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Drop external-byhand.owl
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This file contain axioms about non-OBI terms:
10 object properties and 2 classes.
The annotations about the 2 CLO classes
are no longer needed.
The 10 object properties should be imported from RO.

I did not delete the external-byhand.owl file
in case it's still used by something somewhere.
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@jamesaoverton
jamesaoverton committed Aug 27, 2024
1 parent b93ac97 commit 96ba715
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Showing 3 changed files with 124 additions and 6 deletions.
20 changes: 15 additions & 5 deletions src/ontology/OntoFox_inputs/RO_input.txt
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Expand Up @@ -6,16 +6,26 @@ http://purl.obolibrary.org/obo/obi/dev/import/RO_imports.owl
RO

[Low level source term URIs]
http://purl.obolibrary.org/obo/BFO_0000062 # preceded by
http://purl.obolibrary.org/obo/BFO_0000063 # precedes
http://purl.obolibrary.org/obo/RO_0000079 # function of
http://purl.obolibrary.org/obo/RO_0000080 # quality of
http://purl.obolibrary.org/obo/RO_0000081 # role of
http://purl.obolibrary.org/obo/RO_0000085 # has function
http://purl.obolibrary.org/obo/RO_0000086 # has quality
http://purl.obolibrary.org/obo/RO_0000087 # has role
http://purl.obolibrary.org/obo/RO_0000091 # has disposition
http://purl.obolibrary.org/obo/RO_0000092 # disposition of
http://purl.obolibrary.org/obo/RO_0000085 # has function
http://purl.obolibrary.org/obo/RO_0000079 # function of
http://purl.obolibrary.org/obo/RO_0000086 # has quality
http://purl.obolibrary.org/obo/RO_0000080 # quality of
http://purl.obolibrary.org/obo/RO_0002351 # has member
http://purl.obolibrary.org/obo/RO_0001000 # derives from
http://purl.obolibrary.org/obo/RO_0001025 # located in
http://purl.obolibrary.org/obo/RO_0002087 # immediately preceded by
http://purl.obolibrary.org/obo/RO_0002090 # immediately precedes
http://purl.obolibrary.org/obo/RO_0002180 # has component
http://purl.obolibrary.org/obo/RO_0002215 # capable of
http://purl.obolibrary.org/obo/RO_0002219 # surrounded by
http://purl.obolibrary.org/obo/RO_0002222 # temporal relation
http://purl.obolibrary.org/obo/RO_0002223 # starts
http://purl.obolibrary.org/obo/RO_0002351 # has member

[Top level source term URIs and target direct superclass URIs]

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109 changes: 109 additions & 0 deletions src/ontology/OntoFox_outputs/RO_imports.owl
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Expand Up @@ -69,6 +69,30 @@



<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000062">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">preceded by</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) &lt;= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">preceded by</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/BFO_0000063 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000063">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">precedes</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) &lt;= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0000079 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000079">
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<!-- http://purl.obolibrary.org/obo/RO_0001000 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001000">
<obo:IAO_0000111 xml:lang="en">derives from</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">derives from</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0001025 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001025">
Expand All @@ -169,6 +204,80 @@



<!-- http://purl.obolibrary.org/obo/RO_0002087 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002087">
<obo:IAO_0000111 xml:lang="en">immediately preceded by</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">immediately preceded by</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002090 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002090">
<obo:IAO_0000111 xml:lang="en">immediately precedes</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">immediately precedes</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002180 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002180">
<obo:IAO_0000111 xml:lang="en">has component</obo:IAO_0000111>
<obo:IAO_0000115>w &apos;has component&apos; p if w &apos;has part&apos; p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">has component</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002215 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002215">
<obo:IAO_0000111 xml:lang="en">capable of</obo:IAO_0000111>
<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>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">capable of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002219 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002219">
<obo:IAO_0000111 xml:lang="en">surrounded by</obo:IAO_0000111>
<obo:IAO_0000115>x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">surrounded by</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002222 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002222">
<obo:IAO_0000111 xml:lang="en">temporally related to</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">temporally related to</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002223 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002223">
<obo:IAO_0000111 xml:lang="en">starts</obo:IAO_0000111>
<obo:IAO_0000115>inverse of starts with</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<rdfs:label xml:lang="en">starts</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002351 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002351">
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1 change: 0 additions & 1 deletion src/ontology/obi-edit.owl
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Expand Up @@ -16,7 +16,6 @@
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/obi/dev/obi-edit.owl">
<owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/external-byhand.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/CLO_imports.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/CL_imports.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/dev/import/COB_imports.owl"/>
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