<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obofoundry.org/obo/"
xml:base="http://purl.obofoundry.org/obo/iao/2009-01-23/iao.owl"
xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
xmlns:obo="http://purl.obofoundry.org/obo/"
xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:owl2="http://www.w3.org/2006/12/owl2#"
xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:span="http://www.ifomis.org/bfo/1.1/span#"
xmlns:daml="http://www.daml.org/2001/03/daml+oil#">
<owl:Ontology rdf:about="">
<protege:defaultLanguage rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
<owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
<rdfs:comment
>a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon.</rdfs:comment>
<owl:imports>
<owl:Ontology rdf:about="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
</owl:imports>
<owl:imports>
<owl:Ontology rdf:about="http://purl.obofoundry.org/obo/iao/2009-01-23/ontology-metadata.owl"/>
</owl:imports>
<owl:imports>
<owl:Ontology rdf:about="http://www.ifomis.org/bfo/1.1"/>
</owl:imports>
<owl:imports>
<owl:Ontology rdf:about="http://www.obofoundry.org/ro/ro.owl"/>
</owl:imports>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
<owl:AnnotationProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000114"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obofoundry.org/obo/IAO_0000039 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000039">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:label
>has measurement unit label</rdfs:label>
<rdfs:range rdf:resource="http://purl.obofoundry.org/obo/IAO_0000003"/>
<rdfs:subPropertyOf rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000135 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000135">
<rdfs:label
>specifically denotes</rdfs:label>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000125"/>
<IAO_0000115
>c specifically denotes r =def
r is a portion of reality
& c is a particular quality
& c depends specifically on some independent continuant b
& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly.
Marked means there is a changed or additional quality of the bearer - the quality is the information carrier.
Case 1
Memory trace as mark created when reading some description of some friend. The trace can denote.
Case 2
Pattern of ink arrayed on paper as mark when writing down a friend's name
Case 3
Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.</IAO_0000115>
<IAO_0000119
>Smith, Ceusters, Ruttenberg, 2000 years of philosophy</IAO_0000119>
<IAO_0000117>Alan Ruttenberg</IAO_0000117>
<IAO_0000112
>The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.
Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.
c = pattern in the ink
b = paper + ink
r = friend</IAO_0000112>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000136">
<rdfs:label>is about</rdfs:label>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000125"/>
<IAO_0000117
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000112
>This document is about information artifacts and their representations</IAO_0000112>
<IAO_0000115
>a representation is_about anything exactly when some part of the information_artifact denotes the entity</IAO_0000115>
<IAO_0000119
>Smith, Ceusters, Ruttenberg, 2000 years of philosophy</IAO_0000119>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000219 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000219">
<rdfs:label
>generically denotes</rdfs:label>
<IAO_0000119
>Smith, Ceusters, Ruttenberg, 2000 years of philosophy</IAO_0000119>
<IAO_0000112
>The word Boston on a traffic signn in Massachusetts generically denotes the city of Boston</IAO_0000112>
<IAO_0000115
>g generically 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</IAO_0000115>
<IAO_0000117
>person:Alan Ruttenberg</IAO_0000117>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000220 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000220">
<rdfs:label
>materially denotes</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000221 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000221">
<rdfs:label
>is quality measurement of</rdfs:label>
<IAO_0000115
>m is a quality measurement of q at t when
q is a determinable quality
there is a measurement process p that has_output m
m has a value part that together with the units of the value of q at t.
p is a assay
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.
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.
unit of measure is a quality, e.g. the length of a ruler.
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
Example:
q = height of barry
p is the process using a tape measure extend across the longer part of barry and reading off the number at the far end.
v is that number
# dimension is height
unit of measure is inches
We have had a long discussion about denotes versus describes.</IAO_0000115>
<IAO_0000116
>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.</IAO_0000116>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000222 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000222">
<rdfs:label>describes</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://purl.obofoundry.org/obo/IAO_0000223 -->
<owl:ObjectProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000223">
<rdfs:label>represents</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#has_part -->
<owl:ObjectProperty rdf:about="http://www.obofoundry.org/ro/ro.owl#has_part"/>
<!-- http://www.obofoundry.org/ro/ro.owl#part_of -->
<owl:ObjectProperty rdf:about="http://www.obofoundry.org/ro/ro.owl#part_of">
<IAO_0000116
>There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else</IAO_0000116>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obofoundry.org/obo/IAO_0000004 -->
<owl:DatatypeProperty rdf:about="http://purl.obofoundry.org/obo/IAO_0000004">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
<rdfs:label
>has measurement value</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obofoundry.org/obo/IAO_0000001 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000001">
<rdfs:label xml:lang="en"
>conditional specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000033"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119 xml:lang="en"
>OBI branch derived</IAO_0000119>
<IAO_0000119>OBI_0000349</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PlanAndPlannedProcess Branch</IAO_0000117>
<IAO_0000111 xml:lang="en"
>instruction trigger</IAO_0000111>
<IAO_0000115 xml:lang="en"
>is information about a realizable that specifies that what should happen if the trigger condition is fulfilled</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000003 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000003">
<rdfs:label xml:lang="en"
>measurement unit label</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000009"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000116
>remove? See unit of measure.</IAO_0000116>
<IAO_0000119>OBI_0000176</IAO_0000119>
<IAO_0000115
>A measurement unit label is an label that is part of a measurement datum and denotes a unit of measure.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>Examples of measurement unit labels are liters, inches, weight per volume.</IAO_0000112>
<IAO_0000111 xml:lang="en"
>measurement unit label</IAO_0000111>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000005 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000005">
<rdfs:label xml:lang="en"
>objective specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000033"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000117>Barry Smith</IAO_0000117>
<IAO_0000119>OBI_0000217</IAO_0000119>
<IAO_0000117>Alan Ruttenberg</IAO_0000117>
<IAO_0000115 xml:lang="en"
>An objective specification is an information entity about a realizable entity that describes a 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.</IAO_0000115>
<IAO_0000116 xml:lang="en"
>Answers the question, why did you do this experiment?</IAO_0000116>
<IAO_0000117>Jennifer Fostel</IAO_0000117>
<IAO_0000119 xml:lang="en"
>OBI Plan and Planned Process/Roles Branch</IAO_0000119>
<IAO_0000111 xml:lang="en"
>objective specification</IAO_0000111>
<IAO_0000112 xml:lang="en"
>purpose of a study; support of hypothesis, discovery of new information</IAO_0000112>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000006 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000006">
<rdfs:label xml:lang="en"
>narrative object</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000013</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A narrative object is an information content entity that is a set of propositions.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>Examples of narrative objects are reports, journal articles, and patents submission.</IAO_0000112>
<IAO_0000116 xml:lang="en"
>agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions</IAO_0000116>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000111 xml:lang="en"
>narrative object</IAO_0000111>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000007 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000007">
<rdfs:label
>action specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000033"/>
<IAO_0000117 xml:lang="en">Alan Ruttenberg</IAO_0000117>
<IAO_0000115 xml:lang="en"
>An action specification is information about a realizable that describes an action the bearer will take</IAO_0000115>
<IAO_0000119 xml:lang="en"
>OBI Plan and Planned Process branch</IAO_0000119>
<IAO_0000112 xml:lang="en"
>Pour the contents of flask 1 into flask 2</IAO_0000112>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000008 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000008">
<rdfs:label xml:lang="en">artifact</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115
>An artifact is an independent continuant that is the intended output of an objective driven process</IAO_0000115>
<IAO_0000116
>There is not yet consensus this term</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000009 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000009">
<rdfs:label>label</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000027"/>
<IAO_0000116
>http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n</IAO_0000116>
<IAO_0000115
>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</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000010 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000010">
<rdfs:label xml:lang="en">software</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000104"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000120"/>
<IAO_0000119 xml:lang="en">GROUP: OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PERSON: Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON: Bjoern Peters</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON: Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON: Melanie Courtot</IAO_0000117>
<IAO_0000115 xml:lang="en"
>Series of encoded instructions that can be directly executed by a CPU, or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.</IAO_0000115>
<IAO_0000116 xml:lang="en"
>see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178</IAO_0000116>
<IAO_0000111 xml:lang="en">software</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000012 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000012">
<rdfs:label xml:lang="en">digital entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000141"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.</IAO_0000115>
<IAO_0000119>OBI_0000261</IAO_0000119>
<IAO_0000111 xml:lang="en">digital entity</IAO_0000111>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000013 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000013">
<rdfs:label xml:lang="en"
>journal article content</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000088"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000115 xml:lang="en"
>Journal article content is a narrative object that is the information content encoded in a article published in a serious, scholarly publication, most often peer-reviewed.</IAO_0000115>
<IAO_0000119>OBI_0000159</IAO_0000119>
<IAO_0000112 xml:lang="en"
>Examples of encodings of journal article content are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.</IAO_0000112>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000111 xml:lang="en"
>journal article content</IAO_0000111>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000015 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000015">
<rdfs:label
>information carrier</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000125"/>
<IAO_0000117>Alan Ruttenberg</IAO_0000117>
<IAO_0000115
>an information carrier is that quality of an information bearer that imparts the information content</IAO_0000115>
<IAO_0000112
>The pattern in ink on a page of a paperback novel.</IAO_0000112>
<IAO_0000119
>Smith, Ceusters, Ruttenberg, 2000 years of philosophy</IAO_0000119>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000019 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000019">
<rdfs:label xml:lang="en"
>binary digital entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000012"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000244</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>MS Word document, ZIP file, DICOM file, JPEG file</IAO_0000112>
<IAO_0000111 xml:lang="en"
>binary digital entity</IAO_0000111>
<IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000024 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000024">
<rdfs:label>unit of measure</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000125"/>
<IAO_0000117>Alan Ruttenberg</IAO_0000117>
<IAO_0000112
>The length of a ruler.</IAO_0000112>
<IAO_0000115
>a unit of measure is the quality of some material entity compared to which another quality is some multiple of.</IAO_0000115>
<IAO_0000119
>Smith, Ceusters, Ruttenberg, 2000 years of philosophy</IAO_0000119>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000025 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000025">
<rdfs:label xml:lang="en"
>programming language</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000104"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000058</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.</IAO_0000115>
<IAO_0000112 xml:lang="en">R, Perl, Java</IAO_0000112>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
<IAO_0000111 xml:lang="en"
>programming language</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000027 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000027">
<rdfs:label xml:lang="en">data item</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<IAO_0000116 xml:lang="en"
>JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief</IAO_0000116>
<IAO_0000115
>a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.</IAO_0000115>
<IAO_0000117>Jonathan Rees</IAO_0000117>
<IAO_0000118 xml:lang="en">data</IAO_0000118>
<IAO_0000118 xml:lang="en">datum</IAO_0000118>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000028 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000028">
<rdfs:label>symbol</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000027"/>
<IAO_0000117>Jonathan Rees</IAO_0000117>
<IAO_0000116
>a smallish, word-like datum...</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000029 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000029">
<rdfs:label>numeral</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000028"/>
<IAO_0000117>Jonathan Rees</IAO_0000117>
<IAO_0000116
>a symbol that denotes a number</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000030">
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://www.ifomis.org/bfo/1.1#Entity"/>
</owl:Restriction>
</rdfs:subClassOf>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000112 xml:lang="en"
>Examples of information content entites include journal articles, data, graphical layouts, and graphs.</IAO_0000112>
<IAO_0000119>OBI_0000142</IAO_0000119>
<IAO_0000115 xml:lang="en"
>an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity</IAO_0000115>
<IAO_0000111 xml:lang="en"
>information content entity</IAO_0000111>
<IAO_0000116 xml:lang="en"
>information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000031 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000031">
<rdfs:label>integer numeral</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000029"/>
<IAO_0000117>Jonathan Rees</IAO_0000117>
<IAO_0000115
>a numeral that denotes an integer</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000032 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000032">
<rdfs:label
>scalar measurement datum</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000109"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obofoundry.org/obo/IAO_0000039"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obofoundry.org/obo/IAO_0000004"/>
<owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
</owl:Restriction>
</rdfs:subClassOf>
<IAO_0000116
>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.</IAO_0000116>
<IAO_0000115
>a scalar measurement datum is a measurement datum that is composed of two parts, a single numeral and a unit label.</IAO_0000115>
<IAO_0000112>10 feet. 3 ml.</IAO_0000112>
<IAO_0000117 xml:lang="en">Alan Ruttenberg</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000033 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000033">
<rdfs:label xml:lang="en"
>information entity about a realizable</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obofoundry.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://www.ifomis.org/bfo/1.1/snap#RealizableEntity"/>
</owl:Restriction>
</rdfs:subClassOf>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000116
>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</IAO_0000116>
<IAO_0000115
>An information entity about a realizable is an information content entity about a realizable.</IAO_0000115>
<IAO_0000117 xml:lang="en">Alan Ruttenberg</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000034 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000034">
<rdfs:label xml:lang="en">time trigger</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000001"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119 xml:lang="en"
>OBI branch derived</IAO_0000119>
<IAO_0000119>OBI_0000331</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PlanAndPlannedProcess Branch</IAO_0000117>
<IAO_0000115 xml:lang="en">revisit?</IAO_0000115>
<IAO_0000111 xml:lang="en">time trigger</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000035 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000035">
<rdfs:label xml:lang="en">conclusion</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000006"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000005</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.</IAO_0000115>
<IAO_0000117 xml:lang="en">Jennifer Fostel</IAO_0000117>
<IAO_0000111 xml:lang="en">conclusion</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000037 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000037">
<rdfs:label xml:lang="en">dot plot</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000119>OBI_0000123</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>Dot plot of SSC-H and FSC-H.</IAO_0000112>
<IAO_0000111 xml:lang="en">dot plot</IAO_0000111>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en">person:Allyson</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000038 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000038">
<rdfs:label xml:lang="en">report graph</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000059"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000240</IAO_0000119>
<IAO_0000119>group:OBI</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A report graph is a report figure that presents one or more tuples of information my mapping those tuples in to a two dimensional space in a non arbitrary way.</IAO_0000115>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Allyson Lister</IAO_0000117>
<IAO_0000111 xml:lang="en">report graph</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000047 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000047">
<rdfs:label xml:lang="en"
>text based digital entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000105"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A text based digital entity is a digital entity that is encoded so that it only contains text characters.</IAO_0000115>
<IAO_0000119>OBI_0000132</IAO_0000119>
<IAO_0000112 xml:lang="en"
>XML file, C++ source code file</IAO_0000112>
<IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
<IAO_0000119>group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
<IAO_0000111 xml:lang="en"
>text based digital entity</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000055 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000055">
<rdfs:label xml:lang="en">rule</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000001"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0500021</IAO_0000119>
<IAO_0000116 xml:lang="en">MSI</IAO_0000116>
<IAO_0000119 xml:lang="en">PRS</IAO_0000119>
<IAO_0000117 xml:lang="en">PRS</IAO_0000117>
<IAO_0000115 xml:lang="en"
>a rule is an executable which guides, defines, restricts actions</IAO_0000115>
<IAO_0000112 xml:lang="en"
>example to be added</IAO_0000112>
<IAO_0000111 xml:lang="en">rule</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000057 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000057">
<rdfs:label xml:lang="en">contour plot</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000119>OBI_0000246</IAO_0000119>
<IAO_0000112 xml:lang="en"
>Contour plot of SSC-H, FSC-H, and FL1-H.</IAO_0000112>
<IAO_0000111 xml:lang="en">contour plot</IAO_0000111>
<IAO_0000116 xml:lang="en"
>generically_dependent_continuants</IAO_0000116>
<IAO_0000119 xml:lang="en"
>group:Flow Cytometry community</IAO_0000119>
<IAO_0000117 xml:lang="en">person:Allyson</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000059 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000059">
<rdfs:label xml:lang="en">report figure</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000091"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements</IAO_0000115>
<IAO_0000116 xml:lang="en"
>I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report</IAO_0000116>
<IAO_0000119>OBI_0000027</IAO_0000119>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Allyson Lister</IAO_0000117>
<IAO_0000111 xml:lang="en">report figure</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000064 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000064">
<rdfs:label xml:lang="en">algorithm</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000104"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000270</IAO_0000119>
<IAO_0000112 xml:lang="en"
>PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.</IAO_0000112>
<IAO_0000117 xml:lang="en"
>Philippe Rocca-Serra</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PlanAndPlannedProcess Branch</IAO_0000117>
<IAO_0000119 xml:lang="en"
>adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)</IAO_0000119>
<IAO_0000111 xml:lang="en">algorithm</IAO_0000111>
<IAO_0000115 xml:lang="en"
>an algorithm is a plan which describes inputs, 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.</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000065 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000065">
<rdfs:label
>software interpreter</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000064"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000199</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A software interpreter is a generically dependent realizable entity that takes, as input, some digital entity, and takes action driven by the information content of that digital entity</IAO_0000115>
<IAO_0000116 xml:lang="en"
>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</IAO_0000116>
<IAO_0000112 xml:lang="en"
>R program, Perl interpreter, Java virtual machine</IAO_0000112>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
<IAO_0000111 xml:lang="en"
>software interpreter</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000079 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000079">
<rdfs:label xml:lang="en">density plot</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000119>OBI_0000179</IAO_0000119>
<IAO_0000115 xml:lang="en"
>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.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>Density plot of SSC-H and FSC-H.</IAO_0000112>
<IAO_0000111 xml:lang="en">density plot</IAO_0000111>
<IAO_0000119 xml:lang="en"
>group:Flow Cytometry community</IAO_0000119>
<IAO_0000117 xml:lang="en">person:Allyson</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000088 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000088">
<rdfs:label xml:lang="en"
>report of results</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000006"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000112 xml:lang="en"
>Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.</IAO_0000112>
<IAO_0000119>OBI_0000099</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.</IAO_0000115>
<IAO_0000116 xml:lang="en"
>disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification</IAO_0000116>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
<IAO_0000111 xml:lang="en"
>report of results</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000091 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000091">
<rdfs:label xml:lang="en"
>report display element</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000006"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.</IAO_0000115>
<IAO_0000119>OBI_0000001</IAO_0000119>
<IAO_0000116 xml:lang="en"
>There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text</IAO_0000116>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Allyson Lister</IAO_0000117>
<IAO_0000111 xml:lang="en"
>report display element</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000093 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000093">
<rdfs:label xml:lang="en"
>binary executable</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000012"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)</IAO_0000115>
<IAO_0000119>OBI_0000222</IAO_0000119>
<IAO_0000111 xml:lang="en"
>binary executable</IAO_0000111>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Jennifer Fostel</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000096 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000096">
<rdfs:label xml:lang="en"
>source code module</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000039</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A source code module is an information content entity that specifies, using a programming language, some algorithm.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.</IAO_0000112>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
<IAO_0000111 xml:lang="en"
>source code module</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000097 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000097">
<rdfs:label xml:lang="en">report table</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000091"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000002"/>
<IAO_0000115 xml:lang="en"
>A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content</IAO_0000115>
<IAO_0000119>OBI_0000265</IAO_0000119>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Alan Ruttenberg</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Allyson Lister</IAO_0000117>
<IAO_0000111 xml:lang="en">report table</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000098 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000098">
<rdfs:label xml:lang="en"
>data format specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000033"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000187</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A data format specification is the information content borne by the document published defining the specification.
blah:
for organizing information artifacts. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file</IAO_0000115>
<IAO_0000119 xml:lang="en"
>OBI branch derived</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PlanAndPlannedProcess Branch</IAO_0000117>
<IAO_0000111 xml:lang="en"
>data format specification</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000100 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000100">
<rdfs:label xml:lang="en">data set</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000042</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A data set is an information content entity that is an aggregate of other information_content_entities that have something in common and are considered to form a unit.</IAO_0000115>
<IAO_0000111 xml:lang="en">data set</IAO_0000111>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en">person:Allyson</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000101 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000101">
<rdfs:label xml:lang="en">image</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000030"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000030</IAO_0000119>
<IAO_0000115 xml:lang="en"
>An image is an information content entity which provides a visual representation of for the result of a measurement.</IAO_0000115>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000111 xml:lang="en">image</IAO_0000111>
<IAO_0000117 xml:lang="en">person:Allyson</IAO_0000117>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000104 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000104">
<rdfs:label xml:lang="en"
>plan specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000033"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
<owl:someValuesFrom rdf:resource="http://purl.obofoundry.org/obo/IAO_0000005"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
<owl:someValuesFrom rdf:resource="http://purl.obofoundry.org/obo/IAO_0000007"/>
</owl:Restriction>
</rdfs:subClassOf>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000119>OBI_0000344</IAO_0000119>
<IAO_0000115 xml:lang="en"
>A plan specification is an information entity about a realizable entity. The specification includes parts such as objective specification, action specifications and conditional specifications. When concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.</IAO_0000115>
<IAO_0000117 xml:lang="en">Alan Ruttenberg</IAO_0000117>
<IAO_0000116 xml:lang="en"
>Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved</IAO_0000116>
<IAO_0000119 xml:lang="en"
>OBI Plan and Planned Process branch</IAO_0000119>
<IAO_0000112 xml:lang="en"
>PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.</IAO_0000112>
<IAO_0000111 xml:lang="en"
>plan specification</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000105 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000105">
<rdfs:label xml:lang="en"
>digital document</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000012"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.</IAO_0000115>
<IAO_0000119>OBI_0000195</IAO_0000119>
<IAO_0000111 xml:lang="en"
>digital document</IAO_0000111>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>person:Jennifer Fostel</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000109 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000109">
<rdfs:label xml:lang="en"
>measurement datum</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000027"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115 xml:lang="en"
>A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument.</IAO_0000115>
<IAO_0000119>OBI_0000305</IAO_0000119>
<IAO_0000112 xml:lang="en"
>Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.</IAO_0000112>
<IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
<IAO_0000111 xml:lang="en"
>measurement datum</IAO_0000111>
<IAO_0000117 xml:lang="en"
>person:Chris Stoeckert</IAO_0000117>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000128 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000128">
<rdfs:label>_identifier</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000121"/>
<IAO_0000116
>_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000129 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000129">
<rdfs:label>version number</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000128"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115
>A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.</IAO_0000115>
<IAO_0000116
>Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000131 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000131">
<rdfs:label>serial number</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000128"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000115
>A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.</IAO_0000115>
<IAO_0000116
>Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000132 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000132">
<rdfs:label>lot number</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000128"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000118>batch number</IAO_0000118>
<IAO_0000115
>A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000140 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000140">
<rdfs:label>setting datum</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000027"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000124"/>
<IAO_0000116
>Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.</IAO_0000116>
<IAO_0000115
>A settings datum is a datum that denotes some configuration of an instrument.</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000141 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000141">
<rdfs:label>digital quality</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000121"/>
<IAO_0000116
>Need to rework digital entity. Digital quality was suggested by Barry.</IAO_0000116>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000178 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000178">
<rdfs:label
>material information bearer</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
<IAO_0000115
>An information bearer is an artifact, such as a hard drive, upon which an information content entity generically depends.</IAO_0000115>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000179 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000179">
<rdfs:label xml:lang="en">histogram</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>A histogram is a report graph which is a statistical description of a
distribution in terms of occurrence frequencies of different event classes.</IAO_0000115>
<IAO_0000119 xml:lang="en">GROUP:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000111 xml:lang="en">histogram</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000180 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000180">
<rdfs:label xml:lang="en">heatmap</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>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.</IAO_0000115>
<IAO_0000119 xml:lang="en">GROUP:OBI</IAO_0000119>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000111 xml:lang="en">heatmap</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000181 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000181">
<rdfs:label xml:lang="en">Venn diagram</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>A Venn diagram is a report graph showing all hypothetically possible
logical relations between a finite collection of sets.</IAO_0000115>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000111 xml:lang="en">Venn diagram</IAO_0000111>
<IAO_0000119 xml:lang="en"
>WEB: http://en.wikipedia.org/wiki/Venn_diagram</IAO_0000119>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000182 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000182">
<rdfs:label xml:lang="en">survival curve</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.</IAO_0000115>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000119 xml:lang="en"
>WEB: http://www.graphpad.com/www/book/survive.htm</IAO_0000119>
<IAO_0000111 xml:lang="en">survival curve</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000183 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000183">
<rdfs:label xml:lang="en">dendrogram</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>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.</IAO_0000115>
<IAO_0000112 xml:lang="en"
>Dendrograms are often used in computational biology to
illustrate the clustering of genes.</IAO_0000112>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000119 xml:lang="en"
>WEB: http://en.wikipedia.org/wiki/Dendrogram</IAO_0000119>
<IAO_0000111 xml:lang="en">dendrogram</IAO_0000111>
</owl:Class>
<!-- http://purl.obofoundry.org/obo/IAO_0000184 -->
<owl:Class rdf:about="http://purl.obofoundry.org/obo/IAO_0000184">
<rdfs:label xml:lang="en">scatterplot</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obofoundry.org/obo/IAO_0000038"/>
<IAO_0000114 rdf:resource="http://purl.obofoundry.org/obo/IAO_0000122"/>
<IAO_0000115 xml:lang="en"
>A scatterplot is a report 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.</IAO_0000115>
<IAO_0000117 xml:lang="en"
>PERSON:Chris Stoeckert</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:James Malone</IAO_0000117>
<IAO_0000117 xml:lang="en"
>PERSON:Melanie Courtot</IAO_0000117>
<IAO_0000119 xml:lang="en"
>WEB: http://en.wikipedia.org/wiki/Scatterplot</IAO_0000119>
<IAO_0000118 xml:lang="en">scattergraph</IAO_0000118>
<IAO_0000111 xml:lang="en">scatterplot</IAO_0000111>
</owl:Class>
<!-- http://www.ifomis.org/bfo/1.1#Entity -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1#Entity"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#FiatObjectPart -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#FiatObjectPart"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#Object -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Object"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#ObjectAggregate -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#ObjectAggregate"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#Quality -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
<!-- http://www.ifomis.org/bfo/1.1/snap#RealizableEntity -->
<owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#RealizableEntity"/>
<!-- http://www.w3.org/2002/07/owl#Thing -->
<owl:Class rdf:about="http://www.w3.org/2002/07/owl#Thing"/>
</rdf:RDF>
<!-- Generated by the OWL API (version 2.2.1.974) http://owlapi.sourceforge.net -->