Alfred Hero Anna Maria Masci Chris Stoeckert Adrien Barton Barry Smith Huan Li Jean-François Ethier Jie Zheng Jinjing Guo Marcy Harris Qingzhi Liu Yongqun "Oliver" He Yu Lin OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. OWL-DL A formal ontology in the domain of biological and clinical statistics OBCS: Ontology of Biological and Clinical Statistics 2023-12-08 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. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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. 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor 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 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label definition source 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. 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 . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith 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 elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by A normal distribution probability density function has a formula of: f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2)) An annotation property that represents a mathematical formula. Asiyah Yu Lin, Jie Zheng, Yongqun He mathematical formula ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants 2023-03-03 UK spelling synonym A synonym type for common misspellings 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. 2023-09-30 INN International Nonproprietary Name nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. 2023-11-01 acronym An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation tooth SubClassOf 'never in taxon' value 'Aves' x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . } never in taxon A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. non-overlapping with shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . } mutually spatially disjoint with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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. 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part 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. 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [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]) 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 realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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]) 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 realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. 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. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 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. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about 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. 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 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 person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes 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 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 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. 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. 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. 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. Alan Ruttenberg is quality measurement of inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum A relation between a data set and a probability distribution. Yongqun He, Jie Zheng, Asiyah Yu Lin has probability distribution A relation between a probability distribution and probability. Yongqun He, Jie Zheng, Asiyah Yu Lin has probability density function A student t-test follows the probability distribution of a student distribution. An object property that represents a relation between a statistical test and a probability distribution. Yongqun He, Qingzhi Liu test follows probability distribution is_supported_by_data 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. 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 OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of 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 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' 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. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain 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. 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 PERSON: Alan Ruttenberg 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 has grain objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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). 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). 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. is concretized as 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). 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). 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. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence 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. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence 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. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence 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. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence 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. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence 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. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) 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 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) 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 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'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location 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 Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during https://wiki.geneontology.org/Happens_during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen starts An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true has measurement value has x coordinate value has z coordinate value has y coordinate value has_feature_value has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. James Malone has_feature_value has specified numeric value A relation between a value specification and a number that quantifies it. 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. PERSON: James A. Overton OBI has specified numeric value has specified value A relation between a value specification and a literal. 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. OBI has specified value creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index 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 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity 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 per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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. 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 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 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]) 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]) 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant 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 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]) 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]) 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]) 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]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. 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 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. 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. 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. 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]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent 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. per discussion with Barry Smith 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. 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]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth 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]) 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (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] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant 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]) 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (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] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. 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. 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]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region 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. per discussion with Barry Smith 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]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. 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]) 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) (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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process 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]) (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] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis 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. 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]) 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]) (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] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition 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]) 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]) (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] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet 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. 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]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (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] (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] realizable entity 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]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (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] (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] 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril 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]) 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]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (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] quality 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]) 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]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (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] sdc SpecificallyDependentContinuant 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 of one-sided specifically dependent continuants: the mass of this tomato 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. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 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]) 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. (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] 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. specifically dependent continuant (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] 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]) 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. per discussion with Barry Smith role Role 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. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role 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. 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. 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]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role 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]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. 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]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region 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]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) gdc GenericallyDependentContinuant 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. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] 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. generically dependent continuant 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar 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. 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]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function 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]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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 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. 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. 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]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (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] (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] material entity 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]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (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] (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] cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] immaterial ImmaterialEntity 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 immaterial entity 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] r-quality RelationalQuality 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. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 CAS:9007-49-2 KEGG:C00039 Deoxyribonucleic acid deoxyribonucleic acids chebi_ontology (Deoxyribonucleotide)m (Deoxyribonucleotide)n (Deoxyribonucleotide)n+m DNA DNAn DNAn+1 DNS Desoxyribonukleinsaeure deoxyribonucleic acids desoxyribose nucleic acid thymus nucleic acid CHEBI:16991 deoxyribonucleic acid Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity 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. nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid 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. Wikipedia:Macromolecule macromolecule chebi_ontology macromolecules polymer polymer molecule polymers CHEBI:33839 macromolecule 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. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. MESH:D002478 Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. 2012-01-12T09:58:38Z 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Wikipedia:DNA_methylation biological_process GO:0006306 DNA methylation A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 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. 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. 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. 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." 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. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 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. datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software data item Data items include counts of things, analyte concentrations, and statistical summaries. 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. 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. 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. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ 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 PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 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). 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. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 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. 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. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity dot plot Dot plot of SSC-H and FSC-H. 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. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot graph 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. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. 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. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter curation status specification 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. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). 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. 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 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. person:Allyson Lister person:Chris Stoeckert data list OBI_0000042 group:OBI data set image 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. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 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. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 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 plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 measurement datum 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,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum conclusion textual entity 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 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph obsolescence reason specification The reason for which a term has been deprecated. 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. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities 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. 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. 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. PERSON: Lawrence Hunter text textual entity table | T F --+----- T | T F F | F F 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 PERSON: Lawrence Hunter table figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document 1 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 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 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. 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 Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph time stamped measurement datum pmid:20604925 - time-lapse live cell microscopy 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. Alan Ruttenberg experimental time series time sampled measurement data set A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software method A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software library A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module taxonomic bridge ontology module taxonomic bridge ontology module ontology module subsetted by expressivity ontology module subsetted by expressivity obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module ontology module subsetted by OWL profile ontology module subsetted by OWL profile EL++ ontology module EL++ ontology module GC_ID:1 ncbi_taxonomy Vira Viridae viruses Viruses GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:32628106 PMID:36748408 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes Bacteria GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:32628106 PMID:36748408 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes Archaea GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota A data transformation that has input of mulitple data and report overall trend of the data. Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Statistics statistical data analysis A planned process that gathers and measures information on variables of interest, in an established systematic fashion that enables one to answer stated research questions, test hypotheses, and evaluate outcomes. Data collection results in a collection of data. Jie Zheng, Oliver He WEB: http://en.wikipedia.org/wiki/Data_collection data collection A continuous probability distribution that is associated with the f statistic. Yongqun He Fisher-Snedecor distribution WEB: http://stattrek.com/probability-distributions/f-distribution.aspx STATO:0000204 F distribution A continuous probability distribution that is a two-parameter family of continuous probability distributions. Yongqun He WEB: http://en.wikipedia.org/wiki/Gamma_distribution STATO:0000268 gamma distribution A continuous probability distribution that has a symmetrical curve, whose position and shape is determined by its location and scale parameters, the mean and standard deviation respectively. Yongqun He Gaussian distribution WEB: http://en.wikipedia.org/wiki/Normal_distribution STATO:0000227 normal distribution A continuous probability distribution that is is used to estimate population parameters when the sample size is small and/or when the population variance is unknown. Yongqun He t-distribution WEB: http://stattrek.com/probability-distributions/t-distribution.aspx STATO:0000059 Student's t distribution A continuous probability distribution of two variables that has the traditional bell shape and the distribution of one variable is normal to each and every value of the other variable. Marcy Harris bivariate normality WEB: SAS users guide bivariate normal distribution A continuous probability that is the distribution of a random variable X if ln(X) is normally distributed Marcy Harris log normal, lognormal WEB: http://www.statistics.com log-normal distribution A special case of the Pearson product-moment correlation; calculated when either the independent variable or dependent variable is dichotomous while the other variable is non-dichotomous Marcy Harris point biserial correlation An information content entity that refers to a distribution of a random variable that can be described using a mathematical formula. Yongqun He, Jie Zheng WEB: http://en.wikipedia.org/wiki/Probability_distribution probability distribution An information content entity that represents a type of scale on which a variable is measured, including nominal, ordinal, interval, ratio. Marcy Harris level of measurement scale of measure WEB: http://en.wikipedia.org/wiki/Level_of_measurement measurement scale A data item that is numerically distant from the rest of the data; often indicative either measurement error or that the population has a high kurtosis. Marcy Harris, Yongqun He WEB: http://en.wikipedia.org/wiki/Outlier STATO_0000036 outlier A statistic measure that is a function of the samples and considered as a numberical summary of a data-set that reduces the data to one value that can be used to perform a hypothesis test. It can be used to test a finding for statistical signifiance Marcy Harris, Yongqun He WEB: http://en.wikipedia.org/wiki/Test_statistic test statistic A derived data from inferential statistical analysis that is obtained by applying a weighting process to adjust the impact of cases for representing the population from which the data sample is drawn. Marcy Harris WEB: https://www.fedview.opm.gov/2010/reports/weighteddef.htm weighted data A data item that represents a typical value of a set of values. This term relates to the way in which quantitative data tend to cluster around some value. Marcy Harris, Yongqun He WEB: http://en.wikipedia.org/wiki/Central_tendency STATO:0000029 central tendency A data item that is the value that appears most frequent in a set of data. In a normal distribution the numerical value of the mode is the same as that of the mean and median. Marcy Harris WEB: http://en.wikipedia.org/wiki/Mode_%28statistics%29 mode A statistical measure of agreement for categorical data; a measure of inter-rater agreement or inter-annotator agreement. Marcy Harris inter-rater agreement, inter-annotator agreement WEB: http://en.wikipedia.org/wiki/Cohen%27s_kappa cohen's kappa measurement A statistical model that an abstract, quantitative model of the causal dependencies and other interrelationships among observed or hypothetical models; an ordered triple , where U is a set of exogenous variables whose values are determined by factors outside the model; V is a set of endogenous variables whose values are determined by factors within the model; and E is a set of structural equations that express the value of each endogenous variable as a function of the values of the other variables in U and V. Marcy Harris WEB: http://en.wikipedia.org/wiki/Causal_model causal model A measure of the linear association between two variables that are measured on ordinal, interval or ratio scales Marcy Harris WEB: http://www.statistics.com correlation statistical analysis Marcy Harris hierarchical linear model An inferential statistical data analysis that uses measured variation in genes of known function to examine the causal effect of a modifiable exposure on disease in non-experimental studies. Yongqun He, Jie Zheng, Asiyah Yu Lin URL: https://en.wikipedia.org/wiki/Mendelian_randomization Mendelian randomization A statistical model of parameters that vary at more than one level; a type of regression model that explicitly takes into account structured/nested data Marcy Harris hierarchical models multilevel model An inferential statistical data analysis that is used to analyze data that arises from more than one variable Yongqun He, Jie Zheng MVA WEB: http://www.camo.com/multivariate_analysis.html multivariate analysis A data transformation that is used to calculate the power of a statistical analysis. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms power calculation An inferential statistical data analysis that has only one independent variable Yongqun He univariate analysis An inferential statistical data analysis that analyze the relationship between two measured quantities that renders them statistically dependent Marcy Harris WEB: http://en.wikipedia.org/wiki/Association_%28statistics%29 statistical association A data transformation used in categorical data analysis when the aim is to assess for the presence of an association between a variable with two categories and a variable with k categories. Marcy Harris WEB: http://en.wikipedia.org/wiki/Cochran%E2%80%93Armitage_test_for_trend cochran-armitage test A data transformation that combines categories or ranges of values to produce a smaller number of categories Marcy Harris, Yongqun He bracketing, grouping WEB: SAS users guide data collapsing A measure of the extent to which two variables are associated; the extent to which two random variables vary together Marcy Harris WEB: http://en.wikipedia.org/wiki/Covariation covariation An inferential statistical data analysis used to analyze how well a statistical model fits a set of observations; measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model in question. Marcy Harris WEB: http://en.wikipedia.org/wiki/Goodness_of_fit goodness of fit A Kolmogorov-Smirnov test that compares two samples. Marcy Harris, Huan Li, Qingzhi Liu, Oliver He two-sample K-S test two-sample KS test WEB: http://en.wikipedia.org/wiki/Kolmogorov%E2%80%93Smirnov_test Kolmogorov-Smirnov two sample test A data transformation that is specifically an inferential statistic to assess the equality of variances in different sample; tests the null hypothesis that the population variances are equal (called homogeneity of variance or homoscedasticity). Marcy Harris WEB: http://en.wikipedia.org/wiki/Levene%27s_test levene's test A data transformation used for both hypothesis testing and model building to examine the relationship between more than two categorical variables; uses a likelihood ratio statistic that has an approximate chi-square distribution when the sample size is large. Marcy Harris WEB: http://en.wikipedia.org/wiki/Loglinear_analysis loglinear analysis A normal approximation used on nominal data; applied to 2x2 contingency tables to determine whether the row and column marginal frequencies are equal ("marginal homogeneity"). Marcy Harris WEB: http://en.wikipedia.org/wiki/McNemar%27s_test mcnemar's test A directive information entity that represents a mathematical relationship which relates changes in a given response to changes in one or more factors. A statistical model is a formalization of relationships between variables in the form of mathematical equations. Marcy Harris, Yongqun He model WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm; http://en.wikipedia.org/wiki/Statistical_model statistical model Partitioning of the overall variation into assignable components variance components WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm partitioning of variance components A directive information entity that shows how changing the settings of a factor changes the response. The effect of a single factor is also called a main effect. Marcy Harris, Yongqun He effect WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm statistical effect A directive information entity that specifies a data item that can be measured or counted and is used in a statistical analysis. Yongqun He variable WEB: http://en.wikipedia.org/wiki/Variable_%28mathematics%29 WEB: http://www.abs.gov.au/websitedbs/a3121120.nsf/home/statistical+language+-+what+are+variables statistical variable A variable specification that specifies a variable that may have a causal impact on both the independent variable and dependent variable; ignoring a confounding variable may bias empirical estimates of the causal effect of the independent variable. Marcy Harris confounders WEB: http://en.wikipedia.org/wiki/Mediation_%28statistics%29#Mediator_Variable confounding variable specification A variable specification that specifies a variable used in statistical analysis to correct, adjust, or modify the values of a dependent variable; an independent variable not manipulated by the investigator Marcy Harris covariate WEB: http://www.statistics.com covariate specification A variable that has only two categories. Marcy Harris dichotomous variable WEB: SAS users guide dichotomous variable specification A statistical variable with only two categories that reflect only part of the information available in a more comprehensive variable Marcy Harris WEB: SAS users guide dummy variable A variable postulated to be a predictor of one or more dependent variables, and simultaneously predicted by one or more independent variables Marcy Harris intervening variable, mediating variable WEB: SAS Users Guide intervening variable specification A discrete probability distribution that has the number of successes in a sequence of n independent yes/no experiments, each of which yields success with probability p. Such a success/failure experiment is also called a Bernoulli experiment or Bernoulli trial. Yongqun He WEB: http://en.wikipedia.org/wiki/Binomial_distribution binomial distribution A discrete probability distribution that expresses the probability of a given number of events occurring in a fixed interval of time and/or space if these events occur with a known average rate and independently of the time since the last event. The Poisson distribution can also be used for the number of events in other specified intervals such as distance, area or volume. Yongqun He WEB: http://en.wikipedia.org/wiki/Poisson_distribution Poisson distribution A likelihood ratio that is calculated by dividing 1 minus sensitivity by specificity ((1-sensitivity)/specificity). Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms negative likelihood ratio A likelihood ratio that is calculated by dividing sensitivity by 1 minus specificity (sensitivity/(1-specificity)). Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms positive likelihood ratio A data item of an observed or calculated probability of occurrence of an event, X, in a population related to exposure to a specific hazard, infection, trauma; the number of persons suffering from a disease when the exposed population is known with certainty. Yongqun He WEB: http://medical-dictionary.thefreedictionary.com/absolute+risk absolute risk A data item that refers to the number of true positives and true negatives divided by the total number of observations. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms accuracy A data item collected from censoring that the value of a measurement or observation is only partially known. Marcy Harris, Jie Zheng censoring WEB: https://en.wikipedia.org/wiki/Censoring_(statistics) censored data A probability density function that is for normal distribution probability Jie Zheng, Asiyah Yu Lin, Yongqun He WEB: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Normal.html f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2)) normal distribution probability density function A data item that refers to the number of new events that have occurred in a specific time interval divided by the population at risk at the beginning of the time interval. The result gives the likelihood of developing an event in that time interval. Yongqun He incidence WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms Incidence rate A validity that refers to the degree to which evidence and theory support the interpretations of test scores (as entailed by proposed uses of tests). Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) test validity A data item that refers to the odds that an individual with a specific condition has been exposed to a risk factor divided by the odds that a control has been exposed. The odds ratio is used in case-control studies. The odds ratio provides a reasonable estimate of the relative risk for uncommon conditions. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms STATO:0000182 odds ratio A data item that refers to the number of individuals with a given disease at a given point in time divided by the population at risk at a specified point in time or over a specified period of time. Yongqun He, Jie Zheng prevalence WEB: http://health.mo.gov/training/epi/PrevalenceRates.html WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms prevalence rate A data item that equals the incidence in exposed individuals divided by the incidence in unexposed individuals. The relative risk can be calculated from studies in which the proportion of patients exposed and unexposed to a risk is known, such as a cohort study. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms relative risk A data item that refers to the extent to which repeated measurements of a relatively stable phenomenon fall closely to each other. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms reliability A data item that measures the proportion of actual positives which are correctly identified as such (e.g. the percentage of sick people who are correctly identified as having the condition). Yongqun He sensitivity estimate true positive rate, recall WEB: http://en.wikipedia.org/wiki/Sensitivity_and_specificity STATO:0000233 sensitivity A data item that refers to the proportion of negatives in a binary classification test which are correctly identified Yongqun He true negative rate WEB: http://en.wikipedia.org/wiki/Sensitivity_and_specificity STATO:0000134 specificity A data item that refers to the extent to which a concept conclusion or measurement is well-founded and corresponds accurately to the real world. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms http://en.wikipedia.org/wiki/Validity_(statistics) Here is another definition: Validity is the extend to which an observation reflects the "truth" of the phenomenon being measured. Reference: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms validity A special case of multiple linear regression in which the relationship between the independent variable x and the dependent variable y is modeled as an nth order polynomial Marcy Harris WEB: http://en.wikipedia.org/wiki/Polynomial_regression polynomial regression A plan specification that provides a detailed outline of which measurements will be taken at what times, on which material, in what manner, and by whom. Sampling plans should be designed in such a way that the resulting data will contain a representative sample of the parameters of interest and allow for all questions, as stated in the goals, to be answered. Marcy Harris sampling design sampling plan WEB: http://www.itl.nist.gov/div898/handbook/ppc/section3/ppc33.htm data sampling design A data collection by sampling process that uses some form of random selection, that is, one that will ensure that all units in the population have an equal probability or chance of being selected. Marcy Harris WEB: http://srmo.sagepub.com/view/the-sage-dictionary-of-social-research-methods/SAGE.xml random selection A prevalence rate that occurs at a specific period of time. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms period prevalence rate A prevalence rate that occurs at a specific point of time. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms point prevalence rate A probability distribution that is associated with continuous variables and has a probability density function. Yongqun He WEB: http://en.wikipedia.org/wiki/Continuous_probability_distribution#Continuous_probability_distribution continuous probability distribution A probability distribution that is associated with discrete variables and is characterized by a probability mass function. Yongqun He WEB: http://en.wikipedia.org/wiki/Continuous_probability_distribution#Discrete_probability_distribution discrete probability distribution A tabular summary of a set of data showing the number of items in each of several non-overlapping classes or groupings Marcy Harris WEB: http://statistics.com frequency distribution A statistical measure of inter-rater agreement or inter-annotator agreement for qualitative (categorical) items. WEB: http://en.wikipedia.org/wiki/Cohen%27s_kappa cohen's kappa coefficient A quantitative confidence value that refers to an interval give values within which there is a high probability (95 percent by convention) that the true population value can be found. The calculation of a confidence interval considers the standard deviation of the data and the number of observations. Thus, a confidence interval narrows as the number of observations increases, or its variance (dispersion) decreases. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms confidence interval A quantitative confidence value that is used in Bayesian analysis to describe the range in which a posterior probability estimate is likely to reside. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms credible interval A quantitative confidence value that refers to the upper and lower values defining the central 50 percent of observations. The boundaries are equal to the 25th and 75th percentiles. The interquartile range can be depicted in a box and whiskers plot. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms interquartile range A quantitative confidence value that equals the percentage of a distribution that is below a specific value. As an example, a child is in 90th percentile for weight if only 10 percent of children the same age weigh more than she does. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms percentile A quantitative confidence value that refers to the ability of a study to detect a true difference. Negative findings may reflect that the study was underpowered to detect a difference. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms power A component of experimental error that occurs due to natural variation in the process. Marcy Harris WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm random error A quantitative confidence value that equals the difference between the largest and smallest observation. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms range A quantitative confidence value that measures the variability of data around the mean. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms standard deviation A quantitative confidence value that refers to the probability of incorrectly concluding that there is a statistically significant difference in a dataset. Alpha is the number after a p-value. Thus, a statistically significant difference reported as p<0.05 means that there is less than a 5 percent chance that the difference could have occurred by chance. Yongqun He alpha error false positive rate WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms STATO:0000053 type 1 error rate A quantitative confidence value that refers to the probability of incorrectly concluding that there was no statistically significant difference in a dataset. This error often reflects insufficient power of the study. Yongqun He beta error false negative rate WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms STATO:0000220 type 2 error rate A quantitative confidence value that is a general statistical term meaning a systematic (not random) deviation from the true value Marcy Harris WEB: http://www.statistics.com bias A quantitative confidence value that is the standard deviation of a data set divided by the mean of the same data set; a normalized measure of dispersion of a probability distribution Marcy Harris, Yongqun He variation coefficient WEB: http://www.statistics.com coefficient of variation A quantitative confidence value that represents unexplained variation in a collection of observations; comopnents of error include random error and lack of fit error Marcy Harris, Yongqun He error WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm statistical error A quantitative confidence value that represents theoretical average value of a statistic over an infinite number of samples from the same population; the weights correspond to the probabilities in the case of a discrete random variable or densities in the case of a continuous random variable. Marcy Harris WEB: http://en.wikipedia.org/wiki/Expected_value expected value A quantitative confidence value that is a descriptive statistic and can be used to describe how strongly units in the same group resemble each other; unlike other correlation measures it operates on data structured as groups, rather than data structured as paired observations. Marcy Harris, Yongqun He ICC WEB: http://en.wikipedia.org/wiki/Intraclass_correlation intraclass correlation coefficient A quantitative confidence value that has been standardized so that they have variances of 1.0; produces standardized regression coefficients (betas) Marcy Harris WEB: SAS users guide standardized coefficient A type of regression analysis used for predicting the outcome of a categorical dependent variable Marcy Harris logistic regression WEB: http://en.wikipedia.org/wiki/Logistic_regression logit regression A form of regression analysis in which observational data are modeled by a function which is a nonlinear combination of the model parameters and depends on one or more independent variables Marcy Harris WEB: http://en.wikipedia.org/wiki/Nonlinear_regression nonlinear regression A data sampling design that does not use randomization for sample selection Marcy Harris, Jie Zheng, Yongqun He non-randomization sampling plan non-randomization sampling design A data sampling design that uses randomization for sample selection Marcy Harris, Jie Zheng, Yongqun He randomization sampling plan randomization sampling design A measurement scale consisting of equal-sized units; the distance between any two positions is of known size. Marcy Harris WEB: SAS Users Guide WEB: WEB: http://en.wikipedia.org/wiki/Level_of_measurement interval scale A measurement scale that placing of data into categories, without any order or structure (see related OBI term of categorical measurement datum). Marcy Harris http://en.wikipedia.org/wiki/Nominal_scale#Nominal_scale nominal scale A measurement scale that rankings on which data can be sorted however the size or magnitude of differences between any data points in a class is unknown, just that one ranking is greater than the other Marcy Harris WEB: http://en.wikipedia.org/wiki/Nominal_scale#Ordinal_scale ordinal scale A measurement scale that is similar to an interval scale, i.e. a magnitude of a continuous quantity and a unit magnitude of the same kind; the distinguishing feature of a ratio scale is a meaningful zero value that means the absence of whatever is measured. Marcy Harris WEB: http://en.wikipedia.org/wiki/Nominal_scale#Ratio_scale ratio scale A sensitivity that refers to the number of patients with a positive test who have a disease divided by all patients who have the disease. A test with high sensitivity will not miss many patients who have the disease (i.e., few false negative results). Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms disease test sensitivity A specificity that refers to the number of patients who have a negative test and do not have the disease divided by the number of patients who do not have the disease. A test with high specificity will infrequently identify patients as having a disease when they do not (i.e., few false positive results). Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms disease test specificity A statistical effect that is associated with an input variable that has a limited number of levels or in which only a limited number of levels are of interest to the experimenter. Marcy Harris WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm fixed effect A statistical effect that represents the role of a variable in an estimated model (most often a regression model) and its effect on the dependent variable. A variable that has an interaction effect will have a different effect on the dependent variable, depending on the level of some third variable. Marcy Harris moderation WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm interaction effect A statistical effect that is associated with input variables chosen at random from a population having a large or infinite number of possible values. Marcy Harris WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm random effect A statistical error that occurs when the analysis omits one or more important terms or factors from the model. Marcy Harris WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm lack of fit error A statistical error that the null hypothesis is true but has been rejected; a test result that indicates a given condition has been fulfilled, when it actually has not been fulfilled Marcy Harris false positive WEB: http://en.wikipedia.org/wiki/Type_I_and_type_II_errors type I error A statistical error that the null hypothesis is false but has been accepted; a test result indicates that a condition failed, while it actually was successful. Marcy Harris false negative WEB: http://en.wikipedia.org/wiki/Type_I_and_type_II_errors type II error A statistical hypothesis test in which the test statistic has an F-distribution under the null hypothesis Marcy Harris WEB: http://en.wikipedia.org/wiki/F_test F test A non-parametric test of the null hypothesis that two populations are the same against an alternative hypothesis Marcy Harris Wilcoxon rank-sum test WEB: http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U mann-whitney U test An experimental design where all cells (i.e. treatment combinations) have the same number of observation Marcy Harris WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm balanced design A study design that starts with the outcome of interest and works backward to the exposure. For instance, patients with a disease are identified and compared with controls for exposure to a risk factor. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms case-control study design A study design that starts with an exposure and moves forward to the outcome of interest, even if the data are collected retrospectively. As an example, a group of patients who have variable exposure to a risk factor of interest can be followed over time for an outcome. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms cohort study design A study design in which patients are randomly assigned to two or more interventions. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms randomized controlled trial design A data sampling design that is designed to generate complex samples where sample members do not have equal probability of being selected. Marcy Harris, Yongqun He, Jie Zheng WEB: http://www.theanalysisfactor.com/complex-sample-what-and-why/ complex sample design A statistic test for several similar measures of agreement used with categorical data; typically used in assessing the degree to which two or more raters, examining the same data, agree on assigning data to categories Marcy Harris WEB: http://www.statistics.com kappa statistic A test statistic of whether k samples are from populations with equal variances. Marcy Harris WEB: http://en.wikipedia.org/wiki/Bartlett%27s_test bartlett's test A statistical variable that specifies a variable describing how, rather than when, effects will occur by accounting for the relationship between the independent and dependent variables. A mediating relationship is one in which the path relating A to C is mediated by a third variable (B). Marcy Harris, Yongqun He intervening variable mediating variable, mediation WEB: http://en.wikipedia.org/wiki/Mediation_%28statistics%29#Mediator_Variable mediating variable A statistical variable that specifies a variable affecting the direction and/or strength of the relation between dependent and independent variables; occurs when the relationship between two variables depends on a third variable Marcy Harris moderator, interaction WEB: http://en.wikipedia.org/wiki/Moderator_variable moderator variable A weighted data that measures the agreement for categorical data; a generalization of the Kappa statistics to situations in which the categories are not equal in some respect so weighted by an objective or subjective function Marcy Harris WEB: http://www.statistics.com weighted kappa A center value that separates the higher half from the lower half of the data sample, population, or probability distribution Marcy Harris WEB: http://en.wikipedia.org/wiki/Median median A statistical model containing both fixed effects and random effects, that is mixed effects; Marcy Harris WEB: http://en.wikipedia.org/wiki/Mixed_model mixed model A data transformation that represents a mathematical function describing the relative likelihood of a continuous random variable to take on a value. Marcy Harris, Yongqun He density function WEB: http://en.wikipedia.org/wiki/Probability_density_function probability density function A data item that represents an arrangement according to a rank, i.e., the position of a particular case relative to other cases on a defined scale. Marcy Harris, Yongqun He WEB: http://www.merriam-webster.com/dictionary/rank%20order rank order A quantitative confidence value that expresses how many times more likely the data are under one model than the other. Yongqun He WEB: http://en.wikipedia.org/wiki/Likelihood-ratio_test likelihood ratio A probability distribution that with k degrees of freedom is the distribution of a sum of the squares of k independent standard normal random variables. Yongqun He WEB: http://en.wikipedia.org/wiki/Chi-square_distribution STATO:0000229 chi-square distribution 2 A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns. Person: Oliver He, Jie Zheng set of data sets WEB: https://en.wikipedia.org/wiki/Matrix_(mathematics) data matrix A statistical data analysis that uses patterns in the sample data to draw inferences about the population represented, accounting for randomness. Jie Zheng, Oliver He significantly statistical data analysis WEB: http://en.wikipedia.org/wiki/Statistics inferential statistical data analysis 2 A data item that consists of two or more data sets that are produced as the output of a data transformation. Person: Oliver He, Jie Zheng set of transformed data sets transformed data matrix A data set that is produced as the output of a data transformation. Person: Jie Zheng, Oliver He transformed data set A statistical data analysis objective where the aim is to make inference using population sample data. Jie Zheng, Oliver He inferential statistical data analysis objective A continuous 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. Yongqun He WEB: http://en.wikipedia.org/wiki/Exponential_distribution STATO:0000160 exponential distribution A statistical variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense). Jie Zheng, Yongqun He WEB: http://en.wikipedia.org/wiki/Random_variable random variable An objective specification where the aim is to collect data. Jie Zheng, Oliver He data collection objective A data collection process that results in a collection of data generated from an experiment(s). Jie Zheng, Oliver He data collection from experiment A data collection by sampling process that results in a collection of data generated from an survey(s). Jie Zheng, Oliver He data collection from survey A data collection process that results in a collection of data from the literature. Jie Zheng, Oliver He data collection from literature A statistical variable that is manipulated or controlled in a scientific study to test its effect on a dependent variable(s). Jie Zheng, Yongqun He, Barry Smith WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables https://www.thoughtco.com/i-ndpendent-and-dependent-variables-differences-606115 independent variable A data collection process that results in a collection of data from a sampling process. Jie Zheng, Oliver He data sampling data collection by sampling A statistical variable that represents the output or effect, or is tested to see if it is the effect in an experiment or a modeling. Jie Zheng, Yongqun He dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables dependent variable A random variable which can take an infinite number of possible values. Jie Zheng, Yongqun He WEB: http://www.stats.gla.ac.uk/steps/glossary/probability_distributions.html#contvar continuous random variable Examples of discrete random variables include the number of children in a family, the Friday night attendance at a cinema, the number of patients in a doctor's surgery, the number of defective light bulbs in a box of ten. A random variable which may take on only a countable number of distinct values such as 0, 1, 2, 3, 4, ... Jie Zheng, Yongqun He WEB: http://www.stats.gla.ac.uk/steps/glossary/probability_distributions.html#contvar discrete random variable A data item which consists of digits as opposed to letters of the alphabet of special characters Jie Zheng, Yongqun He numeric data WEB: http://www.ask.com/question/what-is-numerical-data numerical data item A plan specification that provides a detailed outline of how data is collected. Jie Zheng, Yongqun He data collection design A validity that refers to the validity of a diagnosis, and associated diagnostic tests or screening tests in a clinical field such as medicine. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) diagnostic validity A data collection by sampling process that results in a collection of data generated from an censoring. Jie Zheng, Oliver He data collection by censoring A normalization data transformation that used to create normalized gene expression level from microarray raw data. The raw intensity values are background corrected, log2 transformed and then quantile normalized in the RMA normalization process. Person:Jie Zheng, Oliver He RMA RMA normalization http://www.ncbi.nlm.nih.gov/pubmed/12925520 http://www.molmine.com/magma/loading/rma.htm robust multi-array average normalization An inferential statistical data analysis that is established in 2001 by Virginia Tusher, Robert Tibshirani and Gilbert Chu, for determining whether changes in gene expression are statistically significant. Person: Jie Zheng, Oliver He SAM http://www.ncbi.nlm.nih.gov/pmc/articles/PMC33173/ http://en.wikipedia.org/wiki/Significance_analysis_of_microarrays significance analysis of microarrays A univariate analysis that calculates the level of a desired signal to the level of background noise to identify which detected signal is more signal than noise. It can be used to identify differentially expressed genes. Person: Jie Zheng, Oliver He S2N signal-2-noise statistic http://en.wikipedia.org/wiki/Signal-to-noise_ratio http://www.ncbi.nlm.nih.gov/pubmed/10521349 signal-2-noise statistical analysis A validity that refers to whether an experiment (or a study) is able to scientifically answer the questions it is intended to answer. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) experimental validity A quantitative confidence value that indicates how well data points fit a statistical model - sometimes simply a line or curve. It is a statistic used in the context of statistical models whose main purpose is either the prediction of future outcomes or the testing of hypotheses, on the basis of other related information. It provides a measure of how well observed outcomes are replicated by the model, as the proportion of total variation of outcomes explained by the model. Person: Jie Zheng, Oliver He R squared coefficient of determination http://en.wikipedia.org/wiki/Coefficient_of_determination R squared value A data item with a specific table layout that allows visualization of the performance of an algorithm. Each column of the matrix represents the instances in a predicted class, while each row represents the instances in an actual class. Person: Jie Zheng, Oliver He confusion matrix error matrix http://en.wikipedia.org/wiki/Confusion_matrix contingency table A contingency table with two rows and two columns that reports the number of false positives, false negatives, true positives, and true negatives. This allows more detailed analysis than mere proportion of correct guesses (accuracy). Person: Jie Zheng, Oliver He http://en.wikipedia.org/wiki/Confusion_matrix STATO:0000138 2x2 contingency table An inferential statistical data analysis that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). Person: Jie Zheng, Oliver He GSEA http://www.pnas.org/content/102/43/15545.abstract Gene Set Enrichment Analysis An inferential statistical data analysis used when comparing two related samples, matched samples, or repeated measurements on a single sample to assess whether their population mean ranks differ (i.e. it is a paired difference test). It can be used as an alternative to the paired Student's t-test, t-test for matched pairs, or the t-test for dependent samples when the population cannot be assumed to be normally distributed. Person: Jie Zheng, Oliver He http://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test Wilcoxon signed-rank test A data collection process that results in a collection of data generated from observation(s). Person: Jie Zheng, Oliver He data collection from observation A data item which is the ratio of observed deaths in the study group to expected deaths in the general population. Person: Jie Zheng, Oliver He SMR http://en.wikipedia.org/wiki/Standardized_mortality_ratio standardized mortality ratio An experimental validity that refers to the degree to which conclusions about the relationship among variables based on the data are correct or ‘reasonable’. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) statistical conclusion validity An experimental validity that refers to the degree to which conclusions about causal relationships can be made (e.g. cause and effect), based on the measures used, the research setting, and the whole research design. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) internal validity An experimental validity that refers to the extent to which the (internally valid) results of a study can be held to be true for other cases, for example to different people, places or times. In other words, it is about whether findings can be validly generalized. If the same research study was conducted in those other cases, would it get the same results? Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) external validity An external validity that refers to the extent to which research results can be applied to real life situations outside of research settings. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) ecological validity A test validity that refers to the extent to which operationalizations of a construct (i.e., practical tests developed from a theory) do actually measure what the theory says they do. For example, to what extent is a questionnaire actually measuring "intelligence"? Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) construct validity A construct validity that refers to the degree to which a measure is correlated with other measures that it is theoretically predicted to correlate with. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) convergent validity A construct validity that tests whether concepts or measurements that are supposed to be unrelated are, in fact, unrelated. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) discriminant validity A test validity that determine whether it covers a representative sample of the behavior domain to be measured through systematic examination of the test content. For example, does an IQ questionnaire have items covering all areas of intelligence discussed in the scientific literature? Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) content validity A test validity that refers to the correlation between the test and a criterion variable (or variables) taken as representative of the construct. In other words, it compares the test with other measures or outcomes (the criteria) already held to be valid. For example, employee selection tests are often validated against measures of job performance (the criterion), and IQ tests are often validated against measures of academic performance (the criterion). Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) If the test data and criterion data are collected at the same time, this is referred to as concurrent validity evidence. If the test data are collected first in order to predict criterion data collected at a later point in time, then this is referred to as predictive validity evidence. criterion validity A criterion validity that refers to the degree to which the operationalization correlates with other measures of the same construct that are measured at the same time. When the measure is compared to another measure of the same type, they will be related (or correlated). In the selection test example, this would mean that the tests are administered to current employees and then correlated with their scores on performance reviews. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) concurrent validity A criterion validity that refers to the degree to which the operationalization can predict (or correlate with) other measures of the same construct that are measured at some time in the future. With the selection test example, this would mean that the tests are administered to applicants, all applicants are hired, their performance is reviewed at a later time, and then their scores on the two measures are correlated. Yongqun He http://en.wikipedia.org/wiki/Validity_(statistics) predictive validity A content validity that refers to the extent to which an abstract theoretical construct can be turned into a specific practical test. Yongqun He translation validity http://en.wikipedia.org/wiki/Validity_(statistics) representation validity A content validity that estimates whether a test appears to measure a certain criterion. It is not guaranteed that the test actually measures phenomena in that domain. When the test does not appear to be measuring what it is, it has low face validity. Yongqun He translation validity http://en.wikipedia.org/wiki/Validity_(statistics) face validity A software that is used for the differential gene expression significance analysis of DNA microarray experiments for both standard and time course experiments. The outputs consist of bothe p-values and q-values. Elisabetta Manduchi EDGE Storey J.D. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing, Journal of the Royal Statistical Society, Series B, 69: 347-368. Storey J.D., Dai J.Y., and Leek J.T. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments, Biostatistics, 8: 414-432. Leek J.T,. Monsen E.C., Dabney A.R., and Storey J.D. (2006) EDGE: Extraction and analysis of differential gene expression, Bioinformatics, 22: 507-508. Storey J.D., Xiao W., Leek J.T., Tompkins R.G., and Davis R.W. (2005) Significance analysis of time course microarray experiments, Proceedings of the National Academy of Sciences, 102: 12837-12842. Beta Cell Biology Consortium Extraction of Differential Gene Expression software A software that can be used to produce lists of differentially expressed genes with confidence measures attached. These lists are generated via a False Discovery Rate (FDR) method of controlling the false positives. Patterns from Gene Expression (PaGE) is more than a differential expression analysis tool. PaGE is a tool to attach descriptive, dependable, and easily interpretable expression patterns to genes across multiple conditions, each represented by a set of replicated array experiments. The input consists of (replicated) intensities from a collection of array experiments from two or more conditions (or from a collection of direct comparisons on 2-channel arrays). The output consists of patterns, one for each row identifier in the data file. One condition is used as a reference to which the other types are compared. The length of a pattern equals the number of non-reference sample types. The symbols in the patterns are integers, where positive integers represent up-regulation as compared to the reference sample type and negative integers represent down-regulation. The patterns are based on the false discovery rates for each position in the pattern, so that the number of positive and negative symbols that appear in each position of the pattern is as descriptive as the data variability allows. The patterns generated are easily interpretable in that integers are used to represent different levels of up- or down-regulation as compared to the reference sample type. Elisabetta Manduchi PaGE PMID:15797908 Grant G.R., Liu J., Stoeckert C.J.Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data, Bioinformatics, 21(11): 2684-2690. Beta Cell Biology Consortium Patterns from Gene Expression software A software that is used to identify transcription factor binding sites in a genome that have been enriched with aligned reads generated from ChIP-Seq technology. Elisabetta Manduchi, Jie Zheng GLITR PMID:19553195 Tuteja G., White P., Schug J., Kaestner K.H. (2009) Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res., 37(17): e113. doi:10.1093/nar/gkp536. Beta Cell Biology Consortium GLobal Identifier of Target Regions software An inferential statistical data analysis to identify protein-binding regions in a genome sequence from the data generated from a ChIP-sequencing or ChIP-chip experiment. When the protein is a transcription factor, the region is a transcription factor binding site (TFBS). Jie Zheng http://en.wikipedia.org/wiki/Peak_calling peak calling A differential expression analysis using LIMMA linear model to identify differential expression for microarray data. Person: Oliver He, Jie Zheng LIMMA LIMMA data analysis Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK (2015). “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research, 43, pp. doi: 10.1093/nar/gkv007. WEB: http://www.bioconductor.org/packages/release/bioc/html/limma.html differential expression analysis using LIMMA linear models for microarry data A data transformation that add two or more numbers, magnitudes, quantities, or particulars as determined by or as if by the mathematical process of addition. tracker: https://github.com/obcs/obcs/issues/7 Person: Jie Zheng summing data transformation http://dictionary.reference.com/browse/summing PRISM summing data values A data item that is produced as the output of a summing data transformation and represents the total value of the input data. Tracker:https://github.com/obcs/obcs/issues/7 Person: Jie Zheng Jie Zheng PRISM sum value A data collection process that is conducted through an online process. Jie Zheng, Oliver He data collection from online resource An online data collection process that extracts data from an online database Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Online_database data collection from online database An online data collection process that extracts data from online using a web crawler. A Web crawler is an Internet bot which systematically browses the World Wide Web and gets data from WWW. Jie Zheng, Oliver He data collection using Web spider https://en.wikipedia.org/wiki/Web_crawler data collection by web crawling A data collection process that deals with incommensurate fields in the data. Jie Zheng, Oliver He WEB: http://www.ncbi.nlm.nih.gov/pubmed/26428398 Jinjing Guo；Oliver He collection of incommensurate data A software that is used to browses the World Wide Web in a methodical, automated manner. Jie Zheng, Yongqun He web crawler web robot web scutter web spider URL: http://www.sciencedaily.com/terms/web_crawler.htm URL: https://en.wikipedia.org/wiki/Web_crawler web crawling software A data transformation process that re-arrange the order of all or part of a set of data items. Jie Zheng, Oliver He WEB: http://stattrek.com/statistics/dictionary.aspx?definition=Permutation WEB: https://en.wikipedia.org/wiki/Permutation permutation A planned process that generates possible values of missing data Jie Zheng, Oliver He WEB: https://www.niehs.nih.gov/about/visiting/events/pastmtg/assets/docs_k_m/missingdatar.r generation of missing data A data transformation process that transforms incompatible data to compatible data. Jie Zheng, Yongqun He WEB: http://en.wikipedia.org/wiki/Loglinear_analysis processing incompatible data A permutation process that randomly orders a set of data items. Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Random_permutation random permutation A multivariate analysis that uncovers the latent structure (dimensions) of a set of variables. It reduces attribute space from a larger number of variables to a smaller number of factors. Yongqun He, Jie Zheng WEB: https://en.wikipedia.org/wiki/Factor_analysis WEB: https://en.wikipedia.org/wiki/Multivariate_analysis factor analysis A multivariate analysis that compares multivariate sample means. As a multivariate procedure, it is used when there are two or more dependent variables. Yongqun He, Jie Zheng WEB: https://en.wikipedia.org/wiki/Multivariate_analysis_of_variance multivariate analysis of variance MANOVA A regression method of interpolation for which the interpolated values are modeled by a Gaussian process governed by prior covariances, as opposed to a piecewise-polynomial spline chosen to optimize smoothness of the fitted values. Jie Zheng, Yongqun He Gaussian process regression WEB: https://en.wikipedia.org/wiki/Kriging Kriging An inferential statistical data analysis that estimates parameters of an underlying distribution based on the observed distribution Jie Zheng, Oliver He WEB: http://mathworld.wolfram.com/BayesianAnalysis.html Bayesian analysis A random permutation process that generates a permutation of n items uniformly at random without retries. Specifically, it is to start with any permutation (for example, the identity permutation), and then go through the positions 1 through n − 1, and for each position i swap the element currently there with a randomly chosen element from positions i through n, inclusive. Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Random_permutation knuth shuffle A data transformation process that puts the data items in a set in a certain order. Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Sorting_algorithm sorting A sorting process that sorts a set of data items based on the numberical order. Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Sorting_algorithm sorting based on numerical order A sorting process that sorts a set of data items based on a lexicorgraphic order Jie Zheng, Oliver He WEB: https://en.wikipedia.org/wiki/Sorting_algorithm sorting based on lexicorgraphic order A data processing that applies a deterministic mathematical function to each point in a data set; that is, each data point zi is replaced with the transformed value yi = f(zi), where f is a function. Jie Zheng, Yongqun He WEB: https://en.wikipedia.org/wiki/Data_transformation_(statistics) data transformation in statistics A logarithmic transformation that uses the base-2 logarithm. Jie Zheng, Yongqun He WEB: http://en.wikipedia.org/wiki/Logarithm log2 transformation A data transformation that performs an operation of square root. Jie Zheng, Yongqun He WEB: https://en.wikipedia.org/wiki/Square_root square root transformation A variance-stabilizing transformation that transforms a random variable with a Poisson distribution into one with an approximately standard Gaussian distribution. Jie Zheng, Yongqun He WEB: https://en.wikipedia.org/wiki/Anscombe_transform Anscombe transformation A data transformation that lists data items in a sequential arrangement Jie Zheng, Yongqun He rank-order transformation An information content entity that refers to a number value of a data item. Yongqun He, Jie Zheng mathematical data value mathematical value numerical data value A data value that is continuous from an interval of possible outcomes. Yongqun He, Jie Zheng WEB: https://onlinecourses.science.psu.edu/stat414/node/87 continuous data value A data value that is discrete, ie, counted. Yongqun He, Jie Zheng WEB: https://www.mathsisfun.com/data/data-discrete-continuous.html discrete data value A data value that is an ordinal number, ie., a number that tells the position of something in a list. Yongqun He, Jie Zheng ordinal data value A data value that is a cardinal number, i.e., a number that says how many of something there are, such as one, two, three, four, five. Yongqun He, Jie Zheng WEB: https://www.mathsisfun.com/numbers/cardinal-ordinal-nominal.html cardinal data value A mathematic graph that a set of objects (vertices or nodes) that are connected together, where all the edges between two objects are bidirectional. Yongqun He, Jie Zheng undirected network WEB: http://mathinsight.org/definition/undirected_graph undirected graph A data value that is a nominal number, ie., a number used only as a name, or to identify something (not as an actual value or position). Yongqun He, Jie Zheng WEB: https://www.mathsisfun.com/numbers/cardinal-ordinal-nominal.html nominal data value A continuous variable over a particular range of the real numbers is one whose value in that range must be such that, if the variable can take values a and b in that range, then it can also take any value between a and b. We will link continuous variable to measurement scale. Jie Zheng, Yongqun He WEB: https://en.wikipedia.org/wiki/Continuous_and_discrete_variables continuous variable A statistical variable over a particular range of real values is one for which, for any value in the range that the variable is permitted to take on, there is a positive minimum distance to the nearest other permissible value. We will link discrete variable to measurement scale. Jie Zheng, Yongqun He categorical variable WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm WEB: https://en.wikipedia.org/wiki/Continuous_and_discrete_variables discrete variable A continuous variable that has order and equal intervals. Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm interval-scale variable A continuous variable that occur when the measurement is continuous Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm continuous ordinal variable A continuous variable that is a continuous positive measurement on a nonlinear scale Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm ratio-scale variable A discrete variable that allows for only qualitative classification Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm nominal variable A nominal variable, but its different states are ordered in a meaningful sequence Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm discrete ordinal variable A quantitative variable can be transformed into a categorical variable, called a dummy variable by recoding the values Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm dummy variable A preference variable is a specific discrete variable, whose value is either in a decreasing or increasing order. Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm preference variable A discrete variable which can assume more than one value. A typical example is a survey questionnaire about the use of computers in research. The respondents were asked to indicate the purpose(s) for which they use computers in their research work. The respondents could score more than one category. Jie Zheng, Yongqun He WEB: http://www.unesco.org/webworld/idams/advguide/Chapt1_3.htm multiple response variable A probability distribution that represents the probability distribution corresponding to a histogram of data values. Yongqun He, Jie Zheng WEB: https://reference.wolfram.com/language/ref/HistogramDistribution.html histogram distribution A normal distribution that is the distribution of a random variable X for which the Box–Cox transformation on X follows a truncated normal distribution. Yongqun He Gaussian distribution power-normal distribution WEB: http://en.wikipedia.org/wiki/Normal_distribution Box-Cox distribution A mathematic graph that a set of objects (vertices or nodes) that are connected together, where all the edges are directed from one object to another. A directed graph is sometimes called a digraph or a directed network. Yongqun He, Jie Zheng WEB: http://mathinsight.org/definition/directed_graph directed graph A mathematic graph that a set of objects (vertices or nodes) that are connected via numerous semantic relations. Yongqun He, Jie Zheng WEB: http://arxiv.org/abs/1412.2378 relational graph A disposition that inheres in a population of continuant and is realized in a test process (e.g., disease diagnosis). https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0099-4 AB, JZ, JFE, YH This term is generated in OBCS based on BIPO: https://github.com/OpenLHS/BIPO. See more from OBCS track issue: https://github.com/obcs/obcs/issues/9 Traditionally, sensitivity inheres in a population of material entity like human. However, it raises a concern in the existance of such sensitivity disposition in the context of machine learning using syntheti data generated with mathematical formula. In this case, the population of disposition bearer are not population of organisms or material entities. Here the bearer of the disposition is not independent continuant. sensitivity disposition A mathematic graph that contains a set of objects (vertices or nodes) decomposed into two disjoint sets such that no two objects within the same set are adjacent. Yongqun He, Jie Zheng bigraph WEB: http://mathworld.wolfram.com/BipartiteGraph.html bipartite graph An information content entity that represents a set of objects (vertices or nodes) where some pairs of objects are connected by links. Yongqun He, Jie Zheng WEB: https://en.wikipedia.org/wiki/Graph_(mathematics) mathematic graph A mathematic graph that a set of objects (vertices or nodes) that are connected in a hierarchical from. Yongqun He, Jie Zheng WEB: https://en.wikipedia.org/wiki/Tree_structure hierarchical tree A data item that is derived from a statistical data analysis. Jie Zheng, Yongqun He, Marcy Harris, Asiyah Yu Lin statistic WEB: http://en.wikipedia.org/wiki/Statistic WEB: http://www.ask.com/question/what-is-numerical-data derived data from statistical analysis A data item that is derived from a descriptive statistical data analysis. Jie Zheng, Yongqun He descriptive statistic WEB: http://www.ask.com/question/what-is-numerical-data WEB: https://en.wikipedia.org/wiki/Descriptive_statistics derived data from descriptive statistical analysis A data item that is derived from an inferential statistical data analysis. Jie Zheng, Yongqun He inferential statistic WEB: http://psc.dss.ucdavis.edu/sommerb/sommerdemo/stat_inf/intro.htm WEB: http://www.ask.com/question/what-is-numerical-data derived data from inferential statistical analysis A data transformation process that transforms a data set to a normal distribution. Jie Zheng, Oliver He, Asiyah Yu Lin WEB: https://en.wikipedia.org/wiki/Normal_distribution normal distribution transformation A data set that follows a probability distribution Yongqun He, Jie Zheng, Yu Lin data set following probability distribution A data set that follows a normal distribution Yongqun He, Jie Zheng, Yu Lin normally distributed data set data set following normal distribution A data set that is an aggregate of numerical data item. Jie Zheng numerical data set A data collection process that results in a collection of data generated from document(s). Jie Zheng, Oliver He data collection from document A data collection process that results in a collection of data generated from eMedical record(s). data collection from eMedical record A rate of deaths (in general, or due to a specific cause) that in a particular population, scaled to the size of that population, per unit of time. Jie Zheng https://en.wikipedia.org/wiki/Mortality_rate mortality rate A rate of unit shif in a hospital. Jie Zheng hospital unit shift rate A data item that is produced as the output of a data transformation. Person: Jie Zheng, Oliver He transformed data item A data transformation in statistics that processes the data matrix collected from eMedical records to a form that is ready for further data analysis. eMedical record data transformation A sensitivity disposition that is related to a medical test and inheres in a population of organism. AB, JZ, JFE, YH medical test sensitivity disposition A statistical hypothesis test that is not based on any parameterized family of probability distributions. QL, YH https://en.wikipedia.org/wiki/Nonparametric_statistics non-parametric test A non-parametric test that was proposed by James Durbin and is used for for balanced incomplete designs. QL, YH https://en.wikipedia.org/wiki/Durbin_test Durbin test A special case of the Durbin test that was proposed by Milton Frieman and is applicable to complete block designs. Friedman test detects the differences in treatments across multiple test attempts. The procedure involves ranking each row (or block) together, then considering the values of ranks by columns. QL, YH, HL https://en.wikipedia.org/wiki/Friedman_test Friedman test An inferential statistical data analysis that includes all randomized patients in the groups to which they were randomly assigned. The intent-to-treat analysis is based on the initial treatment assignment and not on the treatment eventually received. ITT analysis includes every subject who is randomized according to randomized treatment assignment. It ignores noncompliance, protocol deviations, withdrawal, and anything that happens after randomization. HL, QL, YH ITT analysis https://en.wikipedia.org/wiki/Intention-to-treat_analysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159210/ intent-to-treat analysis A non-parametric test of the equality of continuous, one-dimensional probability distributions that can be used to compare a sample with a reference probability distribution (one-sample K–S test), or to compare two samples (two-sample K–S test). The distributions considered under the null hypothesis are continuous distributions but are otherwise unrestricted. HL, QL, YH K-S test KS test https://en.wikipedia.org/wiki/Kolmogorov%E2%80%93Smirnov_test Kolmogorov–Smirnov test A Kolmogorov-Smirnov test that compares a sample with a reference probability distribution. Huan Li, Qingzhi Liu, Oliver He one-sample K-S test one-sample KS test WEB: http://en.wikipedia.org/wiki/Kolmogorov%E2%80%93Smirnov_test Kolmogorov-Smirnov one sample test A non-parametric test that compares the survival distributions of two samples, and iis appropriate to use when the data are right skewed and censored (technically, the censoring must be non-informative). It is widely used in clinical trials to establish the efficacy of a new treatment in comparison with a control treatment when the measurement is the time to event (such as the time from initial treatment to a heart attack). HL, QL, YH KS test Mantel–Cox test log-rank analysis https://en.wikipedia.org/wiki/Log-rank_test log-rank test A chi square test that is applied to sets of categorical data to evaluate how likely it is that any observed difference between the sets arose by chance. It is suitable for unpaired data from large samples. It is also the most widely used of many chi-squared tests. HL, QL, YH Pearson's Chi square test Pearson's X^2 test https://en.wikipedia.org/wiki/Pearson%27s_chi-squared_test Pearson's chi-square test A chi square test that is used in certain situations when testing for independence in a contingency table. In some cases, Yates' correction may adjust too far, and so its current use is limited. HL, QL, YH Yates' correction for continuity https://en.wikipedia.org/wiki/Yates%27s_correction_for_continuity Yates' chi-squared test A chi square test that is used in the analysis of stratified or matched categorical data. It allows an investigator to test the association between a binary predictor or treatment and a binary outcome such as case or control status while taking into account the stratification. Unlike the McNemar test which can only handle pairs, the CMH test handles arbitrary strata size. It is named after William G. Cochran, Nathan Mantel and William Haenszel. HL, QL, YH CMH test https://en.wikipedia.org/wiki/Cochran%E2%80%93Mantel%E2%80%93Haenszel_statistics Cochran–Mantel–Haenszel test A chi square test that is 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. HL, QL, YH CMH test https://en.wikipedia.org/wiki/McNemar%27s_test McNemar's test A data transformation that is used to calculate a ROC curve. Yongqun He, Jie Zheng ROC curve analysis WEB: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755824/ Receiver operating characteristic curve analysis An inferential statistical data analysis which is used to find the independent components (also called factors, latent variables or sources) by maximizing the statistical independence of the estimated components. Person: Oliver He and Jie Zheng ICA https://en.wikipedia.org/wiki/Independent_component_analysis independent component analysis A regression analysis method that the overall solution minimizes the sum of the squares of the residuals made in the results of every single equation. Person: Jie Zheng https://en.wikipedia.org/wiki/Least_squares least square regression A disposition that inheres in some objects, which prevents accurate prediction or determination of the quality of a material entity. It is realized in objective process or subjective process. Jie Zheng Jinjing Guo Oliver He 不确定性 uncertainty An uncertainty that inheres in an objective continuant. Jie Zheng Jinjing Guo Oliver He Aleatory uncertainty Chance External uncertainty Natural variability Ontological uncertainty Random or stochastic variation Statistical probability 客观不确定性 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2002561/ objective uncertainty An uncertainty that inheres in an organism (in especial human) and results from subjective cognition. Jie Zheng Jinjing Guo Oliver He Epistemic uncertainty Functional uncertainty Inductive probability Internal uncertainty Knowledge uncertainty probability 主观不确定性 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2002561/ subjective uncertainty An object with subjective cognition. Jie Zheng Jinjing Guo Oliver He 带有主观性的客体 subjective object A process in which tangible substances or objects undergo movement or change in a way that can be observed and measured independently, regardless of subjective interpretations or perceptions. It is a concept often used in scientific and objective contexts to describe the physical changes and movements of matter in the external world. Jie Zheng Jinjing Guo Oliver He 客观过程 https://iep.utm.edu/objectiv/ objective process A process refers to the mental processes involved in gaining knowledge and comprehension. Some of the many different cognitive processes include thinking, knowing, remembering, judging, and problem-solving. Jie Zheng Jinjing Guo Oliver He 主观过程 https://www.verywellmind.com/what-is-cognition-2794982 subjective process Jie Zheng Jinjing Guo Oliver He 决策 definition to be confirmed decision making Jie Zheng Jinjing Guo Oliver He 不确定性分析 definition to be confirmed uncertainty analysis Study of how the uncertainty in the output of a mathematical model or system (numerical or otherwise) can be divided and allocated to different sources of uncertainty in its inputs.Conducted to understand the factors and processes that most (or least) control a model’s outputs  Jie Zheng Jinjing Guo Oliver He 灵敏度分析 https://en.wikipedia.org/wiki/Sensitivity_analysis sensitivity analysis Model evaluation performed by varying uncertain factors around specific reference values. Jie Zheng Jinjing Guo Oliver He 局部灵敏度分析 https://uc-ebook.org/docs/html/6_glossary.html local sensitivity analysis Model evaluation performed by varying uncertain factors throughout their entire feasible value space. Jie Zheng Jinjing Guo Oliver He 全局灵敏度分析 https://uc-ebook.org/docs/html/6_glossary.html global sensitivity analysis Jie Zheng Jinjing Guo Oliver He to be confirmed screening sensitivity analysis Equations aimed to assess how the quantified uncertainties in model inputs propagate in model calculations to produce and uncertainty range in a given model outcome of interest.In statistics, propagation of uncertainty (or propagation of error) is the effect of variables' uncertainties (or errors, more specifically random errors) on the uncertainty of a function based on them. When the variables are the values of experimental measurements they have uncertainties due to measurement limitations (e.g., instrument precision) which propagate due to the combination of variables in the function. Jie Zheng Jinjing Guo Oliver He propagation of error propagation of uncertainty 误差传播方程 https://en.wikipedia.org/wiki/Propagation_of_uncertainty error propagation equation A broad class of computational algorithms that rely on repeated random sampling to obtain numerical results.The goal of Monte Carlo analysis is to trace out the structure of the distributions of model output that results from specified uncertainty distributions of model inputs and model parameters. Jie Zheng Jinjing Guo Oliver He Monte Carlo experiment Monte Carlo method 蒙特卡罗分析 https://en.wikipedia.org/wiki/Monte_Carlo_method Monte Carlo analysis A structured process to elicit subjective judgements from experts. Expert elicitation in the context of uncertainty quantification aims at a credible and traceable account of specifying probabilistic information regarding uncertainty, in a structured and documented way. Jie Zheng Jinjing Guo Oliver He 专家启发法 http://www.nusap.net/downloads/toolcatalogue.pdf expert elicitation The NUSAP (Numeral Unit Spread Assessment, Pedigree) method aims to provide an analysis and diagnosis of uncertainty. It captures both quantitative dimensions and qualitative dimensions of uncertainty (Funtowicz and Ravetz 1990). Jie Zheng Jinjing Guo Oliver He NUSAP 数字单元传播评估谱系 https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3855&context=iemssconference;https://link.springer.com/book/10.1007/978-94-009-0621-1 Numeral Unit Spread Assessment Pedigree A method that tries to describe logical and internally consistent sequences of events to explore how the future might, could or should evolve from the past and present. Jie Zheng Jinjing Guo Oliver He 情境分析 http://www.nusap.net/downloads/toolcatalogue.pdf scenario analysis A meta approach (organising framework) to structure the process of uncertainty management Jie Zheng Jinjing Guo Oliver He PRIMA 综合不确定性管理和风险分析的多元框架 https://link.springer.com/chapter/10.1007/978-94-017-2583-5_6 Pluralistic fRamework of Integrated uncertainty Management and risk Analysis An instrument for internal use to assist modellers and users of models in the process of quality control. Jie Zheng Jinjing Guo Oliver He 模型质量协助清单 http://www.nusap.net/downloads/toolcatalogue.pdf Checklist for Model Quality Assistance A method that enables to systematically identify and prioritize critical assumptions in (chains of linked) models and provides a framework for the critical appraisal of model assumptions.This method aims to systematically identify, prioritise and analyse importance and strength of assumptions in models. Jie Zheng Jinjing Guo Oliver He 模型中假设的批判性审查 http://www.nusap.net/downloads/toolcatalogue.pdf critical review of assumptions in model Jie Zheng Jinjing Guo Oliver He elimiation of uncertainty 不确定性消除 https://www.ctillc.com/blog/rd-four-part-test-and-elimination-of-uncertainty to be confirmed uncertainty elimination Jie Zheng Jinjing Guo Oliver He source of uncertainty 不确定性缘由 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed uncertainty arise condition Jie Zheng Jinjing Guo Oliver He solutions of uncertainty 不确定性应对措施 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed uncertainty response activity Rare or extreme events are events that occur with low frequency, and often refers to infrequent events that have a widespread effect and which might destabilize systems Jie Zheng Jinjing Guo Oliver He 事件罕见 https://en.wikipedia.org/wiki/Rare_events rarity of event Jie Zheng Jinjing Guo Oliver He 单一原因的多重影响 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed multiple effects from single cause Jie Zheng Jinjing Guo Oliver He 个体差异 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed individual difference Jie Zheng Jinjing Guo Oliver He 材料难以获取 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed material difficult to obtain Jie Zheng Jinjing Guo Oliver He 事件不稳定（偶发、自我逆转、扩散） Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed instability of event (episodic, self-reversing, spreading) Jie Zheng Jinjing Guo Oliver He limited and inaccurate data 部分可用数据 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition and classification to be confirmed partially available data Jie Zheng Jinjing Guo Oliver He 研究人群不同 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed diverse populations for study Jie Zheng Jinjing Guo Oliver He 因果现象界限不清 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed unclear boundaries of causal phenomena Jie Zheng Jinjing Guo Oliver He 缺乏因果模型 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed lack of causal model Jie Zheng Jinjing Guo Oliver He 不可控的实验条件 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed uncontrollable experimental condition Jie Zheng Jinjing Guo Oliver He 缺乏可供比较的信息 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed lack of information for comparison Jie Zheng Jinjing Guo Oliver He 不稳定和不断扩散的症状和副作用 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed labile and spreading symptom and side effect Jie Zheng Jinjing Guo Oliver He 延迟的信息 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition and classification to be confirmed delayed information Jie Zheng Jinjing Guo Oliver He 同一案例的专业/非专业处理 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed specialist/nonspecialist handling of the same case Jie Zheng Jinjing Guo Oliver He 调查者间地位不平等 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed unequal status between investigators Jie Zheng Jinjing Guo Oliver He 管理层与员工关系不佳 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed poor management-staff relation Jie Zheng Jinjing Guo Oliver He 资金不足 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed lack of funding Jie Zheng Jinjing Guo Oliver He 资金分散 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed sporadic funding Jie Zheng Jinjing Guo Oliver He 缺乏制度保障 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed lack of institutional security Jie Zheng Jinjing Guo Oliver He 调查人员间的延误和缺乏沟通 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed delay and lack of communication between investigators Jie Zheng Jinjing Guo Oliver He Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed reacting subject Jie Zheng Jinjing Guo Oliver He 手术并发症（实验性） Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed operative complication (experimental) Jie Zheng Jinjing Guo Oliver He 无法控制的程序 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed uncontrollable procedure Jie Zheng Jinjing Guo Oliver He 观察困难 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed observational difficulty Jie Zheng Jinjing Guo Oliver He 按顺序或空间位置对数据进行排序 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed order data sequentially or by spatial location Jie Zheng Jinjing Guo Oliver He 标准化 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed standardize Jie Zheng Jinjing Guo Oliver He 范例筛选 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed find exemplars-filter for clear-cut case Jie Zheng Jinjing Guo Oliver He 不确定性分割 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed segmentation of uncertainty Jie Zheng Jinjing Guo Oliver He 诊断分类替代 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed substitution of taxonomy for diagnosis Jie Zheng Jinjing Guo Oliver He 劳动分工 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed division of labor Jie Zheng Jinjing Guo Oliver He 寻找病症 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed search for pathognomonic sign Jie Zheng Jinjing Guo Oliver He 散弹枪疗法 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed shotgun treatment Jie Zheng Jinjing Guo Oliver He 按照政治路线清晰划分数据 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed division of data along political line for clarity Jie Zheng Jinjing Guo Oliver He 按照技术/实质性原则分工 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed division of labor along technical/substantive line Jie Zheng Jinjing Guo Oliver He 观察限于现有材料 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed observations limited to available material Jie Zheng Jinjing Guo Oliver He 强调实际结果的功利主义 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed utilitarian emphasis on practical result Jie Zheng Jinjing Guo Oliver He 技术和材料标准化 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed standardization of techniques and material Jie Zheng Jinjing Guo Oliver He 观察技术（形式）和协议标准化 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed standardization of observational technique (form) and protocol Jie Zheng Jinjing Guo Oliver He 观察向下聚焦到更小的领域 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed observations down-focused to smaller area Jie Zheng Jinjing Guo Oliver He 用理论有效性替代技术一致性 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. definition to be confirmed substitution of theoretical validity for technical consistency Jie Zheng Jinjing Guo Oliver He 测量误差 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition to be confirmed measurement error Jie Zheng Jinjing Guo Oliver He 不完整的知识 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition to be confirmed incomplete knowledge Jie Zheng Jinjing Guo Oliver He 有限的理解 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition to be confirmed limited understanding Jie Zheng Jinjing Guo Oliver He 不完美的模型 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition to be confirmed imperfect model Jie Zheng Jinjing Guo Oliver He 主观判断 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition to be confirmed subjective judgement the chaotic and unpredictable nature of natural processes Jie Zheng Jinjing Guo Oliver He 自然固有的随机性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 inherent randomness of nature ‘non-rational’behaviour, discrepancies between what people say and what they actually do (cognitive dissonance), or deviations of ‘standard’ behavioural patterns (micro-level behaviour). Jie Zheng Jinjing Guo Oliver He Human behaviour 行为可变性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 behavioural variability the chaotic and unpredictable nature of societal processes (macro-level behaviour). The need to consider societal and institutional processes as a major contributor to uncertainty due to variability can be inferred from various papers of Funtowicz, Ravetz, and de Marchi. Jie Zheng Jinjing Guo Oliver He Social, economic, and cultural dynamic 社会可变性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 societal variability New developments or breakthroughs in technology or unexpected consequences (‘side-effects’) of technologies. Jie Zheng Jinjing Guo Oliver He https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 technological surprise Sampling error is the error associated with the degree to which the sample is representative. Jie Zheng Jinjing Guo Oliver He 抽样误差 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 sampling error in the measurement Jie Zheng Jinjing Guo Oliver He 可能 definition and classification to be confirmed probability Jie Zheng Jinjing Guo Oliver He 复杂引起的不确定性 definition to be confirmed complexity-induced uncertainty vagueness is associated with the lack of precise or sharp distinctions or boundaries Jie Zheng Jinjing Guo Oliver He cloudiness fuzziness haziness imprecision indefiniteness indistinctiveness sharplessness unclearness 模糊 GEORGE J. KLIR (1989) IS THERE MORE TO UNCERTAINTY THAN SOME PROBABILITY THEORISTS MIGHT HAVE US BELIEVE?*, International Journal Of General System, 15:4, 347-378, DOI: 10.1080/03081078908935057. classification to be confirmed vagueness Ambiguity, on the other hand, is associated with one-to-many relations, that is, situations in which several alternatives are left unspecified or a desired categorization of an element is left undecided due to ignorance. Jie Zheng Jinjing Guo Oliver He disagreement discrepancy dissonance divergence diversity equivocation generality imprecision incongruity nonspecificity variety 歧义 GEORGE J. KLIR (1989) IS THERE MORE TO UNCERTAINTY THAN SOME PROBABILITY THEORISTS MIGHT HAVE US BELIEVE?*, International Journal Of General System, 15:4, 347-378, DOI: 10.1080/03081078908935057. classification to be confirmed ambiguity Taxonomic uncertainty arose as they tried to develop classification systems (for example, what kind of thing was epilepsy?). Jie Zheng Jinjing Guo Oliver He 分类不确定性 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. taxonomic uncertainty Diagnostic uncertainty arose when investigators attempted to fit a particular case into their taxonomies. Jie Zheng Jinjing Guo Oliver He 诊断不确定性 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. diagnostic uncertainty Organizational uncertainty arose when information was lost or trapped owing to the local division of labor or the circumstances of alliances and collaborations. Jie Zheng Jinjing Guo Oliver He 组织不确定性 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. organizational uncertainty Technical uncertainty developed as a result of inadequate tools or ambiguous information about techniques. Technical uncertainty arose from difficulties with subjects, equipment, and procedures, including the lack of standard measurement techniques. Jie Zheng Jinjing Guo Oliver He 技术不确定性 Star, S. L. (1989). Regions of the mind: Brain research and the quest for scientific certainty. Stanford Univ. Press. technical uncertainty Jie Zheng Jinjing Guo Oliver He 预后不确定性 https://uts.nlm.nih.gov/uts/umls/vocabulary/NANDA-I/03312 definition and classification to be confirmed prognosis uncertainty Jie Zheng Jinjing Guo Oliver He 确定性（正面或中性） https://pubmed.ncbi.nlm.nih.gov/1608829/ definition and classification to be confirmed positive or neutral certainty Jie Zheng Jinjing Guo Oliver He 确定性（有害的） https://pubmed.ncbi.nlm.nih.gov/1608829/ definition and classification to be confirmed detrimental certainty Jie Zheng Jinjing Guo Oliver He 中等不确定性 https://pubmed.ncbi.nlm.nih.gov/1608829/ definition and classification to be confirmed moderate degree of certainty Jie Zheng Jinjing Guo Oliver He 不确定性（有害的） https://pubmed.ncbi.nlm.nih.gov/1608829/ definition and classification to be confirmed detrimental uncertainty Jie Zheng Jinjing Guo Oliver He 不确定性（正面） https://pubmed.ncbi.nlm.nih.gov/1608829/ definition and classification to be confirmed positive uncertainty Determinism is the ideal situation in which we know everything precisely. It is not attainable, but acts as a limiting characteristic at one end of the spectrum. Jie Zheng Jinjing Guo Oliver He 决定论 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 classification to be confirmed determinism Statistical uncertainty is any uncertainty that can be described adequately in statistical terms. Statistical uncertainty can apply to any location in the model, even to model structure uncertainties, as long as the deviation from the true value can be characterised statistically.Statistical uncertainty is what is usually referred to as‘‘uncertainty’’in the natural sciences. Jie Zheng Jinjing Guo Oliver He 统计不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 statistical uncertainty Measurement uncertainty stems from the fact that measurements can practically never precisely represent the ‘‘true’’ value of that which is being measured. Jie Zheng Jinjing Guo Oliver He 测量不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 measurement uncertainty Scenario uncertainty can manifest itself in various ways – for example, (a) as a range in the outcomes of an analysis due to different underlying assumptions, (b) as uncertainty about which changes and developments (e.g., in driving forces or in system characteristics) are relevant for the outcomes of interest, or (c) as uncertainty about the levels of these relevant changes. Jie Zheng Jinjing Guo Oliver He 情景不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 classification to be confirmed scenario uncertainty Recognised ignorance is fundamental uncertainty about the mechanisms and functional relationships being studied. We know neither the functional relationships nor the statistical properties and the scientific basis for developing scenarios is weak. Jie Zheng Jinjing Guo Oliver He 公认的无知 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 classification to be confirmed recognized ignorance Reducible ignorance may be resolved by conducting further research, which implies that it might be possible to somehow achieve a better understanding. Jie Zheng Jinjing Guo Oliver He 可还原的无知 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 reducible ignorance Irreducible ignorance applies when neither research nor development can provide sufficient knowledge about the essential relationships. Jie Zheng Jinjing Guo Oliver He indeterminacy 不可还原的无知 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 irreducible ignorance Total ignorance is the other extreme from determinism on the scale of uncertainty, which implies a deep level of uncertainty, to the extent that we do not even know that we do not know. Jie Zheng Jinjing Guo Oliver He 完全无知 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 classification to be confirmed total ignorance Context uncertainty includes uncertainty about the external economic, environmental, political, social, and technological situation that forms the context for the problem being examined. The context could fall within the past, the present, or the future. Jie Zheng Jinjing Guo Oliver He Situational uncertainty 场景不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 context uncertainty Model uncertainty is associated with both the conceptual model (i.e., the variables and their relationships that are chosen to describe the system located within the boundaries and thus constituting the model complex) and the computer model. Jie Zheng Jinjing Guo Oliver He 模型不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 model uncertainty uncertainty about the form of the model itself. Model structure uncertainty arises from a lack of sufficient understanding of the system (past, present, or future) that is the subject of the policy analysis, including the behaviour of the system and the interrelationships among its elements. Jie Zheng Jinjing Guo Oliver He 模型结构不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 model structure uncertainty uncertainty arising from the computer implementation of the model.Model technical uncertainty is the uncertainty generated by software or hardware errors, i.e. hidden flaws in the technical equipment. Software errors arise from bugs in software, design errors in algorithms and typing errors in model source code. Hardware errors arise from bugs, such as the bug in the early version of the Pentium processor, which gave rise to numerical error in a broad range of floating-point calculations performed on the processor. Jie Zheng Jinjing Guo Oliver He 模型技术不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 model technical uncertainty Jie Zheng Jinjing Guo Oliver He 输入不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition and classification to be confirmed input uncertainty Uncertainty about the external driving forces that produce changes within the system (the relevant scenario variables and policy variables) and the magnitude of the forces (the values of the scenario and policy variables). Jie Zheng Jinjing Guo Oliver He 外部驱动力量不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 external driving forces uncertainty Uncertainty about the systemdata that ‘drive’ themodel and typically quantify relevant features of the reference system and its behaviour (e.g. land-use maps, data on infrastructure (roads, houses)). Uncertainty about system data is generated by a lack of knowledge of the properties (including both the deterministic and the stochastic properties) of the underlying system and deficiencies in the description of the variability that can be an inherent feature of some of the phenomena under observation. Jie Zheng Jinjing Guo Oliver He 系统数据不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 system data uncertainty Jie Zheng Jinjing Guo Oliver He 参数不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 definition and classification to be confirmed parameters uncertainty This is the accumulated uncertainty caused by the uncertainties in all of the above locations (context, model, inputs, and parameters) that are propagated through the model and are reflected in the resulting estimates of the outcomes of interest. Jie Zheng Jinjing Guo Oliver He prediction error 模型产出不确定性 https://www.tandfonline.com/doi/abs/10.1076/iaij.4.1.5.16466 classification to be confirmed model outcome uncertainty Scientific uncertainty refers to uncertainty which emanates from the scientific and technical dimensions of a problem as opposed to the legal, moral, societal, institutional, proprietary, and situational dimensions outlined by De Marchi et al. Scientific uncertainty is intrinsic to the processes of risk assessment and forecasting. Jie Zheng Jinjing Guo Oliver He 科学不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed scientific uncertainty Legal uncertainty is relevant "wherever agents must consider future contingencies of personal liability for their actions (or inactions)". High legal uncertainty can result in defensive responses in regard to both decision making and release of information. Legal uncertainty may also play a role where actions are conditioned on the clarity or otherwise of a legal framework in allowing one to predict the consequences of particular actions. Jie Zheng Jinjing Guo Oliver He 法律不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed legal uncertainty Moral uncertainty stems from the underlying moral issues related to action and inaction in any given case. De Marchi notes that, though similar to legal responsibility, moral guilt may occur absent legal responsibility when negative consequences might have been limited by the dissemination of prior information or more effective management for example. "Moral uncertainty is linked to the ethical tradition of a given country be it or not enacted in legislation (juridical and societal norms, shared moral values, mores), as well as the psychological characteristics of persons in charge, their social status and professional roles" (De Marchi, 1994). Moral uncertainty would typically be high when moral and ethical dimensions of an issue are central and participants have a range of understandings of the moral imperatives at stake. Jie Zheng Jinjing Guo Oliver He 道德不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed moral uncertainty Communities from one region to another may differ in the set of norms, values, and manner of relating characteristic of their societies. This in turn can result in differences in approach to decision making and assessment. Some salient characteristics of these differences will be different views about the role of consensus versus conflict, on locating responsibility between individuals and larger groups, on views about the legitimacy and role of social and private institutions, and on attitudes to authority and expertise. From De Marchi (1994). Societal uncertainty would typically be high when decisions involve substantial collaboration among groups characterized by divergent decision making styles. Jie Zheng Jinjing Guo Oliver He 社会不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed societal uncertainty Institutional uncertainty is in some sense a subset of societal uncertainty, and refers more specifically to the role and actions of institutions and their members. Institutional uncertainty stems from the "diverse cultures and traditions, divergent missions and values, different structures, and work styles among personnel of different agencies" (De Marchi, 1994). High institutional uncertainty can hinder collaboration or understanding among agencies, and can make the actions of institutions difficult to predict. Jie Zheng Jinjing Guo Oliver He 机制不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed institutional uncertainty Proprietary uncertainty occurs due to the fact that information and knowledge about an issue are not uniformly shared among all those who could potentially use it. That is, some people or groups have information that others don't and may assert ownership or control over it. "Proprietary uncertainty becomes most salient when it is necessary to reconcile the general needs for safety, health, and environment protection with more sectorial needs pertaining, for instance, to industrial production and process, or to licensing and control procedures" (De Marchi, 1994). De Marchi notes that 'whistle blowing' is another source of proprietary uncertainty in that there is a need for protection of those who act in sharing information for the public good. Proprietary uncertainty would typically be high when knowledge plays a key role in assessment, but is not widely shared among participants. An example of such would be the case of external safety of military nuclear production facilities. Jie Zheng Jinjing Guo Oliver He 所有权不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed proprietary uncertainty Situational uncertainty relates to "the predicament of the person responsible for a crisis, either in the phase of preparation and planning, or of actual emergency. It refers to individual behaviours or personal interventions in crisis situations" (De Marchi, 1994) and as such represents a form of integration over the other six types of uncertainty. That is, it tends to combine the uncertainties one has to face in a given situation or on a particular issue. High situational uncertainty would be characterized by situations where individual decisions play a substantial role and there is uncertainty about the nature of those decisions. Jie Zheng Jinjing Guo Oliver He context uncertainty 情境不确定性 http://www.nusap.net/modules.php?op=modload&name=NS-Glossary&file=index classification to be confirmed situational uncertainty A belief is psychologically certain when the subject who has it is supremely convinced of its truth. Certainty in this sense is similar to incorrigibility, which is the property a belief has of being such that the subject is incapable of giving it up. But psychological certainty is not the same thing as incorrigibility. A belief can be certain in this sense without being incorrigible; this may happen, for example, when the subject receives a very compelling bit of counterevidence to the (previously) certain belief and gives it up for that reason. Moreover, a belief can be incorrigible without being psychologically certain. For example, a mother may be incapable of giving up the belief that her son did not commit a gruesome murder, and yet, compatible with that inextinguishable belief, she may be tortured by doubt. Jie Zheng Jinjing Guo Oliver He 心理不确定性 https://plato.stanford.edu/entries/certainty/?fbclid=IwAR3vA0iSWlxBOy5xH5IJ6kJCpqxGtweFO07bJCEzgw4cnF7viviAkt006qo#pagetopright classification to be confirmed psychological uncertainty Jie Zheng Jinjing Guo Oliver He identity disorder https://uts.nlm.nih.gov/uts/umls/vocabulary/MEDCIN/1416 classification to be confirmed identity uncertainty Jie Zheng Jinjing Guo Oliver He https://uts.nlm.nih.gov/uts/umls/vocabulary/MEDCIN/1417 classification to be confirmed uncertainty about gender role Jie Zheng Jinjing Guo Oliver He https://uts.nlm.nih.gov/uts/umls/vocabulary/MEDCIN/1418 classification to be confirmed uncertainty about long-term goal Jie Zheng Jinjing Guo Oliver He https://uts.nlm.nih.gov/uts/umls/vocabulary/MEDCIN/1419 classification to be confirmed uncertainty about value system Jie Zheng Jinjing Guo Oliver He definition to be confirmed uncertainty degree level Jie Zheng Jinjing Guo Oliver He No equivocation 绝对确定 https://pubmed.ncbi.nlm.nih.gov/29274047/ definition to be confirmed definitive certainty level Jie Zheng Jinjing Guo Oliver He Minimal equivocation 高度确定 https://pubmed.ncbi.nlm.nih.gov/29274047/ definition to be confirmed high certainty level Jie Zheng Jinjing Guo Oliver He Intermediate degree of equivocation 中度确定 https://pubmed.ncbi.nlm.nih.gov/29274047/ definition to be confirmed intermediate certainty level Jie Zheng Jinjing Guo Oliver He High degree of equivocation 最高程度不确定 https://pubmed.ncbi.nlm.nih.gov/29274047/ definition to be confirmed highest uncertainty degree Jie Zheng Jinjing Guo Oliver He 非常高度不确定 definition to be confirmed very high uncertainty level Jie Zheng Jinjing Guo Oliver He 低程度不确定 definition to be confirmed low uncertainty level Jie Zheng Jinjing Guo Oliver He 非常低程度不确定 definition to be confirmed very low uncertainty level Representation of model output uncertainty using probability distributions. Jie Zheng Jinjing Guo Oliver He 不确定性量化 https://uc-ebook.org/docs/html/6_glossary.html classification to be confirmed uncertainty quantification fluorescent reporter intensity A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. person:Chris Stoeckert group:OBI 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. fluorescent reporter intensity planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. '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.) 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. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent 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) planned process biological feature identification objective 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. Jennifer Fostel biological feature identification objective classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material ratio of collected to emitted light 10% A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role person:Chris Stoeckert person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification 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 study investigation evaluant role 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. 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 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) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 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. Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay quantitative confidence value A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert group:OBI quantitative confidence value eMedical record An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel article-without-pmid-or-doi:CDISCglossary eMedical record culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. 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. Person: Jennifer Fostel, Jie Zheng OBI culture medium reagent role Buffer, dye, a catalyst, a solvating agent. 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. PERSON:Matthew Brush reagent PERSON:Matthew Brush 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. (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). reagent role material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert OBI Data Transformation branch measured expression level specimen role 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. 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 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. 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. 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. 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. GROUP: Role Branch OBI specimen role intervention design 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. 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. Philppe Rocca-Serra OBI branch derived intervention design gene list 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. 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. person:Chris Stoeckert group:OBI 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. gene list number of particles in subset 500, 200, 0 A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events electronic molecular feature identification objective 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. Jennifer Fostel molecular feature identification objective parameter threshold 0.01, 0.03 A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt parameter threshold p-value PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value imaging assay An assay that produces a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived imaging assay methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. Jennifer Fostel methodology testing objective standard error A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. person:Chris Stoeckert group:OBI see P-Value standard error software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. Jennifer Fostel software testing objective cluster Cluster of the lymphocytes population. A data set which is a subset of data that are a similar to each other in some way. person:Allyson person:Chris Stoeckert group:OBI cluster DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction organism feature identification objective Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. Jennifer Fostel organism feature identification objective number of lost events computer 0, 125, 787 events lost due to computer busy. A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer protocol 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. 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. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. 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'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target material to be added role drug added to a buffer contained in a tube; substance injected into an animal; A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target). Role Branch OBI 9 March 09 from discussion with PA branch material to be added role interpreting data 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. 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 PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning 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. a process of creating or modifying a plan specification 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'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning inductive reasoning Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. Proposal is to obsolete. Bjoern Peters wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning inductive reasoning hypothesis driven investigation is an investigation with the goal to test one or more hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis driven investigation hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis generating investigation information processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. Frank Gibson data processor function information processor function extract 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 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract averaging objective 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. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective adding material objective creating a mouse infected with LCM virus 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 BP adding material objective analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective analyte assay 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 An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson Philippe Rocca-Serra Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch Philippe Rocca-Serra analyte assay target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. 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. GROUP: Role Branch OBI target of material addition role normalized data set A data set that is produced as the output of a normalization data transformation. PERSON: James Malone PERSON: Melanie Courtot normalized data set measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. 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. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function consume data function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot consume data function material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out a study design 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. branch derived 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. study design execution NMR instrument An Instrument which is used to carry out a NMR analysis of some sample. PERSON:Daniel Schober MRI scanner NMR instrument magnetic resonance imaging scanner GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 NMR instrument NMR instrument DNA methylation profiling assay Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. Philippe Rocca-Serra DNA methylation profiling OBI branch derived DNA methylation profiling assay material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective clustered data set A clustered data set is the output of a K means clustering data transformation 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set data set of features 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. PERSON: James Malone PERSON: Monnie McGee data set of features differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals. Dan Berrios James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen a portion of urine collected from an organism 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active are we happy calling collection of urine a material separation? urine specimen material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination fuzzy clustering objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. James Malone PERSON: James Malone PERSON: Ryan Brinkman fuzzy clustering objective blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen data set of predicted values according to fitted curve A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. PERSON: James Malone PERSON: Monnie McGee data set of predicted values according to fitted curve data representational model gene regulatory graph model phylogenetic tree protein interaction network Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. Melanie Courtot data structure data structure specification GROUP: OBI 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 data representational model specimen collection process 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 A planned process with the objective of collecting a specimen. 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. 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. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process background corrected data set A data set that is produced as the output of a background correction data transformation. PERSON: James Malone PERSON: Melanie Courtot background corrected data set error corrected data set 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). PERSON: James Malone PERSON: Monnie McGee error corrected data set class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation background correction data transformation A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. James Malone PERSON: James Malone background correction data transformation error correction data transformation 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. James Malone Monnie McGee EDITORS error correction data transformation sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now 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. sample from organism statistical hypothesis test A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. James Malone PERSON: James Malone statistical hypothesis test center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value statistical hypothesis test objective 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. James Malone Person:Helen Parkinson hypothesis test objective WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing statistical hypothesis test objective reduced dimension data set A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. PERSON: James Malone PERSON: Monnie McGee reduced dimension data set portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean mean average value separation into different composition objective The objective to obtain cells contained in a sample of blood. 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). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine self-organizing map A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. James Malone Ryan Brinkman SOM PERSON: Ryan Brinkman self-organizing map decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors 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. James Malone k-NN PERSON: James Malone k-nearest neighbors Student's t-test 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. James Malone WEB: http://en.wikipedia.org/wiki/T-test Student's t-test material sample role 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. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 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. material sample role topologically preserved clustered data set the output data set generated from a self-organizing map. A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. James Malone PERSON: James Malone topologically preserved clustered data set material sample 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. A material entity that has the material sample role OBI: workshop sample population sample material sample CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART independent variable specification 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. 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 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. 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 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. study factor study design independent variable dependent variable specification 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. 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. 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. 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 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. study design dependent variable survival rate A measurement data 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. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate multiple testing correction objective Application of the Bonferroni correction A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction multiple testing correction objective statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation spike train datum Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. needs more work to see exactly what the data set looks like - HP Helen Parkinson, Alan Ruttenberg spike train measurement Jessica Turner, NIF spike train datum material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance Likelihood-ratio test 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. Tina Boussard Likelihood-ratio test pattern matching objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen study intervention A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. PERSON: Bjoern Peters GROUP: OBI study intervention categorical measurement datum A measurement datum that is reported on a categorical scale. Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum compound treatment design an intervention design in which the treatment is the administration of a compound This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. PERSON: Bjoern Peters MO_555 compound_treatment_design compound treatment design processed specimen 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. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label 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. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 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. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device dose specification a protocol specifying to administer 1 ml of vaccine to a mouse a directive information entity that describes the dose that will be administered to a target dose specification 1 scalar score from composite inputs A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. Person: Jessica Turner questionaire score Person: Jessica Turner JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? scalar score from composite inputs sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data handedness categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally PERSON:Alan Ruttenberg PERSON:Jessica Turner handedness categorical measurement datum dose An organism has been injected 1ml of vaccine 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. dose growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing PERSON: Bjoern Peters MO_588 growth_condition_design growth condition intervention design 1 Edinburgh score A score that measures the dominance of a person's right or left hand in everyday activities. Person: Alan Ruttenberg Person:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edinburgh score administration of material to specimen Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen growth environment The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. Right now this may be incomplete. Should also cover e.g. sound, light as well. PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters OBI group growth environment nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract feature extraction A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction feature extraction DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract binding constant The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed. 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. PERSON: Jie Zheng GROUP: OBI term is proposed by BP on Oct 25, 2010 dev call genetically modified material genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective 3D structural organization datum The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. A measurement datum that describes the structural orientation of a material entity in 3D space. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters 3D structural organization datum age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. PERSON:Chris Stoeckert, Jie Zheng MO_495 planting Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call age since planting measurement datum age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. PERSON:Chris Stoeckert, Jie Zheng MO_745 hatching age since hatching measurement datum age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. PERSON:Chris Stoeckert, Jie Zheng MO_767 egg laying age since egg laying measurement datum age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. PERSON:Chris Stoeckert, Jie Zheng MO_590 germination age since germination measurement datum age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. PERSON:Chris Stoeckert, Jie Zheng MO_876 eclosion age since eclosion measurement datum age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. PERSON:Chris Stoeckert, Jie Zheng MO_748 sowing age since sowing measurement datum age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. PERSON:Chris Stoeckert, Jie Zheng MO_783 coitus age since coitus measurement datum age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage. PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. PERSON:Chris Stoeckert, Jie Zheng MO_701 fertilization age since fertilization measurement datum age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) dose response curve 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. Bjoern Peters; Randi Vita dose response curve half maximal effective concentration (EC50) Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. Bjoern Peters; Randi Vita wikipedia half maximal effective concentration (EC50) binding datum A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. Bjoern Peters; Randi Vita binding datum negative binding datum A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. negative binding datum half maximal inhibitory concentration (IC50) Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. Bjoern Peters; Randi Vita wikipedia half maximal inhibitory concentration (IC50) normalization testing design A study design that tests different normalization procedures. Person: Chris Stoeckert, Jie Zheng MO_729 normalization_testing_design normalization testing design genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information epigenetic modification identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. Chris Stoeckert, Jie Zheng Person: Chris Stoeckert epigenetic modification identification objective FWER adjusted p-value http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html 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 PERS:Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) FWER adjusted p-value wild type organism genotype information C57BL/6J wild type a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group wild type organism genotype information genotype information 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 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. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information 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. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information post-transcriptional modification design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases Person: Chris Stoeckert, Jie Zheng MO_392 cellular_modification_design post-transcriptional modification design genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information wild type allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information stimulus or stress design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. Person: Chris Stoeckert, Jie Zheng MO_568 stimulus_or_stress_design stimulus or stress design genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics 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) genetic characteristics information dose response design A study design that examines the relationship between the size of the administered dose and the extent of the response. Person: Chris Stoeckert, Jie Zheng MO_485 dose_response_design dose response design q-value 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)" 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. PERS:Philippe Rocca-Serra FDR adjusted p-value Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html q-value genetic modification design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. Person: Chris Stoeckert, Jie Zheng MO_447 genetic_modification_design genetic modification design lowess group transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. Person: Elisabetta Manduchi MO_861 lowess_group_normalization lowess group transformation lowess transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. Person: Elisabetta Manduchi MO_720 lowess_normalization lowess transformation specimen from organism 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). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism lowess global transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. Person: Elisabetta Manduchi MO_692 lowess_global_normalization lowess global transformation specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus specimen with pre- or post-mortem status sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum minimal inhibitory concentration A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. Created following request by Albert Goldfain PERSON:Bjoern Peters Bjoern Peters, coordinated with Albert Goldfain minimal inhibitory concentration sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm PDB file The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum PDB file equilibrium dissociation constant (KD) KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium dissociation constant (KD) comparative phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference Philly workshop 2011 Philly workshop 2011 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 comparative phenotypic assessment equilibrium association constant (KA) KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium association constant (KA) rate measurement datum 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. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum 50% dissociation of binding temperature (Tm) Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. PERSON: Bjoern Peters, Randi Vita melting temperature (Tm) IEDB 50% dissociation of binding temperature (Tm) equilibrium dissociation constant (KD) approximated by IC50 A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. PERSON: Bjoern Peters, Randi Vita http://dx.doi.org/10.1016/0006-2952(73)90196-2 equilibrium dissociation constant (KD) approximated by IC50 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 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. DNA sequence data assigning gene property based on phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. Philly workshop 2011 Philly workshop 2011 assigning gene property based on phenotypic assessment equilibrium dissociation constant (KD) approximated by EC50 A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. PERSON: Bjoern Peters, Randi Vita Assay Development: Fundamentals and Practices, By Ge Wu, page 74 equilibrium dissociation constant (KD) approximated by EC50 half life of binding datum The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. PERSON: Bjoern Peters, Randi Vita IEDB half life of binding datum binding A peptide binding to an MHC molecule to form a complex. The process of material entities forming complexes. 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters, Randi Vita IEDB binding PDB file chain The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum IEDB PDB file chain binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) average depth of sequence coverage An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Depth of Coverage - Average NIAID GSCID-BRC average depth of sequence coverage specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum drawing a conclusion 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. A planned process in which new information is inferred from existing information. drawing a conclusion sequence assembly process A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert Philippe Rocca-Serra NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence assembly process number of errors Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2 a data item that is the number of times that a given process failed, as an integer Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB number of errors random access memory size Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB random access memory size random access memory Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location Alejandra Gonzalez-Beltran Philippe Rocca-Serra RAM http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02 random access memory testable hypothesis 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 An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis Group:2013 Philly Workshop group testable hypothesis conclusion based on data 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". An information content entity that is inferred from data. 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. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data cell freezing medium 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. PERSON: Matthew Brush cell freezing medium computation run time Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4 computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. Alejandra Gonzalez-Beltran Philippe Rocca-Serra computation run time datum PRS,AGB computation run time categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. 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. PERSON:Bjoern Peters value specification genome coverage Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%" A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. Alejandra Gonzalez-Beltran Philippe Rocca-Serra A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764 genome coverage N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" N50 contig N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html contig N50 scaffold N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html scaffold N50 sequence library data demultiplexing is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library PERSON: Philippe Rocca-Serra PRS for OBI sequence library data demultiplexing operational taxonomic unit matrix http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. PERSON:Philippe Rocca-Serra PRS for OBI operational taxonomic unit matrix epigenetic modification assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Chris Stoeckert Jie Zheng Penn group epigenetic modification assay RNA Integrity Number calculation A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. Chris Stoeckert, Bjoern Peters RIN calculation https://www.agilent.com/cs/library/applications/5989-1165EN.pdf RNA Integrity Number calculation RNA Integrity Number value specification A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). Chris Stoeckert, Bjoern Peters RIN value specification OBI RNA Integrity Number value specification antigen specific antibodies assay Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens An analyte assay that measures the presence or amount of antibodies to a specified antigen. Bjoern Peters Chris Stoeckert James Overton Randi Vita OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB antigen specific antibodies assay tissue section thickness A length measurement datum that is the result of an assay measuring the thickness of a tissue section. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB tissue section thickness diagnosis of cancer A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. Chris Stoeckert, Helena Ellis cancer diagnosis OBIB NCI BBRB diagnosis of cancer diagnosis of infectious disease A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of infectious disease diagnosis of hepatitis B A diagnosis of infectious disease caused by the hepatitis B virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of hepatitis B diagnosis of hepatitis C A diagnosis of infectious disease caused by the hepatitis C virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of hepatitis C diagnosis of HIV A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of HIV number of pregnancies A measurement datum of the total number of pregnancies a woman has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of pregnancies number of live births A measurement datum of the total number of live births a female has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of live births age when gave birth to first child An age measurement datum performed on a female when her first biological child was born. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB age when gave birth to first child measurand role 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. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role age since culture seeding measurement datum An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). Stephen A. Fisher, Junhyong Kim, Dan Berrios age of culture age since culture seeding measurement datum date process started A data item that is the date when a process was initiated. Chris Stoeckert, Daniel Berrios, Stephen A. Fisher date process started number of PCR cycles during library construction A data item that is the number of PCR cycles used during the construction of a sequencing library. Stephen A. Fisher, Junhyong Kim, Dan Berrios library construction PCR cycles https://en.wikipedia.org/wiki/Polymerase_chain_reaction number of PCR cycles during library construction number of rounds of amplification A data item that is the number of times an amplification reaction happened. Stephen A. Fisher, Junhyong Kim, Dan Berrios number of rounds of amplification sequence read length measurement datum A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. Stephen A. Fisher, Junhyong Kim, Dan Berrios read length, read length measurement datum sequence read length measurement datum sequencing library input quantity measurement datum A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. Stephen A. Fisher, Junhyong Kim library input amount sequencing library input quantity measurement datum specimen harvest quantity A scalar measurement datum that indicates the amount of specimen collected. Stephen A. Fisher, Junhyong Kim, Dan Berrios harvest quantity specimen harvest quantity spike-in dilution factor A data item that indicates the dilution of spike-in added to a specimen. Stephen A. Fisher, Junhyong Kim, Dan Berrios spike-in dilution factor cerebrospinal fluid specimen A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen feces specimen A specimen that is derived from feces. Chris Stoeckert stool specimen Chris Stoeckert, Penn Medicine Biobank feces specimen milk specimen A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen sputum specimen A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen bone marrow specimen A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen pleural fluid specimen A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen skin of body specimen A specimen that is derived from skin. Chris Stoeckert skin specimen Chris Stoeckert, NCI BBRB skin of body specimen lung specimen A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios adapter-sequence trimming file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios file merge sequence alignment A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios sequence alignment sequence data feature count tabulation The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. Dan Berrios Dan Berrios sequence data feature count tabulation trimmed sequence data The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. Dan Berrios Dan Berrios trimmed sequence data adapter sequence data Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. Dan Berrios Dan Berrios adapter sequence data adapter-trimmed sequence data The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. Dan Berrios Dan Berrios adapter-trimmed sequence data aligned sequence data The results of a sequence alignment. Dan Berrios Dan Berrios aligned sequence data merged aligned sequence data The results of a data transformation of sequence data in which files containing aligned sequence data are merged together Dan Berrios Dan Berrios merged aligned sequence data sequence library feature count data The results of a sequence data feature count tabulation. Dan Berrios Dan Berrios sequence library feature count data DNA methylation profiling data The results of a DNA methylation profiling assay DNA methylation profiling data differential expression analysis data The results of a differential expression analysis. differential expression analysis data sequence trimming A data transformation in which subsequences of a molecular sequence are cut (removed). sequence trimming swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 OBIB swab specimen collecting specimen with swab A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 OBIB collecting specimen with swab demultiplexed sequence data Sequence data in which an identifier subsequence has been used to categorize each reads by source. Dan Berrios Dan Berrios demultiplexed sequence data multiplexed sequence data Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. Dan Berrios Dan Berrios multiplexed sequence data nasopharyngeal swab specimen A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert Chris Stoeckert, OBIB nasopharyngeal swab specimen oropharyngeal swab specimen A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert Chris Stoeckert, OBIB oropharyngeal swab specimen blood microbiology assay An organism detection assay that detects microorganisms in a blood specimen. John Judkins https://github.com/obi-ontology/obi/issues/1064 blood microbiology assay biopsy Biopsy of a potentially cancerous mole. A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy bone marrow biopsy A bone marrow biopsy removes bone with the marrow inside to look at under a microscope A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. Nicole Vasilevsky http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy bone marrow biopsy induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins PMC3297553 induced sputum specimen passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. John Judkins https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage process passage history record A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process. John Judkins https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage history record karyotype information A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell. Jie Zheng EFO_0004426 karyotype https://github.com/obi-ontology/obi/issues/1097 VEuPathDB karyotype information partial karyotype information A karyotype information that is about the structural variation of partial genome rather than whole genome. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1097 VEuPathDB partial karyotype information full karyotype information A karyotype information that is about the structural variation of the whole genome. Jie Zheng OBI group https://github.com/obi-ontology/obi/issues/1097 full karyotype information cytometry analysis by automated gating A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest. Bjoern Peters CMI-PB https://github.com/obi-ontology/obi/issues/1226 cytometry analysis by automated gating cytometry analysis by manual gating A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest. Bjoern Peters CMI-PB https://github.com/obi-ontology/obi/issues/1226 cytometry analysis by manual gating nasal aspirate specimen A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal wash specimen|nasopharyngeal aspirate Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen aspiration specimen collection Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 aspiration procedure https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 aspiration specimen collection endotracheal aspirate specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. John Judkins ORCID:0000-0001-6595-0902 https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal aspirate specimen input protein sequence start site When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. The position of the first amino acid in a protein sequence being analyzed (input protein sequence). Emma Griffiths input protein start query protein start site Emma Griffiths input protein sequence start site input protein sequence stop site When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. The position of the last amino acid in a protein sequence being analyzed (input protein sequence). Emma Griffiths input protein stop query protein stop site Emma Griffiths input protein sequence stop site input gene sequence start site When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene start query gene start site Emma Griffiths input gene sequence start site input gene sequence stop site When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene stop query gene stop site Emma Griffiths input gene sequence stop site reference protein sequence start site When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. The position of the first amino acid in a reference protein sequence (sequence being used for comparison). Emma Griffiths reference protein start subject protein start site Emma Griffiths reference protein sequence start site reference protein sequence stop site When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. The position of the last amino acid in a reference protein sequence (sequence being used for comparison). Emma Griffiths reference protein stop subject protein stop site Emma Griffiths reference protein sequence stop site reference gene sequence start site When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). Emma Griffiths reference gene start subject gene start site Emma Griffiths reference gene sequence start site reference gene sequence stop site When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. The position of the last nucelotide in a reference sequence (sequence being used for comparison). Emma Griffiths reference gene stop subject gene stop site Emma Griffiths reference gene sequence stop site altitude measurement datum A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum magnetic resonance imaging assay An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. Alexander D. Bartnik, ORCID:0000-0001-9676-7377 Alexander D. Diehl, ORCID:0000-0001-9990-8331 Lauren M. Wishnie, ORCID:0000-0002-7245-3450 Lucas M. Serra, ORCID:0000-0002-2104-0568 Mackenzie T. Smith, ORCID:0000-0002-9821-4132 Rebecca Jackson William D. Duncan, ORCID:0000-0001-9625-1899 MRI url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging https://github.com/obi-ontology/obi/issues/1290 magnetic resonance imaging assay duration of specimen collection Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. specimen collection duration VEuPathDB specimen collection duration prevalence of pathogen in specimens prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. Chris Stoeckert prevalence of pathogen VEuPathDB prevalence of pathogen in specimens prevalence of blood meal specimens from a host organism prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. Chris Stoeckert host blood index VEuPathDB prevalence of blood meal specimens from a host organism presence of blood from host organism in blood meal specimen presence of blood meal host organism indicated by boolean values of yes or no. A data item that indicates whether blood in a blood meal specimen came from a specified host organism. Chris Stoeckert presence of blood meal host organism VEuPathDB presence of blood from host organism in blood meal specimen feces microbiology assay An organism detection assay that detects microorganisms in a feces specimen. John Judkins stool test for microorganisms VEuPathDB https://github.com/obi-ontology/obi/issues/1322 feces microbiology assay blood assay An assay that has a blood specimen as evaulant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 blood assay urine assay An assay that has a urine specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 urine assay proportion mapped reads A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. John Judkins VEuPathDB proportion mapped reads insecticide resistance datum A data item that is about resistance to an insecticide. John Judkins VEuPathDB insecticide resistance datum organism detection datum A data item that is the specified output of an organism detection assay. John Judkins VEuPathDB organism detection datum easting coordinate measurement datum A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system easting coordinate measurement datum northing coordinate measurement datum A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system northing coordinate measurement datum axillary temperature measurement datum A temperature measurement datum that is about an axilla. John Judkins VEuPathDB axillary temperature measurement datum organismal body temperature measurement datum A temperature measurement datum that is about an organism. Chris Stoeckert Jie Zheng Penn Group organismal body temperature measurement datum age since birth at time of enrollment An age since birth measurement datum at the time of subject enrollment. Jie Zheng Penn Group age since birth at time of enrollment age since birth at time of visit An age since birth measurement datum at the time of a clinical visit. Chris Stoeckert Grant Dorsey Jie Zheng Shon Cade Penn Group age since birth at time of visit entomological data item A data item that is about a collection of insects. John Judkins entomological measurement datum VEuPathDB entomological data item temperature measurement datum A scalar measurement datum that is the result of measuring temperature. John Judkins VEuPathDB temperature measurement datum extraction date A time measurement datum that specifies when some material was extracted from an input material. Chris Stoeckert, ORCID: 0000-0002-5714-991X FLU, VEuPathDB https://github.com/obi-ontology/obi/issues/1286 extraction date extraction duration time A time measurement datum that is the result of measuring the duration of an extraction process. Chris Stoeckert, ORCID: 0000-0002-5714-991X Meredith Keybl, Shane Babcock https://github.com/obi-ontology/obi/issues/1286 extraction duration time specimen collection time post disease onset A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. Chris Stoeckert, ORCID: 0000-0002-5714-991X GROUP:FLU, Shane Babcock https://github.com/obi-ontology/obi/issues/1286 specimen collection time post disease onset specimen collection time post infection A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. Chris Stoeckert, ORCID: 0000-0002-5714-991X VEuPathDB, EUPATH:0000613 https://github.com/obi-ontology/obi/issues/1286 specimen collection time post infection categorical binding datum A binding datum that is expressed as a categorical value. IEDB qualitative binding datum IEDB categorical binding datum quantitative binding datum A binding datum that is expressed using numbers. IEDB IEDB quantitative binding datum EC50 binding datum A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). Bjoern Peters Hector Guzman-Orozco IEDB EC50 binding datum IC50 binding datum A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). Bjoern Peters Hector Guzman-Orozco IEDB IC50 binding datum cerebrospinal fluid assay An assay that has a cerebrospinal fluid specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid assay endotracheal aspirate assay An assay that has an endotracheal aspirate specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal aspirate assay induced sputum assay An assay that has an induced sputum specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum assay lung assay An assay that has a lung specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung assay milk assay An assay that has a milk specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 milk assay feces assay An assay that has a feces specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 feces assay umbilical cord blood assay An assay that has an umbilical cord blood specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood assay cerebrospinal fluid microbiology assay An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid microbiology assay endotracheal tube aspirate microbiology assay An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal tube aspirate microbiology assay induced sputum microbiology assay An organism detection assay that detects microorganisms in an induced sputum specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum microbiology assay blood assay datum A data item that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood assay datum blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood microbiology datum feces assay datum A data item that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces assay datum feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces microbiology datum urine assay datum A data item that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine assay datum urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine microbiology datum induced sputum assay datum A data item that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum assay datum induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum microbiology datum cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid assay datum cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid microbiology datum endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal aspirate assay datum endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal tube aspirate microbiology datum lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 lung microbiology datum nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 nasopharyngeal or oropharyngeal swab microbiology datum pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 pleural fluid microbiology datum umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood assay datum umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood microbiology datum bacteria in blood datum A blood microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in blood datum virus in blood datum A blood microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in blood datum eukaryota in blood datum A blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in blood datum bacteria in feces datum A feces microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in feces datum eukaryota in feces datum A feces microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in feces datum virus in feces datum A feces microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in feces datum eukaryota in urine datum A urine microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in urine datum bacteria in induced sputum datum An induced sputum microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in induced sputum datum eukaryota in induced sputum datum An induced sputum microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in induced sputum datum virus in induced sputum datum An induced sputum microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in induced sputum datum bacteria in endotracheal tube aspirate datum An endotracheal tube aspirate microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in endotracheal tube aspirate datum bacteria in lung datum A lung microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in lung datum eukaryota in lung datum A lung microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in lung datum virus in lung datum A lung microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in lung datum bacteria in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in nasopharyngeal or oropharyngeal swab datum eukaryota in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in nasopharyngeal or oropharyngeal swab datum virus in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in nasopharyngeal or oropharyngeal swab datum bacteria in pleural fluid datum A pleural fluid microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in pleural fluid datum eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in pleural fluid datum virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in pleural fluid datum eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in umbilical cord blood datum lung microbiology assay An organism detection assay that detects microorganisms in a lung specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung microbiology assay pleural fluid microbiology assay An organism detection assay that detects microorganisms in a pleural fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 pleural fluid microbiology assay umbilical cord blood microbiology assay An organism detection assay that detects microorganisms in an umbilical cord blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood microbiology assay nasopharyngeal or oropharyngeal swab microbiology assay An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 nasopharyngeal or oropharyngeal swab microbiology assay urine microbiology assay An organism detection assay that detects microorganisms in a urine specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 urine microbiology assay positive binding datum A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. Bjoern Peters Hector Guzman-Orozco IEDB positive binding datum image data set The output produced by a digital imaging technique, such as microscopy, MRI, or CT. A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set magnetic resonance image data set The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. An image data set whose information content originates from some MR imaging assay and is about some MRI participant. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" MRI at a Glance, ISBN 10: 1119053552 https://github.com/obi-ontology/obi/issues/1481 magnetic resonance image data set magnetic resonance imaging participant The subject being scanned in an MRI study, and bearor of data derived from that study. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance imaging participant magnetic resonance imaging evaluant role An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance imaging evaluant role raw image data set The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw image data set magnetic resonance pulse sequence protocol The NMR/MRI machine protocol about the radiofrequency pulse sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance pulse sequence protocol computed image data set The production of JPEG file by a digital camera. An image data set that is the output of an image data set analysis. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 computed image data set reconstructed magnetic resonance image data set The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain. An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 reconstructed magnetic resonance image data set raw magnetic resonance image data set The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set image data set analysis The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set analysis raw magnetic resonance image data set reconstruction A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set reconstruction milk assay datum A data item that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 milk assay datum organism diagnostic process A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 organism diagnostic process diagnosis of an organism A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 diagnosis of an organism remote patient assessment A telephone or video remote patient assessment conducted between a physician and patient. An organism diagnostic process which involves a remote assessment of a patient by a clinician. telehealth patient assessment 2022-05-02T14:15:39Z remote patient assessment placental blood specimen A specimen that is derived from placental blood. John Judkins VEuPathDB placental blood specimen placental blood microbiology assay A blood microbiology assay that detects microorganisms in a placental blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology assay placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology datum eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 eukaryota in placental blood datum mid-upper arm circumference datum A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. The Mother and Child Health and Education Trust mid-upper arm circumference datum antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies assay datum antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in blood assay datum antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in milk assay datum organism detection assay An assay that detects a type of organism and/or the quantity of individuals of a type of organism. This term is a generalized version of the term previously known as 'organism identification assay', to include classification other than species and to include quantities as outputs. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1633 organism detection assay skin of body microbiology assay An organism detection assay that detects microorganisms in a skin of body specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 skin of body microbiology assay skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 skin of body microbiology datum bone marrow microbiology assay An organism detection assay that detects microorganisms in a bone marrow specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 bone marrow microbiology assay bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 bone marrow microbiology datum nasal aspirate microbiology assay An organism detection assay that detects microorganisms in a nasal aspirate specimen. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 nasal aspirate microbiology assay nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 nasal aspirate microbiology datum chronic allograft damage index score A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. Sebastian Duesing CADI chronic allograft damage index score sequential organ failure assessment score A clinical data item that quantifies the degree of function of a critically ill patient's organs. Sebastian Duesing SOFA score https://en.wikipedia.org/wiki/SOFA_score sequential organ failure assessment score physician's global assessment of disease activity A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. Sebastian Duesing MD global, PGA physician's global assessment of disease activity human leukocyte antigen mismatch count A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. Sebastian Duesing HLA mismatch count, HLA mismatch human leukocyte antigen mismatch count organism animal fungus plant virus 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. 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') 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. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. 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. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population 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). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 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. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush 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. cultured cell population data transformation 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. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data operation data processing Branch editors data transformation geometric mean calculation A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). Mathias Brochhausen PERSON: Mathias Brochhausen A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). geometric mean calculation logistic-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 logistic-log curve fitting logit-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 logit-log curve fitting log-log curve fitting Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 log-log curve fitting feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective biexponential transformation This type of transformation is typically used in flow cytometry. A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf biexponential transformation box-cox transformation A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. Ryan Brinkman ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. box-cox transformation hyperlog transformation This type of transformation is typically used in flow cytometry A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." http://flowcyt.sourceforge.net/gating/latest.pdf hyperlog transformation loess scale group transformation one-channel Loess scale group normalization applied to data from two one-channel expression microarray assays. A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. Elisabetta Manduchi OTHER: Editor's adjustment based on MGED Ontology term loess scale group transformation one-channel logical transformation This type of transformation is typically used in flow cytometry. A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf logical transformation loess scale group transformation two-channel Loess scale group normalization applied to data from a two-channel expression microarray assay. A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. Elisabetta Manduchi OTHER: Adjusted from MGED Ontology loess scale group transformation two-channel loess global transformation one-channel Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess global transformation one-channel split-scale transformation This type of transformation is typically used in flow cytometry A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf split-scale transformation loess global transformation two-channel Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess global transformation two-channel sine transformation sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Sine.html sine transformation cosine transformation cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. Elisabetta Manduchi Philippe Rocca-Serra WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation loess group transformation one-channel A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation one-channel loess group transformation two-channel A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation two-channel homogeneous polynomial transformation a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html homogeneous polynomial transformation linlog transformation This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi Philippe Rocca-Serra PMID: 16646782 linlog transformation variance stabilizing transformation This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. Elisabetta Manduchi James Malone Melanie Courtot variance stabilising transformation PMID: 12169536 variance stabilizing transformation loess global transformation A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess global transformation loess group transformation A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess group transformation loess scale group transformation A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation total intensity transformation single This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single total intensity transformation paired This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation paired quantile transformation This 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. A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. Elisabetta Manduchi PERSON: Elisabetta Manduchi quantile transformation mean centering This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. Elisabetta Manduchi Philippe Rocca-Serra mean centring PERSON: Elisabetta Manduchi mean centering median centering This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. Elisabetta Manduchi Philippe Rocca-Serra median centring PERSON: Elisabetta Manduchi median centering differential expression analysis objective 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 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective K-fold cross validation method K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used Person:Helen Parkinson Tina Boussard K-fold cross validation method leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method jackknifing method simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method Helen Parkinson jackknifing http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing method boostrapping Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient Helen Parkinson Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points boostrapping Benjamini and Hochberg false discovery rate correction method 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) 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 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Hochberg false discovery rate correction method pareto scaling A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. Elisabetta Manduchi Philippe Rocca-Serra PMID:16762068 pareto scaling modular decomposition Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. Tina Hernandez-Boussard editor modular decomposition k-means clustering 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). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering hierarchical clustering 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). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering average linkage hierarchical clustering 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi average linkage hierarchical clustering complete linkage hierarchical clustering 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi complete linkage hierarchical clustering single linkage hierarchical clustering 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi single linkage hierarchical clustering Benjamini and Yekutieli false discovery rate correction method The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing Helen Parkinson Philippe Rocca-Serra Helen Parkinson Benjamini and Yekutieli false discovery rate correction method dimensionality reduction 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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction 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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction probabilistic algorithm A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. James Malone PERSON: James Malone probabilistic algorithm expectation maximization EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. James Malone PERSON: James Malone expectation maximization global modularity calculation A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. Richard Scheuermann PERSON: Richard Scheuermann global modularity calculation dye swap merge A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge moving average The moving average is often used to handle data from tiling arrays. A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson Philippe Rocca-Serra PERSON: Elisabetta Manduchi PERSON: Helen Parkinson moving average replicate analysis Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi replicate analysis b cell epitope prediction A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. Helen Parkinson PERSON: Helen Parkinson b cell epitope prediction mhc binding prediction An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. Helen Parkinson PERSON: Helen Parkinson mhc binding prediction t cell epitope prediction A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. Helen Parkinson PERSON: Helen Parkinson t cell epitope prediction data imputation Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. Monnie McGee ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. data imputation continuum mass spectrum A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. PERSON: James Malone PERSON: Tina Hernandez-Boussard PERSON: Tina Boussard continuum mass spectrum analysis characteristic path length calculation Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices PERSON: Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard characteristic path length calculation centroid mass spectrum A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data. Person:Tina Hernandez-Boussard centroid mass spectrum calculation centroiding centroid mass spectrum centroid mass spectrum analysis Holm-Bonferroni family-wise error rate correction method 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 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 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 Person:Helen Parkinson Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method Holm-Bonferroni family-wise error rate correction method edge weighting Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. Tina Hernandez-Boussard editor was classified under algorithm class which is not acceptable super-class TO BE DEALT WITH STILL BY RICHARD. JAMES edge weighting loess transformation A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess transformation curve fitting data transformation A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Curve_fitting curve fitting data transformation family wise error rate correction method A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt Monnie McGee Philippe Rocca-Serra FWER correction Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 family wise error rate correction method submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. Elisabetta Manduchi James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Submatrix submatrix extraction row submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot row submatrix extraction column submatrix extraction When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot column submatrix extraction gating Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. James Malone Josef Spidlen Melanie Courtot Richard Scheuermann Ryan Brinkman PERSON: James Malone PERSON: Josef Spidlen PERSON: Richard Scheuermann PERSON: Ryan Brinkman PERSON:Melanie Courtot gating descriptive statistical calculation objective 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. Elisabetta Manduchi James Malone Melanie Courtot Monnie McGee PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation objective arithmetic mean calculation An arithmetic mean calculation 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. James Malone Monnie McGee Philippe Rocca-Serra PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008) arithmetic mean calculation network analysis A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. Richard Scheuermann network topology analysis PERSON: Richard Scheuermann network analysis sequence analysis objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. James Malone PERSON: James Malone sequence analysis objective longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. PERSON: James Malone PERSON: Tina Boussard correlation analysis longitudinal data analysis longitudinal data analysis survival analysis objective Kaplan meier data transformation 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 PERSON: James Malone PERSON: Tina Boussard survival analysis http://en.wikipedia.org/wiki/Survival_analysis survival analysis objective mass spectrometry analysis A data transformation which has the objective of spectrum analysis. mass spectrometry analysis spread calculation data transformation A spread calculation is a data transformation that has objective spread calculation. James Malone EDITOR spread calculation data transformation Kaplan Meier a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) PERSON: James Malone PERSON: Tina Boussard http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier multiple testing correction method 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 Monnie McGee multiple testing procedure PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method inter-rater reliability objective A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. a data transformation objective of determining the concordance or agreement between human judges. Person:Alan Ruttenberg Person:Helen Parkinson inter-rater agreement http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater reliability objective Westfall and Young family wise error rate correction Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation Helen Parkinson Westfall and Young FWER correction Westfall and Young family wise error rate correction polynomial transformation a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Polynomial.html polynomial transformation logarithmic transformation 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. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Logarithm logarithmic transformation exponential transformation An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function WEB: http://en.wikipedia.org/wiki/Exponential_function exponential transformation non-negative matrix factorization Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization soft independent modeling of class analogy analysis Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. Tina Hernandez-Boussard SIMCA WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies soft independent modeling of class analogy analysis discriminant function analysis Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant function analysis canonical variate analysis canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. Tina Hernandez-Boussard CVA WEB: http://en.wikipedia.org/wiki/Canonical_analysis canonical variate analysis linear discriminant functional analysis Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. Tina Hernandez-Boussard PERSON: Tina Hernandez-Boussard linear discriminant functional analysis regression analysis method 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. Tina Hernandez-Boussard BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 regression analysis method multiple linear regression analysis multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. Tina Hernandez-Boussard WEB:http://en.wikipedia.org/wiki/Linear_regression multiple linear regression analysis principal component regression 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. Tina Hernandez-Boussard WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html principal component regression partial least square regression analysis Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that Y = b0 + b1X1 + b2X2 + ... + bpXp In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. Tina Hernandez-Boussard PLS-RA ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. partial least square regression analysis discriminant analysis Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. Tina Hernandez-Boussard WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis partial least square discriminant analysis PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. James Malone PLS-DA WEB: http://www.camo.com/rt/Resources/pls-da.html partial least square discriminant analysis eh transformation This type of transformation is typically used in flow cytometry. An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf eh transformation b transformation This type of transformation is typically used in flow cytometry. A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf b transformation s transformation This type of transformation is typically used in flow cytometry. An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. Elisabetta Manduchi Joseph Spliden Ryan Brinkman WEB: http://flowcyt.sourceforge.net/gating/latest.pdf s transformation data visualization Generation of a heatmap from a microarray dataset A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization similarity calculation A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. Elisabetta Manduchi PERSON: Elisabetta Manduchi similarity calculation euclidean distance calculation An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. Elisabetta Manduchi PERSON: Elisabetta Manduchi euclidean distance calculation pearson correlation coefficient calculation A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. Elisabetta Manduchi PERSON: Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Correlation pearson correlation coefficient calculation loess fitting A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). Monnie McGee Philippe Rocca-Serra ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. loess fitting mode calculation 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. James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) mode calculation quantile calculation A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. Monnie McGee WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html quantile calculation median calculation 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. James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) median calculation variance calculation A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) variance calculation standard deviation calculation A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) standard deviation calculation interquartile-range calculation The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. Monnie McGee PERSON: Monnie McGee From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) interquartile-range calculation skewness calculation A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment Monnie McGee WEB: http://www.riskglossary.com/link/skewness.htm From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) skewness calculation kurtosis calculation A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html Monnie McGee WEB: http://davidmlane.com/hyperstat/A53638.html From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) kurtosis calculation data combination A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. Richard Scheuermann data pooling editor data combination network graph construction A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann network graph construction weighted network graph construction A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann weighted network graph construction directed network graph construction A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. Richard Scheuermann PERSON: Richard Scheuermann directed network graph construction node quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. Richard Scheuermann PERSON: Richard Scheuermann node quality calculation node degree calculation A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node degree calculation quantitative node degree calculation A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann quantitative node degree calculation node in-degree calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node in-degree calculation node out-degree calculation A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. Richard Scheuermann PERSON: Richard Scheuermann node out-degree calculation node shortest path identification A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. Richard Scheuermann PERSON: Richard Scheuermann node shortest path identification edge quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. Richard Scheuermann PERSON: Richard Scheuermann edge quality calculation edge betweenness calculation An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. Richard Scheuermann PERSON: Richard Scheuermann edge betweenness calculation network subgraph quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. Richard Scheuermann PERSON: Richard Scheuermann network subgraph quality calculation subgraph degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph degree calculation quantitative subgraph degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann quantitative subgraph degree calculation mathematical feature feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) James Malone PERSON: James Malone mathematical feature log base The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. Elisabetta Manduchi logarithm base logarithmic base WEB: http://en.wikipedia.org/wiki/Logarithm log base subgraph in-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph in-degree calculation subgraph out-degree calculation A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. Richard Scheuermann PERSON: Richard Scheuermann subgraph out-degree calculation intra subgraph connectivity calculation A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. Richard Scheuermann PERSON: Richard Scheuermann intra subgraph connectivity calculation subgraph modularity calculation A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. Richard Scheuermann PERSON: Richard Scheuermann subgraph modularity calculation network graph quality calculation A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. Richard Scheuermann PERSON: Richard Scheuermann network graph quality calculation unit-variance scaling A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. Elisabetta Manduchi Philippe Rocca-Serra autoscaling PMID:16762068 unit-variance scaling MA transformation MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. Elisabetta Manduchi Philippe Rocca-Serra PERSON: Elisabetta Manduchi MA transformation exponential base The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base polynomial degree The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. Elisabetta Manduchi PERSON: Elisabetta Manduchi polynomial degree number of variables The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. Elisabetta Manduchi PERSON: Elisabetta Manduchi number of variables agglomerative hierarchical clustering 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. Elisabetta Manduchi James Malone bottom-up hierarchical clustering PERSON: Elisabetta Manduchi agglomerative hierarchical clustering divisive hierarchical clustering 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. Elisabetta Manduchi James Malone top-down hierarchical clustering PERSON: Elisabetta Manduchi divisive hierarchical clustering data partitioning Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. James Malone PERSON: Melanie Courtot PERSON: Richard Scheuermann PERSON: Ryan Brinkman data partitioning data vector reduction objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. James Malone Richard H. Scheuermann PERSON: Richard H. Scheuermann data vector reduction objective generalized family wise error rate correction method A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. Monnie McGee gFWER correction Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 generalized family wise error rate correction method quantile number of false positives correction method A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' Monnie McGee QNFP Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 quantile number of false positives correction method tail probability for the proportion of false positives correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. Monnie McGee TPPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 tail probability for the proportion of false positives correction method false discovery rate correction method 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. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt Monnie McGee Philippe Rocca-Serra FDR correction method 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 false discovery rate correction method proportion of expected false positives correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. Monnie McGee PEFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 proportion of expected false positives correction method quantile proportion of false positives correction method A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). Monnie McGee QPFP correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 quantile proportion of false positives correction method data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective data normalization objective 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. 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. Elisabetta Manduchi Helen Parkinson James Malone PERSON: Elisabetta Manduchi PERSON: Helen Parkinson PERSON: James Malone data normalization objective correction objective Type I error correction 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 James Malone PERSON: James Malone PERSON: Melanie Courtot correction objective normalization data transformation A normalization data transformation is a data transformation that has objective normalization. James Malone PERSON: James Malone normalization data transformation averaging data transformation An averaging data transformation is a data transformation that has objective averaging. James Malone PERSON: James Malone averaging data transformation partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective background correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi background correction objective curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi curve fitting objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation Fisher's exact test Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. James Malone WEB:http://mathworld.wolfram.com/FishersExactTest.html Fisher's exact test center calculation objective 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. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone PERSON: James Malone center calculation objective class discovery objective 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. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective spread calculation objective Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set. Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson spread calculation objective center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. James Malone PERSON: James Malone center calculation data transformation data vector reduction data transformation A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. James Malone PERSON: James Malone data vector reduction data transformation scaling objective Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone Person:Helen Parkinson scaling objective descriptive statistical calculation data transformation 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. James Malone PERSON: James Malone descriptive statistical calculation data transformation scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation error correction objective Application of a multiple testing correction method 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. James Malone, Helen Parkinson PERSON: James Malone error correction objective sequence analysis data transformation A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. James Malone EDITOR sequence analysis data transformation cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective merging objective merging of columns from two different data sets A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. James Malone combining objective PERSON: Data Transformation Branch merging objective clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization gene list visualization 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. James Malone gene list visualization classified data visualization A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. James Malone classified data visualization background corrected data visualization A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. James Malone Monnie McGee background corrected data visualization survival analysis data transformation A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation proportional hazards model estimation Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. PERSON: James Malone PERSON: Tina Boussard Cox model Cox proportional hazards model WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model proportional hazards model estimation correlation study objective A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. PERSON: Tina Boussard correlation study objective spectrum analysis objective Calculation of characteristic path length in mass spectrometry is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. PERSON: Tina Boussard Person:Helen Parkinson spectrum analysis objective gas chromatography mass spectrometry Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. PERSON: James Malone PERSON: Tina Boussard PERSON: Tina Boussard gas chromatography mass spectrometry chi square test 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. PERSON: James Malone PERSON: Tina Boussard chi square test ANOVA A statistical hypothesis test in which the means of several groups are all equal. James Malone https://en.wikipedia.org/wiki/Analysis_of_variance ANOVA sequential design PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does Philippe Rocca-Serra MUSC Provenance: OCI sequential design observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived observation design genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 an organism that is the output of a genetic transformation process PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism predicted data item A data item that was generated on the basis of a calculation or logical reasoning BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. Philippe Rocca-Serra; Bjoern Peters predicted data item mean-centered data a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value Person:Helen Parkinson Person:Philippe Rocca-Serra mean-centered data extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder 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. Person:Bjoern Peters Philippe Rocca-Serra extraction group randomization PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 a process by which an event or an entity is described before it actually happens or is being discovered and identified. Philippe Rocca-Serra OBI prediction computer Apple PowerBook, Dell OptiPlex A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Melanie Courtot Trish Whetzel http://en.wikipedia.org/wiki/Computer computer study design 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. 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. 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. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design repeated measure design 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. 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 PlanAndPlannedProcess Branch http://www.holah.karoo.net/experimentaldesigns.htm repeated measure design cross over design 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. 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 Philippe Rocca-Serra (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) cross over design n-to-1 design N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). Philippe Rocca-Serra Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) n-to-1 design randomized complete block design 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)) 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. Philippe Rocca-Serra http://www.tufts.edu/~gdallal/ranblock.htm randomized complete block design latin square design 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. 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. Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and latin square design graeco latin square design 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. Greco-Latin square design is a study design which relates to Latin square design Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and only 2 articles in pubmed ->probably irrelevant graeco latin square design hyper graeco latin square design PRS to do Philippe Rocca-Serra Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and no example found in pubmed->not in use in the community hyper graeco latin square design replicate design A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Philippe Rocca-Serra on behalf of MO MO_885 replicate design time series design 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. Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 time series design collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism material component separation 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 a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation group assignment 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 group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra cohort assignment study assignment OBI Plan group assignment maintaining cell culture 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 A planned process with the objective to keep cells alive in a defined environment outside of an organism. PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture 'establishing cell culture' 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). PERSON:Matthew Brush PERSON:Matthew Brush 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. establishing cell culture genetic transformation The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 the introduction. alteration or integration of genetic material into a cell or organism PERSON:Kevin Clancy genetic modification OBI branch derived genetic transformation nucleic acid extraction 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. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction bodily fluid specimen A specimen that is derived from some bodily fluid Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen umbilical cord blood specimen A specimen that is derived from some umbilical cord blood Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 umbilical cord blood specimen arterial blood specimen A specimen that is derived from some arterial blood Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066 arterial blood specimen The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis A data item that is about a patient and is the specified output of a health care process assay or diagnostic process creation date: 2018-11-27 clinical data item A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000072 quality PATO:0000001 quality A time quality inhering in a bearer by virtue of how long the bearer has existed. quality PATO:0000011 age A 1-D extent quality which is equal to the distance between two points. https://github.com/pato-ontology/pato/issues/337 quality PATO:0000122 Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. length A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. quality PATO:0000125 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. mass A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. quality PATO:0000169 viability A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A viability quality inhering in a bearer by virtue of the bearer's condition before death. quality PATO:0001421 alive A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. quality PATO:0001422 dead A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. 2010-03-22T05:48:33Z quality PATO:0002201 Adapted from Wikipedia and the birnlex term that is dbxref'd. Added on behalf of OBI at March 2010 workshop. handedness A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein PR:000050567 Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). protein-containing material entity 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. sequence sequence SO:0000001 region One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. sequence scaffold SO:0000148 supercontig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. http://en.wikipedia.org/wiki/Contig sequence SO:0000149 contig A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. http://en.wikipedia.org/wiki/Sequence_assembly sequence assembly sequence SO:0000353 sequence_assembly A region of the genome of known length that is composed by ordering and aligning two or more different regions. http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly sequence SO:0001248 assembly A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. experimental output artefact experimental_output_artefact sequence analysis feature SO:0001410 experimental_feature 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. Wilk's lambda distribution 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. studentized range distribution 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. MA plot one-way anova is an analysis of variance where the different groups being compared are associated with the factor levels of only one independent variable. 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. one-way ANOVA two-way anova is an analysis of variance where the different groups being compared are associated the factor levels of exatly 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. two-way ANOVA 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. multiway ANOVA 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] null hypothesis 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 hypergeometric distribution 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 Cleveland dot plot 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) paired t-test 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. multinomial distribution 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. Funnel plot 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. bean plot a pedigree chart is a graph which plots parent child relations pedigree chart 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 r2 measure of linkage desequilibrium 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. Wilkinson dot plot 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. volcano plot 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. Altman box and whisker plot 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. Hotelling T2 distribution 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. correlation coefficient 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. geometric distribution Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap LD plot 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. violin plot 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. stacked bar chart 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. pie chart the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent. bar chart 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 real time quantitative pcr plot 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. Spear box and whisker plot A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question. Forest plot 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 beta distribution standard normal distribution is a normal distribution with variance = 1 and mean=0 standard normal distribution 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 Lineweaver-Burk plot 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 Spearman's rank correlation coefficient 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 within subject comparison statistical test a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables. tetrachoric correlation coefficient 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 RT-PCR standard curve 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) Kendall's correlation coefficient 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 Q-Q plot a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers. box and whisker plot 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. manhattan plot for gwas 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. repeated measure ANOVA 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 Bernoulli distribution 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). Galbraith plot 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. grouped bar chart 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. polychoric correlation coefficient 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) receiver operational characteristics curve 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. Pearson's correlation coefficient 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. negative binomial distribution 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. one tailed test 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). two tailed test 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. Matthews correlation coefficient Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure anatomical structure Anatomical structure that performs a specific function or group of functions [WP]. BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) anatomical unit body organ element organ A multicellular structure that is a part of an organ. AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part regional part of organ organ part An section of a respiratory tract. EMAPA:16737 FMA:45660 MA:0000434 respiratory tract subdivision of respiratory tract proximo-distal subdivision of respiratory tract A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance excretion excreta A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood whole blood blood A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 SCTID:361693009 UMLS:C0026724 Wikipedia:Mucous_membrane galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa region of mucosa tunica mucosa mucosa Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance organism substance Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 material anatomical entity Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 IDOMAL:0002461 VHOG:0001737 anatomical cluster Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue tissue Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 Wikipedia:Pleural_fluid ncithesaurus:Pleural_Fluid pleural fluid Excretion that is the output of a kidney. BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 UMLS:C0042036 Wikipedia:Urine galen:Urine urine A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:D002555 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 Wikipedia:Cerebrospinal_fluid ZFA:0001626 CSF cerebral spinal fluid liquor cerebrospinalis spinal fluid cerebrospinal fluid The part of the forelimb extending from the shoulder to the autopod[cjm]. BTO:0001435 CALOHA:TS-2204 EFO:0001410 EHDAA2:0000140 EHDAA:4164 EHDAA:6210 EHDAA:8275 EMAPA:17413 GAID:52 MA:0000033 MESH:D001132 VHOG:0000339 Wikipedia:Arm brachium upper extremity arm The section of the pharynx that lies above the soft palate. BTO:0000662 CALOHA:TS-0663 EHDAA2:0001239 EHDAA:7086 EMAPA:17670 EV:0100066 FMA:54878 GAID:339 MA:0000443 MAT:0000447 MESH:D009305 NCIT:C12423 SCTID:181200003 UMLS:C0027442 VHOG:0000375 Wikipedia:Nasopharynx nasal part of pharynx rhinopharynx Nasenrachenraum epipharynx pars nasalis pharyngis nasopharynx The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. BTO:0005257 CALOHA:TS-0718 EFO:0001976 EHDAA2:0004082 EMAPA:25094 EV:0100067 FMA:54879 GAID:340 MA:0000351 MAT:0000446 MESH:D009960 NCIT:C12762 SCTID:263376008 UMLS:C0521367 VHOG:0000457 VSAO:0000034 Wikipedia:Oropharynx XAO:0004048 oral part of pharynx mesopharynx pars oralis pharyngis oropharynx The mucous membrane that lines the nasal cavity[MP]. BTO:0000912 CALOHA:TS-0657 EMAPA:36026 FMA:59684 GAID:302 SCTID:310211009 Wikipedia:Mucous_membrane_of_nose mucosa of nose mucous membrane of nose tunica mucosa nasalis tunica mucosa nasi nasal mucosa nasal cavity mucosa An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. BTO:0000868 CALOHA:TS-0636 EMAPA:36540 ENVO:02000031 EV:0100126 FMA:62100 GAID:1230 MA:0002552 MAT:0000056 MESH:D008892 MIAA:0000056 NCIT:C13401 UMLS:C1511310 VHOG:0001263 Wikipedia:Breast_milk galen:Milk mammary gland milk milk Portion of semisolid bodily waste discharged through the anus[MW,modified]. excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 UMLS:C0015733 Wikipedia:Feces galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint droppings excrement ordure spoor feces Respiration organ that develops as an outpocketing of the esophagus. AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 SCTID:181216001 UMLS:C0024109 VHOG:0000310 Wikipedia:Lung XAO:0000119 galen:Lung pulmo lung The organ covering the body that consists of the dermis and epidermis. BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 SCTID:181469002 UMLS:C1123023 Wikipedia:Skin XAO:0000023 galen:Skin entire skin skin organ entire integument integument integumental organ pelt skin skin of body The soft tissue that fills the cavities of bones. AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 SCTID:421320006 UMLS:C0005953 VHOG:0001218 Wikipedia:Bone_marrow XAO:0000123 galen:BoneMarrow medulla ossea medulla ossium medulla of bone medullary bone bone marrow An anatomical structure that develops (entirely or partially) from the endoderm. endoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative ectoderm-derived structure Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 Wikipedia:Body_fluid galen:BodyFluid body fluid bodily fluid A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 respiratory system fluid respiratory system secretion respiratory system fluid/secretion Matter ejected from the lungs, bronchi, and trachea, through the mouth. BTO:0001297 CALOHA:TS-0963 EMAPA:36553 FMA:312401 GAID:1171 MA:0002536 MESH:D013183 NCIT:C13278 UMLS:C0038056 expectoration sputum Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate plasma ultrafiltrate transudate An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure multicellular anatomical structure Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. BTO:0004053 CALOHA:TS-1079 EFO:0001942 MESH:D005312 Wikipedia:Cord_blood cord blood fetal blood umbilical cord blood umbilical cord blood subdivision of tube A blood that is part of a artery. BTO:0006188 FMA:83066 arterial blood blood in artery portion of arterial blood arterial blood Blood located in the placenta. placental blood length unit mass unit time derived unit time unit temperature derived unit temperature unit concentration unit example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete 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. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release 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." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting 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. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core true placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion 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. Alan Ruttenberg group:OBI requires discussion An confidence interval with 95 percent probability that the true population value can be found. Jie Zheng 95% confidence interval right handed right handed ambidexterous ambidexterous left handed left handed The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). https://github.com/information-artifact-ontology/ontology-metadata/issues/136 https://orcid.org/0000-0002-4142-7153 domain entity does not exist