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PANDA.owl
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1368 lines (813 loc) · 57.9 KB
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/net/brunel/panda#"
xml:base="http://purl.bioontology.org/net/brunel/panda"
xmlns:panda="http://purl.bioontology.org/net/brunel/panda#"
xmlns:void="http://rdfs.org/ns/void#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:uno="http://purl.bioontology.org/net/brunel/uno#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://purl.bioontology.org/net/brunel/panda">
<owl:imports rdf:resource="http://purl.bioontology.org/net/brunel/uno"/>
<dc:title>Probabilistic Knowledge Assembly Ontology </dc:title>
<owl:versionInfo>0.9.0</owl:versionInfo>
<void:dataDump rdf:resource="http://purl.bioontology.org/net/brunel/panda.owl"/>
<dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://klarman.synthasite.com/</dc:contributor>
<dc:subject xml:lang="en">molecular biology</dc:subject>
<skos:altLabel>panda</skos:altLabel>
<dc:subject xml:lang="en">biological events</dc:subject>
<skos:prefLabel>panda</skos:prefLabel>
<skos:definition xml:lang="en">Probabilistic Knowledge Assembly (PANDA) Ontology has been developed in the context of the DARPA's Big Mechanism research program. It provides a semantic interface for capturing information on molecular interactions extracted from scientific texts. Conceptually, PAF ontology supports 3 layers of representation:
1) Domain knowledge: molecular interactions, their participants, structure, and (possibly) formal relationships to some external biological models.
2) Textual evidence: sentences extracted from text, speaking about those interactions, and their provenance-related information.
3) Probabilisitic information associated with different aspects of the representation (see the imported Uncertainty Ontology).</skos:definition>
<void:dataBrowse rdf:resource="http://purl.bioontology.org/net/brunel/panda.graph"/>
<dc:subject xml:lang="en">text mining</dc:subject>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://www.brunel.ac.uk/people/larisa-soldatova</dc:creator>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.bioontology.org/net/brunel/panda#hasDefinition -->
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasDefinition">
<rdfs:label xml:lang="en">has definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasSynonym -->
<owl:AnnotationProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasSynonym"/>
<!-- http://purl.org/dc/elements/1.1/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
<!-- http://purl.org/dc/elements/1.1/creator -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
<!-- http://purl.org/dc/elements/1.1/subject -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/subject"/>
<!-- http://www.w3.org/2004/02/skos/core#altLabel -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>
<!-- http://www.w3.org/2004/02/skos/core#definition -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<!-- http://www.w3.org/2004/02/skos/core#prefLabel -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.bioontology.org/net/brunel/panda#containedIn -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#containedIn">
<owl:inverseOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#containsStatement"/>
<rdfs:comment>a statment is contained in an index card
</rdfs:comment>
<rdfs:label>contained in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#containsStatement -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#containsStatement">
<rdfs:comment>An index card contains a statement</rdfs:comment>
<rdfs:label>contains statement</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#contradicts -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#contradicts">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#relationToModel"/>
<rdfs:label xml:lang="en">contradicts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#corroborates -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#corroborates">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#relationToModel"/>
<rdfs:label xml:lang="en">corroborates</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#evidence -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#evidence">
<hasDefinition>Scientific evidence supporting the existence of the entity as described.</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://www.biopax.org/release/biopax-level2.owl#EVIDENCE"/>
<rdfs:label xml:lang="en">evidence</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#extends -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#extends">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#relationToModel"/>
<rdfs:label xml:lang="en">extends</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasAnnotator -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasAnnotator">
<rdfs:comment>an index card has an annotator (computer+machine, human, or both)</rdfs:comment>
<rdfs:label xml:lang="en">has annotator</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasBody -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasBody">
<hasDefinition>The relationship between oa:Annotation and body. The body is somehow "about" the oa:hasTarget of the annotation.
The Body may be of any media type, and contain any type of content. The Body SHOULD be identified by HTTP URIs unless they are embedded within the Annotation.
Embedded bodies SHOULD be instances of cnt:ContentAsText and embed their content with cnt:chars. They SHOULD declare their media type with dc:format, and MAY indicate their language using dc:language and a RFC-3066 language tag.
There is no OA class provided for "Body" as a body might be a target of a different annotation. However, there SHOULD be 1 or more content-based classes associated with the body resources of an Annotation, and the dctypes: vocabulary is recommended for this purpose, for instance dctypes:Text to declare textual content.</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://www.w3.org/ns/oa#"/>
<rdfs:label xml:lang="en">has body</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasCell -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasCell">
<rdfs:comment>Statements qualify the truth of biological events in the context of certain cell types. Hence a statment should be by defeault connected to some cell type via "has cell type" property.</rdfs:comment>
<rdfs:label>has cell type</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasCellLine -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasCellLine">
<rdfs:comment>Statements qualify the truth of biological events in the context of certain cell lines. Hence a statment should be by defeault connected to some cell line via "has cell line" property.</rdfs:comment>
<rdfs:label>has cell line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasComponent -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasComponent">
<rdfs:comment>Complex chemicals conist of (simple) components. </rdfs:comment>
<rdfs:label>has component</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasFeature -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasFeature">
<rdfs:comment>values accepted (by DARPA) protein modification; binding; mutation
should be attached to a chemical entity - a participant of an event</rdfs:comment>
<rdfs:label xml:lang="en">has feature</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasModificationFeature -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasModificationFeature">
<rdfs:comment>A molecular interaction of type adds_modification or inhibits_modification should by default have some modification feature of type protein modification.</rdfs:comment>
<rdfs:label>has modification feature</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasParticipant -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasParticipant">
<rdfs:isDefinedBy>OBI, IAO</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasParticipantA -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasParticipantA">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#hasParticipant"/>
<rdfs:label xml:lang="en">has participant A</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasParticipantB -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasParticipantB">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#hasParticipant"/>
<rdfs:label xml:lang="en">has participant B</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasRelatedExperimentalResults -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasRelatedExperimentalResults">
<rdfs:comment>An event has been evaluated in a wet lab experiment, whose results are reported</rdfs:comment>
<rdfs:label>has related experimental results</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasSubmitter -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasSubmitter">
<rdfs:label>has submitter</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasTarget -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasTarget">
<hasDefinition>The relationship between oa:Annotation and target. The target resource is what the oa:hasBody is somewhat "about".
The target may be of any media type, and contain any type of content. The target SHOULD be identified by HTTP URIs unless they are embedded within the Annotation.
Embedded targets SHOULD be instances of cnt:ContentAsText and embed their content with cnt:chars. They SHOULD declare their media type with dc:format, and MAY indicate their language using dc:language and a RFC-3066 language tag.
There is no OA class provided for "Target" as a target might be a body in a different annotation. However, there SHOULD be 1 or more content-based classes associated with the target resources of an Annotation, and the dctypes: vocabulary is recommended for this purpose, for instance dctypes:Text to declare textual content.</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://www.w3.org/ns/oa#"/>
<rdfs:label xml:lang="en">has target</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasTissue -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasTissue">
<rdfs:comment>Statements qualify the truth of biological events in the context of certain tissue types. Hence a statment should be by defeault connected to some tissue type via "has tissue type" property.</rdfs:comment>
<rdfs:label>has tissue type</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#inOrganism -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#inOrganism">
<rdfs:comment>Statements qualify the truth of biological events in the context of certain organisms. Hence a statment should be by defeault connected to some organism via "in organism" property.</rdfs:comment>
<rdfs:label>in organism</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#isAbout -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#isAbout">
<hasDefinition>is_about is a (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/IAO_0000136 </hasDefinition>
<rdfs:label xml:lang="en">is about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#isExtractedFrom -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#isExtractedFrom">
<rdfs:comment xml:lang="en">a statement is extracted from an article</rdfs:comment>
<rdfs:label>is extracted from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#isRepresentedBy -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#isRepresentedBy">
<owl:inverseOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#represents"/>
<rdfs:comment>an event is represented by a statement</rdfs:comment>
<rdfs:label xml:lang="en">is represented by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#partOf -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#partOf">
<rdfs:comment>a core relation that holds between a part and its whole</rdfs:comment>
<rdfs:label>part of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#petriNetLabel -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#petriNetLabel">
<rdfs:comment>The nodes of petri net models are labeled with biological entities: places with chemicals or interactions, while transitions with regulation types (classes).</rdfs:comment>
<rdfs:label>has petri net label</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#publishedIn -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#publishedIn">
<rdfs:comment>A journal article is published in a journal</rdfs:comment>
<rdfs:label>published in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#relationToModel -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#relationToModel">
<rdfs:label xml:lang="en">relation to model</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#represents -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#represents">
<rdfs:comment>a statement represents an event</rdfs:comment>
<rdfs:label>represents</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#specifies -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#specifies">
<rdfs:subPropertyOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#relationToModel"/>
<rdfs:label xml:lang="en">specifies</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#transitionFrom -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#transitionFrom">
<rdfs:comment>The transitions in petri net models follow the direction: 'transition from' a place; 'transition to' a place.</rdfs:comment>
<rdfs:label>transition from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#transitionTo -->
<owl:ObjectProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#transitionTo">
<rdfs:comment>The transitions in petri net models follow the direction: 'transition from' a place; 'transition to' a place.</rdfs:comment>
<rdfs:label>transition to</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.bioontology.org/net/brunel/panda#hasEntityId -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasEntityId">
<rdfs:comment>associates an identifier with a chemical entity, e.g.: GAB1_HUMAN, MK03_HUMAN</rdfs:comment>
<rdfs:label>has entity ID</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasEntityName -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasEntityName">
<rdfs:comment>entity's name as accepted in one of the official databases</rdfs:comment>
<rdfs:label>has entity name</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasEntityText -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasEntityText">
<rdfs:comment>associates a chemical entity with its textual representation in the extracted text fragment</rdfs:comment>
<rdfs:label>has entity text</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasHindex -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasHindex">
<rdfs:comment>a journal has an H index</rdfs:comment>
<rdfs:label>has H-index</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasISSN -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasISSN">
<rdfs:label>has ISSN</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasIndexCardId -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasIndexCardId">
<rdfs:label xml:lang="en">has index card ID</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasPmcId -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasPmcId">
<rdfs:label xml:lang="en">has PMC ID</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasPublicationYear -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasPublicationYear">
<rdfs:comment>a publication has publication year</rdfs:comment>
<rdfs:label>has publication year</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasSJRscore -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasSJRscore">
<hasDefinition>https://en.wikipedia.org/wiki/SCImago_Journal_Rank</hasDefinition>
<rdfs:comment>A journal has its SJR score</rdfs:comment>
<rdfs:label>has SJR score</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasSite -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasSite">
<rdfs:comment>Certain interactions, e.g. modificiations or bindings, are additionally qualified by the site (by default of the participant B) where the interaction takes palce. </rdfs:comment>
<rdfs:label>has site</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasStartTime -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasStartTime">
<rdfs:label xml:lang="en">has start time</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasStopTime -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasStopTime">
<rdfs:label xml:lang="en">has stop time</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasSubmitterId -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasSubmitterId">
<rdfs:comment>a submitter has an id</rdfs:comment>
<rdfs:label>has submitter ID</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasTextualEvidence -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasTextualEvidence">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topDataProperty"/>
<rdfs:label xml:lang="en">has textual evidence</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasTitle -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasTitle">
<rdfs:comment>A journal/publication has title.</rdfs:comment>
<rdfs:label>has title</rdfs:label>
</owl:DatatypeProperty>
<!-- http://purl.bioontology.org/net/brunel/panda#hasTruthValue -->
<owl:DatatypeProperty rdf:about="http://purl.bioontology.org/net/brunel/panda#hasTruthValue">
<rdfs:comment>- a statement states the truth value of an event
- an experimental result states the truth value of the tested hypothesis
Values: true/false
</rdfs:comment>
<rdfs:label xml:lang="en">has truth value</rdfs:label>
</owl:DatatypeProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.bioontology.org/net/brunel/panda#Abstract -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Abstract">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#DocumentPart"/>
<rdfs:comment>A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000315"/>
<rdfs:label>abstract</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Acetylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Acetylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0192</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">acetylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#AddsModification -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#AddsModification">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#PositiveRegulation"/>
<rdfs:label>adds modification</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Annotation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Annotation">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<hasDefinition>Typically an Annotation has a single Body (oa:hasBody), which is the comment or other descriptive resource, and a single Target (oa:hasTarget) that the Body is somehow "about". The Body provides the information which is annotating the Target.
This "aboutness" may be further clarified or extended to notions such as classifying or identifying with oa:motivatedBy.</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://www.w3.org/ns/oa#"/>
<rdfs:label xml:lang="en">annotation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Annotator -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Annotator">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<rdfs:comment>The agent that provided an annotation (extracted a sentence). </rdfs:comment>
<rdfs:label xml:lang="en">annotator</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Binding -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Binding">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#MolecularInteraction"/>
<hasDefinition>The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/GO_0005488"/>
<rdfs:label xml:lang="en">binding</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Cell -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Cell">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:label>cell</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#CellLine -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#CellLine">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:label>cell line</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Chemical -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Chemical">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
<rdfs:label xml:lang="en">chemical</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#ChemicalFamily -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#ChemicalFamily">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Chemical"/>
<rdfs:label>chemical family</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Complex -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Complex">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Chemical"/>
<rdfs:label xml:lang="en">complex</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Computer -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Computer">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Annotator"/>
<rdfs:label xml:lang="en">computer</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Database -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Database">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:label>database</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Deacetylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Deacetylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0197</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">deacetylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#DecreasesActivity -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#DecreasesActivity">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#NegativeRegulation"/>
<rdfs:label xml:lang="en">decreases activity</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Defarnesylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Defarnesylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0198</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">defarnesylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Deglycosylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Deglycosylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0558</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">deglycosylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Demethylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Demethylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0871</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">demethylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Dephosphorylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Dephosphorylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0203</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">dephosphorylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Desumoylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Desumoylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0568</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">desumoylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Deubiquitination -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Deubiquitination">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0204</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">deubiquitination</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#DiscussionSectionOfaPublication -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#DiscussionSectionOfaPublication">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#DocumentPart"/>
<rdfs:comment>A part of a publication about an investigation that is about the study interpretation of the investigation</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000319"/>
<rdfs:label>discussion section of a publication</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Document -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Document">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:comment>A collection of information content entities intended to be understood together as a whole</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<rdfs:label>document</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#DocumentPart -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#DocumentPart">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.bioontology.org/net/brunel/panda#partOf"/>
<owl:someValuesFrom rdf:resource="http://purl.bioontology.org/net/brunel/panda#Document"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:comment>an information content entity that is part of a document</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000314"/>
<rdfs:label>document part</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Event -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Event">
<rdfs:comment>A biological event, such as molecular interaction or gene expression. Events are desccribed in statements. </rdfs:comment>
<rdfs:label xml:lang="en">biological event</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#ExperimentalResults -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#ExperimentalResults">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:comment>Experimental results are the set of facts and conclusions, obtained as a result of the interpretation of the experimental observations, which increase/decrease the probability of a research hypothesis of the experiment.</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="https://sourceforge.net/projects/expo/files/EXPO-OWL/"/>
<rdfs:label>experimental results</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Farnesylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Farnesylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0206</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">farnesylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#FigureLegend -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#FigureLegend">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#DocumentPart"/>
<rdfs:comment>A legend associated with a figure in a document
</rdfs:comment>
<rdfs:label>figure legend</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Gene -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Gene">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Chemical"/>
<rdfs:label xml:lang="en">gene</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#GeneExpression -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#GeneExpression">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Event"/>
<rdfs:comment>The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.</rdfs:comment>
<rdfs:isDefinedBy>http://purl.obolibrary.org/obo/GO_0010467</rdfs:isDefinedBy>
<rdfs:label>gene expression</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Glycosylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Glycosylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0559</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">glycosylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Human -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Human">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Annotator"/>
<rdfs:label xml:lang="en">human</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#HumanComputer -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#HumanComputer">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Annotator"/>
<rdfs:label>human with computer</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Hydroxylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Hydroxylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0210</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">hydroxylation</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#IncreasesActivity -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#IncreasesActivity">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#PositiveRegulation"/>
<rdfs:label xml:lang="en">increases activity</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#IndexCard -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#IndexCard">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#TextualEntity"/>
<rdfs:label xml:lang="en">index card</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#InhibitsModification -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#InhibitsModification">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#NegativeRegulation"/>
<rdfs:label>inhibits modification</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#IntroductionToaPublication -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#IntroductionToaPublication">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#DocumentPart"/>
<rdfs:comment>A part of a publication about an investigation that is about the objective specification (why the investigation is being done)</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000316"/>
<rdfs:label>introduction to a publication</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Journal -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Journal">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#TextualEntity"/>
<rdfs:label>journal
</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#JournalArticle -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#JournalArticle">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#Publication"/>
<hasDefinition>a report that is published in a journal</hasDefinition>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000013"/>
<rdfs:label xml:lang="en">journal article</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#MethodsSection -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#MethodsSection">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#DocumentPart"/>
<rdfs:comment>A part of a publication about an investigation that is about the study design of the investigation</rdfs:comment>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/IAO_0000317"/>
<rdfs:label>methods section</rdfs:label>
</owl:Class>
<!-- http://purl.bioontology.org/net/brunel/panda#Methylation -->
<owl:Class rdf:about="http://purl.bioontology.org/net/brunel/panda#Methylation">
<rdfs:subClassOf rdf:resource="http://purl.bioontology.org/net/brunel/panda#ProteinModification"/>
<rdfs:isDefinedBy>MI:0213</rdfs:isDefinedBy>
<rdfs:label xml:lang="en">methylation</rdfs:label>
</owl:Class>