberg)
> x <- c(298,489,213)
> HW.test <- HWChisq(x,verbose=TRUE)
http://cran.r-project.org/web/packages/HardyWeinberg/index.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Hardy-Weinberg equilibrium testing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000182 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000182">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000300"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000622"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000627"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000627"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001404"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000314"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">4</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome.
It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/
http://www.stats.org/stories/2008/odds_ratios_april4_2008.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">OR</obo:STATO_0000032>
<rdfs:label>odds ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000183 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000183">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000217"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">sphericity testing objective is a statistical objective of a data transformation which aims to test a null hypothesis of sphericity holds.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">sphericity testing objective</obo:STATO_0000032>
<rdfs:label xml:lang="en">sphericity testing objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000184 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000184">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">review formal definition as both numerator and denominator should be of the same type, not just some data item</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wolfram Alpha:
https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7</obo:IAO_0000119>
<rdfs:label>ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000185 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000185">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000087"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001927"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000140"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a 2 by n contingency table is a contingency table built for one dichotomous variable (a categorical variable with only 2 outcomes) and one polychotomous variable (a polychomotomous variable with at least 2 outcomes)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">2 by n contingency table</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000186 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000186">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000072"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000071"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000427"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0003824"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Lineweaver-Burk plot is a graph which is the graphical representation of the Lineweaver–Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. The plot provides a useful graphical method for analysis of the Michaelis–Menten equation.
It was widely used to determine important terms in enzymology and enzyme kinetics as the x-intercept of the graph represents −1/Km and the y-intercept of such a graph is equivalent to the inverse of Vmax</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">TODO: create 'inverse function' and replace 'data transformation' in the assertions.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en">double reciprocal plot</obo:STATO_0000032>
<rdfs:label xml:lang="en">Lineweaver-Burk plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000187 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000187">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000133"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000023"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000700"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000061"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000230"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Tukey Honestly Significant Difference (HSD) test is a statistical test used following an ANOVA test yielding a statistically significant p-value in order to determine which means are different, to a given level of significance. The Tukey HSD test relies on the q-distribution.
The procedure is conservative, meaning that if sample sizes (the sizes of different study groups) are equal, the risk of a Type I error is exactly α, and if sample sizes are unequal it’s less than α.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">IMPORTANT: Do Not to confuse the Tukey HSD test with Tukey Mean Difference Test (Bland-Altman test)</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.tc3.edu/instruct/sbrown/stat/anova1.htm#ANOVAprereq</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Tukey's honestly significant difference</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TukeyHSD.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Tukey HSD for Post-Hoc Analysis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000188 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000188">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000451"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200094"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000169"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">average log signal intensity is a data time which corresponds to the sum of 2 distinct logarithm base 2 transformed signal intensity, each corresponding to a distinct condition of signal acquisition, divided by 2.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/MA_plot
last accessed: 2014-03-13</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">A-value</obo:STATO_0000032>
<rdfs:label xml:lang="en">average log signal intensity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000189 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000189">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000082"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000099"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A mixed model is a statistical model containing both fixed effects and random effects. These models are useful in a wide variety of disciplines in the physical, biological and social sciences. They are particularly useful in settings where repeated measurements are made on the same statistical units (longitudinal study), or where measurements are made on clusters of related statistical units. Because of their advantage in dealing with missing values, mixed effects models are often preferred over more traditional approaches such as repeated measures ANOVA.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS: this is a stub and more work is needed to reconcile conflicting definitions</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">mixed effect model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000190 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000190">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000232"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Cq</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Ct</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml</obo:IAO_0000119>
<rdfs:label xml:lang="en">threshold cycle</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000191 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000191">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label>goodness of fit statistical test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000192 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000192">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a cartesian product is a data transformation which operates on a n Sets to produce a set of all possible ordered n-tuples where each element of the tuple comes from a Set</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from math wolfram (http://mathworld.wolfram.com/CartesianProduct.html)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">cartesian product</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000193 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000193">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">statistical sample</obo:STATO_0000032>
<rdfs:label>study group population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000194 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000194">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000192"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">self explanatory</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">cartesian product 2 sets</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000195 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000195">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000264"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A non-negative integer defining how many combination of factor levels (or treatments in the statistical sense) are to be used in a study.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">number of factor level combinations</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000196 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000196">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000561"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000314"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000315"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000182"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000574"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A confidence interval is a data item which defines an range of values in which a measurement or trial falls corresponding to a given probability.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/ConfidenceInterval.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">confidence interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000197 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000197">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000010"/>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">ensembl, ucsc</obo:IAO_0000119>
<rdfs:label xml:lang="en">genomic coordinate system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000198 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000198">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000118"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a statistical test which makes no assumption about the underlying data distribution</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">non-parametric test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000199 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000199">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000131"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000183"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Mauchly's test for sphericity is a statistical test which evaluates if the variance of the differences between all combinations of the groups are equal, a property known as 'sphericity' in the context of repeated measures. It is used for instance prior to repeated measure ANOVA.
The test works by assessing if a Wishart-distributed covariance matrix (or transformation thereof) is proportional to a given matrix.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB-PRS, adapted from wikipedia (http://en.wikipedia.org/wiki/Mauchly's_sphericity_test)
polled on june,10th, 2013
and from R manual:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Mauchly's test for sphericity</obo:STATO_0000032>
<obo:STATO_0000041>mauchly.test(object, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html</obo:STATO_0000041>
<rdfs:label>Mauchly's test for sphericity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000200 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000200">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the statistical test power is data item which is about a statistical test and is obtained by subtracting the false negative rate (type II error rate) to 1. The power of a statistical test is the probability that it will correctly lead to the rejection of a false null hypothesis (Greene 2000). The statistical power is the ability of a test to detect an effect, if the effect actually exists (High 2000).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia (http://en.wikipedia.org/wiki/Statistical_power), polled June 10th, 2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">statistical test power</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000201 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000201">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000228"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other.
Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Spearman's rho</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">cor(x, y = NULL, use = "everything",method = c("spearman"))</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.spearmanr(a, b=None, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2643</obo:STATO_0000391>
<rdfs:label xml:lang="en">Spearman's rank correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000202 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000202">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000253"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">within subject comparison statistical test is a kind of statistical test which evaluates if a change occurs within one experimental unit over time following a treatment or an event</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">within subject comparison statistical test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000203 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000203">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">possibly submit to 'Population and Community Ontology'</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label>cohort</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000204 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000204">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the F-distribution is a continuous probability distribution which arises in the testing of whether two observed samples have the same variance.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Fisher distribution</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Snedecor Fisher distribution</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/F-Distribution.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">df(x, df1, df2, ncp, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Fdist.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f.html#scipy.stats.f</obo:STATO_0000391>
<rdfs:label xml:lang="en">F-distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000206 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000206">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0010467"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001271"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000736"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">RPKM is a kind of count which numbers the sequence reads found per kilobase of transcript reported to million of sequence reads. RPKM is a metric generated by ERANGE software tool as reported by Mortazi et al, in 2008.
The metric has been enhanced and replaced by FPKM to better take into account splice variant. FKPM uses a statistical model to perform the computation.
Recommended use:
-RPKM measure may be used for gene count comparisons within a sample.
-RPKM measure is NOT suited for between sample comparisons.
-RPKM measure is NOT suited for Differential Expression analysis.</obo:IAO_0000115>
<obo:IAO_0000116>The definition of RPKM has been modified in October 2019 to reflect the possible uses as detailed in https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html
and distinguish more clearly RPKM from measures such as TPM</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">RPKM</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">RPKM-reads per kilobase of transcript per million fragments mapped</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000207 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000207">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000208"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a planned process which etablishes and states the different hypothesis to be evaluated during a null hypothesis statistical test</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">specifying null and alternate hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000208 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000208">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An alternative hypothesis is an hypothesis defined in a statistical test that is the opposite of the null hypothesis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">alternative hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000209 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000209">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000112 xml:lang="en">PMID:12892658
"Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change."</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">area under curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000210 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000210">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000169"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000010"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000010"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">channel1/channel2 fluorescence intensity ratio</obo:STATO_0000032>
<rdfs:label xml:lang="en">channel1/channel2 fluorescence intensity ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000211 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000211">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">odds ratio homogeneity hypothesis is a null hypothesis stating that all odds ratio are homogenous, that is remain within the same range.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">odds ratio homogeneity hypothesis</obo:STATO_0000032>
<rdfs:label xml:lang="en">odds ratio homogeneity hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000212 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000212">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000269"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.rasch.org/rmt/rmt193c.htm
and
http://en.wikipedia.org/wiki/Polychoric_correlation</obo:IAO_0000119>
<rdfs:label xml:lang="en">tetrachoric correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000213 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000213">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000251"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000102"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000055"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000087"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">discretization as a processing converting a continuous variable into a polychotomous variable by concretizing a set of discretization rules</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB,PRS adapted from wikipedia (http://en.wikipedia.org/wiki/Discretization)</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://cran.r-project.org/web/packages/discretization/index.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">continuous variable discretization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000214 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000214">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000561"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0002135"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">50</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a confidence interval which covers 50% of the sampling distribution, meaning that there is a 50% risk of false positive (type I error)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">confidence interval at 10% of type I error rate</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">50% confidence interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000215 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000215">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000107"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000228"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">probit regression model is a model which attempts to explain data distribution associated with *ordinal* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the ordered probit function.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">ordered probit regression for analysis of ordinal dependent variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000216 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000216">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000096"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label>stratum population</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000217 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000217">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000065"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000183"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a null hypothesis which states that a given matrix is proportional to a Wishart-distributed covariance matrix</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">hypothesis of sphericity</obo:STATO_0000032>
<rdfs:label xml:lang="en">sphericity hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000218 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000218">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000119"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000472"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000063"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000143"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000191"/>
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Model fitting is a data transformation process which evaluates if a model appropriately represents a dataset. A model fitting process tests the goodness of fit of the model to the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">model fitting</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000219 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000219">
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000414"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33696"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a real time pcr standard curve is a line graph which plots the fluorescence intensity signal as a function of the concentration of a sample used as reference and used to determine relative abundance of test samples</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/qpcr_technical_guide.pdf
and
http://www.lifetechnologies.com/uk/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">RT-PCR standard curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000220 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000220">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO, adapted from</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">type II error rate</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">β</obo:STATO_0000032>
<rdfs:label xml:lang="en">false negative rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000221 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000221">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000258"/>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">aleatory variable</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">stochastic variable</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">wikipedia:
http://en.wikipedia.org/wiki/Random_variable</obo:IAO_0000119>
<rdfs:label xml:lang="en">random variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000222 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000222">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500007"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000517"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">3</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000248"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">graeco-latin square design is_a study design which allows in its simpler form controlling 3 levels of nuisance variables (also known as blocking variables). The 3 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">graeco-latin square design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000223 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000223">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600015"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">group assignment based on blocking variable specification is a kind of group assignment process which takes into account the levels assumed by a blocking variable to allocate subjects or experimental units to a treatment group</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">group assignment based on blocking variable specification</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000224 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000224">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000058"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A testing objective to ensure that the sample used in a statistical test actually follows a normal distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">goodness of fit testing objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000225 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000225">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000068"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000237"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000435"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000436"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000500"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A probability distribution is a information content entity that specifies the probability of the value of a random variable.
For a discrete random variable, a mathematical formula that gives the probability of each value of the variable.
For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000226 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000226">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000054"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>It is a testing objective to ensure the variances of the different groups used in a statistical test are similar (i.e. not too different).</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>homoschedacity testing objective</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">equal variance testing objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000227 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000227">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000329"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000068"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a normal distribution is a continuous probability distribution described by a probability distribution function described here:
http://mathworld.wolfram.com/NormalDistribution.html</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Gaussian distribution</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/NormalDistribution.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.norm.html#scipy.stats.norm</obo:STATO_0000391>
<rdfs:label xml:lang="en">normal distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000228 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000228">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000118"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltan</obo:IAO_0000117>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">ranked variable</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statvartypes.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">ordinal variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000229 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000229">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Chi-square probability distribution with k degrees of freedom is a theoretical probability distribution which corresponds to the distribution of a sum of the squares of k independent standard normal random variables.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000041 xml:lang="en">dchisq(x, df, ncp = 0, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Chisquare.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2.html#scipy.stats.chi2</obo:STATO_0000391>
<rdfs:label xml:lang="en">Chi-square probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000230 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000230">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000221"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the expected value (or expectation, mathematical expectation, EV, mean, or the first moment) of a random variable is a data item which corresponds to the weighted average of all possible values that this random variable can take on. The weights used in computing this average correspond to the probabilities in case of a discrete random variable, or densities in case of a continuous random variable. From a rigorous theoretical standpoint, the expected value is the integral of the random variable with respect to its probability measure.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">first moment</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">mean</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">μ</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Expected_value</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">expected value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000231 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000231">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000561"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0002135"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">95</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a confidence interval which covers 95% of the sampling distribution, meaning that there is a 5% risk of false positive (type I error). If the number of observations made is large enough, the sampling distribution can be assumed to be normal, which entails that 95% of the sampling distributions falls within roughly2 (1.96) standard deviations from the mean.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">confidence interval at 5% of type I error rate</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">95% confidence interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000232 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000232">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from various sources including:
http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml</obo:IAO_0000119>
<rdfs:label xml:lang="en">number of PCR cycle</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000233 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000233">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">recall</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">sensitivity</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/Sensitivity_and_specificity
and
http://mathworld.wolfram.com/Sensitivity.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">true positive rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000234 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000234">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000242"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a residual is a data item which is the output of an error estimate or model fitting process and which is an observable estimate of the unobservable error</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">residual</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000235 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000235">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A genetic association study is a kind of study whose objective is to detect associations between phenotypes, between a phenotype and a genetic polymorphism or between two genetic polymorphisms.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Genetic_association</obo:IAO_0000119>
<rdfs:label xml:lang="en">genetic association study</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000236 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000236">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the coefficient of variation is a normalized measure of dispersion of a probability distribution of frequency distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Coefficient_of_variation
last accessed: 2013-10-18</obo:IAO_0000119>
<obo:STATO_0000391 xml:lang="en">scipy.stats.variation(a, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.variation.html#scipy.stats.variation
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L951</obo:STATO_0000391>
<rdfs:label xml:lang="en">coefficient of variation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000237 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000237">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The standard deviation of a random variable, statistical population, data set, or probability distribution is a measure of variation which correspond to the average distance from the mean of the data set to any given point of that dataset. It also corresponds to the square root of its variance.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">σ</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Standard_deviation</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">sd(x, na.rm = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/sd.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">standard deviation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000238 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000238">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000239"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000964"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200169"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000277"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000185"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000916"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000164"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100064"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">high content screening is a kind of investigation which uses a standardized cellular assays to test the effect of substances (RNAi or small molecules) held in libraries on a cellular phenotype. it relies on microscopy imaging and or flow-cytometry, robotic handling to ensure fast and high-throughput.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/High-content_screening</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">high-content screening</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000239 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000239">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000277"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000164"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100064"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_1000029"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000443"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000964"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000700"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200102"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000279"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000135"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">high throughput screening is a kind of investigation which uses a standardized assays (cell based, enzymatic or chemometric) to test the effect of substances (RNAi or small molecules) held in libraries on a very specific and measureable outcome (e.g fluorence intensity). it relies on robotic handling to ensure fast and high-throughput in assay performance, data acquisition and hit selection.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB,PRS</obo:IAO_0000119>
<rdfs:label xml:lang="en">high throughput screening</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000240 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000240">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000228"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Kendall rank correlation coefficient</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Kendall's tau (τ) coefficient</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient), polled in june 2013
and from:
http://stamash.org/pearsons-correlation-coefficient/
http://stamash.org/kendalls-tau-correlation/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">cor(x, y = NULL, use = "everything",method = c("kendall"))</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.kendalltau(x, y, initial_lexsort=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kendalltau.html#scipy.stats.kendalltau
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2827</obo:STATO_0000391>
<rdfs:label xml:lang="en">Kendall's correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000241 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000241">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000291"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000291"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Q-Q plot or quantile-quantile plot is the output of a graphical method for comparing two probability distributions by plotting their quantiles against each other</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">PRS,AGB: need to add the notion of quantile</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">quantile-quantile plot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">qqplot(x, y, plot.it = TRUE, xlab = deparse(substitute(x)),
ylab = deparse(substitute(y)), ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/qqnorm.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Q-Q plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000242 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000242">
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<obo:IAO_0000115 xml:lang="en">statistical error is an data item denoting the amount by which an observation differs from the expected value, being based on the whole statistical population from which the statistical unit was chosen randomly</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Errors_and_residuals_in_statistics
last accessed: 18-11-2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">disturbance</obo:STATO_0000032>
<rdfs:label xml:lang="en">statistical error</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000243 -->
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<obo:IAO_0000112>A box and whisker plot is appropriate to represent the characteristics oc a distribution.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Tukey box and whisker plot</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">box plot</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Tukey, J. W. "Box-and-Whisker Plots." §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, pp. 39-43, 1977.</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">boxplot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">boxplot(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/boxplot.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">box and whisker plot</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000244 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">(Rn +) − (Rn −), where Rn + = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR with template and Rn − = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR without template or early cycles of a real-time reaction. Ct = threshold cycle, i.e., cycle at which a statistically significant increase in ΔRn is first detected</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://jcm.asm.org/content/38/7/2516.figures-only</obo:IAO_0000119>
<rdfs:label xml:lang="en">ΔRn</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000245 -->
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<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
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<obo:IAO_0000115>Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>risk ratio</obo:IAO_0000118>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label>relative risk</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000246 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000247"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000697"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Woolf's test is a statistical test which evaluates the null hypothesis that odds ratio are the same accross all strata of population under investigation</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://people.umass.edu/biep640w/pdf/4.%20%20Categorical%20Data%20Analysis%202012.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">woolf_test(x) where x is 2 x 2 x k contingency table
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vcd/html/woolf_test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Woolf's test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000247 -->
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<obo:IAO_0000115 xml:lang="en">odds ratio homogeneity test is a statistical test which aims to evaluate that null the hypothesis of consistency odds ratio accross different strata of population is true or not</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">odds ratio homogeneity test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000248 -->
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<obo:IAO_0000112>https://onlinecourses.science.psu.edu/stat503/node/19
Often in medical studies, the blocking factor used is the type of institution. This provides a very useful blocking factor, hopefully removing institutionally related factors such as size of the institution, types of populations served, hospitals versus clinics, etc., that would influence the overall results of the experiment.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a blocking variable is a independent variable which is used in a blocking process part of an experiment with the purpose of maximizing the signal coming from the main variable.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>nuisance variable</obo:IAO_0000118>
<obo:IAO_0000119>https://onlinecourses.science.psu.edu/stat503/node/18</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">blocking variable</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000249 -->
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<obo:IAO_0000115 xml:lang="en">a DNA microarray hybridization is an assay relying on nucleic acid hybridization , which uses a DNA microarray device and a nucleic acid as input. It precedes a data acquisition process</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">DNA microarray hybridization</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000250 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000250">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">group comparison objective is a data transformation objective which aims to determine if 2 or more study group differ with respect to the signal of a response variable</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">group comparison objective</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000251 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000251">
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<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/STATO_0000252"/>
<obo:IAO_0000112 xml:lang="en">"Time to solve an anagram problem" is continuous since it could take 2 minutes, 2.13 minutes etc. to finish a problem</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A continuous variable is one for which, within the limits the variable ranges, any value is possible.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://davidmlane.com/hyperstat/A97418.html</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statvartypes.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">continuous variable</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000252 -->
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">discrete variable</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">nominal variable</obo:IAO_0000118>
<obo:IAO_0000118>qualitative factor</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://udel.edu/~mcdonald/statvartypes.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<dc:source>https://onlinecourses.science.psu.edu/stat503/node/7</dc:source>
<rdfs:label xml:lang="en">categorical variable</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000253 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000253">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">within subject comparison objective</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000254 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.nature.com/scitable/definition/allele-frequency-298</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">gene frequency</obo:STATO_0000032>
<rdfs:label>allele frequency</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000255 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000255">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000061"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the objective of a data transformation to test a null hypothesis of absence of difference withing subject holds.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">between group comparison objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000256 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000256">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000184"/>
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<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000063"/>
</owl:Restriction>
</owl:intersectionOf>
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</owl:someValuesFrom>
</owl:Restriction>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OGMS_0000023"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200094"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
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<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000091"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000091"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a manhattan plot for gwas is a kind of scatter plot used to facilitate presentation of genome-wide association study (GWAS) data. Genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism displayed on the Y-axis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Manhattan_plot</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL,
cutoff = NULL, cutoff.color = "red", cutoff.size = 1,
legend = FALSE, xlim, ylim, xlab, ylab, main)
http://www.tengfei.name/ggbio/docs/man/plotGrandLinear.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">manhattan plot for gwas</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000257 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000257">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000181"/>
<obo:IAO_0000115 xml:lang="en">A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">import from Population and Community Ontology:
http://www.ontobee.org/browser/rdf.php?o=PCO&iri=http://purl.obolibrary.org/obo/PCO_0000020</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://purl.obolibrary.org/obo/PCO_0000020</obo:IAO_0000119>
<rdfs:label xml:lang="en">family</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000258 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000258">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000751"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000251"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2.
and from Oxford English Dictionary:
http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">variable</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000260 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000260">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000202"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000086"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
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<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000199"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000253"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000003"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000750"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000584"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">repeated measure ANOVA is a kind of ANOVA specifically developed for non-independent observations as found when repeated measurements on the sample experimental unit.
repeated measure ANOVA is sensitive to departure from normality (evaluation using Bartlett's test), more so in the case of unbalanced groups (i.e. different sizes of sample populations).
Departure from sphericity (evaluation using Mauchly'test) used to be an issue which is now handled robustly by modern tools such as R's lme4 or nlme, which accommodate dependence assumptions other than sphericity.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">discussion in https://github.com/ISA-tools/stato/issues/28</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">ANOVA for correlated samples</obo:IAO_0000118>
<obo:IAO_0000119>adapted from wikipedia and https://statistics.laerd.com/statistical-guides/repeated-measures-anova-statistical-guide-3.php</obo:IAO_0000119>
<obo:IAO_0000119>http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm</obo:IAO_0000119>
<obo:STATO_0000032>ANOVA for correlated samples</obo:STATO_0000032>
<obo:STATO_0000041>http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html</obo:STATO_0000041>
<rdfs:label>repeated measure ANOVA</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000261 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000261">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000133"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000023"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000230"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Newman–Keuls or Student–Newman–Keuls (SNK) method is a stepwise multiple comparisons procedure used to identify sample means that are significantly different from each other. It was named after Student (1927), D. Newman, and M. Keuls. This procedure is often used as a post-hoc test whenever a significant difference between three or more sample means has been revealed by an analysis of variance (ANOVA). The Newman–Keuls method is similar to Tukey's range test as both procedures use Studentized range statistics.Compared to Tukey's range test, the Newman–Keuls method is more powerful but less conservative.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
last accessed: 2013-11-15</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">SNK.test(y, trt, DFerror, MSerror, alpha = 0.05, group=TRUE, main = NULL)
http://artax.karlin.mff.cuni.cz/r-help/library/agricolae/html/SNK.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Newman-Keuls test post-hoc analysis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000262 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000262">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000276"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Bernoulli distribution is a binomial distribution where the number of trials is equal to 1.
notation: B(1,p)
The mean is p
The variance is p*q</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">Bernoulli distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000263 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000263">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000184"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000037"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
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</rdfs:subClassOf>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000155"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Galbraith (Radial) plot is a scatter plot which can be used in the meta-analytic context to examine the data for heterogeneity. For a fixed-effects model, the plot shows the inverse of the standard errors on the horizontal axis against the individual observed effect sizes or outcomes standardized by their corresponding standard errors on the vertical axis.
Radial plots were introduced by Rex Galbraith (1988a, 1988b, 1994).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Galbraith, Rex (1988). "Graphical display of estimates having differing standard errors". Technometrics (Technometrics, Vol. 30, No. 3) 30 (3): 271–281. doi:10.2307/1270081. JSTOR 1270081</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">radial Galbraith plot</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/Luminescence/docs/plot_RadialPlot
plot_RadialPlot(data, na.exclude = TRUE, negatives = "remove",
log.z = TRUE, central.value, centrality = "mean.weighted",
plot.ratio, bar.col, grid.col, legend.text, summary = FALSE,
stats, line, line.col, line.label, output = FALSE, ...)</obo:STATO_0000041>
<obo:STATO_0000041 xml:lang="en">http://www.metafor-project.org/doku.php/plots:radial_plot</obo:STATO_0000041>
<rdfs:label xml:lang="en">Galbraith plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000264 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000264">
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</owl:Restriction>
</owl:intersectionOf>
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</rdfs:subClassOf>
<obo:IAO_0000112>http://isogenic.info/html/9__treatments.html#factorial</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a factor level combination is one a possible sets of factor levels resulting from the cartesian product of sets of factor and their levels as defined in a factorial design</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>treatment combination</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">factor level combination</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000265 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000265">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000112>http://isogenic.info/html/9__treatments.html#factorial</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A factor level is data item which corresponds to one of the value assumed by a factor or independent variable manipulated and set by the experimentalist. In the context of factorial design, a factor level is assumed to be or treated as a category in a categorical variable</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>treatment</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">AGB-PRS</obo:IAO_0000119>
<obo:IAO_0000119>https://onlinecourses.science.psu.edu/stat503/node/7</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">factor level</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000266 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000266">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported.
The Bayes factor is about the plausibility of 2 different models</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia
last accessed 2013-11-13</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">Bayes factor</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000267 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000267">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000166"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from
http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts
and
http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/
[last accessed: 2014-03-04]</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">barplot(height....)
set argument " beside = TRUE "
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html</obo:STATO_0000041>
<rdfs:label>grouped bar chart</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000268 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000268">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000435"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000436"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A gamma distribution is a general type of continous statistical distribution (related to the beta distribution) that arises naturally in processes for which the waiting times between Poisson distributed events are relevant. Gamma distributions have two free parameters shape k and scale denoted theta .</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/GammaDistribution.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gamma.html#scipy.stats.gamma</obo:STATO_0000391>
<rdfs:label xml:lang="en">Gamma distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000269 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000269">
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<rdfs:subClassOf>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000251"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom>
<owl:Class>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000019"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
</owl:Restriction>
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</owl:someValuesFrom>
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</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000087"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.rasch.org/rmt/rmt193c.htm
and
http://en.wikipedia.org/wiki/Polychoric_correlation</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://cran.r-project.org/web/packages/polycor/
polychor(x, y, ML = FALSE, control = list(), std.err = FALSE, maxcor=.9999)</obo:STATO_0000041>
<rdfs:label xml:lang="en">polychoric correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000270 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000270">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000195"/>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000192"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000192"/>
</owl:Restriction>
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</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/OBI_0000750"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a full factorial design is a factorial design which ensures that all possible factor level combinations are defined and used so all between group differences can be explored</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">full factorial design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000271 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000271">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">permutation numbering is a data tranformation allowing to count the number of possible permutations of elements in a set of size n, each element occurring exactly once. This number is factorial n.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">permutation numbering</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000272 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000272">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Michaelis constant is the substrate concentration at which the reaction rate is at half-maximum, and is an inverse measure of the substrate's affinity for the enzyme—as a small indicates high affinity, meaning that the rate will approach more quickly.[5] The value of is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Michaelis–Menten_constant
last accessed: 22-11-2013</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">half maximal reaction rate substrate concentration (Km)</obo:STATO_0000032>
<rdfs:label xml:lang="en">Michaelis-Menten constant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000273 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000273">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000257"/>
<obo:IAO_0000115>A population of two parents and a child.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">possibly submit to 'Population and Community Ontology'</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032>child-parent trio</obo:STATO_0000032>
<obo:STATO_0000032>parent-child trio</obo:STATO_0000032>
<obo:STATO_0000032>parents-child trio</obo:STATO_0000032>
<rdfs:label xml:lang="en">child-parents trio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000274 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000274">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
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<owl:someValuesFrom>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000233"/>
</owl:Restriction>
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<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000134"/>
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000031"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200111"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">receiver operational characteristics curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold (aka cut-off point) is varied by plotting sensitivity vs (1 − specificity)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>ROC curve</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Receiver_operating_characteristic</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">roc.from.table(table, graph = TRUE, add = FALSE, title = FALSE,
line.col = "red", auc.coords = NULL, ...)
http://rss.acs.unt.edu/Rdoc/library/epicalc/html/roc.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">receiver operational characteristics curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000275 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000275">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000053"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">The transmission disequilibrium test is a statistical test for genetic linkage between genetic marker and a trait in families. The test is robust to population structure.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">TDT</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO , adapted wikipedia (from http://en.wikipedia.org/wiki/Transmission_disequilibrium_test), polled on June,2013</obo:IAO_0000119>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">transmission disequilibrium test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000276 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000117"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N.
The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N.
The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p )
notation: B(n,p)
The mean is N*p
The variance is N*p*q</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Binomial_distribution</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dbinom(x, size, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom.html#scipy.stats.binom</obo:STATO_0000391>
<rdfs:label xml:lang="en">binomial distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000277 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">hit selection is a planned process which in screening processes such as high-throughput screening, lead to the identification of perturbing agent which cause the typical signal generated by a standardized assay to significantly differ from the negative control. The selection hitself results from meeting or exceeding selection threshold (for instance 6 sigma from the mean or SSMD value beyond 5 when compared to positive controls or below -5 when compared to negative controls</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">AGB, PRS</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/SSMD</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">hit selection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000278 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000278">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000055"/>
<obo:IAO_0000112 xml:lang="en">age-matched participants</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">pairing rule is a rule which specifies the criteria for deciding on how to associated any 2 entities.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">pairing rule</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000279 -->
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<owl:equivalentClass>
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">between group comparison statistical test is a statistical test which aims to detect difference between the means computing for each of the study group populations</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label>between group comparison statistical test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000280 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000280">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
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</owl:Restriction>
</rdfs:subClassOf>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
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<owl:Class>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000019"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists.
The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Pearson product-moment correlation coefficient</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Pearson's r</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">r statistics</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO, adapted from
http://www.r-tutor.com/elementary-statistics/numerical-measures/correlation-coefficient
and from:
http://stamash.org/pearsons-correlation-coefficient/
http://stamash.org/kendalls-tau-correlation/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">cor(x, y = NULL, use = "everything",method = c("pearson"))</obo:STATO_0000041>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.pearsonr(x, y)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2427</obo:STATO_0000391>
<rdfs:label xml:lang="en">Pearson's correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000282 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000282">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000404>F</obo:STATO_0000404>
<rdfs:label xml:lang="en">F-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000283 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000283">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000117"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur. The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Pascal distribution</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Pólya distribution</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/NegativeBinomialDistribution.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dnbinom(x, size, prob, mu, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/NegBinomial.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.nbinom.html#scipy.stats.nbinom</obo:STATO_0000391>
<rdfs:label xml:lang="en">negative binomial distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000284 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000284">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
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</owl:Restriction>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Breusch-Pagan test is a statistical test which computes a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the response (fitted values), or with a linear combination of predictors.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Breusch, T. S. and Pagan, A. R. (1979) A simple test for heteroscedasticity and random coefficient variation. Econometrica 47, 1287--1294.
and adapted from:
http://www.inside-r.org/packages/cran/car/docs/ncvTest
last accessed [2014-03-15]</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/bptest.html
bptest(formula, varformula = NULL, studentize = TRUE, data = list())
or
http://www.inside-r.org/packages/cran/car/docs/ncvTest</obo:STATO_0000041>
<rdfs:label xml:lang="en">Breusch-Pagan test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000285 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000287"/>
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</owl:Restriction>
</rdfs:subClassOf>
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<owl:someValuesFrom>
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000675"/>
<owl:Restriction>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000296"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000297"/>
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</owl:intersectionOf>
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<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/?term=17182697
Bioinformatics. 2007 Feb 15;23(4):401-7.
Enrichment or depletion of a GO category within a class of genes: which test?
Rivals I1, Personnaz L, Taing L, Potier MC.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">hypergeometric test is a null hypothesis test which evaluates if a random variable follows a hypergeometric distribution. It is a test of goodness of fit to that distribution. The test is suited for situation aimed at assessing cases of sampling from a finite set without replacements. For instance, testing for enrichment or depletion of elements (e.g GO categories, genes)</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000041 xml:lang="en">phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE)
lower.tail
logical; if TRUE (default), probabilities are P[X ≤ x], otherwise, P[X > x].
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">hypergeometric test</rdfs:label>
</owl:Class>
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a one-tailed test is a statistical test which, assuming an unskewed probability distribution, allocates all of the significance level to evaluate only one hypothesis to explain a difference.
The one-tailed test provides more power to detect an effect in one direction by not testing the effect in the other direction.
one-tailed test should be preceded by two-tailed test in order to avoid missing out on detecting alternate effect explaining an observed difference.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">one sided test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">one tailed test</rdfs:label>
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<obo:IAO_0000112 xml:lang="en">For example, we may wish to compare the mean of a sample to a given value x using a t-test. Our null hypothesis is that the mean is equal to x. A two-tailed test will test both if the mean is significantly greater than x and if the mean significantly less than x. The mean is considered significantly different from x if the test statistic is in the top 2.5% or bottom 2.5% of its probability distribution, resulting in a p-value less than 0.05.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a two tailed test is a statistical test which assess the null hypothesis of absence of difference assuming a symmetric (not skewed) underlying probability distribution by allocating half of the significance level selected to each of the direction of change which could explain a difference (for example, a difference can be an excess or a loss).</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">two sided test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">two tailed test</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">A null hypothesis which states that no difference exists between 2 or more groups being considered.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">absence of difference hypothesis</rdfs:label>
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<obo:IAO_0000112 xml:lang="en">let's consider an experiment evaluating 2 compounds (aspirin & ibuprofen) at 3 distinct dose levels (low, medium, high) and 4 time points post exposure (0h, 6h, 12h, 24h). Assuming the treatments are applied only once (no replication), the number of observation in a full factorial design is 2 x 3 x 4 = 24 so the design matrix would have 24 rows and 3 columns (1 per factor (independent variable).</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a design matrix is an information content entity which denotes a study design. The design matrix is a n by m matrix where n the number of rows, corresponds to the number of observations (4 rows if quadruplicates) and where m, the number of columns corresponds to the number of independent variables. Each element in the matrix correspond to a discretized value representing one of the factor levels for a given factor.
A design matrix can be used as input to statistical modeling or statistical analysis.
The design matrix contains data on the independent variables (also called explanatory variables) in statistical models which attempt to explain observed data on a response variable (often called a dependent variable) in terms of the explanatory variables. The theory relating to such models makes substantial use of matrix manipulations involving the design matrix: see for example linear regression. A notable feature of the concept of a design matrix is that it is able to represent a number of different experimental designs and statistical models, e.g., ANOVA, ANCOVA, and linear regression</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/9</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">model matrix</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
Design of Experiments: Principles and Applications
edited by Lennart Eriksson, 1999-2008 Umetrics. ISBN-13:978-91-973730-4-3
and
http://en.wikipedia.org/wiki/Design_matrix
[last accessed: 22-05-2014]</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">model.matrix(object, data = environment(object),
contrasts.arg = NULL, xlev = NULL, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/model.matrix.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">design matrix</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115 xml:lang="en">A contrast is the weighted sum of group means, the c_j coefficients represent the assigned weights of the means (these must sum to 0 for orthogonal contrasts)</obo:IAO_0000115>
<obo:IAO_0000116>Term request by Nolan Nichols via https://github.com/ISA-tools/stato/issues/9</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Contrast_%28statistics%29</obo:IAO_0000119>
<obo:STATO_0000041>contrasts(x, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrasts.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">contrast</rdfs:label>
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a quantile is a data item which corresponds to specific elements x in the range of a variate X.
the k-th n-tile P_k is that value of x, say x_k, which corresponds to a cumulative frequency of Nk/n (Kenney and Keeping 1962). If n=4, the quantity is called a quartile, and if n=100, it is called a percentile.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Evans, M.; Hastings, N.; and Peacock, B. Statistical Distributions, 3rd ed. New York: Wiley, 2000.</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://mathworld.wolfram.com/Quantile.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">quantile</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000292 -->
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a decile is a quantile where n=10 and which splits data into sections accrued of 10% of data, so the first decile delineates 10% of the data, the second decile delineates 20% of the data and the nineth decile, 90 % of the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">decile</rdfs:label>
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a percentile is a quantile which splits data into sections accrued of 1% of data, so the first percentile delineates 1% of the data, the second quartile delineates 2% of the data and the 99th percentile, 99 % of the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">percentile</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000294 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly less than a threshold does not exist.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">absence of negative difference hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000295 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly greater than a threshold does not exist.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">absence of positive difference hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000296 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000296">
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<obo:IAO_0000115 xml:lang="en">absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly greater than a threshold does not exist.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">absence of over representation hypothesis</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">absence of enrichment hypothesis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000297 -->
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<obo:IAO_0000115 xml:lang="en">absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly less than a threshold does not exist.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">absence of under representation hypothesis</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">absence of depletion hypothesis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000298 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a binomial test is a statistical hypothesis test which evaluates if the observations made about a Bernoulli experiment , that is an experiment which tests the statistical significance of deviations from a theoretically expected distribution (the binomial distribution) of observations into 2 categories. It is a goodness of fit test.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/Binomial_test</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">binomial test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">binom.test(x, n, p = 0.5,
alternative = c("two.sided", "less", "greater"),
conf.level = 0.95)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/binom.test.html</obo:STATO_0000041>
<rdfs:comment>scipy.stats.binom_test(x, n=None, p=0.5)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom_test.html#scipy.stats.binom_test
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1605</rdfs:comment>
<rdfs:label xml:lang="en">exact binomial test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000299 -->
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000144"/>
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<obo:IAO_0000112 xml:lang="en">Evaluation of statistical inference on empirical resting state fMRI.
IEEE Trans Biomed Eng. 2014 Apr;61(4):1091-9. doi: 10.1109/TBME.2013.2294013.
http://www.ncbi.nlm.nih.gov/pubmed/24658234</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Statistical inference is the process of deducing properties of an underlying probability distribution by analysis of data.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Added following a term request by Nolan Nichols:
https://github.com/ISA-tools/stato/issues/12</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Definition changed according to discussions in https://github.com/ISA-tools/stato/issues/55</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>The definition cited from Wikipedia is from: Upton, G., Cook, I. (2008) Oxford Dictionary of Statistics, OUP. ISBN 978-0-19-954145-4</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Statistical_inference</obo:IAO_0000119>
<rdfs:label xml:lang="en">statistical inference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000300 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000300">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A ratio where the numerator and denominator are expressed in the same unit.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">dimensionless ratio</obo:STATO_0000032>
<rdfs:label>dimensionless ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000301 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000301">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000611"/>
<rdfs:subClassOf>
<owl:Restriction>
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<owl:minQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:minQualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000230"/>
</owl:Restriction>
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<owl:Restriction>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The covariance is a measurement data item about the strength of correlation between a set (2 or more) of random variables.
The covariance is obtained by forming:
cov(X,Y)=E([X-E(X)][Y-E(Y)] where E(X), E(Y) is the expected value (mean) of variable X and Y respectively.
covariance is symmetric so cov(X,Y)=cov(Y,X).
The covariance is usefull when looking at the variance of the sum of the 2 random variables since:
var(X+Y) = var(X) +var(Y) +2cov(X,Y)
The covariance cov(x,y) is used to obtain the coefficient of correlation cor(x,y) by normalizing (dividing) cov(x,y) but the product of the standard deviations of x and y.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://mathworld.wolfram.com/Covariance.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">covariance</obo:STATO_0000032>
<obo:STATO_0000041>cov(x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman"))
from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">covariance</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000302 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000302">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000739"/>
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</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
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<rdfs:subClassOf>
<owl:Restriction>
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</owl:Restriction>
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<rdfs:subClassOf>
<owl:Restriction>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">one sample t-test is a kind of Student's t-test which evaluates if a given sample can be reasonably assumed to be taken from the population.
The test compares the sample statistic (m) to the population parameter (M).
The one sample t-test is the small sample analog of the z test, which is suitable for large samples.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from various sources, including:
Practical Statistics for Medical Research by D.Altman.
ISBN: 0-412-27630-5
http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tone.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">one sample t-test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">t.test(x = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = FALSE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html</obo:STATO_0000041>
<obo:STATO_0000391>scipy.stats.ttest_1samp(a, popmean, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_1samp.html#scipy.stats.ttest_1samp
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3194</obo:STATO_0000391>
<rdfs:label xml:lang="en">one sample t-test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000303 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
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<owl:Restriction>
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<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:hasValue>
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<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">two sample t-test is a null hypothesis statistical test which is used to reject or accept the hypothesis of absence of difference between the means over 2 randomly sampled populations.
It uses a t-distribution for the test and assumes that the variables in the population are normally distributed and with equal variances.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">two sample t-test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/Student's_t-test#Independent_.28unpaired.29_samples
and from:
http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tind.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">t-test for independent means assuming equal variance</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">t.test(x, y = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = TRUE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html</obo:STATO_0000041>
<obo:STATO_0000391>scipy.stats.ttest_ind(a, b, axis=0, equal_var=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271</obo:STATO_0000391>
<rdfs:label xml:lang="en">two sample t-test with equal variance</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000304 -->
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<obo:IAO_0000115 xml:lang="en">Welch t-test is a two sample t-test used when the variances of the 2 populations/samples are thought to be unequal (homoskedasticity hypothesis not verified). In this version of the two-sample t-test, the denominator used to form the t-statistics, does not rely on a 'pooled variance' estimate.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Welsh t-test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Welch, B. L. (1947). "The generalization of "Student's" problem when several different population variances are involved". Biometrika 34 (1–2): 28–35. doi:10.1093/biomet/34.1-2.28</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Welch's_t_test
last accessed: 2014-05-06</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">t-test for independent means assuming unequal variance</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">t.test(x, y = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = FALSE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html</obo:STATO_0000041>
<obo:STATO_0000391>scipy.stats.ttest_ind(a, b, axis=0, equal_var=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271</obo:STATO_0000391>
<rdfs:label xml:lang="en">two sample t-test with unequal variance</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">A Helmert contrast is a contrast in which the coefficients for the Helmert regressors compare each level with the average of the “preceding” ones</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.clayford.net/statistics/tag/helmert-contrasts/
An R and S-Plus Companion to Applied Regression. John Fox
ISBN-13: 978-0761922803</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">contr.helmert(n, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Helmert contrast</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000306 -->
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<obo:IAO_0000115 xml:lang="en">a polynomial contrast is a contrast which...</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">contr.poly(n, scores = 1:n, contrasts = TRUE, sparse = FALSE)
from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">polynomial contrast</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000307 -->
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<obo:IAO_0000115 xml:lang="en">treatment contrast is a contrast which allows to test how linear model coefficients of categorical variables are interpreted in case where the “first” level (aka, the baseline) is included into the intercept and all subsequent levels have a coefficient that represents their difference from the baseline.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from multiple sources:
http://pic.dhe.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_idd_genlin_emmeans.htm
http://www.clayford.net/statistics/tag/helmert-contrasts/
http://www.aliquote.org/articles/tech/contrasts.html</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">contr.treatment(n, base = 1, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">treatment contrast</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000308 -->
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<obo:IAO_0000115 xml:lang="en">the sum contrast is a contrast in which each coefficient compares the corresponding level of the factor to the average of the other levels</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.clayford.net/statistics/tag/helmert-contrasts/
An R and S-Plus Companion to Applied Regression. John Fox
ISBN-13: 978-0761922803</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">contr.sum(n, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">sum contrast</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Pearson's Chi-Squared test for goodnes of fit is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Chi2 test for goodness of fit</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
and
http://en.wikipedia.org/wiki/Pearson's_chi-squared_test</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
chisq.test(x = NULL, correct = FALSE,
p = rep(1/length(x), length(x)), rescale.p = FALSE,
simulate.p.value = FALSE, B = 2000)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Pearson's Chi square test of goodness of fit</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">Barnard's test is an exact statistical test used to determine if there are non-random associations between two categorical variables. It was developed in 1949 by Barnard and is a test which is, most times, more powerful that the Fisher exact test</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Barnard's_test
and
G A Barnard (1945) "A New Test for 2X2 Tables", Nature, 156, 177 & 783.</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Barnard's test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">barnardw.test(n1, n2, n3, n4, dp = 0.001, verbose = FALSE)
from
http://www.inside-r.org/packages/cran/Barnard/docs/barnardw.test</obo:STATO_0000041>
<rdfs:label xml:lang="en">Barnard's test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000311 -->
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<obo:IAO_0000115 xml:lang="en">a central composite design is a study design which contains an imbedded factorial or fractional factorial design with center points that is augmented with a group of so-called 'star points' that allow estimation of curvature.
A CCD design with k factors has 2k star points.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.itl.nist.gov/div898/handbook/pri/section3/pri3361.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Box-Wilson Central Composite Design</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">cd(basis, generators, blocks = "Block", n0 = 4, alpha = "orthogonal",
wbreps = 1, bbreps = 1, randomize = TRUE, inscribed = FALSE, coding)
http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/ccd.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">central composite design</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000312 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000312">
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<obo:IAO_0000115 xml:lang="en">The Box-Behnken design is an independent quadratic design in that it does not contain an embedded factorial or fractional factorial design. In this design the treatment combinations are at the midpoints of edges of the process space and at the center. These designs are rotatable (or near rotatable) and require 3 levels of each factor. The designs have limited capability for orthogonal blocking compared to the central composite designs.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.itl.nist.gov/div898/handbook/pri/section3/pri3362.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">bbd(k, n0 = 4, block = (k == 4 | k == 5), randomize = TRUE, coding)
from:
http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/bbd.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Box–Behnkens design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000313 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000313">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Plackett-Burman design is a type of study design optimizing multifactorial experiments characterized by their parsimony and economy with the run number a multiple of 4 (rather than a power of 2).
Plackett-Burman design is often used for screening experiments where the main effect is often heavily confounded with two-factor interactions.
This type of design is very useful for economically detecting large main effects, assuming all interactions are negligible when compared with the few important main effects.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.itl.nist.gov/div898/handbook/pri/section3/pri335.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">pb(nruns, nfactors = nruns - 1, factor.names = if (nfactors <= 50)
Letters[1:nfactors] else paste("F", 1:nfactors, sep = ""),
default.levels = c(-1, 1), ncenter=0, center.distribute=NULL,
boxtyssedal = TRUE, n12.taguchi = FALSE,
replications = 1, repeat.only = FALSE,
randomize = TRUE, seed = NULL, oldver = FALSE, ...)
from:
http://www.inside-r.org/packages/cran/FrF2/docs/pb</obo:STATO_0000041>
<rdfs:label xml:lang="en">Plackett-Burman design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000314 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000314">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000633"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">upper confidence limit is a data item which is a largest value bounding a confidence interval</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">upper confidence limit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000315 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000315">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000633"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000196"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">lower confidence limit is a data item which is a lowest value bounding a confidence interval</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">lower confidence limit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000316 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000316">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">root-mean-square standardized effect is a statistic which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Ψ</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.statpower.net/Steiger%20Biblio/Steiger04.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">RMSSE</obo:STATO_0000032>
<rdfs:label xml:lang="en">root-mean-square standardized effect</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000317 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000317">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Effect_size#Eta-squared.2C_.CE.B72</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">η2</obo:STATO_0000032>
<rdfs:label xml:lang="en">eta-squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000318 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000318">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000085"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://en.wikipedia.org/wiki/Effect_size#Omega-squared.2C_.CF.892</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">ω2</obo:STATO_0000032>
<rdfs:label xml:lang="en">omega-squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000319 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000319">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hedges's g is an estimator of effect size, which is similar to Cohen's d and is a measure based on a standardized difference. However, the denominator, corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from :
http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d
and
http://blog.stata.com/tag/cohens-d/</obo:IAO_0000119>
<rdfs:label xml:lang="en">Hedges's g</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000320 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000320">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000175"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from :
http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d
and
http://blog.stata.com/tag/cohens-d/</obo:IAO_0000119>
<rdfs:label xml:lang="en">Glass's delta</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000321 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000321">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000329"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000068"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000129"/>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">0</owl:hasValue>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Karl Helmer</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<rdfs:comment>Initially discussed at https://github.com/incf-nidash/nidm/pull/191</rdfs:comment>
<rdfs:label>non-parametric distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000322 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000322">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000112 xml:lang="en">http://artax.karlin.mff.cuni.cz/r-help/library/nparcomp/html/weight.matrix.html</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a contrast weight is a coefficient which multiplies a group mean, part of a linear combinaison defining a constrast as a weighted sum of group means, giving a 'weight' to a specific group mean hence the name.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
http://en.wikipedia.org/wiki/Contrast_%28statistics%29</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">contrast coefficient</obo:STATO_0000032>
<rdfs:label xml:lang="en">contrast weight</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000323 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000323">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000322"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000290"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">[1,0,0]</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">contrast weights</obo:STATO_0000032>
<rdfs:label xml:lang="en">contrast weight matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000324 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000324">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000144"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000322"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000403"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">contrast weight estimate is a model parameter estimate which results from the computation from the data and that is used as input to a model fitting process</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">contrast weight estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000325 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000325">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000328"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/7791040</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Akaike information criterion (AIC) is a measure of the relative quality of a statistical model for a given set of data. As such, AIC provides a means for model selection. AIC is defined as:
AIC = 2K - 2log(L)
where K is the number of predictors and L is the maximized likelihood value.
AIC deals with the trade-off between the goodness of fit of the model and the complexity of the model. It is founded on information theory: it offers a relative estimate of the information lost when a given model is used to represent the process that generates the data. AIC does not provide a test of a model in the sense of testing a null hypothesis; i.e. AIC can tell nothing about the quality of the model in an absolute sense. If all the candidate models fit poorly, AIC will not give any warning of that.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Akaike_information_criterion
and
http://users.ecs.soton.ac.uk/jn2/teaching/aic.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">AIC</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">AIC(object, ..., k = 2)
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/AIC.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Akaike information criterion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000326 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000326">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000325"/>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/19761098</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">corrected Akaike information criteria is a modified version of the Akaike information criterion.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032 xml:lang="en">CAIC</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">corrected Akaike information criterion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000327 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000327">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000328"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/7791040</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">Bayesian information criterion or Schwartz's Bayesian information criterion is a criterion for model selection among a finite set of models. It is based, in part, on the likelihood function and it is closely related to the Akaike information criterion (AIC).
Given any two estimated models, the model with the lower value of BIC is the one to be preferred. The BIC is an increasing function of sigma_e^2 and an increasing function of k. That is, unexplained variation in the dependent variable and the number of explanatory variables increase the value of BIC. Hence, lower BIC implies either fewer explanatory variables, better fit, or both.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
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<obo:IAO_0000115 xml:lang="en">Probability distribution estimated empirically from a censored lifetime data</obo:IAO_0000115>
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<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
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<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Henderson C. R., 1984 Applications of Linear Models in Animal Breeding. University of Guelph, Guelph, Ontario, Canada.
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<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suiteable model</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119>http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf</obo:IAO_0000119>
<rdfs:label xml:lang="en">covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000347 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">Given two sets of locations computes the Matern cross covariance matrix for covariances among all pairings.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Matern covariance function</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.rdocumentation.org/packages/fields/versions/2.3/topics/matern.cov</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">matern.cov</obo:STATO_0000041>
<rdfs:label xml:lang="en">Matern function anisotropic covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000348 -->
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<obo:IAO_0000115 xml:lang="en">The rational quadratic covariance function is used in spatial statistics, geostatistics, machine learning, image analysis, and other fields where multivariate statistical analysis is conducted on metric spaces. It is commonly used to define the statistical covariance between measurements made at two points that are d units distant from each other. Since the covariance only depends on distances between points, it is stationary. If the distance is Euclidean distance, the rational quadratic covariance function is also isotropic.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Rational_quadratic_covariance_function</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corRatio.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">rational quadratic anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000349 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000349">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">spatial linear geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give linear features.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SP(LINGA)</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corLin.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">spatial linear geometric anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000350 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000350">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">spatial spherical geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give spherical features.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">SP(SPHGA)</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corSpher.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">spatial spherical geometric anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000351 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000351">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">spatial gaussian geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give gaussian features.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SP(GAUGA)</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corGaus.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">spatial gaussian geometric anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000352 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000352">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">spatial exponential geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give exponential features.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SP(EXPGA)</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">spatial exponential geometric anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000353 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000353">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">spatial exponential anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give exponential features.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SP(EXPA)(c-list)</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Sacks et al. (1989)</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corExp.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">spatial exponential anisotropic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000354 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000354">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>the banded heterogeneous Toeplitz covariance structure is a type of coviance structure which is often used to analyzed and intepret repeated measure design.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">TOEPH(q)</obo:STATO_0000032>
<rdfs:label xml:lang="en">banded heterogeneous Toeplitz covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000355 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000355">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">This covariance structure has heterogenous variances and heterogenous correlations between elements. The correlation between adjacent elements is homogenous across pairs of adjacent elements. The correlation between elements separated by a third is again homogenous, and so on.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">TOEPH</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
as well as:
https://www.ibm.com/support/knowledgecenter/en/SSLVMB_23.0.0/spss/advanced/covariance_structures.html</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">heterogeneous Toeplitz covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000356 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000356">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A banded Toeplitz structure, defined by parameter q, can be viewed as a moving-average structure with order q-1.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">TOEP(q)</obo:STATO_0000032>
<rdfs:label xml:lang="en">banded Toeplitz covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000357 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000357">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">The Toeplitz covariance structure has homogenous variances and heterogenous correlations between elements. The correlation between adjacent elements is homogenous across pairs of adjacent elements. The correlation between elements separated by a third is again homogenous, and so on.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.ibm.com/support/knowledgecenter/en/SSLVMB_23.0.0/spss/advanced/covariance_structures.html</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">TOEP</obo:STATO_0000032>
<rdfs:label xml:lang="en">Toeplitz covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000358 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000358">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a form of covariance structure used to provide analysis ground s in the context of repeated measures datasets (longitudinal, time series)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">HF</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Huynh and Feldt 1970</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">Huynh-Feldt covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000359 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000359">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000361"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">factor-analytic structure is a covariance structure which is specified for q factors
equal diagonal factor-analytic covariance structure is a type of factor analytic covariance structure specified for q factors, which includes a diagonal component for repeated measures.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">FA1(q)</obo:STATO_0000032>
<rdfs:label xml:lang="en">equal diagonal Factor Analytic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000360 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000360">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000361"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">no diagonal factor-analytic covariance structure is a type of factor analytic covariance structure specified for q factors, which does not include a diagonal component for repeated measures.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">FA0(q)</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">no diagonal Factor Analytic covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000361 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000361">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">factor-analytic structure is a type of heterogeneous covariance structure which is specified for q factors</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
Heterogeneous Variance: Covariance Structures for Repeated Measures
Russell D. Wolfinger. Journal of Agricultural, Biological, and Environmental Statistics
Vol. 1, No. 2 (Jun., 1996), pp. 205-230.
https://doi.org/10.2307/1400366
and
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Jennrich and Schluchter 1986</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">FA(q)</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">Factor Analytic covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000362 -->
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<obo:IAO_0000115 xml:lang="en">compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">CS</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">compound symmetry covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000363 -->
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<obo:IAO_0000115 xml:lang="en">heterogenous compound symmetry structure is a compound symmetry covariance structure which has a different variance parameter for each diagonal element, and it uses the square roots of these parameters in the off-diagonal entries.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">CSH</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">heterogeneous compound symmetry covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000364 -->
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<obo:IAO_0000115 xml:lang="en">first order autoregressive moving average covariance structure is a type of covariance structure which is used in the context of time series analysis</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">ARMA(1,1)</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corARMA.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">first order autoregressive moving average covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000365 -->
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<obo:IAO_0000115 xml:lang="en">first order autoregressive covariance structure is a covariance structure where correlations among errors decline exponentially with distance</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">AR(1)</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corAR1.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">first order autoregressive covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000366 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">This is an homogeneous structure, i.e. the variance along the main diagonal is constant. The covariances decline exponentially. It has only 2 parameters.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">ARH(1)</obo:STATO_0000032>
<rdfs:label xml:lang="en">heterogeneous first-order autoregressive covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000367 -->
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<obo:IAO_0000115 xml:lang="en">Ante-dependence covariance structure is a covariance structure which specifies that the covariance between two time points is a function of the product of variances at both points (hence allowing hetrogenity of error variance across measures to affect the correlation) and the product of the correlations at the distances up to the one chosen.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">ANTE(1)</obo:STATO_0000032>
<rdfs:label xml:lang="en">Ante-dependence covariance structure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000368 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Mallows' Cp is a data item which compares the precision and bias of the full model to models with a subset of the predictors thus helping to choose between multiple regression models.
the mallows cp is a function of the number of parameter used in the model relying on the residuals sum of squares to compute a score.
the smaller Cp is, the better the model fit is.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/regression-and-correlation/goodness-of-fit-statistics/what-is-mallows-cp/</obo:IAO_0000119>
<obo:STATO_0000041>http://ugrad.stat.ubc.ca/R/library/locfit/html/cp.html</obo:STATO_0000041>
<rdfs:label>Mallows' Cp</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000369 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">repeated measure analysis is a kind of data transformation which deals with signals measured in the same experimental units at different times and, possibly, under different conditions over a period of time. Data produced by longitudinal studies qualify for such analysis. Since measurements are made on the same experimental units a number of times, they are likely to be correlated. Repeated measure analysis usually takes into consideration the possibility of correlation with time. It does so by specifying covariance structure in the analysis</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from https://ciser.cornell.edu/sasdoc/saspdf/analyst/chap16.pdf</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">repeated measure analysis</obo:STATO_0000032>
<rdfs:label xml:lang="en">repeated measure analysis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000370 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000370">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols</obo:IAO_0000119>
<obo:STATO_0000032>OLS estimation</obo:STATO_0000032>
<obo:STATO_0000041>https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">ordinary least squares estimation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000371 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols</obo:IAO_0000119>
<obo:STATO_0000032>WLS estimation</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">weighted least squares estimation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000372 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to "whiten" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols</obo:IAO_0000119>
<obo:STATO_0000032>GLS estimation</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">generalized least squares estimation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000373 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Tom Nichols</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">iteratively reweighted least squares estimation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000374 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119>Tom Nichols</obo:IAO_0000119>
<rdfs:label xml:lang="en">feasible generalized least squares estimation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000375 -->
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<obo:IAO_0000112>used as an unbiased estimator of the variance for a regression model</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a residual mean square is a data item which is obtained by dividing the sum of squared residuals (SSR) by the number of degrees of freedom</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Mean_squared_error#Regression</obo:IAO_0000119>
<obo:IAO_0000119>http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/anova/anova-statistics/understanding-mean-squares/</obo:IAO_0000119>
<obo:IAO_0000119>https://github.com/ISA-tools/stato/issues/35</obo:IAO_0000119>
<obo:STATO_0000032>MSE</obo:STATO_0000032>
<obo:STATO_0000032>error mean square</obo:STATO_0000032>
<rdfs:label>residual mean square</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000376 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maument</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Z-test</obo:IAO_0000119>
<rdfs:label>Z-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000377 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Deviance is an indicator of fit and can be estimated by computing -2 times the log-likelihood ratio of the fitted model compared to a saturated(full) model.
It is a generalization of the idea of using the sum of squares of residuals in ordinary least squares to cases where model-fitting is achieved by maximum likelihood.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Deviance_%28statistics%29</obo:IAO_0000119>
<obo:STATO_0000032>deviance</obo:STATO_0000032>
<obo:STATO_0000041>https://stat.ethz.ch/R-manual/R-devel/library/stats/html/deviance.html</obo:STATO_0000041>
<rdfs:label>deviance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000378 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000378">
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<obo:IAO_0000112 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682718/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The deviance information criterion (DIC) is a hierarchical modeling generalization of the AIC (Akaike information criterion) and BIC (Bayesian information criterion, also known as the Schwarz criterion). It is particularly useful in Bayesian model selection problems where the posterior distributions of the models have been obtained by Markov chain Monte Carlo (MCMC) simulation. Like AIC and BIC it is an asymptotic approximation as the sample size becomes large. It is only valid when the posterior distribution is approximately multivariate normal.
The deviance information criterion was published in 2002 by Spiegelhalter et al.
Spiegelhalter, D. J., N. G. Best, B. P. Carlin, and A. van der Linde, 2002. Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society, B, 64, 583-639.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Deviance_information_criterion</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">DIC</obo:STATO_0000032>
<obo:STATO_0000041>http://artax.karlin.mff.cuni.cz/r-help/library/SpatialExtremes/html/DIC.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">deviance information criterion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000379 -->
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</owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">The focused information criterion is a measurement data item which aims at facilitating model selection. It was published in 2003 by Claeskens, G. and Hjort, N.L. (2003). "The focused information criterion".</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Journal of the American Statistical Association, volume 98, pp. 879–899. doi:10.1198/016214503000000819</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">FIC</obo:STATO_0000032>
<rdfs:label xml:lang="en">focused information criterion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000383 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000383">
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000322"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000384"/>
</owl:Restriction>
<owl:Restriction>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a data transformation that finds a contrast value (the contrast estimate) by computing the weighted sum of model parameter estimates using a set of contrast weights.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119>https://github.com/ISA-tools/stato/pull/37</obo:IAO_0000119>
<rdfs:label xml:lang="en">contrast estimation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000384 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000384">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf>
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</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
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</owl:Restriction>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">estimate of a contrast obtained by computing the weighted sum of model parameter estimates using a set of contrast weights.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119>https://github.com/ISA-tools/stato/pull/37</obo:IAO_0000119>
<rdfs:label xml:lang="en">contrast estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000385 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000385">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000562"/>
<rdfs:subClassOf>
<owl:Class>
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<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000384"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000383"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000403"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an estimate of the standard deviation of a contrast estimate sampling distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119>https://github.com/ISA-tools/stato/pull/37</obo:IAO_0000119>
<rdfs:label xml:lang="en">standard error of a contrast estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000386 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000386">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A scree plot is a graphical display of the variance of each component in the dataset which is used to determine how many components should be retained in order to explain a high percentage of the variation in the data</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.stats.gla.ac.uk/glossary/?q=node/451</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Cattell scree test plot</obo:STATO_0000032>
<obo:STATO_0000041>screeplot(x, npcs = min(10, length(x$sdev)),
type = c("barplot", "lines"),
main = deparse(substitute(x)), ...)
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/screeplot.html</obo:STATO_0000041>
<rdfs:label>scree plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000387 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000387">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A scatterplot matrix contains all the pairwise scatter plots of a set of variables on a single page in a matrix format.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Adapted from http://itl.nist.gov/div898/handbook/eda/section3/eda33qb.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">scatterplot matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000388 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000388">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">The alpha distribution is a continuous probability distribution whose density function is as defined at: https://docs.scipy.org/doc/scipy-1.0.0/reference/tutorial/stats/continuous_alpha.html</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://docs.scipy.org/doc/scipy-1.0.0/reference/tutorial/stats/continuous_alpha.html</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.alpha.html#scipy.stats.alpha</obo:STATO_0000391>
<rdfs:label xml:lang="en">alpha distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000389 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000389">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a power-law probability distribution is a probability distribution whose density function (or mass function in the discrete case) has the form
p(x) = L(x) . x^{-alpha}
where alpha is a parameter >1 and L(x) is a slowly varying function.</obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia and wolfram alpha:
https://en.wikipedia.org/wiki/Power_law#Power-law_probability_distributions
last accessed: 2015-11-03</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">https://cran.r-project.org/web/packages/poweRlaw/index.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.powerlaw.html#scipy.stats.powerlaw</obo:STATO_0000391>
<rdfs:label xml:lang="en">power law distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000390 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000390">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A regression model is a statistical model used in a type of analysis knowns as regression analysis, whereby a function is used to determine the relation between a response variable and an independent variable , with a set of unknown parameters.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Regression_analysis#Regression_models
last accessed: 2015-11-03</obo:IAO_0000119>
<rdfs:label xml:lang="en">regression model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000392 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000392">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000435"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Pareto distribution is a continuous probability distribution, which is defined by the follwoing probability density (1) function and distribution function (2)
(1): P(x)=(ab^a)/(x^(a+1))
(2): D(x)=1-(b/x)^a
defined over the interval x>=b.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapter from:
http://mathworld.wolfram.com/ParetoDistribution.html
last accessed: 2015-11-04</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://artax.karlin.mff.cuni.cz/r-help/library/LaplacesDemon/html/dist.Pareto.html
last accessed: 2015-11-04
Usage
>dpareto(x, alpha, log=FALSE)
>ppareto(q, alpha)
>qpareto(p, alpha)
>rpareto(n, alpha)
Arguments
x,q
These are each a vector of quantiles.
p
This is a vector of probabilities.
n
This is the number of observations, which must be a positive integer that has length 1.
alpha
This is the shape parameter alpha, which must be positive.
log
Logical. If log=TRUE, then the logarithm of the density or result is returned.</obo:STATO_0000041>
<rdfs:label xml:lang="en">Pareto type-I probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000393 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000393">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Pareto type-II probability distribution is a continuous probability distribution which is defined by a probability density function characterized by 2 parameters, alpha and lambda, 2 real, strictly positive numbers. alpha is known as the shape parameter while lambda is known as the scale parameter.
the function defines the probably of a continous random variable according to the following:
p(x) = {\alpha \over \lambda} \left[{1+ {x \over \lambda}}\right]^{-(\alpha+1)}, \qquad x \geq 0,</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Lomax_distribution</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Lomax distribution</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/actuar/docs/Pareto
dpareto(x, shape, scale, log = FALSE)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Pareto type-II probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000394 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000394">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Pareto(III) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form:
F(x) = 1 − [1 + ((x − mu)/sigma)1/gamma]−1
for x > mu, sigma > 0, gamma > 0 and s =1.
a is the location parameter,
b is the scale parameter,
g is the inequality parameter
s is the shape parameter of value 1
The Pareto III distribution corresponds to a Pareto Type IV distribution where the shape parameter has a value of 1.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Pareto_distribution#Pareto_types_I.E2.80.93IV
last accessed: 2015-11-04</obo:IAO_0000119>
<rdfs:label xml:lang="en">Pareto type-III probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000395 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000395">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000205"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000435"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Pareto(IV) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form:
F(y) = 1 − [1 + ((y − a)/b)1/g]−s
for y > a, b > 0, g > 0 and s > 0.
a is the location parameter,
b is the scale parameter,
g is the inequality parameter
s is the shape parameter
The distribution is used in actuarial science, economics, finance and telecommunications, but not restricted to those fields.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://cran.r-project.org/web/packages/VGAM/VGAM.pdf
page 517</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">dparetoIV(x, location = 0, scale = 1, inequality = 1, shape = 1, log = FALSE)
https://cran.r-project.org/web/packages/VGAM/VGAM.pdf</obo:STATO_0000041>
<rdfs:label xml:lang="en">Pareto type-IV probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000396 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000396">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000112 xml:lang="en">The geometric mean of two numbers, say 2 and 8, is just the square root of their product; that is sqrt(2 x 8)=4.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The geometric mean is defined as the nth root of the product of n numbers, i.e., for a set of numbers \{x_i\}_{i=1}^N, the geometric mean is defined as \left(\prod_{i=1}^N x_i\right)^{1/N}.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
https://en.wikipedia.org/wiki/Mean#Geometric_mean_.28GM.29
https://en.wikipedia.org/wiki/Geometric_mean</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://personality-project.org/r/html/geometric.mean.html
Usage: >geometric.mean(x,na.rm=TRUE)
Arguments: x , a vector or data.frame</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.gmean.html</obo:STATO_0000391>
<rdfs:label xml:lang="en">geometric mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000397 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000397">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000115 xml:lang="en">The harmonic mean is a kind of mean which is calculated by dividing the total number of observations by the reciprocal of each number in a series.
Harmonic Mean = N/(1/a1+1/a2+1/a3+1/a4+.......+1/aN)
where a(i)= Individual score and N = Sample size (Number of scores)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia and
https://www.easycalculation.com/statistics/learn-harmonic-mean.php
last accessed: 2015-11-04</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Harmonic_mean</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Mean#Harmonic_mean_.28HM.29</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://personality-project.org/r/html/harmonic.mean.html
Usage: > harmonic.mean(x,na.rm=TRUE)
Arguments:
x, a vector, matrix, or data.frame
na.rm, na.rm=TRUE remove NA values before processing.</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.hmean.html</obo:STATO_0000391>
<rdfs:label xml:lang="en">harmonic mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000398 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000398">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value.
The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others.
The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Matthew Diller</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Weighted_arithmetic_mean</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">weighted average</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">weighted.mean(x, w, ...)
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/weighted.mean.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">From numpy
https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html
np.average(range(1,11), weights=range(10,0,-1))</obo:STATO_0000391>
<doap:bug-database xml:lang="en">https://github.com/ISA-tools/stato/issues/59</doap:bug-database>
<rdfs:label xml:lang="en">weighted arithmetic mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000399 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000399">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000163"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">The interquartile mean (IQM) (or midmean) is a statistical measure of central tendency based on the truncated mean of the interquartile range.
In the calculation of the IQM, only the data in the second and third quartiles is used (as in the interquartile range), and the lowest 25% and the highest 25% of the scores are discarded. These points are called the first and third quartiles, hence the name of the IQM.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">IQM</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Mean#Interquartile_mean</obo:IAO_0000119>
<rdfs:label xml:lang="en">interquartile mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000400 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000400">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The root mean square (abbreviated RMS or rms), also known as the quadratic mean, in statistics is a statistical measure of central tendency defined as the square root of the mean of the squares of a sample.
( To find the root mean square of a set of numbers, square all the numbers in the set and then find the arithmetic mean of the squares. Take the square root of the result. This is the root mean square.)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">RMS</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">root mean square</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Root_mean_square
and
http://www.mathwords.com/r/root_mean_square.htm
last accessed: 2015-11-04</obo:IAO_0000119>
<rdfs:label xml:lang="en">quadratic mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000401 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000401">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000679"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000573"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000651"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000403"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000402"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">the sample mean of sample of size n with n observations is an arithmetic mean computed over n number of observations on a statistical sample.
The sample mean, denoted x¯ and read “x-bar,” is simply the average of the n data points x1, x2, ..., xn:
x¯=x1+x2+⋯+xnn=1n∑i=1nxi
The sample mean summarizes the "location" or "center" of the data.
the sample mean is a measure of dispersion of the observations made on the sample and provides an unbias estimate of the population mean</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
https://onlinecourses.science.psu.edu/stat414/node/66
and
http://mathworld.wolfram.com/SampleMean.html
last accessed: 2015-11-05</obo:IAO_0000119>
<rdfs:label xml:lang="en">sample mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000402 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000402">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000029"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">the population mean or distribution mean is a parameter of a probability distribution or population indicative of the data dispersion. For continous probabibility distribution, the population mean is computed using the probability density function, for discrete probability distributions, a mass density function is used instead.
A population mean can be estimated by computing a sample mean</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>distribution mean</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://mathworld.wolfram.com/PopulationMean.html
last accessed: 2015-11-05</obo:IAO_0000119>
<rdfs:label xml:lang="en">population mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000405 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000405">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A covariance structure where no restrictions are made on the covariance between any pair of measurements.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Camille Maumet</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Thomas Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct</obo:IAO_0000119>
<rdfs:label xml:lang="en">unstructured covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000406 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000406">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000163"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000193"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Yuen's t-test is a two sample t-test with populations of unequal variance which provides a more robust t-test procedure under normal distribution and long tailed distributions.
The test computes a t statistics not using 'arithmetic means' but using 'trimmed means' instead as well as winsorized variances.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Yuen-Welch's t-test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Biometrika (1974) 61 (1): 165-170
10.1093/biomet/61.1.165</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://finzi.psych.upenn.edu/library/DescTools/html/YuenTTest.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Yuen t-Test with trimmed means</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000407 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000407">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000007"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000409"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000417"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Fagan nomogram is a graph plotting pre-test probabilities, likelyhood ratios and post-test probabilities on 3 parallel axis. The plot was first proposed by Fagan in 1975 as a way to visualize Baye's Theorem data where
P(D) is the probability that the patient has the disease before the test. P(D|T) is the probability that the patient has the disease after the test result. P(T|D) is the probability of the test result if the patient has the disease, and P(T|D̄) is the probability of the test result if the patient does not have the disease. With this terminology the usefulness of both positive and negative test results can be assessed. A line drawn from P(D) on the right through the ratio of P(T|D) to P(T|D̄) gives P(D|T) on the left of the nomogram.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/1143310
N Engl J Med 1975; 293:257July 31, 1975
DOI: 10.1056/NEJM197507312930513</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">Fagan nomogram</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000408 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000408">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000134"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000233"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000409"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000007"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000417"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Two-Step Fagan Nomogram, which adds two extra axis between the LR axis that represents sensibility and specificity to calculate negative and positive likelihood ratios in the same nomogram</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/23468201</obo:IAO_0000119>
<rdfs:label xml:lang="en">2 step Fagan nomogram</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000409 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000409">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000622"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000314"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the likelihood ratio is a ratio which is formed by dividing the post-test odds with the pre-test odds in the context of a Bayesian formulation</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<rdfs:label xml:lang="en">likelihood ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000410 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000410">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the likelihood ratio of negative results is a ratio which is formed by dividing the difference between 1 and sensitivity of the test by the specificity value of a test. This can be expressed also as dividing the probability of a person who has the disease testing negative by the probability of a person who does not have the disease testing negative.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">likelihood ratio for negative results</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing
last accessed: May 2016</obo:IAO_0000119>
<rdfs:label xml:lang="en">negative likelihood ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000411 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000411">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000409"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the likelihood ratio of positive results is a ratio which is form by dividing the sensitivity value of a test by the difference between 1 and specificity of the test. This can be expressed also as dividing the probability of the test giving a positive result when testing an affected subject versus the probability of the test giving a positive result when a subject is not affected.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">likelihood ratio for positive results</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing
last accessed: May 2016</obo:IAO_0000119>
<rdfs:label xml:lang="en">positive likelihood ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000412 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000412">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000112>disease prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A proportion in which the numerator represents all events of interest (for example, both new and preexisting cases of a disease) in the population, which is represented by the denominator.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">prevalence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000413 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000413">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000112>For instance, Disease Incidence is the ratio of the number of new cases of a disease divided by the number of persons at risk for the disease.</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A proportion in which the numerator represents new events.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-01-12 vote 6-0 by Harold Lehman, Mario Tristan, janice tufte, Andrew Beck, Robin Ann Yurk, Paul Harris</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>cumulative incidence</obo:IAO_0000118>
<obo:IAO_0000118>incidence proportion</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">incidence</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000414 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000414">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">mortality is a ratio formed by the number of deaths due to a disease divided by the total population size.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">mortality</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000415 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000415">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000639"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">in the context of binary classification, accuracy is defined as the proportion of true results (both true positives and true negatives) to the total number of cases examined (the sum of true positive, true negative, false positive and false negative).
It can be understood as a measure of the proximity of measurement results to the true value.
Accuracy is a metric used in the context of classification tasks to evaluate the proportion of correctly predicted instances among the total instances.
Key Points:
Use Case: Classification performance evaluation.
Metric: Measures the proportion of correct predictions.
Interpretation: Higher values indicate better classification performance.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">In the context of unsupervised learning, such as in clustering, the same formula is used to calculate the Rand Index or Rand accuracy.
The Rand Index is primarily used to measure the similarity between two data clusterings. It is commonly employed in clustering validation to compare the similarity between a predicted clustering and a ground truth clustering.
Key Points:
Use Case: Clustering validation.
Metric: Measures pairwise agreement between two clusterings.
Interpretation: Higher values indicate more similar clusterings</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification
last accessed: May 2016
adapted from ChatGPT using the following prompt: [what is the difference between "Rand Index" and "Accuracy" in statistics]
last accessed: July 2024</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Rand index</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">Accuracy(y_pred, y_true)
from:
https://www.rdocumentation.org/packages/MLmetrics/versions/1.1.1/topics/Accuracy</obo:STATO_0000041>
<rdfs:label xml:lang="en">accuracy</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000416 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000416">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">precision or positive predictive value is defined as the proportion of the true positives against all the positive results (both true positives and false positives)
A proportion in which the numerator represents the correctly detected items within the denominator that represents all items detected.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">positive predictive value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification
last accessed: May 2016</obo:IAO_0000119>
<rdfs:label xml:lang="en">precision</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000417 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000417">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The probability of a patient having the target disorder before a diagnostic test result is known</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.cebm.net/pre-test-probability/</obo:IAO_0000119>
<rdfs:label xml:lang="en">pretest probability</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000418 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000418">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a measure of heterogeneity in meta-analysis is a data item which aims to describe the variation in study outcomes between studies.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from http://www.statsdirect.com/help/default.htm#meta_analysis/heterogeneity.htm
last accessed: May 2016</obo:IAO_0000119>
<rdfs:label xml:lang="en">measure of heterogeneity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000419 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000419">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000418"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Cochran's Q statistic is a measure of heterogeneity accros study computed by summing the squared deviations of each study's estimate from the overall meta-analytic estimate, weighting each study's contribution in the same manner as in the meta-analysis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Cochran WG. The combination of estimates from different experiments. Biometrics 1954;10: 101-29.
https://doi.org/10.2307/3001666</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/RVAideMemoire/docs/cochran.qtest</obo:STATO_0000041>
<rdfs:label xml:lang="en">Cochran's Q statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000420 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000420">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000418"/>
<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The quantity called I2, describes the percentage of total variation across studies that is due to heterogeneity rather than chance. I2 can be readily calculated from basic results obtained from a typical meta-analysis as I2 = 100%×(Q - df)/Q, where Q is Cochran's heterogeneity statistic and df the degrees of freedom. Negative values of I2 are put equal to zero so that I2 lies between 0% and 100%. A value of 0% indicates no observed heterogeneity, and larger values show increasing heterogeneity.
Unlike Cochran's Q, it does not inherently depend upon the number of studies considered. A confidence interval for I² is constructed using either i) the iterative non-central chi-squared distribution method of Hedges and Piggott (2001); or ii) the test-based method of Higgins and Thompson (2002). The non-central chi-square method is currently the method of choice (Higgins, personal communication, 2006) – it is computed if the 'exact' option is selected.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">I2</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC192859/
and
http://www.statsdirect.com/help/default.htm#meta_analysis/heterogeneity.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">I-squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000421 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000421">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000418"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Tau-squared is an estimate of the between-study variance in a random-effects meta-analysis. The square root of this number (i.e. tau) is the estimated standard deviation of underlying effects across studies.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://handbook.cochrane.org/chapter_9/9_5_4_incorporating_heterogeneity_into_random_effects_models.htm</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/metacor</obo:STATO_0000041>
<rdfs:label xml:lang="en">Tau squared</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000422 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000422">
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<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200111"/>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The L’Abbé plot was introduced in 1987 in the context of meta-analyses of clinical trials with dichotomous (binary) outcomes, as a plot of observed risks in the treatment group against observed risks in the control group.
Another formulation is that it plots the event rate in the experimental (intervention) group against the event rate in the control group, as an aid to exploring the heterogeneity of effect estimates within a meta-analysis.
It is diagram used in meta-analysis that compares the risks observed in the experimental and control arms of clinical trials. Each trial is located in the space of a diagram where the sizes of the circles indicate the sizes of the trials. Trials in which the experimental treatment had a higher risk than the control will be in the upper left of the plot. If risk in the both groups is the same the circle will fall on the line of equality. If the control treatment has a higher risk than the experimental treatment then the point will be in the lower right of the plot. It is often used as an indicator of heterogeneity and hence as an indicator of the likelihood that results from different trials can be validly combined. Named after Kristin L'Abbé.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">10.1002/jrsm.6
Graphical displays for meta-analysis: An overview with suggestions for practice</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/3300460
and
http://www.dictionarycentral.com/definition/l-abb-plot.html</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/labbe.metabin</obo:STATO_0000041>
<rdfs:label xml:lang="en">L'Abbe plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000423 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000423">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000620"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the proportion of individuals in a population with the outcome of interest</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://handbook.cochrane.org/chapter_9/9_2_2_4_measure_of_absolute_effect_the_risk_difference.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">observed risk</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000424 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000424">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000614"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The risk difference is the difference between the observed risks (proportions of individuals with the outcome of interest) in the two groups.
The risk difference is straightforward to interpret: it describes the actual difference in the observed risk of events between experimental and control interventions.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Harold Lehmann, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>ARD</obo:IAO_0000118>
<obo:IAO_0000118>RD</obo:IAO_0000118>
<obo:IAO_0000118>absolute risk difference</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://handbook.cochrane.org/chapter_9/9_2_2_4_measure_of_absolute_effect_the_risk_difference.htm</obo:IAO_0000119>
<rdfs:label xml:lang="en">risk difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000425 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000425">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Sidik-Jonkman estimator is a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/16955539</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="FALSE",
method.tau="SJ",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Sidik-Jonkman estimator</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000426 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000426">
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Hunter-Schmidt estimator is a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Methods of Meta-Analysis: Correcting Error and Bias in Research Findings. by John E. Hunter, Frank L. Schmidt
doi:10.2307/2289738</obo:IAO_0000119>
<obo:STATO_0000041>http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="FALSE",
method.tau="HS",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">Hunter-Schmidt estimator</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000427 -->
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<obo:IAO_0000115 xml:lang="en">restricted maximum likelihood estimation is a kind of maximum likelihood estimation data transformation which estimates the variance components of random-effects in univariate and multivariate meta-analysis. in contrast to 'maximum likelihood estimation', reml can produce unbiased estimates of variance and covariance parameters.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.1093/biomet/58.3.545</obo:IAO_0000119>
<obo:STATO_0000032>REML</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">reml(y, v, x, data, RE.constraints = NULL, RE.startvalues = 0.1,
RE.lbound = 1e-10, intervals.type = c("z", "LB"),
model.name="Variance component with REML",
suppressWarnings = TRUE, silent = TRUE, run = TRUE, ...)
https://www.rdocumentation.org/packages/metaSEM/versions/1.0.0/topics/reml</obo:STATO_0000041>
<rdfs:label xml:lang="en">restricted maximum likelihood estimation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000428 -->
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<obo:IAO_0000115 xml:lang="en">maximum likelihood estimation (MLE) is a method of estimating the parameters of a statistical model, given observations. MLE attempts to find the parameter values that maximize the likelihood function, given the observations.
The method of maximum likelihood is based on the likelihood function, {\displaystyle {\mathcal {L}}(\theta \,;x)} {\displaystyle {\mathcal {L}}(\theta \,;x)}. We are given a statistical model, i.e. a family of distributions {\displaystyle \{f(\cdot \,;\theta )\mid \theta \in \Theta \}} {\displaystyle \{f(\cdot \,;\theta )\mid \theta \in \Theta \}}, where {\displaystyle \theta } \theta denotes the (possibly multi-dimensional) parameter for the model. The method of maximum likelihood finds the values of the model parameter, {\displaystyle \theta } \theta , that maximize the likelihood function, {\displaystyle {\mathcal {L}}(\theta \,;x)} {\displaystyle {\mathcal {L}}(\theta \,;x)}. I</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Maximum_likelihood_estimation</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">maximum likelihood estimation</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">DerSimonian-Laird estimator s a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis. The estimator is used in simple noniterative procedure for characterizing the distribution of treatment effects in a series of studies</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">doi:10.1016/j.cct.2006.04.004</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">http://www.ncbi.nlm.nih.gov/pubmed/3802833
doi:10.1016/0197-2456(86)90046-2</obo:IAO_0000119>
<obo:STATO_0000041>http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="FALSE",
method.tau="DL",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">DerSimonian-Laird estimator</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000430 -->
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<obo:IAO_0000115 xml:lang="en">a random effect meta analysis procedure defined by Hartung and Knapp and by Sidik and Jonkman which performs better than DerSimonian and Laird approach, especially when there is heterogeneity and the number of studies in the meta-analysis is small.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">HKSJ method</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">doi:10.1186/1471-2288-14-25</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="TRUE",
method.tau="HS",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">meta analysis by Hartung-Knapp-Sidik-Jonkman method</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000431 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">a meta analysis which relies on the computation of the DerSimonian and Leard estimator as a measure of heterogeneity over a set of studies.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="FALSE",
method.tau="DL",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">meta analysis by DerSimonian and Leard method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000432 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">a meta analysis which relies on the computation of the Hunter and Schmidt estimator as a measure of heterogeneity over a set of studies by considering the weighted mean of the raw correlation coefficient. Hunter and Schmidt developed what is commonly termed validity generalization procedures (Schmidt and Hunter, 1977). These involve correcting the effect sizes in the meta-analysis for sampling, and measurement error
and range restriction.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Hunter JE, Schmidt FL. Methods of Meta-analysis: correcting error and bias in research findings. Newbury Park, CA: Sage 1990.</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">http://www.inside-r.org/packages/cran/meta/docs/metacor
metacor(cor, n, studlab,
data=NULL, subset=NULL,
sm=.settings$smcor,
level=.settings$level, level.comb=.settings$level.comb,
comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random,
hakn="FALSE",
method.tau="HS",
tau.common=.settings$tau.common,
prediction=.settings$prediction, level.predict=.settings$level.predict,
method.bias=.settings$method.bias,
backtransf=.settings$backtransf,
title=.settings$title, complab=.settings$complab, outclab="",
byvar, bylab, print.byvar=.settings$print.byvar,
keepdata=.settings$keepdata
)</obo:STATO_0000041>
<rdfs:label xml:lang="en">meta analysis by Hunter-Schmidt method</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">McNemar's test is a statistical test used on paired nominal data. It is applied to 2 × 2 contingency tables with a dichotomous trait, with matched pairs of subjects, to determine whether the row and column marginal frequencies are equal (that is, whether there is "marginal homogeneity"). It is named after Quinn McNemar, who introduced it in 1947.
An application of the test in genetics is the transmission disequilibrium test for detecting linkage disequilibrium</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">McNemar's Chi-squared Test for Count Data</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">test of the marginal homogeneity of a contingency table</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">within-subjects chi-squared test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/McNemar%27s_test
last accessed: May 2016</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.ncbi.nlm.nih.gov/pubmed/20254758</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">mcnemar.test(x, y = NULL, correct = TRUE)
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/mcnemar.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">McNemar test</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Cochran's Q test is a statistical test used for unreplicated randomized block design experiments with a binary response variable and paired data.
In the analysis of two-way randomized block designs where the response variable can take only two possible outcomes (coded as 0 and 1), Cochran's Q test is a non-parametric statistical test to verify whether k treatments have identical effects.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.inside-r.org/packages/cran/CVST/docs/cochranq.test
and
https://en.wikipedia.org/wiki/Cochran%27s_Q_test
last accessed: May 2016</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">cochran.qtest(formula, data, alpha = 0.05, p.method = "fdr")
from:
http://www.inside-r.org/packages/cran/RVAideMemoire/docs/cochran.qtest</obo:STATO_0000041>
<rdfs:label xml:lang="en">Cochran's q test for heterogeneity</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000435 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
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<obo:IAO_0000112 xml:lang="en"></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a probability distribution scale parameter is a measure of variation which is set by the operator when selecting a parametric probability distribution and which defines how spread the distribution is. The larger the value of the scale parameter is, the more spread out the distribution.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">user request:
https://github.com/ISA-tools/stato/issues/47</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Scale_parameter.
last accessed: 2016/11/11</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">scale</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">statistical dispersion</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">probability distribution scale parameter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000436 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000436">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a probability distribution shape parameter is a data item which is set by the operator when selecting a parametric probability distribution and which dictates the way the profile but not the location or size of the distribution plot looks like.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">user request:
https://github.com/ISA-tools/stato/issues/47</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Shape_parameter
last accessed: 2016-11-11</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">shape</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">probability distribution shape parameter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000437 -->
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<obo:IAO_0000115 xml:lang="en">a scale estimator is a measurement datum (a statistic) which is calculated to approach the actual scale parameter of a probability distribution from observed data.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">user request:
https://github.com/ISA-tools/stato/issues/47</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Scale_parameter
last accessed: 2016/11/11</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">https://stat.ethz.ch/R-manual/R-devel/library/mgcv/html/gam.scale.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">scale estimator</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed. Thus, if the random variable {\displaystyle X} X is log-normally distributed, then {\displaystyle Y=\ln(X)} Y=\ln(X) has a normal distribution. Likewise, if {\displaystyle Y} Y has a normal distribution, then {\displaystyle X=\exp(Y)} X=\exp(Y) has a log-normal distribution. A random variable which is log-normally distributed takes only positive real values. The distribution is occasionally referred to as the Galton distribution or Galton's distribution, after Francis Galton.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">user request:
https://github.com/ISA-tools/stato/issues/47</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Log-normal_distribution
last accessed: 2016/11/11</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">dlnorm(x, meanlog = 0, sdlog = 1, log = FALSE)
plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)
qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)
rlnorm(n, meanlog = 0, sdlog = 1)
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Lognormal.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">log normal distribution</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">outlier detection testing objective is a statistical objective of a data transformation which aims to test a null hypothesis that an observation is not an outlier.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">outlier detection testing objective</obo:STATO_0000032>
<rdfs:label xml:lang="en">outlier detection testing objective</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">Dixon test is a statistical test used to detect outliers in a univariate data set assumed to come from a normally distributed population.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="fr">Le test de Dixon est un test statistique destiné à identifier des données abérrantes dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Dixon test</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Q test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Robert B. Dean and Wilfrid J. Dixon (1951) "Simplified Statistics for Small Numbers of Observations". Anal. Chem., 1951, 23 (4), 636–638.</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Dixon%27s_Q_test
last accessed: 2016-11-19</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">dixon.outliers(data)
from:
http://finzi.psych.upenn.edu/library/referenceIntervals/html/dixon.outliers.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Dixon Q test</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Grubbs' test is a statistical test used to detect one outlier in a univariate data set assumed to come from a normally distributed population.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="fr">Le test de Grubb est un test statistique destiné à identifier une (et une seule) abérration dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">maximum normed residual test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Grubbs'_test_for_outliers
last accessed: 2016-11-19</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">rgrubbs.test(x, alpha = 0.05)
from:
http://finzi.psych.upenn.edu/library/OutlierDM/html/rgrubbs.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Grubbs' test</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">Tietjen-Moore test for outlier is a statistical test used to detect outliers and corresponds to a generalization of the Grubb's test, thus allowing detection of more than one outlier in a univariate data set assumed to come from a normally distributed population.
If testing for a single outlier, the Tietjen-Moore test is equivalent to the Grubbs' test.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="fr">Le test de Tietjen-Moore est un test statistique destiné à identifier des données abérrantes dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale.
Ce test est une généralisation du test de Grubb dans le sens où il permet de tester pour la présence de plus d'une seule et unique abérration.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Tietjen-Moore test</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from NIST:
http://www.itl.nist.gov/div898/handbook/eda/section3/eda35h2.htm
last accessed: 2016-11-19</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">FindOutliersTietjenMooreTest(dataSeries,k,alpha=0.05)
from:
https://rdrr.io/rforge/climtrends/man/findOutliers.Tietjen.Moore.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Tietjen-Moore test for outliers</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The Extreme Studentized Deviate Test is a statistical test used to detect outliers in a univariate data set assumed to come from a normally distributed population.
The ESD Test differs from the Grubbs' test and the Tietjen-Moore test in the sense that it contains built-in correction for multiple testing.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">ESD test for outliers</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">generalized ESD test for outliers</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Rosner, Bernard (May 1983), Percentage Points for a Generalized ESD Many-Outlier Procedure,Technometrics, 25(2), pp. 165-172.</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">adapted from NIST:
http://www.itl.nist.gov/div898/handbook/eda/section3/eda35h3.htm
last accessed: 2016-11-19</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">rgrubbs.test(x, alpha = 0.05)
from:
http://finzi.psych.upenn.edu/library/OutlierDM/html/rgrubbs.test.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">generalized extreme studentized deviate test</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a split-plot design is kind of factorial design which is used when running a full factorial completely randomized design is inpractical, either for cost or practicalities (e.g. equipment, fields), in other words, when a restricted randomization has to be applied. A split-plot design is used whenever practioners fix the level of 'hard to change factor' and run all the combinations of the other factors. The hard to change factor is also refered to as the 'whole plot' factor, while the remainders of the factors are refered to as 'split plot factor'.
Performing a split-plot design therefore means fixing one factor level, and then applying the treatments formed by the cartesian products of the levels for the other factors. A mininum of 2 factors are required and one being applied before the other(s).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://www.minitab.com/uploadedFiles/Content/News/Published_Articles/recognize_split_plot_experiment.pdf
adapted from wikipedia:
https://en.wikipedia.org/wiki/Restricted_randomization
last accessed: 14.12.2016</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://pdfs.semanticscholar.org/bb4b/d979610388c76bb81568f14a886304ce4662.pdf</obo:IAO_0000119>
<rdfs:label xml:lang="en">split-plot design</rdfs:label>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">a split split plot design is a study design where restricted randomization affect 2 study factors (and not 1 as in split-plot design). Such design is only possible if at least 3 independent variables are present.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from https://onlinecourses.science.psu.edu/stat503/node/72
last accessed 2016/12/15</obo:IAO_0000119>
<rdfs:label xml:lang="en">split split plot design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000446 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000446">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">Restricted randomization is a kind of randomization which is used or occured when hard to change factors exist in a study design. In other words, when complete randomization is not possible, a case of restricted randomization exists, for instance in the case of split-plot design.
Restricted randomization allows intuitively poor allocations of treatments to experimental units to be avoided, while retaining the theoretical benefits of randomization.
Restricted randomization can also result from an unplanned event and is then something that should be avoided. RandomizeR R package can be used to detect such events and assess the quality of randomization process.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Adapted from Wikipedia:
https://en.wikipedia.org/wiki/Restricted_randomization
last accessed: 2016/12/15</obo:IAO_0000119>
<rdfs:label xml:lang="en">restricted randomization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000447 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000447">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a 'whole plot number' is a data item used to count and identify the actual piece of land (in the case of real field based trials) used in a split plot design experiment and receiving treatments corresponding to the levels of a factor whose randomization is restricted (these factors are known as 'hard to change' factors).
In the case of non-field based trials, the 'whole plot' is a metaphor.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO
adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf
last accessed: 2016/12/15</obo:IAO_0000119>
<rdfs:label xml:lang="en">whole plot number</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000448 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000448">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a 'sub plot number' is a data item used to count and identify the actual piece of land located within a 'whole plot', in the case of real field based trials using a split-plot design, and received completely randomized treatments corresponding to the factor levels combinations of the remainder factors declared in the experiment.
in the case of 'split-split plot design', sub-plots also receive treatments corresponding to a factor whose randomization is restriction. In such configuration, each 'sub-plot' is itself divided into 'sub sub-plot', which then received the remainder of the treatments in completely randomized fashion.
In the case of non-field based trials, the notion 'sub-plot' is a metaphor.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO
adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf
last accessed: 2016/12/15</obo:IAO_0000119>
<rdfs:label xml:lang="en">sub-plot number</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000449 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000449">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">a 'sub sub-plot number' is a data item used to count and identify the actual piece of land located within a 'sub plot', in the case of real field based trials using a split-split-plot design, and received completely randomized treatments corresponding to the factor levels combinations of the remainder factors declared in the experiment.
in the case of 'split-split plot design', sub-plots also receive treatments corresponding to a factor whose randomization is restriction. In such configuration, each 'sub-plot' is itself divided into 'sub sub-plot', which then received the remainder of the treatments in completely randomized fashion.
In the case of non-field based trials, the notion 'sub sub-plot' is a metaphor.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO
adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf
last accessed: 2016/12/15</obo:IAO_0000119>
<rdfs:label xml:lang="en">sub sub-plot number</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000450 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000450">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000454"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">"Wilks' lambda is a test statistic used in multivariate analysis of variance (MANOVA) to test whether there are differences between the means of identified groups of subjects on a combination of dependent variables."</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.blackwellpublishing.com/specialarticles/jcn_9_381.pdf</obo:IAO_0000119>
<obo:STATO_0000041>https://stat.ethz.ch/R-manual/R-devel/library/stats/html/summary.manova.html
## S3 method for class 'manova'
summary(object,
test = c("Pillai", "Wilks", "Hotelling-Lawley", "Roy"),
intercept = FALSE, tol = 1e-7, ...)</obo:STATO_0000041>
<obo:STATO_0000391>https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.mstats.f_value_wilks_lambda.html#scipy.stats.mstats.f_value_wilks_lambda
scipy.stats.mstats.f_value_wilks_lambda(ER, EF, dfnum, dfden, a, b)</obo:STATO_0000391>
<rdfs:label xml:lang="en">Wilk's Lambda</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000451 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000451">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000454"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Pillai trace is a statistic used for the following three tests during a multivariate analysis of variance: (a) equality of mean vectors of lp‐variate normal distributions with the common but unknown covariance matrix, (b) independence between two sets of variates distributed jointly as a normal distribution with unknown mean vector, and (c) equality of covariance matrices of two p‐variate normal distributions with unknown mean vectors.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.1002/0470011815.b2a13067</obo:IAO_0000119>
<rdfs:label xml:lang="en">Pillai's trace</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000452 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000452">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000454"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">"The Lawley–Hotelling trace is used to test the equality of mean vectors of k p‐variate normal distributions with common but unknown covariance matrix. The explicit form of the null distribution of T$_{0}^{2}$equation image is the F distribution. The asymptotic null distribution is the chi‐square distribution. The power function of the test is described and its power is compared with the likelihood ratio test. "</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.1002/0470011815.b2a13035</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Lawley–Hotelling Trace</obo:STATO_0000032>
<rdfs:label xml:lang="en">Hotelling-Lawley trace</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000453 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000453">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Roy's maximum root is a statistic used in multivariate analysis of variance to find the maximum characteristic root or eigenvalue statistic for testing equality of k p-variate normal distributions with same covariance matrix, independence between two sets of variables jointly distributed as a normal distribution, equality of covariance matrices of two p-variate normal distributions, whether the covariance matrix of a p-variabte normal distribution with unknown mean vector equals a specified matrix.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Oxford Dictionary of Statistical Terms</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://onlinecourses.science.psu.edu/stat505/node/163</obo:IAO_0000119>
<rdfs:label xml:lang="en">Roy’s Maximum Root</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000454 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000454">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000086"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">"The multivariate analysis of variance, or MANOVA, is a procedure for comparing multivariate sample means. As a multivariate procedure, it is used when there are two or more dependent variables, and is typically followed by significance tests involving individual dependent variables separately.
It helps to answer:
1. Do changes in the independent variable(s) have significant effects on the dependent variables?
2. What are the relationships among the dependent variables?
3. What are the relationships among the independent variables?"</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Multivariate_analysis_of_variance</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">MANOVA</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://stat.ethz.ch/R-manual/R-devel/library/stats/html/manova.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">multivariate analysis of variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000455 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000455">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000314"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000315"/>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000144"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">In Bayesian statistics context, a credible interval is an interval of a posterior distribution which is such that the density at any point inside the interval is greater than the density at any point outside and that the area under the curve for that interval is equal to a prespecified probability level. For any probability level there is generally only one such interval, which is also often known as the highest posterior density region. Unlike the usual confidence interval associated with frequentist inference, here the intervals specify the range within which parameters lie with a certain probability.
The Bayesian counterparts of the confidence interval used in Frequentists Statistics.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Bayesian credibility interval</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Adapted from Wikipedia:
https://en.wikipedia.org/wiki/Credible_interval
and from the Cambridge Dictionary of Statistics, fourth edition, ISBN-13 978-0-511-78827-7
last accessed: 2017-07-01</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">HPD</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">region of highest posterior density</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en"></obo:STATO_0000391>
<rdfs:label xml:lang="en">credible interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000456 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000456">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000455"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">In Bayesian statistics context, a 95% credible interval is a credible interval which,given the data, includes the true parameter with probability of 95%.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Bayesian credibility interval at 95%</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Wikipedia:
https://en.wikipedia.org/wiki/Credible_interval
last accessed: 2017-07-01</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en"></obo:STATO_0000391>
<rdfs:label xml:lang="en">95% credible interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000457 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000457">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000614"/>
<obo:IAO_0000112 xml:lang="en">" In clinical trials, it gives you an idea of how much difference there is between the averages of the experimental group and control groups."</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The mean difference, or difference in means, measures the absolute difference between the mean value in two different groups.
The mean difference is a subtraction of one mean from another.
The primary use of this term is in analyzing between-group differences</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2021-12-01 vote 6-0 by Philippe Rocca-Serra, Paola Rosati, Robin Ann Yurk, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.statisticshowto.com/mean-difference/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">MD</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">difference in means</obo:STATO_0000032>
<rdfs:label xml:lang="en">mean difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000458 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000458">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000455"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">In Bayesian statistics context, a 99% credible interval is a credible interval which, given the data, includes the true parameter with probability of 99%.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Bayesian credible interval at 99%</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Wikipedia:
https://en.wikipedia.org/wiki/Credible_interval
last accessed: 2017-07-01</obo:IAO_0000119>
<rdfs:label xml:lang="en">99% credible interval</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000459 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000459">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">group sequential design is a study design used in clinical trial settings in which interim analyses of the data are conducted after groups of patients are recruited. After each interim analysis, the trial may stop early if the evidence so far shows the new treatment is particularly effective or ineffective. Such designs are ethical and cost-effective, and so are of great interest in practice.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from https://www.jstatsoft.org/article/view/v066i02/v66i02.pdf</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">https://cran.r-project.org/web/packages/gsDesign/index.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">group sequential design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000460 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000460">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">interim analysis is a data transformation used to analyzed studies implementing a group-sequential design, to evaluate and interpret the accumulating information during a clinical trial. It means that the analysis of data that is conducted before full data collection has been completed. Clinical trials are unusual in that enrollment of patients is a continual process staggered in time. This means that if a treatment is particularly beneficial or harmful compared to the concurrent placebo group while the study is on-going, the investigators are ethically obliged to assess that difference using the data at hand and to make a deliberate consideration of terminating the study earlier than planned.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from https://onlinecourses.science.psu.edu/stat509/node/75
and from wikipedia:
https://en.wikipedia.org/wiki/Interim_analysis
last accessed: 2017-10-9</obo:IAO_0000119>
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<obo:IAO_0000115 xml:lang="en">the O'brien-Flemming boundary analysis is a kind of interim-analysis method implemented by O'brien and Flemming to account for the
As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.</obo:IAO_0000115>
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<obo:IAO_0000112 xml:lang="en">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856440/</obo:IAO_0000112>
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<obo:IAO_0000115 xml:lang="en">The Pocock boundary analysis gives a p-value threshold for each interim analysis which guides the data monitoring committee on whether to stop the trial. The boundary used depends on the number of interim analyses.
The Pocock boundary is simple to use in that the p-value threshold is the same at each interim analysis. The disadvantages are that the number of interim analyses must be fixed at the start and it is not possible under this scheme to add analyses after the trial has started. Another disadvantage is that investigators and readers frequently do not understand how the p-values are reported: for example, if there are five interim analyses planned, but the trial is stopped after the third interim analysis because the p-value was 0.01, then the overall p-value for the trial is still reported as <0.05 and not as 0.01.
As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.1093%2Fbiomet%2F64.2.191
and Wikipedia:
https://en.wikipedia.org/wiki/Pocock_boundary</obo:IAO_0000119>
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<rdfs:label xml:lang="en">Pocock boundary analysis</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">The Haybittle–Peto boundary analysis is an interim analysis where a rule for deciding when to stop a clinical trial prematurely is defined. It is named for John Haybittle and Richard Peto.
The Haybittle–Peto boundary is one such stopping rule, and it states that if an interim analysis shows a probability of equal to, or less than 0.001 that a difference as extreme or more between the treatments is found, given that the null hypothesis is true, then the trial should be stopped early. The final analysis is still evaluated at the normal level of significance (usually 0.05).[3][4] The main advantage of the Haybittle–Peto boundary is that the same threshold is used at every interim analysis, unlike the O'Brien–Fleming boundary, which changes at every analysis. Also, using the Haybittle–Peto boundary means that the final analysis is performed using a 0.05 level of significance as normal, which makes it easier for investigators and readers to understand. The main argument against the Haybittle–Peto boundary is that some investigators believe that the Haybittle–Peto boundary is too conservative and makes it too difficult to stop a trial.
As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">10.1259/0007-1285-44-526-793
and adapted from Wikipedia:
https://en.wikipedia.org/wiki/Haybittle%E2%80%93Peto_boundary</obo:IAO_0000119>
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<rdfs:label xml:lang="en">Haybittle-Peto boundary analysis</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">A lnear mixed model is a mixed model containing both fixed effects and random effects and in which factors and covariates are assumed to have a linear relationship to the dependent variable. These models are useful in a wide variety of disciplines in the physical, biological and social sciences. They are particularly useful in settings where repeated measurements are made on the same statistical units (longitudinal study), or where measurements are made on clusters of related statistical units. Because of their advantage in dealing with missing values, mixed effects models are often preferred over more traditional approaches such as repeated measures ANOVA.
Fixed-effects factors are generally considered to be the variables whose values of interest are all represented in the data file.
Random-effects factors are variables whose values correspond to unwanted variation. They are useful when trying to understand variability in the dependent variable which was not anticipated and exceeds what was expected.
Linear mixed models also allow to specify specific interactions between factors, and allow the evaluation of the various linear effect that a particular combination of factor levels may have on a response variable.
Finally, linear mixed models allow to specify variance components in order to describe the relation between various random effects levels.</obo:IAO_0000115>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Pawel Krajewski</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>LMM</obo:IAO_0000118>
<obo:IAO_0000119>adapted from Wikipedia:
https://en.wikipedia.org/wiki/Mixed_model</obo:IAO_0000119>
<rdfs:label xml:lang="en">linear mixed model</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">An empirical measure is a random measure arising from a particular realization of a (usually finite) sequence of random variables.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Empirical_measure</obo:IAO_0000119>
<rdfs:label xml:lang="en">empirical measure</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">A model term is a data item set in statistical model formula to apportion source of variation.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
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<obo:IAO_0000115>the model random effect term is model term which aims to account for the unwanted variability in the data associated with a range of independent variables which are not the primary interest in the dataset. It is there also known as the variance component of the model</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>variance component</obo:IAO_0000118>
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<obo:IAO_0000115>a model fixed effect term is a model term which accounts for variation explained by an independent variable and its levels.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
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<obo:IAO_0000115>a model interaction effect term is a model term which accounts for variation explained by the combined effects of the factor levels of more than one (usually 2) independent variables.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
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<obo:IAO_0000115>a model error term is a model term which accounts for residual variation not explained by the other components (fixed and random effect terms)</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
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<obo:IAO_0000115>a estimate is a data item which is computed from a dataset to provide an approximated value (an estimator) for a 'statistical parameter' (a 'characteristics/parameter' of the true underlying distribution) of a real population.</obo:IAO_0000115>
<obo:IAO_0000116>Hanna Cwiek</obo:IAO_0000116>
<obo:IAO_0000116>Tom Nichols</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:IAO_0000233 xml:lang="en">https://github.com/ISA-tools/stato/issues/74</obo:IAO_0000233>
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<obo:IAO_0000115 xml:lang="en">An estimate of the number of degrees of freedom.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">degree of freedom approximation</rdfs:label>
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<obo:IAO_0000115 xml:lang="en">The Kenward-Roger method's fundamental idea is to calculate the approximate mean and variance of their statistic and then match moments with an F distribution to obtain the denominator degrees of freedom.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://support.sas.com/documentation/cdl/en/statug/68162/HTML/default/viewer.htm#statug_glimmix_details40.htm</obo:IAO_0000119>
<obo:IAO_0000119>https://www.jstatsoft.org/article/view/v059i09</obo:IAO_0000119>
<obo:IAO_0000119>https://www.ncbi.nlm.nih.gov/pubmed/9333350</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Kenward-Roger</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/lmerTest/versions/2.0-36/topics/anova-methods
ibrary(lme4)
library(pbkrtest)
fm1 <- lmer(Reaction ~ Days + (Days| Subject), sleepstudy)
get_Lb_ddf(fm1, lme4::fixef(fm1))</obo:STATO_0000041>
<rdfs:label xml:lang="en">Kenward-Roger degree of freedom approximation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000474 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Satterthwaite degree of freedom approximation is a type of degree of freedom approximation which is used to estimate an “effective degrees of freedom” for a probability distribution formed from several independent normal distributions where only estimates of the variance are known. It was originally developed by statistician Franklin E. Satterthwaite.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">satterthwaite</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Satterthwaite, F. E. (1946), "An Approximate Distribution of Estimates of Variance Components.", Biometrics Bulletin, 2: 110–114, doi:10.2307/3002019</obo:IAO_0000119>
<obo:STATO_0000032>Welch-Satterthwaite</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/metRology/versions/0.9-23-2/topics/welch.satterthwaite</obo:STATO_0000041>
<rdfs:label xml:lang="en">Satterthwaite degree of freedom approximation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000475 -->
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<obo:IAO_0000115 xml:lang="en">a data transformation to determine the number of degree of freedom</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">between-within</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">https://www.ncbi.nlm.nih.gov/pubmed/25899170</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">between-within denominator degrees of freedom approximation</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000477 -->
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<obo:IAO_0000115 xml:lang="en">PLS weight (or Partial Least Square weight) is a information content entity which is generated when performing a Partial Least Square analysis</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>PLS weight</obo:IAO_0000118>
<rdfs:label xml:lang="en">partial least square weight</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000478 -->
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<obo:IAO_0000115 xml:lang="en">a dataset which is made up of pedigree information, that is presenting ancestry or lineage information in a set of individuals of an organism.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">pedigree data set</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000480 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>RR-BLUP is a data transformation used in the context of estimating breeding value using a Bayesian ridge regression. It can be obtained from Bayes B procedure by setting pi parameter to zero ( ) and assuming that all the markers have the same variance.</obo:IAO_0000115>
<obo:IAO_0000116>term request by Guillaume Bauchet, cassavabase.org, Cornell University</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat
Paulino Pérez-Rodríguez, Daniel Gianola, Juan Manuel González-Camacho, José Crossa, Yann Manès and Susanne Dreisigacker
G3: GENES, GENOMES, GENETICS December 1, 2012 vol. 2 no. 12 1595-1605; https://doi.org/10.1534/g3.112.003665</obo:IAO_0000119>
<obo:STATO_0000032>RRBLUP</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>ridge regression best linear unbiaised predictor</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000481 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a data transformation which calculate predictions of breeding values using an animal model and a relationship matrix calculated from the genomic/genetic markers (G Matrix), in constrast to using Pedigree information as in BLUP, also known as ABLUP</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382275/
and from:
https://www.rdocumentation.org/packages/pedigree/versions/1.4/topics/gblup
and from</obo:IAO_0000119>
<obo:STATO_0000032>GBLUP</obo:STATO_0000032>
<obo:STATO_0000041>gblup(formula, data, M, lambda)
where:
formula: formula of the model, do not include the random effect due to animal (generally ID).
data: data.frame with columns corresponding to ID and the columns mentioned in the formula.
M: Matrix of marker genotypes, usually the count of one of the two SNP alleles at each markers (0, 1, or 2).
lambda : Variance ratio (σ2e/σ2a)
https://www.rdocumentation.org/packages/pedigree/versions/1.4/topics/gblup</obo:STATO_0000041>
<rdfs:label>genomic best linear unbiased prediction</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000482 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a data transformation which calculate estimates of genomic estimated breeding values (GEBVs) on an animal or plant model utilizing trait-specific marker information.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>from:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012648</obo:IAO_0000119>
<obo:STATO_0000032>TABLUP</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>trait-specific relationship matrix best linear unbiaised prediction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000483 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Bayes A is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model and treats the prior probability π that a SNP has zero effect as unknown (i.e π=0)</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637029/
doi: 10.1186/1297-9686-41-2.
and:
Prediction of total genetic value using genome-wide dense marker maps.
Meuwissen TH, Hayes BJ, Goddard ME.
Genetics. 2001 Apr;157(4):1819-29.
PMID: 11290733</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">Bayes A</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000484 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Bayes B is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model, treats the prior probability π that a SNP has zero effect to a set value (i.e π >0) and uses a mixture distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637029/
doi: 10.1186/1297-9686-41-2.
and:
Prediction of total genetic value using genome-wide dense marker maps.
Meuwissen TH, Hayes BJ, Goddard ME.
Genetics. 2001 Apr;157(4):1819-29.
PMID: 11290733</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">Bayes B</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000485 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the estimated breeding value of an organism is a data item computed to estimate the true breeding value defined as genetic merit of an organism, half of which will be passed on to its progeny. While the exact breeding value can not been known, for performance traits it is possible to make good estimates. These estimates are called Estimated Breeding Values (EBVs). EBVs are expressed in the units of measurement for each particular trait. These estimates are output of various estimation methods which differ depending on the underlying assumptions (equal variance of marker effect, all markers contributing to the trait) , the mathemical methods used (bayesian or non-bayesians) and the genetic inheritance models being considered (additive, dominant, epistatic) selected by the analysts.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://abri.une.edu.au/online/pages/understanding_ebvs_char.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">EBV</obo:STATO_0000032>
<rdfs:label xml:lang="en">estimated breeding value</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000487 -->
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<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an additive genetic model is a data item which refers to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their effects individually.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">additive genetic inheritance model</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000488 -->
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<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an additive genetic model is a data item which refer to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their individual effects and their dominance effect (of alleles at a single locus).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">additive dominant genetic inheritance model</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000489 -->
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<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an additive genetic model is a data item which refer to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their individual effect, their additive dominant (effect (of alleles at a single locus) and their epistasic effect (of alleles at more different loci).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">additive dominant genetic and epistatic inheritance model</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000490 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Dunn’s Multiple Comparison Test is a post hoc (i.e. it’s run after an ANOVA) non parametric test (a “distribution free” test that doesn’t assume your data comes from a particular distribution). It is one of the least powerful of the multiple comparisons tests and can be a very conservative test–especially for larger numbers of comparisons. The Dunn is an alternative to the Tukey test when you only want to test for differences in a small subset of all possible pairs; For larger numbers of pairwise comparisons, use Tukey’s instead. Use Dunn’s when you choose to test a specific number of comparisons before you run the ANOVA and when you are not comparing to controls. If you are comparing to a control group, use the Dunnett test instead.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Dunn, O.J. (1961) Multiple comparisons among means. JASA, 56: 54-64
Dunn, Olive Jean (1964). "Multiple comparisons using rank sums". Technometrics. 6 (3): 241–252. doi:10.2307/1266041
and adapted from:
http://www.statisticshowto.com/dunns-test/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Dunn's test</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">## Default S3 method:
dunnTest(x, g, method = dunn.test::p.adjustment.methods[c(4,
2:3, 5:8, 1)], two.sided = TRUE, altp = two.sided, ...)
from:
http://www.rforge.net/doc/packages/FSA/dunnTest.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Dunn’s multiple comparison test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000491 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Conover-Iman test for stochastic dominance is a stastical test for multiple group comparisons and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other.
The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test.
Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks.
The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Conover, W. J. and Iman, R. L. (1979). On multiple-comparisons procedures. Technical Report LA-7677-MS, Los Alamos Scientific Laboratory.</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">posthoc.kruskal.conover.test(x, …)
# S3 method for default
posthoc.kruskal.conover.test( x, g, p.adjust.method =
p.adjust.methods, …)
# S3 method for formula
posthoc.kruskal.conover.test(formula, data, subset,
na.action, p.adjust.method = p.adjust.methods, …)
https://www.rdocumentation.org/packages/PMCMR/versions/4.2/topics/posthoc.kruskal.conover.test
conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences.</obo:STATO_0000041>
<rdfs:label xml:lang="en">Conover-Iman test of multiple comparisons using rank sums</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000492 -->
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<obo:IAO_0000112>application to breeding value estimation and genomic selection
https://www.ncbi.nlm.nih.gov/pubmed/20122298</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Bayesian LASSO is a data transformation where the regression parameters have independent Laplace (i.e., double-exponential) priors and are used to interprete Lasso estimate for linear regression parameters as Bayesian posterior mode estimates in accordance to a Bayesian framework.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://www.tandfonline.com/doi/abs/10.1198/016214508000000337</obo:IAO_0000119>
<obo:STATO_0000032>Bayes LASSO</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>Bayesian least absolute shrinkage and selection operator</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000493 -->
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</owl:Restriction>
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<obo:IAO_0000115>a genotype matrix is a kind of genomic relationship matrix in the rawest of form and which simply corresponds to a matrix of individuals genotype for a given set of markers or genomic positions. Columns are snps or markers, Rows are individuals. Each column/row cell contains a genotype expressed as, in the genome is diploid, as a pair of characters chosen from ATGC where the dominant variant is uppercased and the recessive variant is lower cased.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://articles.extension.org/pages/68019/genomic-relationships-and-gblup</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>genotype matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000494 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000494">
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</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the MAF matrix is a genomic relationship matrix which is obtained from the genotype matrix by counting the number of minor alleles at each locus</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://articles.extension.org/pages/68019/genomic-relationships-and-gblup</obo:IAO_0000119>
<obo:STATO_0000032>MAF matrix</obo:STATO_0000032>
<obo:STATO_0000032>gene content matrix</obo:STATO_0000032>
<obo:STATO_0000032>matrix of minor allele count</obo:STATO_0000032>
<rdfs:label>MAF matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000495 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the M matrix is a genomic relationship matrix which is obtained by subtracting 1 to every value of the MAF matrix (gene content matrix). The values of the M matrix are only -1, 0 or 1 and makes computation easier.
M = MAF-1</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://articles.extension.org/pages/68019/genomic-relationships-and-gblup
Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008
P. M. VanRaden.
10.31 68/jds.2007-0980</obo:IAO_0000119>
<obo:STATO_0000032>deviation of 1 from the gene content matrix</obo:STATO_0000032>
<obo:STATO_0000041>>M = MAF-1</obo:STATO_0000041>
<rdfs:label>M matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000496 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000496">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>P matrix is a kind of genomic relationship matrix which contains allele frequencies expressed as a difference from 0.5 and multiplied by 2.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://articles.extension.org/pages/68019/genomic-relationships-and-gblup
Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008
P. M. VanRaden.
10.31 68/jds.2007-0980</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>P matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000497 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000497">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the Z-matrix is a genomic relationship matrix which is obtained by substracted the M matrix with the P matrix. It is also known as the incidence matrix for the markers.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://articles.extension.org/pages/68019/genomic-relationships-and-gblup
Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008
P. M. VanRaden.
10.31 68/jds.2007-0980</obo:IAO_0000119>
<obo:STATO_0000032>incidence matrix for genotyping markers</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>Z matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000498 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000498">
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The degree of freedom numerator is the number of degrees of freedom that the estimate of variance used in the numerator is based on. It is one of the parameters for the F-distribution used to compute probabilities in analysis of variance.</obo:IAO_0000115>
<obo:IAO_0000116>term request:
https://github.com/ISA-tools/stato/issues/71</obo:IAO_0000116>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032>df1</obo:STATO_0000032>
<obo:STATO_0000032>num df</obo:STATO_0000032>
<rdfs:label>numerator degrees of freedom</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000499 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000499">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>augmented design is a kind of experimental design where the goal is to compare existing (control) treatments with new treatments that have an experimental constraint of "limited replication". To understand limited replication, consider about experiments that may only allow a single representation of the new treatment, this limitation may be many times due to the cost associated with the experiment, limited resources, or limited number of new units that can be used in the experiment. In contrast, the existing treatments are referred as checks and are generally replicated multiple times. With augmented design one can estimate the following:
a) Differences between checks and new treatments,
b) Differences among new treatments,
c) Differences among check treatments, and
d) Differences among new and check treatments combined.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Federer, W.T. 1956. Augmented (or hoonuiaku) designs. Hawaiian Planters’ Record LV(2): 191–208)
http://rna.genomics.purdue.edu/</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041>an example of dataset representing an augmented design:
https://www.rdocumentation.org/packages/sommer/versions/3.2/topics/augment</obo:STATO_0000041>
<rdfs:label>augmented experimental design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000500 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a probability distribution location parameter is a data item which is set by the operator when selecting a parametric probability distribution and which dictates the way the location but not the profile or size of the distribution plot looks like.</obo:IAO_0000115>
<obo:IAO_0000116>https://github.com/ISA-tools/stato/issues/50</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
https://docs.scipy.org/doc/scipy/reference/tutorial/stats.html#shifting-and-scaling</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">norm.stats(loc=3, scale=4, moments="mv"), where loc is the location parameter indicated how much shift is given</obo:STATO_0000391>
<rdfs:label xml:lang="en">probability distribution location parameter</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000501 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Weibull probability distribution is continuous probabibility distribution which is used to model time to fail, time to repair and material strength in material science. In biomedicine, the Weibull probability is used to in determining 'hazard functions'.
The 'location parameter' of the Weibull probability distribution can be used to define a failure-free zone.
If the quantity X is a "time-to-failure", the Weibull distribution gives a distribution for which the failure rate is proportional to a power of time. The shape parameter, k, is that power plus one, and so this parameter can be interpreted directly as follows:
A value of {\displaystyle k<1\,} {\displaystyle k<1\,} indicates that the failure rate decreases over time. This happens if there is significant "infant mortality", or defective items failing early and the failure rate decreasing over time as the defective items are weeded out of the population. In the context of the diffusion of innovations, this means negative word of mouth: the hazard function is a monotonically decreasing function of the proportion of adopters;
A value of {\displaystyle k=1\,} {\displaystyle k=1\,} indicates that the failure rate is constant over time. This might suggest random external events are causing mortality, or failure. The Weibull distribution reduces to an exponential distribution;
A value of {\displaystyle k>1\,} {\displaystyle k>1\,} indicates that the failure rate increases with time. This happens if there is an "aging" process, or parts that are more likely to fail as time goes on. In the context of the diffusion of innovations, this means positive word of mouth: the hazard function is a monotonically increasing function of the proportion of adopters. The function is first concave, then convex with an inflexion point at {\displaystyle (e^{1/k}-1)/e^{1/k},k>1\,} {\displaystyle (e^{1/k}-1)/e^{1/k},k>1\,}.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>Weibull distribution</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from :
https://en.wikipedia.org/wiki/Weibull_distribution
and from
http://www.engineeredsoftware.com/nasa/weibull.htm</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Weibull probability distribution</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">pweibull(q, shape, scale = 1, lower.tail = TRUE, log.p = FALSE)
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Weibull.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">scipy.stats.weibull_min
from:
https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.weibull_min.html#scipy.stats.weibull_min</obo:STATO_0000391>
<rdfs:label xml:lang="en">Weibull probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000502 -->
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>statistical sampling is a planned process which aims at assembling a population of observation units (samples) in as an unbiaised manner as possible in order to obtain or infer information about the actual population these samples have been drawn.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>statistical sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000503 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000503">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/STATO_0000509"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Simple random sampling is a statistical sampling process which creates a sample of a size n entirely by chance. In such process, each unit has the same probability of being selected. Depending on the size of the population being sampled, the sampling process may be done with or without replacement</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Simple_random_sample</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">random sampling</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">srswor(n,N)
from
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/srswor
[simple random sampling without replacement]
Sampling R package</obo:STATO_0000041>
<obo:STATO_0000041 xml:lang="en">srswr(n,N)
from:
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/srswr
[simple random sampling with replacement]
Sampling R package</obo:STATO_0000041>
<rdfs:label xml:lang="en">simple random sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000504 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000504">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000509"/>
<obo:IAO_0000112 xml:lang="en">It is a sampling process used, among other things, in ecological studies when studying how things change in an given environment</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">line intercept sampling is a sampling process by which an element in a spatial region is included in a sample if it is intersected by a line chosen by the operator.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">LIS</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">LIS sampling</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Lee Kaiser, Biometrics, Vol. 39, No. 4 (Dec., 1983), pp. 965-976
http://www.jstor.org/stable/2531331</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">line intercept sampling</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">line intercept sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000505 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000505">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000509"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Quadrat sampling is a classic tool for the study of ecology, especially biodiversity. In general, a series of squares (quadrats) of a set size are placed in a habitat of interest and the species within those quadrats are identified and recorded. Passive quadrat sampling (done without removing the organisms found within the quadrat) can be either done by hand, with researchers carefully sorting through each individual quadrat or, more efficiently, can be done by taking a photograph of the quadrat for future analysis.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">http://www.coml.org/investigating/observing/quadrat_sampling.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">quadrat sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000506 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000506">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000509"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Cluster sampling is a sampling plan used when mutually homogeneous yet internally heterogeneous groupings are evident in a statistical population.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Cluster_sampling</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">cluster(data, clustername, size, method=c("srswor","srswr","poisson",
"systematic"),pik,description=FALSE)
from:
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/cluster
Sampling R package</obo:STATO_0000041>
<rdfs:label xml:lang="en">cluster sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000507 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000507">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Probability proportional to size ('PPS') sampling is a sampling method in which the selection probability for each element is set to be proportional to its size measure, up to a maximum of 1. In a simple PPS design, these selection probabilities can then be used as the basis for Poisson sampling. However, this has the drawback of variable sample size, and different portions of the population may still be over- or under-represented due to chance variation in selections.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Sampling_(statistics)#Probability-proportional-to-size_sampling</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">PPS sampling</obo:STATO_0000032>
<rdfs:label xml:lang="en">probability-proportional-to-size sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000508 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000508">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000503"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000509"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000096"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>stratified sampling is a statistical sampling method which divides the population into homogenous subpopulations, which are then sampled using random or systematic sampling methods</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Stratified_sampling</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">stratified sampling</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">strata(data, stratanames=NULL, size, method=c("srswor","srswr","poisson",
"systematic"), pik,description=FALSE)
From:
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/strata
R Sampling Package</obo:STATO_0000041>
<rdfs:label xml:lang="en">stratified sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000509 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000509">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">systematic sampling is a process for collecting samples and assembling a statistical sample using a system or method (.e.g unequal probabilities, without replacement, fixed sample size), as opposed to a random sampling.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Madow, W.G. (1949), On the theory of systematic sampling, II, Annals of Mathematical Statistics, 20, 333-354.</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">from:
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/UPsystematic
Sampling R package</obo:STATO_0000041>
<rdfs:label xml:lang="en">systematic sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000510 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000510">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Quota sampling is a method for selecting survey participants that is a non-probabilistic version of stratified sampling.
In quota sampling, a population is first segmented into mutually exclusive sub-groups, just as in stratified sampling. Then judgment is used to select the subjects or units from each segment based on a specified proportion. For example, an interviewer may be told to sample 200 females and 300 males between the age of 45 and 60. This means that individuals can put a demand on who they want to sample (targeting).</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Quota_sampling</obo:IAO_0000119>
<rdfs:label xml:lang="en">quota sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000511 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000511">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Panel sampling is the method of first selecting a group of participants through a random sampling method and then asking that group for (potentially the same) information several times over a period of time. Therefore, each participant is interviewed at two or more time points; each period of data collection is called a "wave". The method was developed by sociologist Paul Lazarsfeld in 1938 as a means of studying political campaigns.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Sampling_(statistics)#Panel_sampling</obo:IAO_0000119>
<rdfs:label xml:lang="en">panel sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000512 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000512">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Snowball sampling (or chain sampling, chain-referral sampling, referral sampling) is a non-probability sampling technique where existing study subjects recruit future subjects from among their acquaintances. Thus the sample group is said to grow like a rolling snowball.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">from:
https://en.wikipedia.org/wiki/Snowball_sampling</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">chain sampling</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">referral sampling</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">snowball sampling</obo:STATO_0000032>
<rdfs:label xml:lang="en">chain-referral sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000513 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000513">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The voluntary sampling method is a type of non-probability sampling. A voluntary sample is made up of people who self-select into the survey. Often, these subjects have a strong interest in the main topic of the survey. Volunteers may be invited through advertisements on Social Media Sites</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Sampling_(statistics)#Voluntary_Sampling</obo:IAO_0000119>
<rdfs:label xml:lang="en">voluntary sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000514 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000514">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Convenience sampling (also known as grab sampling, accidental sampling, or opportunity sampling) is a type of non-probability sampling that involves the sample being drawn from that part of the population that is close to hand. This type of sampling is most useful for pilot testing.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">from wikipedia:
https://en.wikipedia.org/wiki/Convenience_sampling</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">accidental sampling</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">grab sampling</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">opportunity sampling</obo:STATO_0000032>
<rdfs:label xml:lang="en">convenience sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000515 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000515">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000509"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Brewer's sampling is a statistical sampling method which was proposed by Brewer in 1975 and uses unequal probabibility sampling technique</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Brewer, Kenneth RW (1975). A Simple Procedure For Sampling πpswor1. Australian Journal of Statistics, 17(3), 166-172.</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">UPbrewer(pik,eps=1e-06)
from:
https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/UPbrewer
Sampling R package</obo:STATO_0000041>
<rdfs:label xml:lang="en">Brewer sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000516 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000516">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">In imbalanced datasets, where the sampling ratio does not follow the population statistics, one can resample the dataset in a conservative manner called minimax sampling. The minimax sampling has its origin in Anderson minimax ratio whose value is proved to be 0.5: in a binary classification, the class-sample sizes should be chosen equally. This ratio can be proved to be minimax ratio only under the assumption of LDA classifier with Gaussian distributions. The notion of minimax sampling is recently developed for a general class of classification rules, called class-wise smart classifiers.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Sampling_(statistics)#Minimax_sampling</obo:IAO_0000119>
<rdfs:label xml:lang="en">minimax sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000517 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000517">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302900"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>complete randomization is a group randomization where experimental units are randomly assigned to the entire set of groups defined by the experimental treatments.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041>crPar(N, K = 2, ratio = rep(1, K), groups = LETTERS[1:K])
from:
https://www.rdocumentation.org/packages/randomizeR/versions/1.4/topics/crPar</obo:STATO_0000041>
<rdfs:label>complete randomization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000518 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000518">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Data imputation is a data transformation process whereby missing data is replaced with an estimated value for the missing element. The substituted values are intended to create a data record that does not fail edits. Various methods may be used to produce these substituted values.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia and from the OECD glossary of statistical terms
https://stats.oecd.org/glossary/detail.asp?ID=3406</obo:IAO_0000119>
<rdfs:label>data imputation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000519 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000519">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000518"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>last observation carried forward data imputation is a type of data imputation which uses a very simple, self explanatory method for substituted a missing value for an observation. It should be noted that this method gives a biased estimate of the treatment effect and underestimates the variability of the estimated result and should be used cautiously.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from Wikipedia:
https://en.wikipedia.org/wiki/Analysis_of_clinical_trials#Last_observation_carried_forward</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">last observation carried forward data imputation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000520 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000520">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000518"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>regression data imputation is a type of data imputation where missing values are replaced with the value of a regression function coefficient.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">regression data imputation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000521 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000521">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000518"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>substitution by the mean data imputation is a type of data imputation where missing values are replaced with the value the variable mean.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">substitution by the mean data imputation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000522 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000522">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000518"/>
<obo:IAO_0000112>https://www.r-bloggers.com/imputing-missing-data-with-r-mice-package/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>multivariate imputation with chained equations (MICE) is a type of data imputation which uses an algorithm devised by Stef van Buuren and Karin Groothuis-Oudshoorn</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>MICE: Multivariate Imputation by Chained Equations in R by Stef van Buuren and Karin Groothuis-Oudshoorn. Journal of Statistical Software,
http://www.stefvanbuuren.nl/publications/mice%20in%20r%20-%20draft.pdf</obo:IAO_0000119>
<obo:STATO_0000032>MICE</obo:STATO_0000032>
<obo:STATO_0000041>library(mice)
miceMod <- mice(BostonHousing[, !names(BostonHousing) %in% "medv"], method="rf") # perform mice imputation, based on random forests.</obo:STATO_0000041>
<rdfs:label>multivariate imputation with chained equations</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000523 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000523">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000518"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>k-nearest neighbour imputation is a data imputation which uses the k-nearest neighbour algorithm to compute a substitution value for the missing values. For every observation to be imputed, it identifies ‘k’ closest observations based on the euclidean distance and computes the weighted average (weighted based on distance) of these ‘k’ obs.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
http://r-statistics.co/Missing-Value-Treatment-With-R.html</obo:IAO_0000119>
<obo:STATO_0000032>kNN data imputation</obo:STATO_0000032>
<obo:STATO_0000041>library(DMwR)
knnOutput <- knnImputation(BostonHousing[, !names(BostonHousing) %in% "medv"]) # perform knn imputation.
anyNA(knnOutput)
from:
http://r-statistics.co/Missing-Value-Treatment-With-R.html</obo:STATO_0000041>
<rdfs:label>k-nearest neighbour data imputation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000524 -->
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
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<rdfs:subClassOf>
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<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000314"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Matthews Correlation Coefficient (or MCC) is a correlation coefficient which is a measure of the quality of binary (two-class) classifications, introduced by biochemist Brian W. Matthews in 1975.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>phi coefficient</obo:IAO_0000118>
<obo:IAO_0000119>adapted from wikipedia:
https://en.wikipedia.org/wiki/Matthews_correlation_coefficient
and from:
https://doi.org/10.1016/0005-2795(75)90109-9</obo:IAO_0000119>
<obo:STATO_0000032>MCC</obo:STATO_0000032>
<obo:STATO_0000041>mcc(preds = NULL, actuals = NULL, TP = NULL, FP = NULL, TN = NULL, FN = NULL)
from:
https://www.rdocumentation.org/packages/mltools/versions/0.3.4/topics/mcc</obo:STATO_0000041>
<rdfs:label>Matthews correlation coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000525 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000525">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a covariance matrix is a square matrix that contains the variances and covariances associated with several variables. The diagonal elements of the matrix contain the variances of the variables and the off-diagonal elements contain the covariances between all possible pairs of variables.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">dispersion matrix</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">variance-covariance matrix</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">covariance matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000526 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000526">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<obo:IAO_0000112>https://www.r-bloggers.com/setup-up-the-inverse-of-additive-relationship-matrix-in-r/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the numerator relationship matrix is the matrix of *expected* additive genetic relationships between individuals. This matrix was originally used by Henderson (Henderson, C.R. 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32:69-83.) to account for covariances between random effects, and therefore to use information from relatives in estimation of breeding value. Among the properties of the NRM matrix (also known as the A matrix), it is symmetric, the diagonal value correspond to 1+ the inbreeding coefficient for an individual.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>A matrix</obo:IAO_0000118>
<obo:IAO_0000119>adapted from:
https://jvanderw.une.edu.au/Genetic_properties_of_the_animal_model.pdf
and from:
Henderson, C.R. 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32:69-83.
https://doi.org/10.2307/2529339</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">NRM</obo:STATO_0000032>
<obo:STATO_0000041>https://rdrr.io/cran/sommer/man/A.mat.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">numerator relationship matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000527 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000527">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200201"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The degree of freedom denominator is the number of degrees of freedom that the estimate of variance used in the denominator is based on. It is one of the parameters for the F-distribution used to compute probabilities in analysis of variance.</obo:IAO_0000115>
<obo:IAO_0000116>term request:
https://github.com/ISA-tools/stato/issues/71</obo:IAO_0000116>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:STATO_0000032>den df</obo:STATO_0000032>
<obo:STATO_0000032>df2</obo:STATO_0000032>
<rdfs:label>denominator degrees of freedom</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000528 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000528">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A matrix of relationships among a group of individuals, which can be used to predict breeding values, to manage inbreeding and in genetic conservation. It can be calculated from the pedigree, but it is also possible to calculate the relationship matrix from genotypes at genetic markers such as single-nucleotide polymorphisms (SNPs). Elements of the genomic relationship matrix are estimates of the realized proportion of the genome that two individuals share, whereas the pedigree-derived relationship matrix is the expectation of this proportion.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.3168/jds.2007-0980</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.ncbi.nlm.nih.gov/pubmed/22059574</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">realized genomic relationship matrix</obo:STATO_0000032>
<obo:STATO_0000032>relationship matrix</obo:STATO_0000032>
<obo:STATO_0000041>https://cran.r-project.org/web/packages/snpReady/snpReady.pdf</obo:STATO_0000041>
<rdfs:label>G matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000529 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000529">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000059"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a scaled t distribution is a kind of Student's t distribution which is shifted by 'mean' and scaled by standard deviation 'sd'.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>R documentation</obo:IAO_0000119>
<obo:STATO_0000041>t.scaled(x, df, mean = 0, sd = 1, ncp, log = FALSE)
from:
https://www.rdocumentation.org/packages/metRology/versions/0.9-23-2/topics/Scaled%20t%20distribution</obo:STATO_0000041>
<rdfs:label>scaled t distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000530 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000530">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000531"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a Bayesian model is a statistical model where inference is based on using Bayes theorem to obtain a posterior distribution for a quantity (or quantities) of interest for some model (such as parameter values) based on some prior distribution for the relevant unknown parameters and the likelihood from the model.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from several sources:
Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001
http://www.scholarpedia.org/article/Bayesian_statistics
https://stats.stackexchange.com/questions/129017/what-exactly-is-a-bayesian-model</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>Bayesian model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000531 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000531">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000004"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000530"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a prior probability distribution is a probability distribution used as input to a Bayesian model to represent a priori knowledge about a model parameter. Along with the acquired/observed data, it is used to compute a posterior distribution according to the Bayes theorem.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>prior probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000532 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000532">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000225"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000218"/>
<owl:Restriction>
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</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a posterior probability distribution is a probability distribution computed in a Bayesian model approach given a prior distribution and a set of events/observations.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>posterior probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000533 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000533">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000119"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000337"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000227"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000144"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000485"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Bayes C pi is a data transformation used to compute estimated breeding values using a Bayesian model and which assesses the SNP effect using MonteCarlo Markov chain methods. Bayes C pi treats the prior probability π that a SNP has zero effect as unknown.
The method was devised to address short comings of Bayes A and Bayes B approaches</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
BMC Bioinformatics. 2011 May 23;12:186. doi: 10.1186/1471-2105-12-186.
Extension of the bayesian alphabet for genomic selection.
Habier D, Fernando RL, Kizilkaya K, Garrick DJ.
but also
https://cran.r-project.org/web/packages/gdmp/gdmp.pdf
and
https://jvanderw.une.edu.au/RFSlides.pdf</obo:IAO_0000119>
<obo:STATO_0000032>Bayes C pi</obo:STATO_0000032>
<rdfs:label>Bayes C pi</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000534 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000534">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000107"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>genetic inheritance model is a data item defining the assumption used by a breeding value estimation method to consider when running the calculations.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label xml:lang="en">genetic inheritance model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000535 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000535">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>sampling from a probability distribution is a data transformation which aims at obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label>sampling from a probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000536 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000536">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000535"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Gibbs sampling or a Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm for obtaining a sequence of observations which are approximated from a specified multivariate probability distribution, when direct sampling is difficult.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia:
https://en.wikipedia.org/wiki/Gibbs_sampling
Geman, S.; Geman, D. (1984). "Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images". IEEE Transactions on Pattern Analysis and Machine Intelligence. 6 (6): 721–741. doi:10.1109/TPAMI.1984.4767596</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label>Gibbs sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000537 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000537">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000535"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000538"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000539"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the Metropolis–Hastings algorithm is a Markov chain Monte Carlo (MCMC) method for obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Metropolis%E2%80%93Hastings_algorithm
Hastings, W.K. (1970). "Monte Carlo Sampling Methods Using Markov Chains and Their Applications". Biometrika. 57 (1): 97–109. doi:10.1093/biomet/57.1.97</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<rdfs:label>Metropolis–Hastings sampling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000538 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000538">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000067"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a continuous multivariate probability distribution is a continuous probability distribution which describes the possible values, and corresponding probabilities, of two or more (usually three or more) associated random variables.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1095?rskey=355sBu&result=1</obo:IAO_0000119>
<rdfs:label>continuous multivariate probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000539 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000539">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000117"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a discrete multivariate probability distribution is a discrete probability distribution which describes the possible values, and corresponding probabilities, of two or more (usually three or more) associated random variables.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1095?rskey=355sBu&result=1</obo:IAO_0000119>
<rdfs:label>discrete multivariate probability distribution</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000540 -->
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<obo:IAO_0000115 xml:lang="en">A data transformation that produces a reproducing kernel Hilbert space (or RKHS), which is a Hilbert space of functions in which point evaluation is a continuous linear functional.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Reproducing_kernel_Hilbert_space</obo:IAO_0000119>
<obo:STATO_0000032>RKHS</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/KGode/versions/1.0.1/topics/rkhs</obo:STATO_0000041>
<obo:STATO_0000041>rkhs</obo:STATO_0000041>
<rdfs:label xml:lang="en">reproducing kernel Hilbert space procedure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000541 -->
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<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a state space model is a kind of statistical model which describes the probabilistic dependence between the latent state variable and the observed measurement. The state or the measurement can be either continuous or discrete. The term “state space” originated in 1960s in the area of control engineering (Kalman, 1960). SSM provides a general framework for analyzing deterministic and stochastic dynamical systems that are measured or observed through a stochastic process.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.scholarpedia.org/article/State_space_model</obo:IAO_0000119>
<obo:STATO_0000032>SSM</obo:STATO_0000032>
<rdfs:label>state space model</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000542 -->
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<obo:IAO_0000115>genomic estimated breeding value (GEBV) is an estimated breeding value derived from information in an organism DNA (genotype). GEBV is calculated differently to conventional Estimated Breeding Values using advanced modeling technique to deal with high dimensionality data.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
https://businesswales.gov.wales/farmingconnect/posts/genomic-breeding-values</obo:IAO_0000119>
<obo:STATO_0000032>GEBV</obo:STATO_0000032>
<rdfs:label>genomic estimated breeding value</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000544 -->
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<obo:IAO_0000115>In a planned experiment where to covariance (genotype x environment) can be controlled and held at 0, the heritability is defined as the ratio of the variance of the genotypic variables to the variance of the phenotypic variables.
H2 = Var(G)/Var(P)
H2 is the broad-sense heritability. This reflects all the genetic contributions to a population's phenotypic variance including additive, dominant, and epistatic (multi-genic interactions), as well as maternal and paternal effects, where individuals are directly affected by their parents' phenotype, for example, milk production in mammals.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Heritability</obo:IAO_0000119>
<obo:STATO_0000032>H2</obo:STATO_0000032>
<obo:STATO_0000032>broad sense heritability</obo:STATO_0000032>
<rdfs:label>heritability</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000545 -->
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<obo:IAO_0000115 xml:lang="en">A particularly important component of the genetic variance is the additive variance, Var(A), which is the variance due to the average effects (additive effects) of the alleles. Since each parent passes a single allele per locus to each offspring, parent-offspring resemblance depends upon the average effect of single alleles. Additive variance represents, therefore, the genetic component of variance responsible for parent-offspring resemblance. The additive genetic portion of the phenotypic variance is known as Narrow-sense heritability and is defined as:
h2 = Var(A)/Var(P)</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Heritability</obo:IAO_0000119>
<obo:STATO_0000032>h2</obo:STATO_0000032>
<rdfs:label>narrow sense heritability</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000546 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Bayes R is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model to compute 'genomic estimated breeding values'. In contrast to Bayes B methods, the new method assumes that the true SNP effects are derived from a series of normal distributions, the first with zero variance, up to one with a variance of approximately 1% of the genetic variance.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Erbe M, Hayes BJ, Matukumalli LK, Goswami S, Bowman PJ, Reich CM, et al. Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. J Dairy Sci. 2012;95:4114–29
doi: 10.3168/jds.2011-5019.
https://www.ncbi.nlm.nih.gov/pubmed/22720968</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">Bayes R</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000547 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The double exponential distribution (a.k.a. Laplace distribution) is the distribution of differences between two independent variates with identical exponential distributions (Abramowitz and Stegun 1972, p. 930).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://mathworld.wolfram.com/LaplaceDistribution.html</obo:IAO_0000119>
<obo:STATO_0000032>double exponential probability distribution</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">dLaplace(x, mu = 0, b = 1, params = list(mu, b), ...)
https://www.rdocumentation.org/packages/ExtDist/versions/0.6-3/topics/Laplace</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">https://docs.scipy.org/doc/scipy-0.19.0/reference/generated/scipy.stats.laplace.html</obo:STATO_0000391>
<rdfs:label>Laplace probability distribution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000548 -->
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<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>Bootstrapping is the practice of estimating properties of an estimator (such as its variance) by measuring those properties when sampling from an approximating distribution.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia:
https://en.wikipedia.org/wiki/Bootstrapping_(statistics)</obo:IAO_0000119>
<obo:STATO_0000032>bootstrap</obo:STATO_0000032>
<rdfs:label>sampling distribution estimation by bootstrapping</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000549 -->
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<obo:IAO_0000115 xml:lang="en">random forest procedure is a type of data transformation used in classification and statistical learning using regression. The random forest procedure is a meta estimator that fits a number of classifying decision trees on various sub-samples of the dataset (it operates by constructing a multitude of decision trees at training time) and use averaging to improve the predictive accuracy and control over-fitting. The sub-sample size is always the same as the original input sample size but the samples are drawn with replacement if bootstrap=True (default). The random forest procedure outputs the class that is the mode of the classes (classification) or mean prediction (regression) of the individual trees.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
https://en.wikipedia.org/wiki/Random_forest
and http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestRegressor.html</obo:IAO_0000119>
<obo:STATO_0000032>random forest</obo:STATO_0000032>
<obo:STATO_0000041># S3 method for formula
randomForest(formula, data=NULL, ..., subset, na.action=na.fail)
# S3 method for default
randomForest(x, y=NULL, xtest=NULL, ytest=NULL, ntree=500,
mtry=if (!is.null(y) && !is.factor(y))
max(floor(ncol(x)/3), 1) else floor(sqrt(ncol(x))),
replace=TRUE, classwt=NULL, cutoff, strata,
sampsize = if (replace) nrow(x) else ceiling(.632*nrow(x)),
nodesize = if (!is.null(y) && !is.factor(y)) 5 else 1,
maxnodes = NULL,
importance=FALSE, localImp=FALSE, nPerm=1,
proximity, oob.prox=proximity,
norm.votes=TRUE, do.trace=FALSE,
keep.forest=!is.null(y) && is.null(xtest), corr.bias=FALSE,
keep.inbag=FALSE, ...)
# S3 method for randomForest
print(x, ...)
from https://www.rdocumentation.org/packages/randomForest/versions/4.6-14/topics/randomForest</obo:STATO_0000041>
<obo:STATO_0000391>sklearn.ensemble.RandomForestClassifier(n_estimators=10, criterion=’gini’, max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features=’auto’, max_leaf_nodes=None, min_impurity_decrease=0.0, min_impurity_split=None, bootstrap=True, oob_score=False, n_jobs=1, random_state=None, verbose=0, warm_start=False, class_weight=None)
from:
http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html</obo:STATO_0000391>
<obo:STATO_0000391>sklearn.ensemble.RandomForestRegressor(n_estimators=10, criterion=’mse’, max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features=’auto’, max_leaf_nodes=None, min_impurity_decrease=0.0, min_impurity_split=None, bootstrap=True, oob_score=False, n_jobs=1, random_state=None, verbose=0, warm_start=False)
from:
http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestRegressor.html</obo:STATO_0000391>
<rdfs:label>random forest procedure</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000550 -->
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<obo:IAO_0000115>log likelihood is a data item which corresponds to the natural logarithm of the likelihood.
log likelihood is a data item commonly used to provide a measure of accuracy of a model.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041>ogLik(object, ...)
## S3 method for class 'lm'
logLik(object, REML = FALSE, ...)
from:
https://stat.ethz.ch/R-manual/R-patched/library/stats/html/logLik.html</obo:STATO_0000041>
<rdfs:label>log likelihood</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000551 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A data transformation process in which the Holm p-value procedure is applied with the aim of correcting false discovery rate</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics, 6, 65–70. http://www.jstor.org/stable/4615733.</obo:IAO_0000119>
<obo:STATO_0000032>Holm fdr</obo:STATO_0000032>
<obo:STATO_0000041>p.adjust(p, method = holm, n = length(p))
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html</obo:STATO_0000041>
<rdfs:label>Holm false discovery rate correction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000552 -->
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<obo:IAO_0000115>A data transformation process in which the Hommel p-value procedure is applied with the aim of correcting false discovery rate</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Hommel, G. (1988). A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika, 75, 383–386. doi: 10.2307/2336190</obo:IAO_0000119>
<obo:STATO_0000032>Hommel fdr</obo:STATO_0000032>
<obo:STATO_0000041>p.adjust(p, method = hommel, n = length(p))
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html</obo:STATO_0000041>
<rdfs:label>Hommel false discovery rate correction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000554 -->
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<obo:IAO_0000115>number of cross-validation segments is a count which is used as input parameter in a cross validation procedure to evaluate a statistical model.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>number of cross-validation segments</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000555 -->
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<obo:IAO_0000115>number of predictive components is a count used as input to the principle component analysis (PCA)</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>number of predictive components</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000556 -->
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<obo:IAO_0000115>number of orthogonal components is a count used as input to the orthogonal partial least square discriminant analysis (OPLS-DA)</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>number of orthogonal components</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000558 -->
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<obo:IAO_0000115 xml:lang="en">A statistical model term testing is a data transformation that accounts for the evaluation of a component of a statistical model or model term.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">statistical model term testing</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000559 -->
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<obo:IAO_0000115>the Wald test is statistical test which computes a Wald chi-squared test for 1 or more coefficients, given their variance-covariance matrix.
The Wald test (also called the Wald Chi-Squared Test) is a way to find out if explanatory variables in a model are significant. “Significant” means that they add something to the model; variables that add nothing can be deleted without affecting the model in any meaningful way</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041>Wald test for a term in a regression model:
regTermTest(model, test.terms, null=NULL,df=Inf, method=c("Wald","LRT"))
from:
http://r-survey.r-forge.r-project.org/survey/html/regTermTest.html</obo:STATO_0000041>
<obo:STATO_0000041>wald.test(Sigma, b, Terms = NULL, L = NULL, H0 = NULL, df = NULL, verbose = FALSE)
from:
https://www.rdocumentation.org/packages/aod/versions/1.3/topics/wald.test</obo:STATO_0000041>
<rdfs:label>Wald test</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000560 -->
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<obo:IAO_0000115>the Rao-Scott score is a statistic which is used to test the hypothesis that all coefficients associated with a particular regression term are zero (or have some other specified values). the LRT uses a linear combination of chi-squared distributions</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Lagrange multiplier test</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Rao-Scott test</obo:IAO_0000118>
<obo:IAO_0000119>Rao, JNK, Scott, AJ (1984) "On Chi-squared Tests For Multiway Contingency Tables with Proportions Estimated From Survey Data" Annals of Statistics 12:46-60.</obo:IAO_0000119>
<obo:STATO_0000032>Rao score test</obo:STATO_0000032>
<obo:STATO_0000041>regTermTest(model, test.terms, null=NULL,df=Inf, method=c("Wald","LRT"))
from:
http://r-survey.r-forge.r-project.org/survey/html/regTermTest.html</obo:STATO_0000041>
<rdfs:label>Rao's score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000561 -->
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<obo:IAO_0000115>the frequency (i.e., the proportion) of possible confidence intervals that contain the true value of their corresponding parameter. In other words, if confidence intervals are constructed using a given confidence level in an infinite number of independent experiments, the proportion of those intervals that contain the true value of the parameter will match the confidence level.
A probability measure of the reliability of an inferential statistical test that has been applied to sample data and which is provided along with the confidence interval for the output statistic.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia:
https://en.wikipedia.org/wiki/Confidence_interval
and from:
http://www.oxfordreference.com/view/10.1093/acref/9780191792236.001.0001/acref-9780191792236-e-103?rskey=tQCMI6&result=1</obo:IAO_0000119>
<obo:STATO_0000032></obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>confidence level</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000562 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000562">
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</rdfs:subClassOf>
<obo:IAO_0000112>http://davidmlane.com/hyperstat/A121160.html</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The standard error is a measure of dispersion applied to estimates across hypothetical repeated random samples.
It is a measure of how precise an estimate of a statistical parameter is.
The standard error is the estimated standard deviation of an estimate.
It measures the uncertainty associated with the estimate. Compared with the standard deviations of the underlying distribution, which are usually unknown, standard errors can be calculated from observed data.</obo:IAO_0000115>
<obo:IAO_0000117>Harold Lehmann, Kenneth Wilkins, Brian S. Alper, Xing Song, Joanne Dehnbostel, Muhammad Afzal, Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia and from SAGE research method article
http://methods.sagepub.com/reference/encyc-of-research-design/n435.xml</obo:IAO_0000119>
<obo:STATO_0000032>standard error of the estimate</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>standard error of estimate</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000562</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000563 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000563">
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<obo:IAO_0000115 xml:lang="en">Biplots are a type of exploratory graph used in statistics, a generalization of the simple two-variable scatterplot. A biplot is constructed by using the singular value decomposition (SVD) to obtain a low-rank approximation to a transformed version of the data matrix X, whose n rows are the samples (also called the cases, or objects), and whose p columns are the variables. The biplot was introduced by K. Ruben Gabriel (1971).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Gabriel, K. R. (1971). The biplot graphic display of matrices with application to principal component analysis. Biometrika, 58(3), 453–467.
adapted from:
https://en.wikipedia.org/wiki/Biplot
Last accessed: 04/07/2018</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">biplot(x, y, var.axes = TRUE, col, cex = rep(par("cex"), 2),
xlabs = NULL, ylabs = NULL, expand = 1,
xlim = NULL, ylim = NULL, arrow.len = 0.1,
main = NULL, sub = NULL, xlab = NULL, ylab = NULL, ...)
from:
http://stat.ethz.ch/R-manual/R-devel/library/stats/html/biplot.html
last accessed: 04/07/2018</obo:STATO_0000041>
<rdfs:label xml:lang="en">biplot</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000564 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000564">
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<obo:IAO_0000115 xml:lang="en">The coefficient of determination is a data item measuring the proportion of the variance in the dependent variable that is predictable from the independent variable(s).
In the case of a linear regression mode, the coefficient of determination r2 is the quotient of the variances of the fitted values and observed values of the dependent variable.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">r2</obo:IAO_0000118>
<obo:STATO_0000041 xml:lang="en">> eruption.lm = lm(eruptions ~ waiting, data=faithful)
> summary(eruption.lm)$r.squared
from:
http://www.r-tutor.com/elementary-statistics/simple-linear-regression/coefficient-determination</obo:STATO_0000041>
<rdfs:label xml:lang="en">coefficient of determination</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000565 -->
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<obo:IAO_0000115 xml:lang="en">a regression coefficient is a measure of association that is used as the coefficient of an independent variable in a regression model, of the dependent variable, which is linear in its parameters.
A value of zero means no association. The sign (positive or negative) reflects the direction of association.
a regression coefficient is a measure of association generated by a type of data transformation called a regression, which aims to model a response variable by expression the predictor variables as part of a function where variable terms are modified by a number. A regression coefficient is one such number.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2023-02-07 vote 5-0 by Cauê Monaco, Harold Lehmann, Mario Tristan, Jesus Lopez-Alcalde, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000116>Harold Lehmann, Brian S. Alper, Kenneth Wilkins, Muhammad Afzal</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en"></obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label>regression coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000566 -->
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<obo:IAO_0000115 xml:lang="en">An eigenvalue is a data item resulting from a data transformation known as eigen value decomposition. It also corresponds to a process of matrix diagonalization or any equivalent operation, ie. transforming the underlying system of equations into a special set of coordinate axes in which the matrix takes this canonical form. Each eigenvalue is paired with a corresponding so-called eigenvector.</obo:IAO_0000115>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from:
http://mathworld.wolfram.com/Eigenvalue.html
last accessed: 04/07/2018</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">eigen(x, symmetric, only.values = FALSE, EISPACK = FALSE)
https://stat.ethz.ch/R-manual/R-devel/library/base/html/eigen.html</obo:STATO_0000041>
<obo:STATO_0000391 xml:lang="en">In Python numpy linear algebra package (numpy.linalg)
https://docs.scipy.org/doc/numpy-1.13.0/reference/routines.linalg.html
linalg.eig(a) Compute the eigenvalues and right eigenvectors of a square array.
linalg.eigh(a[, UPLO]) Return the eigenvalues and eigenvectors of a Hermitian or symmetric matrix.
linalg.eigvals(a) Compute the eigenvalues of a general matrix.
linalg.eigvalsh(a[, UPLO]) Compute the eigenvalues of a Hermitian or real symmetric matrix.</obo:STATO_0000391>
<rdfs:label xml:lang="en">eigen value</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000567 -->
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<obo:IAO_0000115 xml:lang="en">Factor analysis is a dimension reduction data transformation that is used to describe variability among observed, correlated variables in terms of a potentially lower number of unobserved variables called factors. Factor analysis is related to principal component analysis (PCA), but the two are not identical. Both PCA and factor analysis aim to reduce the dimensionality of a set of data, but the approaches taken to do so are different for the two techniques. Factor analysis is clearly designed with the objective to identify certain unobservable factors from the observed variables, whereas PCA does not directly address this objective; at best, PCA provides an approximation to the required factors.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from Wikipedia:
https://en.wikipedia.org/wiki/Factor_analysis
last accessed: 04/07/2018
Cattell, R. B. (1952). Factor analysis. New York: Harper</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">factanal(x, factors, data = NULL, covmat = NULL, n.obs = NA,
subset, na.action, start = NULL,
scores = c("none", "regression", "Bartlett"),
rotation = "varimax", control = NULL, ...)</obo:STATO_0000041>
<obo:STATO_0000041 xml:lang="en">https://stat.ethz.ch/R-manual/R-devel/library/stats/html/factanal.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">factor analysis</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000568 -->
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<obo:IAO_0000115 xml:lang="en">In factor analysis, factor loadings express the relationship of each variable to the underlying factor.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Serra-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Factor_analysis</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.theanalysisfactor.com/factor-analysis-1-introduction/</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">factor loadings</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">https://stat.ethz.ch/R-manual/R-devel/library/stats/html/loadings.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">loadings</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000569 -->
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<obo:IAO_0000115 xml:lang="en">The score indicates how sensitive a likelihood function L(\Theta,X) is to its parameter \Theta. Explicitly, the score for \Theta is the gradient of the log-likelihood with respect to \Theta.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Serra-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://en.wikipedia.org/wiki/Score_(statistics)</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">https://www.rdocumentation.org/packages/bnlearn/versions/4.3/topics/score</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">efficient score</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">informant</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">score function</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">score</obo:STATO_0000041>
<rdfs:label xml:lang="en">score</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000570 -->
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<obo:IAO_0000115>The selectivity ratio (SR) is defined as the ratio of explained vexpl,i to residual variance vres,i for
the variable i on the target projection (TP) component in the context of Partial Least Squares Analysis.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.1289</obo:IAO_0000119>
<obo:STATO_0000032>selectivity ratio</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>selectivity ratio</rdfs:label>
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<!-- http://purl.obolibrary.org/obo/STATO_0000571 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Partial least squares regression (PLS regression) is a data transformation that bears some relation to principal components regression; instead of finding hyperplanes of maximum variance between the response and independent variables, it finds a linear regression model by projecting the predicted variables and the observable variables to a new space. Because both the X and Y data are projected to new spaces, the PLS family of methods are known as bilinear factor models. Partial least squares Discriminant Analysis (PLS-DA) is a variant used when the Y is categorical.
PLS is used to find the fundamental relations between two matrices (X and Y), i.e. a latent variable approach to modeling the covariance structures in these two spaces. A PLS model will try to find the multidimensional direction in the X space that explains the maximum multidimensional variance direction in the Y space. PLS regression is particularly suited when the matrix of predictors has more variables than observations, and when there is multicollinearity among X values. By contrast, standard regression will fail in these cases (unless it is regularized).
Partial least squares was introduced by the Swedish statistician Herman O. A. Wold, who then developed it with his son, Svante Wold. An alternative term for PLS (and more correct according to Svante Wold[1]) is projection to latent structures, but the term partial least squares is still dominant in many areas. Although the original applications were in the social sciences, PLS regression is today most widely used in chemometrics and related areas. It is also used in bioinformatics, sensometrics, neuroscience and anthropology.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>PLS</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
last accessed on 24/07/2018 from:
https://en.wikipedia.org/wiki/Partial_least_squares_regression</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Partial least squares analysis</obo:STATO_0000032>
<obo:STATO_0000041>https://rpubs.com/omicsdata/pls</obo:STATO_0000041>
<obo:STATO_0000391>http://scikit-learn.org/stable/modules/generated/sklearn.cross_decomposition.PLSRegression.html</obo:STATO_0000391>
<rdfs:label xml:lang="en">Partial Least Square regression</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000572 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a version of PLS used for classification, where the input y-block are group labels (categorical variable) rather than a continuous variable</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>PLS-DA</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">partial least squares discriminant analysis</obo:STATO_0000032>
<obo:STATO_0000041># S3 method for default
plsda(x, y, ncomp = 2, probMethod = "softmax",
prior = NULL, ...)
https://www.rdocumentation.org/packages/caret/versions/6.0-80/topics/plsda</obo:STATO_0000041>
<obo:STATO_0000391>http://scikit-learn.org/stable/modules/generated/sklearn.cross_decomposition.PLSRegression.html</obo:STATO_0000391>
<rdfs:label xml:lang="en">Partial Least Square Discriminant Analysis</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000573 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The arithmetic mean is defined as the sum of the numerical values of each and every observation divided by the total number of observations. S The arithmetic mean A is defined by the formula
A=sum[Ai] / n where i ranges from 1 to n and Ai represents the value of individual observations.
The arithmetic mean is significantly affected by extreme values and outliers. A better measure of central tendency is the median (http://purl.obolibrary.org/obo/STATO_0000574).</obo:IAO_0000115>
<obo:IAO_0000116>replaced OBI import following addition of restrictions and use in STATO. however the xref to OBI is kept as class metadata</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032>arithmetic mean</obo:STATO_0000032>
<obo:STATO_0000391>http://docs.scipy.org/doc/numpy/reference/generated/numpy.mean.html</obo:STATO_0000391>
<rdfs:label>average value</rdfs:label>
<rdfs:seeAlso>average value (http://purl.obolibrary.org/obo/OBI_0000679)</rdfs:seeAlso>
<rdfs:seeAlso>http://purl.obolibrary.org/obo/OBI_0000679</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000574 -->
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The median is that value of the variate which divides the total frequency into two halves. The median is measure of central tendency of data. It is obtained by arranging the observations in order from smallest to largest value. If there is an odd number of observations, the median is the middle value. If there is an even number of observations, the median is the average of the two middle values.</obo:IAO_0000115>
<obo:IAO_0000116>PRS and AGB added restriction about 'measure of central tendency' and quartile, june 2013 on 'centre value' OBI class.</obo:IAO_0000116>
<obo:IAO_0000116>replaced OBI import following addition of restrictions and use in STATO. however the xref to OBI is kept as class metadata</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>second quartile</obo:IAO_0000118>
<obo:IAO_0000119>A Dictionary of Statistical Terms, 5th edition, prepared for the International Statistical Institute by F.H.C. Marriott. Published for the International Statistical Institute by Longman Scientific and Technical.
and
Wolfram Alpha</obo:IAO_0000119>
<obo:STATO_0000032>median</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>center value</rdfs:label>
<rdfs:seeAlso>center value (http://purl.obolibrary.org/obo/OBI_0000674)</rdfs:seeAlso>
<rdfs:seeAlso>http://purl.obolibrary.org/obo/OBI_0000674</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000575 -->
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</owl:unionOf>
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</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115>a data transformation which finds principal component by applying non-linear iterative partial least squares algorithm</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>NIPALS</obo:IAO_0000118>
<obo:IAO_0000119>https://cran.r-project.org/web/packages/nipals/vignettes/nipals_algorithm.pdf</obo:IAO_0000119>
<obo:STATO_0000041>nipals(x, ncomp = min(nrow(x), ncol(x)), center = TRUE, scale = TRUE,
maxiter = 500, tol = 1e-06, startcol = 0, fitted = FALSE,
force.na = FALSE, gramschmidt = TRUE, verbose = FALSE)
https://www.rdocumentation.org/packages/mixOmics/versions/6.3.2/topics/nipals</obo:STATO_0000041>
<obo:STATO_0000391></obo:STATO_0000391>
<rdfs:label xml:lang="en">non-iterative Partial Least Squares</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000576 -->
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A novel algorithm for partial least squares (PLS) regression, SIMPLS, is proposed which calculates the PLS factors directly as linear combinations of the original variables. The PLS factors are determined such as to maximize a covariance criterion, while obeying certain orthogonality and normalization restrictions. This approach follows that of other traditional multivariate methods. The construction of deflated data matrices as in the nonlinear iterative partial least squares (NIPALS)-PLS algorithm is avoided. For univariate y SIMPLS is equivalent to PLS1 and closely related to existing bidiagonalization algorithms. This follows from an analysis of PLS1 regression in terms of Krylov sequences. For multivariate Y there is a slight difference between the SIMPLS approach and NIPALS-PLS2. In practice the SIMPLS algorithm appears to be fast and easy to interpret as it does not involve a breakdown of the data sets.
The acronym SIMPLS comes from 'straightforward implementation of a statistically inspired modification of the PLS method'</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SIMPLS: An alternative approach to partial least squares regression
Sijmen de Jong
https://doi.org/10.1016/0169-7439(93)85002-X</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">straightforward implementation of a statistically inspired modification of the PLS method</obo:STATO_0000032>
<obo:STATO_0000041>simpls(X, Y, ncomp, stripped = FALSE, ...)
https://www.rdocumentation.org/packages/cocorresp/versions/0.3-0/topics/simpls</obo:STATO_0000041>
<rdfs:label xml:lang="en">SIMPLS</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000577 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000577">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a partial least square regression applied when there is only one variable in Y (the matrix of response variables), or it is desirable to model and optimize separately the performance of each of the variables in Y. This case is usually referred to as PLS1 regression (J = 1).</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>A comparison of nine PLS1 algorithms, Martin Andersson.
https://doi.org/10.1002/cem.1248</obo:IAO_0000119>
<obo:STATO_0000041></obo:STATO_0000041>
<obo:STATO_0000041>plsreg1(x, y, nc = 2, cv = FALSE)
https://www.rdocumentation.org/packages/plspm/versions/0.2-2/topics/plsreg1</obo:STATO_0000041>
<rdfs:label>PLS1</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000578 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000578">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000571"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a partial least square regression applied to a multivariate response variable.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>a partial least square regression applied when there Y matrix of response variables is truely multivariate (J >1)</obo:IAO_0000119>
<obo:IAO_0000119>https://doi.org/10.1016/0003-2670(86)80028-9</obo:IAO_0000119>
<obo:STATO_0000041>plsreg2(X, Y, nc = 2)
https://www.rdocumentation.org/packages/plspm/versions/0.2-2/topics/plsreg2</obo:STATO_0000041>
<rdfs:label>PLS2</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000579 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000579">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>improved kernel PLS is a data transformation which implement a very fast kernel algorithm for updating PLS models in a recursive manner and for exponentially discounting past data.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-128X%28199701%2911%3A1%3C73%3A%3AAID-CEM435%3E3.0.CO%3B2-%23</obo:IAO_0000119>
<obo:STATO_0000041>kernelpls.fit(X, Y, ncomp, stripped = FALSE, ...)
https://www.rdocumentation.org/packages/pls/versions/2.6-0/topics/kernelpls.fit</obo:STATO_0000041>
<rdfs:label>improved Kernel PLS</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000580 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000580">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>variable importance in projection is a measure computed as part of a partial least square regression to accumulate the importance of each variable j being reflected by w from each component.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>VIP</obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.1016/j.chemolab.2012.07.010
and
S. Wold, E. Johansson, M. Cocchi
PLS: Partial Least Squares Projections to Latent Structures, 3D QSAR in drug design, 1 (1993), pp. 523-550</obo:IAO_0000119>
<obo:STATO_0000041>vip(object)
https://www.rdocumentation.org/packages/mixOmics/versions/6.3.2/topics/vip</obo:STATO_0000041>
<rdfs:label>variable importance in projection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000581 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000581">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a data transformation which compute the singular-value decomposition of a rectangular matrix.
The singular-value decomposition is very general in the sense that it can be applied to any m × n matrix whereas eigenvalue decomposition can only be applied to certain classes of square matrices.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Ralf Weber and Gavin Lloyd, University of Birmingham</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia:
https://en.wikipedia.org/wiki/Singular-value_decomposition
last accessed: 24/08/2018</obo:IAO_0000119>
<obo:STATO_0000041>svd(x, nu = min(n, p), nv = min(n, p), LINPACK = FALSE)
https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/svd</obo:STATO_0000041>
<obo:STATO_0000391>numpy.linalg.svd(a, full_matrices=True, compute_uv=True)
https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/numpy.linalg.svd.html</obo:STATO_0000391>
<rdfs:label>singular value decomposition</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000582 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000582">
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>best linear unbiased estimator</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Henderson C. R., 1984 Applications of Linear Models in Animal Breeding. University of Guelph, Guelph, Ontario, Canada.
ftp://tech.obihiro.ac.jp/suzuki/Henderson.pdf</obo:IAO_0000119>
<obo:STATO_0000032>BLUE</obo:STATO_0000032>
<obo:STATO_0000032 xml:lang="en">best linear unbiaised estimator of the fixed effect</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">best linear unbiased estimator</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000583 -->
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<obo:IAO_0000112>https://www.ncbi.nlm.nih.gov/pubmed/24033541
"An experiment was conducted to investigate the effect of a prebiotic on performance of partridge. The experiment was carried out with a total of eighty-day-old male Chukar partridge (Alectoris chukar chukar) chicks in a completely randomized design. The dietary treatments consisted of a control and an experimental treatment, and each treatment was replicated four times with 10 chicks per replicate."</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a completely randomized design is a type of design of experiment where the observation unit receive treatments (independent variable level) entirely at random. In other words, the observations unit are randomly assigned to treatments.
Completely randomized designs differ from randomized complete block design and should not be confused as in the latter, a blocking variable is first use to assign experimental units to blocks. Then only, the members of each block are then randomly assigned to different treatment groups</obo:IAO_0000115>
<obo:IAO_0000116>term request by Hanna Cwiek, https://github.com/ISA-tools/stato/issues/61</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from http://www.stat.yale.edu/Courses/1997-98/101/expdes.htm and from
A Dictionary of Statistics (3 ed.) , Graham Upton and Ian Cook
Publisher: Oxford University Press
Print Publication Date: 2014
Print ISBN-13: 9780199679188</obo:IAO_0000119>
<obo:STATO_0000041>http://animsci.agrenv.mcgill.ca/StatisticalMethodsII/R/crd/index.html</obo:STATO_0000041>
<rdfs:label>completely randomized design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000584 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000584">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000559"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the Wald statistic is a statistic is used during a Wald test, a test of significance of the regression coefficient; it is based on the asymptotic normality property of maximum likelihood estimates, and is computed as:
W = b * 1/Var(b) * b
In this formula, b stands for the parameter estimates, and Var(b) stands for the asymptotic variance of the parameter estimates. The Wald statistic is tested against the Chi-square distribution in the Wald test.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Hanna Cwiek:
https://github.com/ISA-tools/stato/issues/67</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia and http://documentation.statsoft.com/STATISTICAHelp.aspx?path=glossary/GlossaryTwo/W/WaldStatistic</obo:IAO_0000119>
<rdfs:label>Wald statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000585 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000585">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>degree of freedom calculation is a data transformation which is part of a stastical test and which aims to determine or estimate the number of degrees of freedom in a system.</obo:IAO_0000115>
<obo:IAO_0000116>term request from Hanna Cwiek:
https://github.com/ISA-tools/stato/issues/68</obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<rdfs:label>degree of freedom calculation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000586 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000586">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000446"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000001"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000248"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000046"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a restricted randomized design is a kind of study design which uses randomization to allocate observation unit to treatment but where intuitively poor allocations of treatments to experimental units are avoided, while retaining the theoretical benefits of randomization. This is often the case when so-called 'hard to change' factors are used in an experimental design.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia</obo:IAO_0000119>
<rdfs:label xml:lang="en">restricted randomized design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000587 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000587">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000648"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000639"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200104"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>https://www.nature.com/articles/srep35323/tables/1</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the percentage of variance is an output of principal component analysis (PCRA), which is obtained by forming the ratio of an eigen-value divided by the sum of all eigen-values. This produces a "percentage of variance" for each eigen-vector.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
https://stats.stackexchange.com/questions/31908/what-is-percentage-of-variance-in-pca</obo:IAO_0000119>
<obo:STATO_0000032>PoV</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<obo:STATO_0000391>http://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html</obo:STATO_0000391>
<rdfs:label>percentage of variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000588 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000588">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000346"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the scaled identity covariance structure is a type of covariance structure which has constant variance. The assumption is that there is no correlation between any elements.</obo:IAO_0000115>
<obo:IAO_0000117>Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117>Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119>adapted from https://www.ibm.com/support/knowledgecenter/en/SSLVMB_24.0.0/spss/advanced/covariance_structures.html</obo:IAO_0000119>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>scaled identity covariance structure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000589 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000589">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>TPM, which stands for Transcript Per Million, is a data item produced during a normilization procedure of RNA-Seq data (i.e. transcription profiling reads produced by nucleic acid sequencing) and corresponds to the count per length of transcript (kb) per million reads mapped.
-TPM considers the gene length and sequencing depth for normalization
-TPM proposed as an alternative to RPKM due to inaccuracy in RPKM measurement (Wagner et al., 2012)
-TPM is suitable for sequencing protocols where reads sequencing depends on gene length
-TPM is RPKM scaled by a constant to make sure the sum of all values is 1 million.
-TPM (transcript per million) = 1,000,000*θi/(ℓi*c), where c is a constant value, sum_[j](θj/ℓj), sum_[i]TPM=1,000,000
Recommended use:
-TPM measure is suited for gene count comparisons within a sample or between samples of the same sample group.
-TPM measure is NOT suited for Differential Expression analysis.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>TPM</obo:IAO_0000118>
<obo:IAO_0000119>https://www.biostars.org/p/273537/
http://www.arrayserver.com/wiki/index.php?title=TPM
https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html</obo:IAO_0000119>
<obo:IAO_0000233 xml:lang="en">https://github.com/ISA-tools/stato/issues/79
and
https://github.com/mcourtot/FAIRPlus_squad2/issues/50</obo:IAO_0000233>
<obo:IAO_0000600>TPM-transcript per million</obo:IAO_0000600>
<obo:STATO_0000032>TPM</obo:STATO_0000032>
<rdfs:label>TPM-transcript per million</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000590 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000590">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>median of the ratios corrected count is kind of count produced during an RNA-Seq data normalization procedure which corresponds to dividing counts by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene.
It was first described by Anders and Huber in 2010 (https://doi.org/10.1186/gb-2010-11-10-r106)
Recommended use:
-"median of the ratios corrected count" is suited for Differential Expression analysis or between samples.
-"median of the ratios corrected count" is NOT suited for gene count comparisons within a sample.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118></obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.1186/gb-2010-11-10-r106</obo:IAO_0000119>
<obo:STATO_0000032>median of the ratios of observed counts</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>median of the ratios corrected count</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000591 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000591">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>TMM or Trimmed Mean of M-Values is a measurement datum which is the output of the TMM normalization procedure for RNA-Seq data proposed by Robinson and Oshlack (2010). A scaling normalization method for differential expression analysis of RNA-seq data.
The TMM procedure is doubly trimmed, by log-fold-changes (sample k relative to sample r for gene g) and by absolute intensity (A g ).
It was first release as part of the R package edgeR, 10.1093/bioinformatics/btp616
Recommended use:
-TMM measure is suited for gene count comparisons within a sample or between samples of the same sample group.
-TMM measure is suited for Differential Expression analysis.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>TMM</obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.1186/gb-2010-11-3-r25
and
https://doi.org/10.1093/bioinformatics/btp616
and
https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html</obo:IAO_0000119>
<obo:STATO_0000032>TMM</obo:STATO_0000032>
<obo:STATO_0000041>"calcNormFactors"(object, method=c("TMM","RLE","upperquartile","none"), refColumn=NULL, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10, p=0.75, ...)
from:
https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/calcNormFactors</obo:STATO_0000041>
<rdfs:label>TMM-trimmed mean of M-values corrected count</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000592 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000592">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the Rand index is a ratio, related to the notion of accuracy (STATO_0000415), which is used to compare the similarity of two clustering outcomes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">RI</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">Rand, W.M. 1971. Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 66: 846--850. Hubert, L. and Arabie, P. 1985. Comparing partitions. Journal of Classification. 2: 193--218.</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en">Rand index</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">rand.index(group1, group2)
from:
https://www.rdocumentation.org/packages/fossil/versions/0.3.7/topics/rand.index</obo:STATO_0000041>
<rdfs:label xml:lang="en">Rand index</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000593 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000593">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000592"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">the adjusted Rand index is a measure which rescales the Rand index, taking into account that random chance will cause some objects to occupy the same clusters, so the Rand Index will never actually be zero.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">ARI</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:STATO_0000032>ARI</obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en">adj.rand.index(group1, group2)
from:
https://www.rdocumentation.org/packages/fossil/versions/0.3.7/topics/rand.index</obo:STATO_0000041>
<rdfs:label xml:lang="en">adjusted Rand index</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000594 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000594">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000642"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000090"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000252"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001927"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:onClass>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a confusion matrix is a 2 by 2 contingency table used to evaluate the performance of a classifier, often a machine-learning classifier and that allows visualization of the performance of an algorithm, typically a supervised learning one. It defines two dimensions ("actual" and "predicted"), and identical sets of "classes" in both dimensions (each combination of dimension and class is a variable in the contingency table).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000119 xml:lang="en">adapted from wikipedia:
https://en.wikipedia.org/wiki/Confusion_matrix
last accessed: 22.10.2019</obo:IAO_0000119>
<obo:STATO_0000032 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix
from:
https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix</obo:STATO_0000041>
<rdfs:label xml:lang="en">confusion matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000595 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000595">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the number of true positive is a count which denotes how many elements are correctly classified as having a feature they are actually known to be having (e.g. carrier of a pathogen).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">number of true positive</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000596 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000596">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the number of false positive is a count which denotes how many elements known to be void of feature are wrongly classified as having it (e.g. being diagnosed with a disease when one is totally healthy)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">number of false positive</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000597 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000597">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the number of true negative is a count which denotes how many elements are correctly classified as void of a feature they are actually known to be missing (e.g. free of pathogen).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">number of true negative</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000598 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000598">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000047"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the number of false negative is a count which denotes how many elements known to be having a feature are wrongly classified as being devoided of it (e.g. being given an all clear while being actually infected and carrier of a pathogen)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<rdfs:label xml:lang="en">number of false negative</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000599 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000599">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a point estimate is a data item which provides a particular value evaluating a population parameter</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Tom Nichols</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en"></obo:IAO_0000119>
<obo:IAO_0000233 xml:lang="en">https://github.com/ISA-tools/stato/issues/74</obo:IAO_0000233>
<rdfs:label xml:lang="en">point estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000600 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000600">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an interval estimate is a data item corresponding to a range of values likely to contain the population parameter of interest</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Hanna Cwiek</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000233 xml:lang="en">https://github.com/ISA-tools/stato/issues/74</obo:IAO_0000233>
<obo:STATO_0000032 xml:lang="en"></obo:STATO_0000032>
<obo:STATO_0000041 xml:lang="en"></obo:STATO_0000041>
<rdfs:label xml:lang="en">interval estimate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000601 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000601">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200089"/>
<obo:IAO_0000115>simultaneous multiple testing method is a multiple testing correction method which...</obo:IAO_0000115>
<obo:IAO_0000119></obo:IAO_0000119>
<rdfs:label>simultaneous multiple testing correction</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000602 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000602">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200089"/>
<obo:IAO_0000115>sequential multiple testing method is a multiple testing correction method which...</obo:IAO_0000115>
<obo:IAO_0000119></obo:IAO_0000119>
<rdfs:label>sequential multiple testing correction method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000603 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000603">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000602"/>
<obo:IAO_0000115>a sequential multiple correction procedure which does not maintain a constant false positive rate but allows it to grow controllably.</obo:IAO_0000115>
<obo:IAO_0000119>Thompson et al 2019.
doi: http://dx.doi.org/10.1101/801696
https://www.biorxiv.org/content/biorxiv/early/2019/10/22/801696.full.pdf</obo:IAO_0000119>
<rdfs:label>alpha debt</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000604 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000604">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000602"/>
<obo:IAO_0000115>a type of sequential multiple testing correction method</obo:IAO_0000115>
<obo:IAO_0000119>Aharoni, Ehud, and Saharon Rosset. 2014. “Generalized α -investing: definitions, optimality results and application to public databases.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 76 (4): 771–94. https: //doi.org/10.1111/rssb.12048.</obo:IAO_0000119>
<obo:IAO_0000119>Foster, Dean P, and Robert A Stine. 2008. “α-Investing: A procedure for sequential control of expected false discoveries.” Journal of the Royal Statistical Society. Series B: Statistical Methodology 70 (2): 429–44. https://doi.org/10. 1111/j.1467-9868.2007.00643.x.</obo:IAO_0000119>
<rdfs:label>alpha investing procedure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000605 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000605">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000602"/>
<obo:IAO_0000115>a type of sequential multiple testing correction</obo:IAO_0000115>
<obo:IAO_0000119>Aharoni, Ehud, and Saharon Rosset. 2014. “Generalized α -investing: definitions, optimality results and application to public databases.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 76 (4): 771–94. https: //doi.org/10.1111/rssb.12048.</obo:IAO_0000119>
<rdfs:label>alpha spending procedure</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000606 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000606">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115>q is the basic statistic for the studentized range distribution, which is used for multiple comparison procedures, such as the single step procedure Tukey's range test, the Newman–Keuls method, and the Duncan's step down procedure, and establishing confidence intervals that are still valid after data snooping has occurred</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Student (1927). "Errors of routine analysis". Biometrika. 19 (1/2): 151–164. doi:10.2307/2332181</obo:IAO_0000119>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Studentized_range</obo:IAO_0000119>
<obo:STATO_0000032>studentized range</obo:STATO_0000032>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>q-statistic</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000607 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000607">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000115>a proportion is a ratio which corresponds to the fraction of the total presenting a particular feature</obo:IAO_0000115>
<obo:IAO_0000119>COKA group</obo:IAO_0000119>
<rdfs:label>proportion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000608 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000608">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000209"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000274"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An area under the curve where the curve is the true positive rate and the range of interest is the false positive rate.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">AUC</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">AUROC</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">C-statistic</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">Harrell's C</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">c-statistic</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">concordance index</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">concordance statistic</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/yardstick/versions/1.3.1/topics/roc_auc
roc_auc()</obo:STATO_0000041>
<rdfs:label xml:lang="en">area under the receiver operator characteristic curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000609 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000609">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en"></obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">measure of hypothesis testing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000610 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000610">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">measure of association is a statistic which quantitatively represents a relationship between two or more variables</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-03-16 vote 7-0 by Mario Tristan, Paola Rosati, Louis Leff, nisha mathew, Philippe Rocca-Serra, Harold Lehmann, Janice Tufte</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal, Neeraj Ojha</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">measure of association</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000611 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000611">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
<obo:IAO_0000115 xml:lang="en">measure of correlation is a measure of association between ordinal or continuous variables.
A value of 0 means no association.
A positive value means a positive association (as one variable increases, the other variable increases).
A negative value means a negative association (as one variable increases, the other variable decreases).
For correlation coefficients, the possible values range from +1 (perfect positive association) to -1 (perfect negative association)</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-11-16 vote 5-0 by Brian S. Alper, Philippe Rocca-Serra, Harold Lehman, Jesus Lopez-Alcalde, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000118>correlation</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">measure of correlation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000612 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000612">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000142"/>
<obo:IAO_0000115>A measure of correlation, ranging from -1 to 1, that measures the strength and direction of the relationship between ranks by value of two ordinal or continuous variables, and is calculated based on the difference in the number of concordant and discordant pairs of rankings divided by the total number of pairs of rankings, where ties are not counted among the pairs of rankings.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2023-01-25 vote 5-0 by Mario Tristan, Jesus Lopez-Alcalde, Joanne Dehnbostel, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000118>Goodman-Kruskal gamma</obo:IAO_0000118>
<obo:IAO_0000118>gamma coefficient</obo:IAO_0000118>
<obo:IAO_0000118>gamma statistic</obo:IAO_0000118>
<obo:IAO_0000119>adapted from: https://stats.stackexchange.com/questions/18112/how-do-the-Goodman-Kruskal-gamma-and-the-Kendall-tau-or-Spearman-rho-correlation</obo:IAO_0000119>
<rdfs:label>Goodman and Kruskal's gamma</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000613 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000613">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a subtraction of one quantity from another.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2021-12-01 vote 5-0 by Philippe Rocca-Serra, Paola Rosati, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000614 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000614">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000613"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a subtraction of one quantity from another, with no modification of the resulting value.
As a type of statistic, "Absolute Difference" is the actual difference between two quantities and can be positive or negative depending on the order of subtraction. The term "Absolute Difference" should not be confused with the mathematical term 'absolute value' which is a numerical value without a negative sign.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2021-12-01 vote 5-0 by Philippe Rocca-Serra, Paola Rosati, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal, Khalid Shahin, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">absolute difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000615 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000615">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000613"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a difference between 1 and a ratio of the two quantities being compared.
Relative Difference = 1 - ( a / b ). Because 1 - ( a / b ) is not equal to 1 - ( b / a ), Relative Difference may be expressed as "Relative Difference with respect to b" when referring to 1 - ( a / b ).
The relative difference can also be defined as a statistic that is a ratio of the absolute difference (of the two quantities being compared) to the reference value (one of the quantities being compared). Relative Difference = ( b - a ) / ( b ) where b is the reference value and this may also be called "Relative Difference with respect to b".</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-06-29 vote 5-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Kenneth Wilkins, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">relative difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000616 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000616">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000614"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a subtraction of one count from another.
The term Count Difference is used to specify the Absolute Difference is with respect to a count or number of items (such as number of events, platelet counts, sample size e.g. number of people in the group) to distinguish from differences in other types of statistics (mean difference, median difference, risk difference, etc.)</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000116>Expert Working Group Agreement: 2021-12-15 vote 6-0 by Robin Ann Yurk, Janice Tufte, Paola Rosati, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">count difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000617 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000617">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000614"/>
<obo:IAO_0000115 xml:lang="en">A difference that is a subtraction of one median from another.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2021-12-01 vote 6-0 by Philippe Rocca-Serra, Paola Rosati, Robin Ann Yurk, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Janice Tufte, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000118>difference in median</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">median difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000618 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000618">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000100"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A standardized mean difference which is calculated as a difference between two means, divided by a square root of an average of the variances of the two groups.
In Cohen's d statistic, the statistical measure of dispersion is specified as the square root of an average of the variances of the two groups being compared. The variances of the two groups are based on within-group standard deviations.
For sample sizes < 50, a correction factor is used.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-07-20 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO</obo:IAO_0000119>
<rdfs:label xml:lang="en">Cohen's d</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000619 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000619">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000115>A proportion in which the numerator represents the correctly non-detected items within the denominator that represents all items not detected.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-01-26 vote 8-0 by Robin Ann Yurk, Janice Tufte, Harold Lehmann, Philippe Rocca-Serra, Paola Rosati, Mario Tristan, Brian S. Alper, Jesus Lopez-Alcalde</obo:IAO_0000116>
<obo:IAO_0000116>In a population of people with and without a disease, and a test which is positive (suggesting the disease) or negative (suggesting not having the disease), the negative predictive value is the proportion of true negatives (all people without the disease who test negative) within all the people with a negative test (true negatives plus false negatives). NPV = TN / (TN + FN).</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Ken Wilkins, Philippe Rocca-Serra, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO</obo:IAO_0000119>
<rdfs:label>negative predictive value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000620 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000620">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000115>A proportion in which the numerator represents the cases in which an event or characteristic occurs and the denominator represents all possible cases.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-06-29 vote 6-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Janice Tufte, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000116>In the English language, 'risk' may be used synonymously with 'hazard', 'chance', 'likelihood', 'relative likelihood', 'probability' and many other terms. In SEVCO the term 'risk' is explicitly defined for how it is used in other terms such as 'Risk Ratio' and 'Relative Risk Difference' The statistical definition of 'risk' does not have a negative or undesirable connotation.</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO</obo:IAO_0000119>
<rdfs:label>risk</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000621 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000621">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000607"/>
<obo:IAO_0000115>diagnostic yield is a proportion in which the numerator represents the correctly detected items within the denominator that represents all items tested.</obo:IAO_0000115>
<obo:IAO_0000116>2022-08-10 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Harold Lehmann, Eric Harvey, Paola Rosati</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000119>"Diagnostic yield was defined as the number of participants with positive findings for advanced neoplasia relative to all participants" in https://pubs.rsna.org/doi/10.1148/radiol.12112486
Other 'definitions' found include synonymous use with sensitivity, and 'diagnostic yield' describing the statistic array of TP, FP, TN, and FN data.</obo:IAO_0000119>
<rdfs:label>diagnostic yield</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000622 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000622">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000314"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">ratio-based measure of association is a measure of association which relies on a quotient of 2 quantities to indicate the strength of the association.</obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">ratio-based measure of association</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000623 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000623">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000610"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A measure of association of two variables representing measurements of the same attribute of an entity.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-12-21 vote 5-0 by Mario Tristan, Philippe Rocca-Serra, Eric Harvey, Janice Tuft, Harold Lehmann</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO/STATO</obo:IAO_0000119>
<rdfs:label>measure of agreement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000624 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000624">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000028"/>
<obo:IAO_0000115 xml:lang="en">The Gini index, or Gini coefficient, is a statistical measure of dispersion which assesses the pattern of data in a frequency distribution, in particular it measures the inequality among values.
Geometrically, the Gini index can be defined as the ratio of 2 areas delineated by 2 curves, the line of equality (curve 1) and the Lorenz curve (curve 2). The numerator of the ratio corresponds to the area defined between curve 1 and curve 2 , while the denominator corresponds to the entire area below curve 1.
Mathematically, the Gini index is defined as half of the relative mean absolute difference.
It was therefore originally used to assess income inequality and is named after the italian statistician Corrado Gini who published it in 1912.</obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<obo:STATO_0000041>https://search.r-project.org/CRAN/refmans/dineq/html/gini.wtd.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">Gini index</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000625 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000625">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000615"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a difference between 1 and a ratio of the two mean values being compared.
Relative Mean Difference = 1 - ( a / b ) where a and b are mean values.
The relative mean difference can also be defined as a statistic that is a ratio of the difference in means to the reference mean value. Relative Mean Difference = ( b - a ) / ( b ) where b is the reference mean value and a is another mean value.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-06-29 vote 6-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Janice Tufte, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Kenneth Wilkins, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">relative mean difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000626 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000626">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000615"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a difference between 1 and a ratio of the two risk values being compared.
Relative Risk Difference = 1 - ( a / b ) where a and b are risk values.
The relative risk difference can also be defined as a statistic that is a ratio of the risk difference to the risk used as a reference. Relative Risk Difference = ( b - a ) / ( b ) where b is the reference risk value and a is another risk value.</obo:IAO_0000115>
<obo:IAO_0000117>Expert Working Group Agreement: 2022-06-22 vote 6-0 by Mario Tristan, Eric M Harvey, Jesus Lopez-Alcalde, Robin Ann Yurk, Paola Rosati, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">relative risk difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000627 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000627">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>odds correspond to a ratio in which the numerator represents the probability that an event will occur and the denominator represents the probability that an event will not occur.
'Odds' and 'Odds ratio' are different terms. 'Odds' is a ratio of probabilities. 'Odds ratio' is a ratio of two different odds.
Odds are calculated as p / (1-p) where p is the probability of event occurrence. When p = 0, the odds = 0. When p = 1, the odds may be expressed as not calculable or as "odds against = 0".
Odds may be expressed as p:(1-p). Odds may be expressed as p:q where q = 1-p. Odds may be expressed as a:b where a and b are multiples of p and (1-p). Examples of different expressions of the same odds include 3:2, 3/2, 0.6:0.4, 0.6/0.4, and 1.5.
Odds may be expressed as "odds for" or "odds in favor" (e.g. 1:5 for a "3" on a 6-sided die) or "odds against" (e.g. 5:1 against a "3" on a 6-sided die).
The term "betting odds" used in gambling that involves financial amounts in the formulation is not an "Odds" in the definition of the Scientific Evidence Code System.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-03-22 vote 5-0 by Muhammad Afzal, Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Robin Ann Yurk</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Kenneth Wilkins, Muhammad Afzal</obo:IAO_0000117>
<rdfs:label>odds</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000628 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000628">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000663"/>
<obo:IAO_0000112>https://pubmed.ncbi.nlm.nih.gov/35508113/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A ratio representing the harmonic mean of recall and precision.
The F1-score is used as a measure of quality for classification algorithms and information retrieval strategies, where 1 represents the best precision and recall and 0 represents the worst precision and recall.
A harmonic mean of a set of quantities is the reciprocal of the arithmetic mean of the reciprocals of each quantity. The F score is thus calculated as 1 / (the arithmetic mean of the reciprocals), or:
F = 1 / ( ( (1/recall) + (1/precision) ) / 2 )
F = 2*( (precision*recall) / (precision+recall) )
Recall is sensitivity STATO:0000233
Precision (PPV) is STATO:0000416</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-10-19 vote 6-0 by Joanne Dehnbostel, Muhammad Afzal, Jesus Lopez-Alcalde, Mario Tristan, Eric Harvey, Harold Lehmann</obo:IAO_0000116>
<obo:IAO_0000116>term request: https://github.com/ISA-tools/stato/issues/93</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel, Brian S. Alper, Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>F score</obo:IAO_0000118>
<obo:IAO_0000118>F-measure</obo:IAO_0000118>
<obo:IAO_0000118>F-score</obo:IAO_0000118>
<obo:IAO_0000118>F1 measure</obo:IAO_0000118>
<obo:IAO_0000118>F1-score</obo:IAO_0000118>
<obo:IAO_0000119></obo:IAO_0000119>
<obo:STATO_0000391>sklearn.metrics.f1_score(y_true, y_pred, *, labels=None, pos_label=1, average='binary', sample_weight=None, zero_division='warn')
source:
https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html</obo:STATO_0000391>
<rdfs:label>F1 score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000629 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000629">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000682"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A Kappa statistic where the expected agreement between two raters is expressed in terms of the square of arithmetic means of marginal proportions of each assessment category.
Scott's pi is a kappa statistic for two raters that assumes the likelihood of each category for assignment is based on the same distribution of rater responses, leading to the use of squared arithmetic means of the marginal proportion of each assessment category as its estimate of "chance agreement."
Pr(expected) is calculated using squared "joint proportions" which are squared arithmetic means of the marginal proportions of each assessment category, in contrast to Cohen's Kappa which uses squared geometric means.
Scott's pi = ( p[a] - p[e] ) / ( 1 - p[e] ) where p[a] is the observed percent agreement and p[e] is the expected chance agreement expressed as the squared joint proportions of the marginal sums.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-10-19 vote 6-0 by Joanne Dehnbostel, Muhammad Afzal, Jesus Lopez-Alcalde, Mario Tristan, Eric Harvey, Harold Lehmann</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<rdfs:label>Scott's pi</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000630 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000630">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000682"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A Kappa statistic in which the expected agreement by chance is based on an assumption that the likelihood of each category for assignment is based on the proportion observed, and the number of raters is 2.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-09-14 vote 6-0 by Nisha Mathew, Philippe Rocca-Serra, Harold Lehmann, Eric Harvey, Jesus Lopez-Alcalde, Khalid Shahin</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000118>Cohen's kappa statistic</obo:IAO_0000118>
<obo:IAO_0000119>COKA/SEVCO/STATO</obo:IAO_0000119>
<rdfs:label>Cohen's kappa</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000631 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000631">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000682"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A Kappa statistic in which the expected agreement by chance is based on an assumption that the likelihood of each category for assignment is based on the proportion observed, and the number of raters is more than 2.
A Kappa statistic is a measure of agreement among categorical assessments, corrected for chance agreement.
In the modified Cohen's kappa for more than 2 raters, the expected chance agreement is modeled as the summation of the differences, between the square of the expected probability of the category and the quotient of its variance divided by the number of raters, for each category.
The modified Cohen's kappa for more than 2 raters is calculated as ( p[a] - p[e] ) / ( 1 - p[e] ) where p[a] is the observed percent agreement and p[e] is the expected chance agreement.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-09-14 vote 5-0 by Nisha Mathew, Philippe Rocca-Serra, Harold Lehmann, Eric Harvey, Jesus Lopez-Alcalde</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<rdfs:label>modified Cohen’s kappa for more than 2 raters</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000632 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000632">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000623"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A ratio of the number of incorrect results to the total number tested.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-10-19 vote 5-0 by Joanne Dehnbostel, Muhammad Afzal, Janice Tufte, Mario Tristan, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000118>classification error</obo:IAO_0000118>
<obo:IAO_0000119>COKA/SEVCO/STATO</obo:IAO_0000119>
<rdfs:label>misclassification rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000633 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000633">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>a cutoff is an information content entity that represents or sets the boundary at which something changes.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 5/5 as of 10/11/2021: Janice Tufte, Joanne Dehnbostel, Louis Leff, Vignesh Subbian, Robin Ann Yurk</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Kenneth Wilkins, Khalid Shahin</obo:IAO_0000117>
<obo:IAO_0000118>cutoff point</obo:IAO_0000118>
<obo:IAO_0000118>cutoff value</obo:IAO_0000118>
<obo:IAO_0000118>limit</obo:IAO_0000118>
<obo:IAO_0000118>threshold value</obo:IAO_0000118>
<obo:IAO_0000119>COKA/SEVCO</obo:IAO_0000119>
<rdfs:label>cutoff</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000634 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000634">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistic that is a quotient of one and a difference.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-07-20 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO</obo:IAO_0000119>
<rdfs:label>reciprocal of difference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000635 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000635">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000634"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>A statistic that represents the number of units that needs to be treated to prevent one additional undesired outcome. The Number Needed to Treat is calculated as the reciprocal of a treatment effect estimate, where the effect estimate is expressed as a risk difference.
The Number Needed to Treat (NNT) value is often rounded up to the next highest whole integer</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-07-20 vote 7-0 by Cauê Monaco, Janice Tufte, Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000118>NTT</obo:IAO_0000118>
<obo:IAO_0000118>NTTB</obo:IAO_0000118>
<obo:IAO_0000118>number needed to treat to benefit</obo:IAO_0000118>
<obo:IAO_0000119>COKA/SEVCO</obo:IAO_0000119>
<rdfs:label>number needed to treat</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000636 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000636">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000634"/>
<obo:IAO_0000112>Number needed to screen was then calculated by dividing the number needed to treat for treating risk factors by the prevalence of disease that was unrecognised or untreated.
https://www.bmj.com/content/317/7154/307.long</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistic that represents the number of units that needs to be tested to prevent one additional adverse outcome, assuming that positive testing will lead to preventive intervention. The Number Needed to Screen to Prevent is calculated as the Number Needed to Treat divided by the prevalence.
Comment for application:
The Number Needed to Screen (NNS) value is often rounded up to the next highest whole integer. The Number Needed to Screen to Detect is distinct from the Number Needed to Screen to Prevent as the formulas to calculate are different, even though both may be abbreviated as NNS.
The formula may be adjusted for test performance characteristics (e.g. dividing by the sensitivity) or assumptions regarding acceptance or adherence of interventions.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-08-03 vote 5-0 by Jesus Lopez-Alcalde, Janice Tufte, Eric Harvey, Philippe Rocca-Serra, Harold Lehmann</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000118>NNS</obo:IAO_0000118>
<obo:IAO_0000119>Number needed to screen was then calculated by dividing the number needed to treat for treating risk factors by the prevalence of disease that was unrecognised or untreated.
https://www.bmj.com/content/317/7154/307.long</obo:IAO_0000119>
<rdfs:label>number needed to screen to prevent</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000637 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000637">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000634"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistic that represents the number of units that needs to be tested to identify one additional case. The Number Needed to Screen to Detect is calculated as the reciprocal of a difference in rate of detected cases with and without screening.
The Number Needed to Screen (NNS) value is often rounded up to the next highest whole integer. The Number Needed to Screen to Detect is distinct from the Number Needed to Screen to Prevent as the formulas to calculate are different, even though both may be abbreviated as NNS.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-08-03 vote 5-0 by Jesus Lopez-Alcalde, Janice Tufte, Eric Harvey, Philippe Rocca-Serra, Harold Lehmann</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000118>NNS</obo:IAO_0000118>
<rdfs:label>number needed to screen to detect</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000638 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000638">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000634"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>A statistic that represents the number of units that, if treated or exposed to the intervention, lead to one additional undesired outcome. The Number Needed to Harm is calculated as the reciprocal of a treatment effect estimate, where the effect estimate is expressed as a risk difference.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117></obo:IAO_0000117>
<obo:IAO_0000118>NNH</obo:IAO_0000118>
<obo:IAO_0000118>NNTH</obo:IAO_0000118>
<obo:IAO_0000118>number needed to treat to harm</obo:IAO_0000118>
<obo:IAO_0000119>https://www.cebm.ox.ac.uk/resources/ebm-tools/glossary</obo:IAO_0000119>
<rdfs:label>number needed to harm</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000639 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000639">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A ratio formed between a numerator and a denominator (both described by the same unit), and that is multiplied by 100.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2022-01-07 vote 7-0 by Harold Lehmann, Robin Ann Yurk, Janice Tufte, C P Ooi, Louis Leff, Jesus Lopez-Alcalde, Mario Tristan</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>%</obo:IAO_0000118>
<obo:IAO_0000119>COKA/SEVCO/STATO</obo:IAO_0000119>
<rdfs:label>percentage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000640 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000640">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200194"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0200083"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The logrank test is a statistical hypothesis test used to compare the survival distributions of two or more groups. It is commonly employed in survival analysis, where the primary interest lies in comparing the survival experiences of different groups over time.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>Mantel-Cox test</obo:IAO_0000118>
<obo:IAO_0000118>logrank test</obo:IAO_0000118>
<obo:IAO_0000119>adapted from wikipedia: https://en.wikipedia.org/wiki/Logrank_test
AND
adapted from ChatGPT3.5 with the following prompt: "Please define 'logrank Test' in statistics"</obo:IAO_0000119>
<rdfs:label>log-rank test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000641 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000641">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000279"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000255"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112></obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>The Friedman test is a non-parametric statistical test used to determine whether there are statistically significant differences among multiple related groups. It is an extension of the Wilcoxon signed-rank test for more than two related samples.</obo:IAO_0000115>
<obo:IAO_0000116></obo:IAO_0000116>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia https://en.wikipedia.org/wiki/Friedman_test
and
adapted from ChatGPT3.5 with the following prompt: "Please define 'Friedman Test' in statistics"</obo:IAO_0000119>
<rdfs:label>Friedman test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000642 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000642">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a matrix is a rectangular array of numbers, which are called entries of the matrix.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from:
https://en.wikipedia.org/wiki/Matrix_(mathematics)</obo:IAO_0000119>
<rdfs:label>matrix</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000643 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000643">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000651"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the sample variance is a variance computed over the actual observations made, which correspond to a sample drawn from a population in an experiment. the sample variance can be used to estimate the true variance of the underlying population/distribution.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2023-11-20 vote 5-0 by Brian S. Alper, Jesus Lopez-Alcalde, Harold Lehmann, Muhammad Afzal, Eric Harvey</obo:IAO_0000116>
<obo:IAO_0000117>Kenneth Wilkins, Brian S. Alper, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000118>sample variance</obo:IAO_0000118>
<obo:IAO_0000119>STATO and COKA group:
adapted from:
https://guilhermejacob.github.io/2020/06/variance-sampling/</obo:IAO_0000119>
<rdfs:label>variance for sample</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000644 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000644">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000654"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The sign test is a non-parametric hypothesis test used to assess whether the median of a single population is equal to a specified value, typically referred to as the null hypothesis. The sign test is particularly useful when the data are not normally distributed or when the assumptions required for parametric tests are not met.
Note that the 'sign test' is related but different from the "Wilcoxon signed rank test'.
Sign test: It does not assume any specific distribution for the data. It only requires paired data and makes no assumptions about the shape of the underlying distribution.
Wilcoxon signed-rank test: It assumes that the differences between paired observations come from a symmetric distribution. It's also more powerful than the sign test when the distribution is continuous and symmetric.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>adapted from wikipedia
and
adapted from ChatGPT3.5</obo:IAO_0000119>
<obo:STATO_0000391></obo:STATO_0000391>
<rdfs:label>sign test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000645 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000645">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A ratio in which the numerator represents any quantity and the denominator represents an interval of time.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO Group</obo:IAO_0000119>
<rdfs:label xml:lang="en">rate</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000645</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000646 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000646">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
<obo:IAO_0000115>the population variance is a variance of the true population from which a sample is derived.
the population variance describes the variability of a characteristic in the population.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>distribution variance</obo:IAO_0000118>
<obo:IAO_0000119>STATO and COKA group
adapted from :
https://guilhermejacob.github.io/2020/06/variance-sampling/</obo:IAO_0000119>
<rdfs:label>population variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000647 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000647">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000562"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of dispersion applied to proportions across hypothetical repeated random samples.
A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2024-01-22 vote 5-0 by Homa Keshavarz, Eric Harvey, Brian S. Alper, Harold Lehmann, Yasser Sami Amer</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper, Kenneth Wilkins, Xing Song, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">standard error of the proportion</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000647</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000648 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000648">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000562"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of dispersion applied to differences between means of independent groups across hypothetical repeated random samples.
A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2024-02-12 vote 5-0 by Lenny Vasanthan, Xing Song, Eric Harvey, Harold Lehmann, Homa Keshavarz</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Kenneth Wilkins, Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">standard error of the difference between independent means</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000648</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000649 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000649">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000562"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of dispersion applied to differences between proportions arising from independent groups across hypothetical repeated random samples.
A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.</obo:IAO_0000115>
<obo:IAO_0000116>Expert Working Group Agreement: 2024-02-12 vote 5-0 by Lenny Vasanthan, Xing Song, Eric Harvey, Harold Lehmann, Homa Keshavarz.</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Kenneth Wilkins, Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">standard error of the difference between independent proportions</rdfs:label>
<rdfs:seeAlso>https://fevir.net/resources/CodeSystem/27270#STATO:0000649</rdfs:seeAlso>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000650 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000650">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000471"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000403"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000646"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>sampling variance refers to the variability in the estimates of a population parameter that arises from random sampling.
sampling variance is a variance of the sampling distribution of a random variable and estimates the dispersion of sample estimates about their expected value in hypothetical repetitions of the sample.</obo:IAO_0000115>
<obo:IAO_0000119>STATO and COKA group.
adapted from: https://dx.doi.org/10.4135/9781412963947.n515</obo:IAO_0000119>
<rdfs:label>sampling variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000651 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000651">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000502"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000115"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>the output of a statistical sampling, a draw from a distribution or a population of physical or immaterial entities.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<rdfs:label>statistical sample</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000652 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000652">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>calibration in statistics refers to the process of ensuring that the predicted probabilities or scores from a statistical model accurately reflect the true probabilities or outcomes observed in the data. It is an essential aspect of predictive modeling to ensure the reliability and interpretability of model predictions, where the goal is to estimate the likelihood of certain events or outcomes.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>predictive model calibration</obo:IAO_0000118>
<obo:IAO_0000119>STATO
adapted from ChatGPT3.5 with the following prompt: "define 'calibration' in the context of statistics"</obo:IAO_0000119>
<rdfs:label>calibration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000653 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000653">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000149"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000069"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000229"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000390"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000224"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The Hosmer-Lemeshow test is a statistical test used to assess the goodness of fit of a logistic regression model. It evaluates how well the predicted probabilities from the model match the observed outcomes in the data. The test helps determine whether the logistic regression model adequately captures the relationship between the predictor variables and the binary outcome variable.
The test statistic follows a chi-square distribution with degrees of freedom equal to the number of groups minus the number of parameters estimated in the logistic regression model.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO
adapted from ChatGPT3.5 with the following prompt: "define Hosmer-Lemeshow test in statistics"</obo:IAO_0000119>
<obo:STATO_0000041>hltest(model, verbose = TRUE, ...)
from:
https://search.r-project.org/CRAN/refmans/glmtoolbox/html/hltest.html</obo:STATO_0000041>
<rdfs:label>Hosmer-Lemeshow goodness-of-fit test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000654 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000654">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000675"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000288"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<rdfs:label>paired observation comparison objective</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000655 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000655">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>calibration plot is a line graph which plots values resulting from predictions againts values obtained through observation.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000041>https://cran.r-project.org/web/packages/predtools/vignettes/calibPlot.html</obo:STATO_0000041>
<rdfs:label>calibration plot</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000656 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000656">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>the slope of a line graph is a data item denoting the rate of change between the two variables represented on the graph.
the slope is used to visualize and interpret the relationship between two variables.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<rdfs:label>slope</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000657 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000657">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IAO_0000573"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>an intercept is a data item which corresponds to where a graph line cuts (intercepts) an coordinates axis.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<rdfs:label>intercept</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000658 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000658">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000679"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000573"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A mean of values in which each value is the duration of time between the start of observation and the occurrence of an event.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label>mean time-to-event</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000659 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000659">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000674"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000574"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A median of values in which each value is the duration of time between the start of observation and the occurrence of an event.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao</obo:IAO_0000117>
<obo:IAO_0000119>COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label>median time-to-event</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000660 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000660">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<obo:IAO_0000115 xml:lang="en">A hypothesis testing measure that is the predictive probability that a statistic is equal to or more extreme than that observed under the assumptions of the model.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Hypothesis testing measure is defined as a statistic that represents the result of evaluating the congruence between a hypothesis and the statistics derived from the observed data.
A posterior predictive p-value includes assumptions of prior probability of the hypothesis or parameters in the model
Within the frequentist framework, use 'one-sided p-value" or "two sided pvalue"</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Bayesian p-value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">pppvalue(x, parameter = "mu", value = 0.0,
alternative = c("two.sided", "less", "greater"),
statistic = "median",
rejection.region,
n = 10,
prior = FALSE,
quietly = FALSE,
parallel, seed, ...)
from:
https://search.r-project.org/CRAN/refmans/bayesmeta/html/pppvalue.html</obo:STATO_0000041>
<rdfs:label xml:lang="en">posterior predictive value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000661 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000661">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A p-value which represents the probability of obtaining a result at least as far, in one direction, from the value actually obtained as the value expected, assuming the null hypothesis is true.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">P-value is defined as a hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for one-sided test interprets 'at least as far from' with either the direction of 'greater than' or the direction of 'less than' but not with both possible directions.</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">one-sided test p-value</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">one-tailed test p-value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">p-value for one-sided test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000662 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000662">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:qualifiedCardinality>
<owl:onClass rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A p-value which represents the probability of obtaining a result at least as far, in either direction, from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for two-sided test interprets 'at least as far from' with both the direction of 'greater than' and the direction of 'less than'. For hypothesis test interpretation, the two-tailed p-value is compared to the alpha setting divided by 2.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">P-value is defined as a hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for one-sided test interprets 'at least as far from' with either the direction of 'greater than' or the direction of 'less than' but not with both possible directions.</obo:IAO_0000116>
<obo:IAO_0000117>Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">two-sided test p-value</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">two-tailed test p-value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">p-value for two-sided test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000663 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000663">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000623"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The F-beta score is a measure of a model's accuracy, specifically designed to evaluate the performance of binary classification models. It is a generalized form of the F1 score, which itself is the harmonic mean of precision and recall. The F-beta score introduces a way to weigh recall more heavily than precision (or vice versa) depending on the value of beta.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">https://github.com/ISA-tools/stato/pull/86</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Shawn Tan</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from ChatGPT using the following prompt: [what is the F-beta score in statistics]
last accessed: July 2024</obo:IAO_0000119>
<obo:STATO_0000391 xml:lang="en">sklearn.metrics.fbeta_score(y_true, y_pred, *, beta, labels=None, pos_label=1, average='binary', sample_weight=None, zero_division='warn')[source]
https://scikit-learn.org/stable/modules/generated/sklearn.metrics.fbeta_score.htm</obo:STATO_0000391>
<rdfs:label xml:lang="en">F-beta score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000664 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000664">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000679"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000573"/>
<obo:IAO_0000115 xml:lang="en">A mean of values in which each value is the subtraction of one quantity from another.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">The primary use of this term is in analyzing within-individual differences.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Janice Tufte, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">average difference</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">average of differences</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">mean of paired differences</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA/SEVCO working group</obo:IAO_0000119>
<rdfs:label>mean of differences</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000665 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000665">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000614"/>
<obo:IAO_0000115 xml:lang="en">A statistic that is a subtraction of one difference from another.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">The term 'Difference-in-differences' may be used to assess the incremental benefit or harm of an intervention or exposure, where the effect of the exposure is measured as a difference (for example, pre-post testing comparison of values before and after the exposure) in two groups being compared.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">difference in differences</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000666 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000666">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en">A statistic that represents the largest value that could occur.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This term may be used to denote the upper limit of a scale or score.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">maximum possible value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000667 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000667">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en">A statistic that represents the smallest value that could occur.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This term may be used to denote the lower limit of a scale or score.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">minimum possible value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000668 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000668">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en">A statistic that represents the distance of a value from zero.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">The | symbol is used around the value to denote the absolute value, e.g. |x|, such that if x = -3, then |x| = 3.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Kenneth Wilkins, Harold Lehmann.</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">absolute value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000670 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000670">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A rate in which the number of new events per total at risk is divided by an interval of time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Incidence is defined as a proportion in which the numerator represents new events and the denominator represents the total at risk for events. Rate is defined as a ratio in which the numerator represents any quantity and the denominator represents an interval of time. The interval of time used for the denominator may be data-dependent when the duration of observation varies across the observations.
In the method for calculating incidence rate (described at https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section2.html), the numerator is the "Number of new cases of disease or injury during the specified period" and the denominator is the "Time each person was observed, totaled for all persons"</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">average hazard rate</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">incidence density</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">adapted from:
https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section2.html
and
NCIt: Incidence Rate = The frequency of new occurrences of an event during a specified time period.</obo:IAO_0000119>
<rdfs:label xml:lang="en">incidence rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000671 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000671">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A conditional instantaneous rate in which the numerator represents an incidence conditioned on survival to a specified time, and the denominator represents a time interval with a duration approaching zero.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">In the definition of Hazard Rate, the term "survival" is not literally about life and death but is used to represent existence without experiencing the event. "Hazard" as a statistical term is not specific to "bad" or "dangerous" events.
A hazard rate is expressed as a unitless numerator per unit of time, occurring at a specified time, and conditioned on survival to that time.
A hazard rate is mathematically the negative derivative of the log of the survival function. The survival function is the probability of surviving past a specified point in time, expressed as Pr{ T >= t }.
A hazard rate is also mathematically defined as lim(dt -> 0) [ Pr{ ( t <= T < t + dt ) | ( T >= t ) } / dt ]</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">hazard</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">hazard function</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">instantaneous hazard rate</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">hazard rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000672 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000672">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The number of occurrences per unit of time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">An event rate is a ratio in which the numerator represents a count and the denominator represents an interval of time.
When the numerator represents a count:
-If the denominator includes an interval of time, the type of ratio is an Event Rate.
-If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency.
-If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate.
-If the denominator includes an interval of space, the type of ratio is a Number Density</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann.</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">event rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000673 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000673">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000645"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A ratio in which the numerator represents an event frequency and the denominator represents an interval of time.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">When the numerator represents a count:
-If the denominator includes an interval of time, the type of ratio is an Event Rate.
-If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency.
-If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate.
-If the denominator includes an interval of space, the type of ratio is a Number Density</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">event frequency rate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000674 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000674">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A ratio in which the numerator represents a count and the denominator represents a count (without involving an interval of time).</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">When the numerator represents a count:
-If the denominator includes an interval of time, the type of ratio is an Event Rate.
-If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency.
-If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate.
-If the denominator includes an interval of space, the type of ratio is a Number Density</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">frequency</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000675 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000675">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A ratio in which the numerator represents any quantity and the denominator represents an interval of space (distance, area, or volume).</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en"></obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">density</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000676 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000676">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000675"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A ratio in which the numerator represents a count and the denominator represents an interval of space (distance, area, or volume).</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">adapted from:
The number density (symbol: n or ?N) is an intensive quantity used to describe the degree of concentration of countable objects (particles, molecules, phonons, cells, galaxies, etc.) in physical space: three-dimensional volumetric number density, two-dimensional areal number density, or one-dimensional linear number density. Population density is an example of areal number density.
IUPAC Gold Book https://goldbook.iupac.org/terms/view/N04262
number density, n
Number of particles divided by the volume they occupy.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">number density</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000677 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000677">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of association that is the ratio of the hazard rate of an event in one group to the hazard rate of the same event in another group.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Hazard rate is defined as: A conditional instantaneous rate in which the numerator represents an incidence conditioned on survival to a specified time, and the denominator represents a time interval with a duration approaching zero.
The groups being compared are often the exposed group versus the unexposed group, but hazard ratio can also be applied to comparisons of one exposure relative to another exposure.
A hazard ratio of one means there is no difference between two groups in terms of their hazard rates, based on whether or not they were exposed to a certain substance or factor, or how they responded to two interventions being compared. A hazard ratio of greater than one implies an association of greater risk, and a hazard ratio of less than one implies an association of lower risk.
The hazard ratio can be calculated from studies in which the proportion of exposed participants who had the event is known, the proportion of unexposed participants who had the event is known, and the timing of events for each participant is known or estimable, such as a cohort study or clinical trial.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">NCIt:
Hazard ratio = A measure of how often a particular event happens in one group compared to how often it happens in another group, over time. In cancer research, hazard ratios are often used in clinical trials to measure survival at any point in time in a group of patients who have been given a specific treatment compared to a control group given another treatment or a placebo. A hazard ratio of one means that there is no difference in survival between the two groups. A hazard ratio of greater than one or less than one means that survival was better in one of the groups.
https://www.statisticshowto.com/hazard-ratio/
The hazard ratio is a comparison between the probability of events in a treatment group, compared to the probability of events in a control group.
Hazard Ratio in Clinical Trials (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC478551/)
The hazard ratio is an estimate of the ratio of the hazard rate in the treated versus the control group. The hazard rate is the probability that if the event in question has not already occurred, it will occur in the next time interval, divided by the length of that interval. The time interval is made very short, so that in effect the hazard rate represents an instantaneous rate.
The Hazards of Hazard Ratios (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653612/)
The hazard ratio (HR) is the main, and often the only, effect measure reported in many epidemiologic studies. For dichotomous, non–time-varying exposures, the HR is defined as the hazard in the exposed groups divided by the hazard in the unexposed groups. For all practical purposes, hazards can be thought of as incidence rates and thus the HR can be roughly interpreted as the incidence rate ratio. The HR is commonly and conveniently estimated via a Cox proportional hazards model, which can include potential confounders as covariates.</obo:IAO_0000119>
<rdfs:label xml:lang="en">hazard ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000678 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000678">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000622"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000412"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000412"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of association that is the ratio of two prevalences.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Prevalence (SEVCO STATO:0000412) is defined as: A proportion in which the numerator represents all events of interest (for example, both new and preexisting cases of a disease) in the population, which is represented by the denominator.
The Prevalence Ratio indicates the magnitude of the prevalence of an event/outcome in one group of subjects/individuals (with characteristics/attribute) relative to another group (with different characteristics/attributes), such as the prevalence of the disease among the exposed persons to the prevalence of the disease among the unexposed persons.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal, Janice Tufte</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://www.ctspedia.org/do/view/CTSpedia/PrevalenceRatio#:~:text=Reference-,Definition%20of%20Prevalence%20Ratio,the%20proportion%20with%20the%20exposure.
The ratio of the proportion of the persons with disease over the proportion with the exposure.
Calculation is described here:
https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717-Module3-Frequency-Association/PH717-Module3-Frequency-Association12.html</obo:IAO_0000119>
<rdfs:label xml:lang="en">prevalence ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000679 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000679">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000184"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of association that is the ratio of the odds of a positive test in those with disease relative to the odds of a positive test in those without disease.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">DOR</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">AHRQ https://effectivehealthcare.ahrq.gov/products/test-performance-metrics/appendixes:
The diagnostic odds ratio (DOR) describes the odds of a positive test in those with disease relative to the odds of a positive test in those without disease.4 It can be computed in terms of sensitivity and specificity as well as in terms of positive and negative likelihood ratios (DOR = LR+/LR-). Thus this single measure includes information about both sensitivity and specificity and tends to be reasonably constant despite diagnostic threshold. However, it is impossible to use diagnostic odds ratios to weigh sensitivity and specificity separately, and to distinguish between tests with high sensitivity and low specificity and tests with low sensitivity and high specificity.
Another disadvantage is that it is difficult for clinicians to understand and apply, limiting its clinical value. This is partly because they are not often exposed to diagnostic odds ratios. A diagnostic odds ratio is similar to an odds ratio that measures strength of association in an observational study or effect size in a trial. However, contrary to the typical effect size magnitudes of such odds ratios (often between 0.5 and 2), diagnostic odds ratios can attain much larger values (often greater than 100).</obo:IAO_0000119>
<rdfs:label xml:lang="en">diagnostic odd ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000680 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000680">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000622"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000101"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000670"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/STATO_0000259"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000670"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of association that is the ratio of two incidence rates.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Incidence Rate (SEVCO STATO_0000680) is defined as: A rate in which the number of new events per total at risk is divided by an interval of time.
The incidence rates may refer to the same event comparing two different groups, or the same group comparing two different events</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">IRR</obo:IAO_0000118>
<rdfs:label xml:lang="en">incidence rate ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000681 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000681">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000680"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An incidence rate ratio in which the numerator is the incidence rate in a group and the denominator is the incidence rate for a reference population.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">The incidence rate used for the denominator may be an expected incidence rate for a reference population. The reference population may refer to a general population of the geographic area from which the cohort was selected.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">SIR</obo:IAO_0000118>
<rdfs:label xml:lang="en">standardized incidence ratio</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000682 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000682">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000623"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of agreement among categorical assessments, corrected for chance agreement.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">In the literature, the same eponymic term (e.g., 'Cohen's kappa') is used with different formulas. In SEVCO, we define each term with a single formula, and recommend annotators to choose the SEVCO term based on the formula.
This is a widely used term to measure inter-rater reliability. Refer to measures of association to see other terms: for example, intra-class correlation coefficient (ICC).</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">kappa statistic</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">kappa</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000683 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000683">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000682"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A Kappa statistic in which the expected agreement by chance is based on an assumption that all possible categories for assignment are equally likely.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A Kappa statistic is a measure of agreement among categorical assessments, corrected for chance agreement.
In the simple chance-corrected agreement coefficient, the expected chance agreement is modeled as the inverse of the number of categories (1/q) where q is the number of possible categories for assignment.
The simple chance-corrected agreement coefficient is calculated as ( p[a] - 1/q ) / ( 1 - 1/q ) where p[a] is the observed percent agreement and q is the number of possible categories for assignment.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965565
Gwet KL. Testing the Difference of Correlated Agreement Coefficients for Statistical Significance. Educ Psychol Meas. 2016 Aug;76(4):609-637. doi: 10.1177/0013164415596420. Epub 2015 Jul 28. PMID: 29795880; PMCID: PMC5965565.
Brennan and Prediger (1981) proposed a simple chance-corrected agreement coefficient, which generalizes to multiple raters and multiple categories, the G-index previously proposed by Holley and Guilford (1964) for two raters and two categories. What is known as the Holley–Guilford G-index was previously proposed independently by various authors under different names. Among them are Guttman (1945), Bennett, Alpert, and Goldstein (1954), and Maxwell (1977). For an interrater reliability experiment involving r raters who classify n subjects into one of q possible categories, the Brennan-Prediger coefficient is given by
k[BP] = ( p[a] - 1/q ) / ( 1 - 1/q ),
where the percent agreement p[a] is defined by Equation (3 -- see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965565/#disp-formula3-0013164415596420), and the percent chance agreement is a constant representing the inverse of the number of categories.</obo:IAO_0000119>
<rdfs:label xml:lang="en">simple chance-corrected agreement coefficient</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000684 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000684">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000237"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A standard deviation that is the square root of the quotient of the summation across data points of the square of the distance from each data point to the sample mean, and the degrees of freedom (where the degrees of freedom is sample size minus one).</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en"></obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Standard deviation is defined as a measure of dispersion that represents the average of the distances from the mean of the dataset to each data point in the dataset.
Standard deviation for sample is a standard deviation in which the dataset is a sample.
The formula for the standard deviation for sample (
s
s) is:
s
=
∑
n
i
=
1
(
x
i
−
x
‾
)
2
n
−
1
s=
n−1
∑
n
i=1
(x
i
−
x
)
2
where
n
n is the sample size (the number of independent observations, indexed by
i
i),
x
x is observed value, and
x
‾
x
is the sample mean.
The formula to calculate degrees of freedom depends on the model. For the degrees of freedom for a sample standard deviation, given the sample mean, it is n-1, because the nth observation is no longer independent, given the n-1 other observations and the sample mean.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Khalid Shahin, Kenneth Wilkins</obo:IAO_0000117>
<rdfs:label xml:lang="en">standard deviation for sample</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000685 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000685">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of association between a variable representing known or true values and a variable representing measured or predicted values.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Calibration is often used for measurement devices. The known or true values may be called the reference standard.
Calibration is also used for predictive models and other contexts comparing computed or expected probabilities with empirical frequencies.
A measure of calibration indicates the degree to which the computed values are underestimated or overestimated.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Joanne Dehnbostel, Harold Lehmann, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">mesure of calibration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000686 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000686">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000685"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of calibration that is the average of a function of the difference between the expected values and the observed values.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">For predictive modeling of non-continuous variables, the mean calibration is a measure of calibration that is the average of a function of the difference between the expected probabilities and the observed frequencies.
The expected values may be computed (as in predictive models) or may be derived from reference data (as typical for a measurement device).
When the function is the square of the difference and the variables are binary (0 or 1), the measure is called the Brier score.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">mean calibration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000687 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000687">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000685"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of calibration that is the rate of change in the appropriately transformed value per unit change of the correspondingly transformed predicted value.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">For calibration of binary outcome variables (0 or 1), the calibration slope is computed from a statistical model where the log odds of the predicted probabilities is a linear function of the empirical frequencies (logistical regression). The transformation is log odds (logit, the link function for a generalized linear model for the expected value of the outcome).
For calibration of count outcome variables (0, 1, 2, 3, ...), the calibration slope may be computed from a statistical model where the log of the predicted mean counts is a linear function of the empirical frequencies determined by unique combinations of the covariates. The transformation is log, the link function, of the counts.
There are other types of outcome variables for which the calibration slope may be obtained.
Slopes further away from 1.0 indicate, at upper and lower values, over- or under-confidence in the prediction.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Ken Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">calibration in the small</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">calibration slope</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000688 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000688">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000685"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A measure of calibration that is the difference between the mean expected value and the mean observed value.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">For calibration of binary outcome variables (0 or 1), the calibration intercept is computed from a statistical model where the log odds of the predicted probabilities is a linear function of the empirical frequencies.
For calibration of count outcome variables (0, 1, 2, 3, ...), the calibration intercept may be computed from a statistical model where the log of the predicted mean counts is a linear function of the empirical frequencies determined by unique combinations of the covariates.
There are other types of outcome variables for which the calibration-in-the-large measure may be obtained.
The notion of calibration in the large is that the intercept is a gross assessment of whether the average prediction matches the average outcome, however, this interpretation is exquisitely sensitive to the choice of referent factors within the prediction model.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Harold Lehmann, Ken Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin.</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">calibration intercept</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000689 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000689">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000209"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An area under the curve where the curve is the true positive rate and the range of interest is a specified portion of the range of possible values for the false positive rate and/or range of possible values for the true positive rate.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Area under the ROC curve is defined as an area under the curve where the curve is the true positive rate and the range of interest is the false positive rate. ROC stands for Receiver Operating Characteristic. The area under the ROC curve is used to assess the performance of a classifier used to distinguish between two or more groups. Another term for true positive rate is sensitivity and another term for false positive rate is 1-specificity.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Kenneth Wilkins, Brian S. Alper, Muhammad Afzal, Harold Lehmann and SEVCO group</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label>partial area under the receiver operator characteristic curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000690 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000690">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000209"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000696"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>An area under the curve where the curve is the repeated measures of a variable over time and the domain of interest is time.</obo:IAO_0000115>
<obo:IAO_0000117>Kenneth Wilkins, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>area under the value versus time curve</obo:IAO_0000118>
<obo:IAO_0000118>area under the value vs. time curve</obo:IAO_0000118>
<obo:IAO_0000118>area under the value-by-time curve</obo:IAO_0000118>
<obo:IAO_0000119>SEVCO group</obo:IAO_0000119>
<rdfs:label>area under the value-time curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000691 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000691">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000209"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000695"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>An area under the curve where the curve is the precision and the domain of interest is the recall.</obo:IAO_0000115>
<obo:IAO_0000117>Kenneth Wilkins, Harold Lehmann, Brian S. Alper</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>AUC-PR</obo:IAO_0000118>
<obo:IAO_0000118>AUCPR</obo:IAO_0000118>
<obo:IAO_0000118>AUPRC</obo:IAO_0000118>
<obo:IAO_0000119>SEVCO group</obo:IAO_0000119>
<obo:STATO_0000041 xml:lang="en">https://www.rdocumentation.org/packages/PRROC/versions/1.3.1/topics/pr.curve
pr.curve()</obo:STATO_0000041>
<rdfs:label>area under the precision-recall curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000692 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000692">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000679"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000573"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A probability distribution attribute that represents the expected value of a variable that has that distribution.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">For a normal distribution, the distribution parameter mean (also called µ or mu) coincides with the mean of the distribution.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">mu</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">probability distribution mean</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000693 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000693">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000113"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A distribution variance is defined as a probability distribution attribute that is the expected value of the square of the difference of the value of a variable that has that distribution from its expected value.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">probability distribution variance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000694 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000694">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000237"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A probability distribution attribute that is the square root of the distribution variance.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A distribution variance is defined as a probability distribution attribute that is the expected value of the square of the difference of the value of a variable that has that distribution from its expected value.
For a normal distribution, the distribution parameter standard deviation (also called s or sigma) coincides with the standard deviation of the distribution. Standard deviation is defined as a measure of dispersion that represents the average of the distances from the mean of the dataset to each data point in the dataset.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Brian S. Alper, Harold Lehmann, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">probability distribution standard deviation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000695 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000695">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000006"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000233"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000008"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000416"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>The precision-recall curve is a graph which plots the sensitivity or recall on the X-axis and the precision on the Y-axis.
The precision-recall curves focuses on the trade-off between Precision and Recall at various thresholds. It also highlights the performance of the model for the positive class (often the minority or more important class).
It is particularly suited for for imbalanced datasets where the positive class is rare.
The PR-curve is more sensitive to class imbalance. As precision drops significantly if the model predicts too many false positives, it makesthe PR-curve better for evaluating performance on imbalanced datasets.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>PR-curve</obo:IAO_0000118>
<obo:IAO_0000119>adapted from ChatGPT using the prompt: "What is the difference between ROC curve and PR curve"</obo:IAO_0000119>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label>precision-recall curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000696 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000696">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">a value-time curve is a graph which plot time on the x-axis versus the value of a variable of interest as delivered by a process. It is used to represent the relationship there is the value and the time it takes to achieve that value. It is commonly used in project management or business analysis to evaluate and optimize how efficiently value is delivered over time.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">adapted from ChatGPT using the prompt: "what is a value-time curve?"</obo:IAO_0000119>
<rdfs:label>value-time curve</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000697 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000697">
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000417"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000173"/>
</owl:Restriction>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">an homogeneity test is a statistical test aiming at evaluate if the statisical measure from several random samples are similar</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<rdfs:label xml:lang="en">homogeneity test</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000699 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000699">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A t-score generally refers to the value resulting from standardizing a sample statistic (e.g., sample mean) in terms of the t-distribution. It quantifies how far the sample statistic is from the hypothesized population parameter in units of the estimated standard error.
A t-score is a statistic that represents a measure of the divergence of an individual experimental result from a specified mean, taking sample size into account and expressed in terms of the number of standard errors from the mean value.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>T score</obo:IAO_0000118>
<obo:IAO_0000118>T-Score</obo:IAO_0000118>
<obo:IAO_0000118>t score</obo:IAO_0000118>
<obo:IAO_0000118>t-value</obo:IAO_0000118>
<rdfs:label>t-score</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000700 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000700">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000071"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000057"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000673"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Within the frequentist framework, a p-value is typically a p-value for two-sided test and the criterion for rejecting the null hypothesis is typically expressed as a p-value that is less than an alpha setting divided by 2. In some cases, the p-value is a p-value for one-sided test, and the criterion for rejecting the null hypothesis is typically expressed as a p-value that is less than an alpha setting. A p-value is preferably coded more precisely as a p-value for two-sided test or a p-value for one-sided test rather than using the code for p-value without specification. The code for p-value (without specification) may be used in contexts where the p-value reported is ambiguous.
Within the Bayesian framework, use the posterior predictive p-value.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">P value</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">P-value</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">PValue</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">p value</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">p-value</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000701 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000701">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000247"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000697"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/STATO_0000700"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>a statistical test which test for homogeneity of proportions, which is used when comparing proportions observed across multiple groups. It relies on frequencies calculated in contingency tables. It determines is proportions are consistent.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>STATO</obo:IAO_0000119>
<obo:STATO_0000041></obo:STATO_0000041>
<rdfs:label xml:lang="en">Chi-square test for homogeneity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000702 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000702">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistic that represents the likelihood of a parameter of interest, before accounting for the observed data from the study.</obo:IAO_0000115>
<obo:IAO_0000116>This term is core to Bayesian statistics, where the focus is on estimation of the parameter of interest (unlike frequentist statistics, where the focus is on the likelihood of producing an estimate given a specific value of the parameter).
The prior probability may be constructed in several ways: from prior research, from raw data in a database, from expert opinion, or specified as "non-informative" (meaning pure ignorance).
The likelihood of the parameter is usually represented as a distribution over all possible values of the parameter.</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>SEVCO</obo:IAO_0000119>
<rdfs:label>prior probability</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000703 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000703">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistic that represents the likelihood of a parameter of interest, after updating its prior probability with the observed data from the study.</obo:IAO_0000115>
<obo:IAO_0000116>This term is core to Bayesian statistics, where the focus is on estimation of the parameter of interest (unlike frequentist statistics, where the focus is on the likelihood of producing an estimate given a specific value of the parameter). The prior probability is the likelihood of a parameter of interest from before the study. For calculating the posterior probability of a parameter, the prior probability is updated using Bayes' Theorem' and the likelihood function.</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>SEVCO</obo:IAO_0000119>
<rdfs:label>posterior probability</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000704 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000704">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A concentration is the measure of the amount of solute dissolved in a unit quantity of solvent or solution. It describes the strength or intensity of a solution in terms of its solute content.
It is therefore a ratio in which the numerator is a measure of the solute and the denominator is a measure of the solvent.</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann</obo:IAO_0000119>
<rdfs:label>concentration</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000705 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000705">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000639"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000428"/>
<obo:IAO_0000115>Measurement accuracy refers to how close a measured value is to the true or accepted value of the quantity being measured.
It is a percentage in which the numerator represents the absolute value of one minus the difference between the true value and the observed value, and the denominator represents the true value.
Accuracy is often expressed as a percentage of the true value, based on the relative error:
Accuracy (%)= (1 −∣Measured Value−True Value∣/True Value)×100
True Value: The reference or accepted value.
Measured Value: The value obtained during the measurement.</obo:IAO_0000115>
<obo:IAO_0000117>Brian S. Alper, Harold Lehmann, Muhammad Afzal, Joanne Dehnbostel</obo:IAO_0000117>
<rdfs:label>measurement accuracy as a percentage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000706 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000706">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000299"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistical inference paradigm in which the assumptions are that parameters are random variables with probability distributions, that prior knowledge can be represented with such distributions, and that one learns from data by updating those prior distributions using Bayes' Rule.</obo:IAO_0000115>
<obo:IAO_0000116>Regarding random variables with probability distribution: These random variables are often used to represent population parameters, but there are other types of random variables, e.g., representing typical methodological concerns, where the typical notion of “population” does not apply.
Regarding prior knowledge: The notion of representing prior knowledge as a probability distribution is the core of disagreement among statisticians around Bayesian inference. For those interpreting “probability” as “measure of belief”, prior probability distributions encodes belief about the parameters (“subjectivist Bayes”), and ignorance is represented as a “non-informative” prior. For those with a more frequentist interpretation of probability, such priors summarizes frequency knowledge seen in the past (“empirical Bayes”).
Regarding Bayes’ Rule: Probability theory, with no assumptions beyond regular probability, says that P(A|B) = P(B|A) P(A). Bayes Rule says that one can (should) use this formula to update knowledge from data: P(parameter value | data) = P(data | parameter value) P(Data), with P(data | parameter value) being called the “likelihood function,” communicating how likely data are, given parameter values (and what type of distribution the parameter(s) connote), and could be use to reflect sampling, if relevant.</obo:IAO_0000116>
<obo:IAO_0000117>Harold Lehmann, Kenneth Wilkins</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000118>Bayesian approach</obo:IAO_0000118>
<obo:IAO_0000119>SEVCO</obo:IAO_0000119>
<rdfs:label>Bayesian inference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000707 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000707">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000299"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A statistical inference paradigm in which the assumptions are that probabilities reflect relative frequencies of events and that the probability of observing data are governed by fixed yet unknown population parameters.</obo:IAO_0000115>
<obo:IAO_0000116>The frequentist inference is based on hypothetical repeated sampling and the resulting relative frequencies in the long run. Inferences are based on point and interval estimates. For hypothesis testing, the inference is based on the probability of obtaining values equal to or more extreme than the observed data.</obo:IAO_0000116>
<obo:IAO_0000118>classical statistical approach</obo:IAO_0000118>
<obo:IAO_0000118>frequentist approach</obo:IAO_0000118>
<obo:IAO_0000118>frequentist statistical inference paradigm</obo:IAO_0000118>
<obo:IAO_0000119>SEVCO Group</obo:IAO_0000119>
<rdfs:label>frequentist inference</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/STATO_0000708 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/STATO_0000708">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000030"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115>A chi-square statistic used to test whether a dichotomous variable and an ordinal variable are related.
The statistic is calculated using a weighted sum of the differences between observed and expected frequencies, where the weights are based on the scores assigned to the ordered categories. Mathematically, it's often expressed as:
Z = ∑(wi(Oi-Ei)/sqr( wi^2.Ei(1-Ei))
where wi are the scores, Oi observed frequencies, and Ei expected frequencies.</obo:IAO_0000115>
<obo:IAO_0000117>Kenneth Wilkins, Brian S. Alper, Joanne Dehnbostel</obo:IAO_0000117>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>Cochran, W. G., & Armitage, P. (1954). The χ² Test for Trend. Biometrika, 41(1-2), 171–178.</obo:IAO_0000119>
<obo:IAO_0000119>SEVCO & STATO</obo:IAO_0000119>
<rdfs:label>Cochran-Armitage Chi-Square Statistic for Trend</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UBERON_0000465 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000465">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material anatomical entity</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical entity that has mass.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">material anatomical entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UBERON_0000477 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000477">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical cluster</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anatomical group that has its parts adjacent to one another.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical cluster</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length unit</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a standard measure of the distance between two points.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length unit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass unit</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a standard measure of the amount of matter/energy of a physical object.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass unit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/UO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time unit</obo:IAO_0000111>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a standard measure of the dimension in which events occur in sequence.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time unit</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/stato.owl#http://purl.obolibrary.org/obo/STATO_0000669 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/stato.owl#http://purl.obolibrary.org/obo/STATO_0000669">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000039"/>
<obo:IAO_0000115 xml:lang="en">A statistic that represents the result of adding all the values in a collection of values.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en"></obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">total</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">COKA group</obo:IAO_0000119>
<rdfs:label xml:lang="en">sum</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/stato.owl#http://purl.obolibrary.org/obo/STATO_0000698 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/stato.owl#http://purl.obolibrary.org/obo/STATO_0000698">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/STATO_0000030"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A Chi-squared statistic used to test whether observed data from two or more groups follow the same distribution.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">In meta-analysis, a chi-square statistic for homogeneity is often used to determine the appropriateness of combining the statistics to represent a common population.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Kenneth Wilkins, Brian S. Alper, Joanne Dehnbostel, Harold Lehmann</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">SEVCO group</obo:IAO_0000119>
<rdfs:label xml:lang="en">Chi-squared statistic for homogeneity</rdfs:label>
</owl:Class>
<!-- http://www.w3.org/2002/07/owl#Thing -->
<rdf:Description rdf:about="http://www.w3.org/2002/07/owl#Thing">
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Individuals
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000002 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000002">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">example to be eventually removed</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000120 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000120">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.</obo:IAO_0000115>
<rdfs:label xml:lang="en">metadata complete</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000121 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000121">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<rdfs:label xml:lang="en">organizational term</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000122 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000122">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."</obo:IAO_0000115>
<rdfs:label xml:lang="en">ready for release</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000123 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000123">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.</obo:IAO_0000115>
<rdfs:label xml:lang="en">metadata incomplete</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000124 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000124">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">Nothing done yet beyond assigning a unique class ID and proposing a preferred term.</obo:IAO_0000115>
<rdfs:label xml:lang="en">uncurated</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000125 -->
<owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000125">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.</obo:IAO_0000115>
<rdfs:label xml:lang="en">pending final vetting</rdfs:label>
</owl:Thing>
<!-- http://purl.obolibrary.org/obo/IAO_0000423 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000423">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">Terms with this status should eventually replaced with a term from another ontology.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<rdfs:label xml:lang="en">to be replaced with external ontology term</rdfs:label>
</owl:NamedIndividual>
<!-- http://purl.obolibrary.org/obo/IAO_0000428 -->
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000428">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<obo:IAO_0000115 xml:lang="en">A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
<rdfs:label xml:lang="en">requires discussion</rdfs:label>
</owl:NamedIndividual>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<rdf:Description>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
</rdf:Description>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotations
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0001901">
<obo:IAO_0000115>
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
</obo:IAO_0000115>
<rdfs:label xml:lang="en">axiom holds for all times</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000043">
<obo:IAO_0000115 xml:lang="en">a false positive rate whose value is 5 per cent</obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000116 xml:lang="en">Following discussion with OBCS, deprecated of class STATO_0000043 and creation of instance</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<rdfs:label xml:lang="en">5 % false positive rate</rdfs:label>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/STATO_0000281">
<rdfs:label xml:lang="en">1 % false positive rate</rdfs:label>
<obo:IAO_0000117 xml:lang="en">Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000116 xml:lang="en">Following discussion with OBCS, deprecated of class STATO_0000281 and creation of instance</obo:IAO_0000116>
<obo:IAO_0000115 xml:lang="en">a false positive rate whose value is 1 per cent</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alejandra Gonzalez-Beltran</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">STATO</obo:IAO_0000119>
<obo:IAO_0000117 xml:lang="en">Orlaith Burke</obo:IAO_0000117>
</rdf:Description>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/obi.owl">
<dc:creator xml:lang="en">Liju Fan</dc:creator>
<dc:creator xml:lang="en">James A. Overton</dc:creator>
<dc:creator xml:lang="en">Tanya Gray</dc:creator>
<dc:creator xml:lang="en">Frank Gibson</dc:creator>
<dc:creator xml:lang="en">Richard Scheuermann</dc:creator>
<dc:creator xml:lang="en">Matthew Brush</dc:creator>
<dc:creator xml:lang="en">Melanie Courtot</dc:creator>
<dc:creator xml:lang="en">Chris Stoeckert</dc:creator>
<dc:creator xml:lang="en">Alan Ruttenberg</dc:creator>
<dc:creator xml:lang="en">Gilberto Fragoso</dc:creator>
<dc:creator xml:lang="en">Jessica Turner</dc:creator>
<dc:creator xml:lang="en">Lawrence Hunter</dc:creator>
<dc:creator xml:lang="en">John Westbrook</dc:creator>
<dc:creator xml:lang="en">Jie Zheng</dc:creator>
<dc:creator xml:lang="en">Yongqun He</dc:creator>
<rdfs:label>obi.owl</rdfs:label>
<dc:creator xml:lang="en">Monnie McGee</dc:creator>
<protege:defaultLanguage rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
<dc:creator xml:lang="en">Bill Bug</dc:creator>
<dc:creator xml:lang="en">Trish Whetzel</dc:creator>
<dc:format xml:lang="en">OWL-DL</dc:format>
<dc:creator xml:lang="en">Larisa Soldatova</dc:creator>
<dc:creator xml:lang="en">Dirk Derom</dc:creator>
<dc:creator xml:lang="en">Chris Taylor</dc:creator>
<dc:creator xml:lang="en">Susanna-Assunta Sansone</dc:creator>
<dc:creator xml:lang="en">James Malone</dc:creator>
<dc:creator xml:lang="en">Helen C. Causton</dc:creator>
<dc:creator xml:lang="en">Cristian Cocos</dc:creator>
<dc:creator xml:lang="en">Stefan Wiemann</dc:creator>
<dc:creator xml:lang="en">Philippe Rocca-Serra</dc:creator>
<dc:creator xml:lang="en">Norman Morrison</dc:creator>
<dc:creator xml:lang="en">Ryan R. Brinkman</dc:creator>
<dc:creator xml:lang="en">Jay Greenbaum</dc:creator>
<dc:creator xml:lang="en">Dawn Field</dc:creator>
<dc:creator xml:lang="en">Helen Parkinson</dc:creator>
<dc:creator xml:lang="en">Melissa Haendel</dc:creator>
<dc:subject xml:lang="en">An ontology for the annotation of biomedical and functional genomics experiments.</dc:subject>
<dc:creator xml:lang="en">Robert Stevens</dc:creator>
<dc:creator xml:lang="en">Philip Lord</dc:creator>
<dc:creator xml:lang="en">Bjoern Peters</dc:creator>
<dc:creator xml:lang="en">Matthew Pocock</dc:creator>
<dc:creator xml:lang="en">Eric Deutsch</dc:creator>
<dc:contributor xml:lang="en">Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester</dc:contributor>
<dc:creator xml:lang="en">Kevin Clancy</dc:creator>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.</rdfs:comment>
<dc:creator xml:lang="en">Daniel Schober</dc:creator>
<dc:creator xml:lang="en">Chris Mungall</dc:creator>
<dc:creator xml:lang="en">Carlo Torniai</dc:creator>
<dc:creator xml:lang="en">Daniel Rubin</dc:creator>
<dc:creator xml:lang="en">Barry Smith</dc:creator>
<dc:creator xml:lang="en">Joe White</dc:creator>
<dc:creator xml:lang="en">Christian Bolling</dc:creator>
<dc:creator xml:lang="en">Pierre Grenon</dc:creator>
<dc:creator xml:lang="en">Mervi Heiskanen</dc:creator>
<dc:creator xml:lang="en">Richard Bruskiewich</dc:creator>
<dc:description xml:lang="en">The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.</dc:description>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2018-05-23</owl:versionInfo>
<terms:license>http://creativecommons.org/licenses/by/4.0/</terms:license>
<obo:IAO_0000589 xml:lang="en">Ontology for Biomedical Investigations</obo:IAO_0000589>
<dc:creator xml:lang="en">Luisa Montecchi</dc:creator>
<dc:creator xml:lang="en">Jennifer Fostel</dc:creator>
<dc:creator xml:lang="en">Jeffrey Grethe</dc:creator>
<dc:creator xml:lang="en">Elisabetta Manduchi</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2009-07-31</dc:date>
<dc:creator xml:lang="en">Allyson Lister</dc:creator>
<dc:creator xml:lang="en">Tina Hernandez-Boussard</dc:creator>
<dc:creator xml:lang="en">Holger Stenzhorn</dc:creator>
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