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sepio-base.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/sepio/sepio-base.owl#"
xml:base="http://purl.obolibrary.org/obo/sepio/sepio-base.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/sepio/sepio-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/sepio/releases/2023-02-21/sepio-base.owl"/>
<dc:title>Ontology for Scientific Evidence and Provenance Information</dc:title>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-1048-5019"/>
<terms:description>The SEPIO ontology is in its early stages of development, undergoing iterative refinement as new requirements emerge and alignment with existing standards is explored.</terms:description>
<terms:license rdf:resource="https://creativecommons.org/licenses/by/3.0/"/>
<owl:versionInfo>2023-02-21</owl:versionInfo>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000231 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
<!-- http://purl.obolibrary.org/obo/IAO_0100001 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000052 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000052">
<rdfs:label xml:lang="en">consider</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000061 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000061">
<rdfs:comment>Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation).</rdfs:comment>
<rdfs:label xml:lang="en">SEPIO_editor_note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000184 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000184">
<rdfs:label xml:lang="en">usage note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000337 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000337">
<rdfs:label xml:lang="en">in_value_set</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000386 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000386">
<rdfs:label xml:lang="en">sepio_preferred_label</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000118"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000399 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000399">
<obo:IAO_0000115>Annotation indicating whether a property represents a "shortcut" relation that can be used to directly link two objects that are indirectly linked through a longer path of two or more edges. Shortcut relations can be logically expanded to be expressed in terms of this longer path, e.g.
has_evidence_from_source = has_evidence_line o has_evidence_item o source.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_shortcut</rdfs:label>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/license"/>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
<!-- http://purl.org/dc/elements/1.1/type -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
<!-- http://purl.org/dc/terms/contributor -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/contributor"/>
<!-- http://purl.org/dc/terms/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description">
<obo:IAO_0000115>An account of the resource.</obo:IAO_0000115>
<rdfs:comment xml:lang="en">Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."</rdfs:comment>
<rdfs:label xml:lang="en">description</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/dc/terms/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source">
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label xml:lang="en">database_cross_reference</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
<!-- http://www.w3.org/2002/07/owl#deprecated -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2002/07/owl#deprecated"/>
<!-- http://xmlns.com/foaf/0.1/mbox -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/mbox"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">is part of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my brain is part of my body (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this day is part of this year (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a part and its whole</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my body has part my brain (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this year has part this day (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000055 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2002/07/owl#topObjectProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<rdfs:comment>Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process</rdfs:comment>
<rdfs:label>realizes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000136 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115>Is_about is a (currently) primitive relation that relates an information artifact to an entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">is_about</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000999 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000999"/>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<obo:IAO_0000111 xml:lang="en">participates in</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood clot participates in this blood coagulation</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this input material (or this output material) participates in this process</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigator participates in this investigation</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a continuant and a process, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">participates_in</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">participates in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000057 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000057">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000111 xml:lang="en">has participant</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this blood coagulation has participant this blood clot</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this investigation has participant this investigator</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this process has participant this input material (or this output material)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a relation between a process and a continuant, in which the continuant is somehow involved in the process</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_participant</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">has participant</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002215 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215">
<obo:IAO_0000115>A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process</obo:IAO_0000115>
<rdfs:label>capable of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002233 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002233">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002352"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>consumes</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">has input</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002234 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002234">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002353"/>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115>p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.</obo:IAO_0000115>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000118>produces</obo:IAO_0000118>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">has output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002350 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002350">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<obo:IAO_0000115>Is member of is a mereological relation between a item and a collection.</obo:IAO_0000115>
<rdfs:label>member of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002351 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002351">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<obo:IAO_0000115>Has member is a mereological relation between a collection and an item.</obo:IAO_0000115>
<rdfs:label>has member</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002352 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002352">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">input of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002353 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002353">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ro/subsets#ro-eco"/>
<rdfs:label xml:lang="en">output of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002614 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002614">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000115>A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">is_evidence_supported_by</obo:IAO_0000118>
<rdfs:label>is_evidence_with_support_from</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000006 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000427"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<obo:IAO_0000115>A relationship between an assertion or proposition and an evidence line used in evaluating its validity.</obo:IAO_0000115>
<obo:IAO_0000116>Consider re-use of http://purl.obolibrary.org/obo/RO_0002558 ! 'has evidence'.
Definition = "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x."
See also http://semanticscience.org/resource/SIO_000772 ! 'has evidence'.</obo:IAO_0000116>
<obo:IAO_0000118>has_evidence</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000007 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that supports its validity, based on the evaluation of some agent.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000206 ! 'is supported by'</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_supporting_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000008 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000008">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000100"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000007"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that contradicts its validity, based on the evaluation and conclusion of some agent.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000774 ! 'is refuted by'</obo:IAO_0000116>
<obo:IAO_0000118>has_conflicting_evidence</obo:IAO_0000118>
<obo:IAO_0000118>has_refuting_evidence_line</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_disputing_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000009 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000009">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000009"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation between a proposition and information that was used to evaluate a particular proposition, but failed to provide conclusive support for or against its validity.</obo:IAO_0000115>
<obo:IAO_0000116>Mapping to related terms:
Consider: http://semanticscience.org/resource/SIO_000207 ! 'is disputed by'</obo:IAO_0000116>
<obo:IAO_0000118>has_insignificant_evidence_line</obo:IAO_0000118>
<rdfs:comment>A relation between a proposition and information that does not conclusively support or contradict its validity, based on evaluation of some agent.</rdfs:comment>
<rdfs:label xml:lang="en">has_inconclusive_evidence_line</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000015 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000015">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<obo:IAO_0000115>A relation holding between a proposition and an assertion in which it is expressed.</obo:IAO_0000115>
<obo:IAO_0000118>is_asserted_in</obo:IAO_0000118>
<rdfs:comment>A particular proposition can be asserted in more than one assertion - in cases where assertions made by different agents, or on different occasions, put forth the same proposition as true.</rdfs:comment>
<rdfs:label>proposition_asserted_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000017 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000017">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Agent"/>
<obo:IAO_0000116>Consider use of http://purl.obolibrary.org/obo/RO_0002217 ! actively participates in.
Definition = "actively participates in y if and only if x participates in y and x realizes some active role"</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_agent</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000026 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000026">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.org/oban/association_has_subject"/>
</owl:propertyChainAxiom>
<obo:IAO_0000231>Decided that a more generic has_subject property should suffice to cover links from either an assertion or a proposition to an entity representing the subject of the statement made.
But wanted to maintain the text in the comment here for future reference/use.</obo:IAO_0000231>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_subject :thing1).
The assertion_has_subject property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the subject of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_subject).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_subject</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000027 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000027">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000027"/>
</owl:propertyChainAxiom>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_object :thing1).
The assertion_has_object property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the object of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_object).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_object</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000028 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000028">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030"/>
<rdf:Description rdf:about="http://purl.org/oban/association_has_predicate"/>
</owl:propertyChainAxiom>
<rdfs:comment>Propositional statements can be represented in RDF as directional subject-predicate-object (S-P-O) triples. RDF reification vocabularies such as OBAN create named individuals in a graph that represent such S-P-O propositional statements. In OBAN, these are called 'associations', and the semantics of these associations can be represented using properties that link it to the subject, predicate, and object of the triple it represents.
As a proposition-level entity, a particular association can be expressed in more than one assertion made by different agents, or at different times. The meaning of an assertion can be captured through its link to an association whose meaning is formally specified as described above (e.g. :assertion1 is_asserted_in :association1, :association1 has_predicate :thing1).
The assertion_has_predicate property allows more direct specification of assertion meaning, bypassing an association and pointing directly to the predicate of the reified triple. In this sense, it is a shortcut relation over two more fundamental properties (is_asserted_in o association_has_predicate).
This property is useful when a particular dataset wants to describe statements at the level of assertions rather than propositions, and formally describe assertion semantics without needed to represent an proposition-level association.</rdfs:comment>
<rdfs:label xml:lang="en">assertion_has_predicate</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000030 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000030">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<obo:IAO_0000115>A relation holding between an assertion and the proposition that it puts forth as true.</obo:IAO_0000115>
<obo:SEPIO_0000052>Mapping to related terms:
Consider: http://purl.org/see/rdo#is_assertion_asserting</obo:SEPIO_0000052>
<obo:SEPIO_0000386>assertsProposition</obo:SEPIO_0000386>
<rdfs:comment>In practice, SEPIO recommends that data is captured at the assertion level, and post-processed as needed to aggregate assertions making the same claim under a single proposition using this property.</rdfs:comment>
<rdfs:label>asserts_proposition</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000041 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000041">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000407"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
<obo:IAO_0000115>A relation holding between a planned process, or the artifact it generates, and a plan specification that specifies all or part of the process (e.g. a protocol, guideline, rule set)</obo:IAO_0000115>
<obo:IAO_0000116>Consider SIO:00339 (a relation between a product and the information content entity that specifies it.)</obo:IAO_0000116>
<rdfs:comment>In SEPIO, this property is most often used to link an assertion (the generated artifact) to an 'assertion method' that may specified how it was created. This assertion method may describe what types of data may be used as evidence, what weight to give a particular type of evidence, and how to combine different lines of evidence in generating the final assertion.</rdfs:comment>
<rdfs:label xml:lang="en">was_specified_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000046 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000046">
<obo:IAO_0000116>Consider RO:0000087 ! has_role (def = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence). However, this property is defined as a relation between an independent continuant and a role. In BFO, dependent continuants (such as information) cannot bear roles.</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_role</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000084 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000376"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000149"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000257"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation holding between an evidence line and an individual information entity that contributes to the argument it represents.</obo:IAO_0000115>
<obo:IAO_0000118>has_supporting_information</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_evidence_item</rdfs:label>
</owl:ObjectProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#propertyChainAxiom"/>
<owl:annotatedTarget rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000257"/>
</owl:annotatedTarget>
<obo:SEPIO_0000061>If we start using the 'study data set' class in a similar way to organize data items from a partiular study, we should create a similar property chain that traverses the property we use to link study data sets to their data item parts.
Can this just be "has part" . . .or is a specific/unique relation needed here to avoid unwanted entailments?</obo:SEPIO_0000061>
<rdfs:comment>This property chain ensures that any evidence items that are organized into groups using a 'study finding' object will still be classified as evidence items for the relevant evidence line, and returned by queries for evidence items for a particular evidence line.</rdfs:comment>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000085 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000085">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Activity"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002353"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation that links an evidence line to any activities (studies, assays, computational tasks, curation) that generated evidence items contributing to it.</obo:IAO_0000115>
<obo:IAO_0000118>has_evidence_item_output_from</obo:IAO_0000118>
<obo:IAO_0000118>has_supporting_activity</obo:IAO_0000118>
<obo:SEPIO_0000399 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:SEPIO_0000399>
<rdfs:label xml:lang="en">evidence_has_supporting_activity</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000098 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000098">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000116"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000118>has_equivalent_proposition</obo:IAO_0000118>
<rdfs:label xml:lang="en">is_equilavent_to</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000099 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000099">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000116"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<obo:IAO_0000118 xml:lang="en">has_consistent_proposition</obo:IAO_0000118>
<rdfs:label>is_consistent_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000100 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000100">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000115"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<obo:IAO_0000116>Previosly implemented property chains:
is_asserted_in o strongly_contradicts o asserts -> strongly_contradicts
asserts o strongly_contradicts o is_asserted_in -> strongly_contradicts
But these broke reasoner - "the given hierarchy is not regular" error message". Apparently breaks rule that "in property chains of 3 or larger, the inner property must not also appear as the composite property". (https://arxiv.org/pdf/1212.2902.pdf)</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_contradicting_proposition</obo:IAO_0000118>
<rdfs:comment>Relation between two propositions that make opposing claims (e.g. proposition1 holds that variant1 is pathogenic for disease1, and proposition2 holds that variant1 is benign for disease1).</rdfs:comment>
<rdfs:label xml:lang="en">strongly_contradicts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000101 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000101">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000115"/>
<obo:IAO_0000118 xml:lang="en">has_inconsistent_proposition</obo:IAO_0000118>
<rdfs:label>contradicts</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000108 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000108">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000109"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<obo:IAO_0000115>Relationship between a statement or proposition and a document in which it is expressed (e.g. a publication, report, or database record).</obo:IAO_0000115>
<obo:IAO_0000118>is_reported_in</obo:IAO_0000118>
<rdfs:label xml:lang="en">is_expressed_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000109 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000109">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000115>Relationship between a document (e.g. a publication, report, database record) and an assertion or proposition that is stated in its content.</obo:IAO_0000115>
<rdfs:label xml:lang="en">expresses</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000113 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000113">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000406"/>
<obo:IAO_0000116>Grouping class to hold exploratory relationships linking assertions or propositions based on the compatability or degree of agreement in their meaning. Has utility toward inferring links between evidence lines and propositions.</obo:IAO_0000116>
<obo:IAO_0000118>has_concordance</obo:IAO_0000118>
<obo:IAO_0000118>propositional relationships</obo:IAO_0000118>
<rdfs:label xml:lang="en">has_compatability</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000114 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000114">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000406"/>
<obo:IAO_0000115>A relation between a planned process and a parameter that it measures as part of an assay or observation.</obo:IAO_0000115>
<rdfs:label>measures_parameter</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000115 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000115">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">conflicts_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000116 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000116">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">aligns_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000124 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000124">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002614"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
<obo:IAO_0000115>A relation that holds between an evidence line and a citable document from which information supporting the evidence line was obtained (i.e. a "supporting reference").</obo:IAO_0000115>
<obo:IAO_0000116>Note that this relation only links an evidence line to publications actually consulted by the asserting agent to find and interpret evidence items. There may be other publications that describe the same evidence item that the asserting agent did not consult, which would not qualify as supporting references.
For example, consider a GO curator's use of sequence data for the rat Vegfa gene in a line of evidence supporting their assertion that the human VEGFA ortholog exhibited the same angiogeneic activity. There may be multiple publications that report this same rat gene sequence, but only the publication that the curator consulted in making this assertion would qualify as a supporting reference for this evidence line.
For this resaon, we are not able to create a property chain declaring "has_evidence_item o is_described_by -> has_evidence_item_described_by". . . because this would entail that any publication describing this rat Vegfa gene sequence was a supporting reference for the assertion.</obo:IAO_0000116>
<obo:IAO_0000118>has_support_from_source</obo:IAO_0000118>
<obo:IAO_0000118>has_supporting_reference</obo:IAO_0000118>
<obo:SEPIO_0000061>Keeping the label has_supporting_reference instead of has_evidence_item_described_by because the later follows the pattern we use for true shortcut relations (i.e. that can be defined using property chains). For reasons outlined in the editor note, this is not such a shortcut relation.</obo:SEPIO_0000061>
<rdfs:label xml:lang="en">evidence_has_supporting_reference</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000126 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000126">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000113"/>
<rdfs:label xml:lang="en">is_inconsistent_with</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000130 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000130">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<obo:IAO_0000112>As an example, consider the assertion that "Variant X causes Disease Y". At an abstract level this represents a bfo: information content entity (or frbr:Work). This abstract assertion can be concretized / encoded various formats - e.g. a free-text sentence, an rdf graph, a blob of json, or stanza of XML. Each such manifestation might use a different model or structure to represent this knowledge. Each such concrete form is considered a separate resource/digital artifact at the 'manifestation' level, but each expresses the same knowledge.
The authored_by and date_authored properties allow us connect an abstract or concrete representation of this assertion to who and when the knowledge was originally generated. This will be the same agent and date for all formats/manifestations listed above.
The created_by and date_created properties allow us to connect a representation of the abstract or concrete assertion to who and when the specific manifestation was created in a particular format. The agent/dates here will be different for each of the formats/manifestations listed above.</obo:IAO_0000112>
<obo:IAO_0000115>A relation between an information content entity (or concrete manifestation of it as a particular resource/digital artifact), and the agent that originally generated the information content.</obo:IAO_0000115>
<obo:SEPIO_0000061>Older note - remove before releasing:
We intentionally avoid use of a more generic "creator" property here, as this term is used in established standards such as PAV and DC to specifically describe agents who generated a specific representation of an information content entity. For example, the pav:createdBy property is used specifically to describe agents contributing to a specific representation.
SEPIO, by contrast, aims to describe the agent(s) responsible for generating the abstract information content these concretized artifacts express. For this reason, SEPIO creates the more specific "stated_by" relation to explicitly distinguish the act of making a statement (generating its information content) from the act of creating a specific digital representation of the statement (generating a particular concretized artifact).
A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.</obo:SEPIO_0000061>
<rdfs:comment>In the case that the information artifact is an assertion, the responsible agent is the one who originally generated an assertion based on their evaluation of relevant evidence. If more than one agent is involved in this process, we may consider them collectively as a group or organization representing a single agent.</rdfs:comment>
<rdfs:label xml:lang="en">authored_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000132 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000132">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000002"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000133"/>
<obo:IAO_0000115>A relation describing the degree of support provided by an evidence line for a target assertion or proposition.</obo:IAO_0000115>
<obo:IAO_0000116>The value of this property is typically a term from some defined set of values that enumerates categorical degrees of evidence strength (e.g. the CIViC five-teired 'evidence level' scale). Different systems or applications can create terms representing the levels of strength they wish to define for their use case.</obo:IAO_0000116>
<rdfs:label xml:lang="en">evidence_line_strength</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000140 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000140">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000150"/>
<obo:IAO_0000115>A relation holding between a generated artifact and an agent who evaluated its quality, completeness, or utility.</obo:IAO_0000115>
<obo:IAO_0000116>In SEPIO, the agent responsible for a particular evidence line is linked via the "evaluated_by" property. This reflects that perspective that evaluation of the relevance, strength, and direction of an evidence line w.r.t. a particular assertion are the key acts inherent in the evidence line's "creation".
We avoid using a "creator" relation here because this label is used in established standards such as PAV and DC to specifically describe agents contributing to a specific digital representation, as opposed to agents responsible for generating the underlying information content these concrete representations express.
A explicit commitment to this more abstracted level of representation is a core feature of the SEPIO model, and has implications for how instances in the data are described, identified, and distinguished in practice.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">assessed_by</obo:IAO_0000118>
<rdfs:label>evaluated_by</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000144 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000144">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000174"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<obo:IAO_0000115>A relation used to indicate context in which a particular assertion or proposition applies.</obo:IAO_0000115>
<rdfs:label xml:lang="en">has_qualifier</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000145 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000145">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000178"/>
</owl:propertyChainAxiom>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000006"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000084"/>
<rdf:Description rdf:about="http://purl.org/dc/terms/source"/>
</owl:propertyChainAxiom>
<obo:IAO_0000115>A relation used to link an assertion or proposition to a source where evidence for it was found (i.e. a document, document part, database, etc)</obo:IAO_0000115>
<obo:SEPIO_0000052>cito:cites_as_evidence</obo:SEPIO_0000052>
<obo:SEPIO_0000061>Note that this may not qualify as a proper shortcut (i.e. it may not be valid to define using a property chain) for the same reason has_supporting reference is not defined as a property chain called has_evidence_item_described_by.</obo:SEPIO_0000061>
<obo:SEPIO_0000399 rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</obo:SEPIO_0000399>
<rdfs:comment>This is a shortcut relation to be used when publications are referenced as providing support for an assertion, but it is not clear how many evidence lines are described across these publications. In such cases, discrete evidence lines cannot be created, and the has_evidence_from_source relation is used to directly link the assertion to publications providing some form of evidence information.</rdfs:comment>
<rdfs:label xml:lang="en">has_evidence_from_source</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000146 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000146">
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000000"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000001"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000133"/>
<obo:IAO_0000115>A relation used to link an assertion or proposition directly to some indicator of the strength of the total evidence that asserting agent beleives to support it.</obo:IAO_0000115>
<obo:IAO_0000118>has_total_evidence_strength</obo:IAO_0000118>
<rdfs:comment>This relation links an assertion or proposition directly to some indicator of the strength of the total evidence supporting it. It is used when there is not enough information to create evidence line(s) for the assertion, but the source provides some indication of the strength of the evidence supporting it.
Note that this is different than the notion of statement confidence, which describes how confident an agent is that a statement is true. Confidence may depend on factors in addition to the strength of the evidence (e.g. who made the prior probability that the asserted proposition could be true, who made the assertion and when, etc.)</rdfs:comment>
<rdfs:label xml:lang="en">has_evidence_level</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000150 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/SEPIO_0000150">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000188"/>
<rdfs:range rdf:resource="http://www.w3.org/ns/prov#Agent"/>
<obo:IAO_0000115>A relation between an information content entity and an agent who made a contribution to its information content, or to its subsequent modification or assessment.</obo:IAO_0000115>
<obo:IAO_0000116>SEPIO intentionally creates its own hierarchy of contributor properties, instead of re-using terms from existing standards like PAV or Dublin Core - whose domain is structured digital resources. This is because properties such as pav:createdBy specifically describe agents who generated a specific digital representation of information, while SEPIO aims to describe agents responsible for generating the abstract information content that such a concrete representation may express.
The subject of 'contributor' relations in the SEPIO are explicitly abstract in nature - considered at the level of their information content as opposed to concretizations in particular digital resources or representations. For example, the SEPIO "stated_by" relation explicitly refers toan agent originally putting forth a statement as true (generating its information content), as opposed to an agent creating a specific digital representation of the statement (generating a particular concretized artifact such as a json object returned by an API).
Should further clarification become available with respect to whether PAV or DC contributor properties accommodate the nuanced definitions we require, we will re-consider their inclusion in SEPIO. For example, the pav:authoredBy property seems to refer specifically to the agent who generated information content expressed in a resource - and thus may be appropriate in the context of SEPIO. But even here, the range of the property is a particular authored digital resource, and not the information content it expresses. DC properties such as dc:contributor and dc:creator are ambiguous as to which level of contribution they describe.</obo:IAO_0000116>
<rdfs:label xml:lang="en">has_contributor</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/SEPIO_0000151 -->