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Pre-COB-transition cleanup #1838

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Pre-COB-transition cleanup #1838

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d238606
Import versioned OMO
sebastianduesing Nov 18, 2024
d7679f1
Update to devices.owl
sebastianduesing Nov 22, 2024
a0e030f
Relabel specified input/output terms to remove underscores
sebastianduesing Nov 22, 2024
3197d0d
Replace alternative term with alternative label in all templates
sebastianduesing Nov 22, 2024
4cbb517
Update IAO import module
sebastianduesing Dec 19, 2024
c83ff10
Remove references to BFO_0000001
sebastianduesing Dec 19, 2024
dec6bf8
Remove references to BFO_0000002
sebastianduesing Dec 19, 2024
2c34312
Remove references to BFO_0000003
sebastianduesing Dec 19, 2024
66fa0bb
Remove references to BFO_0000004
sebastianduesing Dec 19, 2024
75644d9
Remove references to BFO_0000035
sebastianduesing Dec 19, 2024
6f6b23b
Update RO import and switch out 'bearer of' and 'inheres in'
sebastianduesing Dec 19, 2024
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5 changes: 2 additions & 3 deletions src/ontology/OntoFox_inputs/IAO_input.txt
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Expand Up @@ -11,10 +11,8 @@ http://purl.obolibrary.org/obo/IAO_0000003 # measurement unit label
http://purl.obolibrary.org/obo/IAO_0000004 # has measurement value
http://purl.obolibrary.org/obo/IAO_0000005 # objective specification
http://purl.obolibrary.org/obo/IAO_0000006 # narrative object
http://purl.obolibrary.org/obo/IAO_0000007 # action specification
http://purl.obolibrary.org/obo/IAO_0000009 # datum label
http://purl.obolibrary.org/obo/IAO_0000010 # software
http://purl.obolibrary.org/obo/IAO_0000015 # information carrier
http://purl.obolibrary.org/obo/IAO_0000027 # data item
http://purl.obolibrary.org/obo/IAO_0000028 # symbol
http://purl.obolibrary.org/obo/IAO_0000030 # information content entity
Expand Down Expand Up @@ -46,6 +44,7 @@ http://purl.obolibrary.org/obo/IAO_0000235 # denoted by
http://purl.obolibrary.org/obo/IAO_0000300 # textual entity
http://purl.obolibrary.org/obo/IAO_0000306 # table
http://purl.obolibrary.org/obo/IAO_0000310 # document
http://purl.obolibrary.org/obo/IAO_0000311 # publication
http://purl.obolibrary.org/obo/IAO_0000312 # publication about an investigation
http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000407 # has coordinate unit label
Expand Down Expand Up @@ -73,7 +72,7 @@ http://purl.obolibrary.org/obo/IAO_0000572 # documenting
subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process

[Source term retrieval setting]
includeAllIntermediates
includeComputedIntermediates

[Source annotation URIs]
http://www.w3.org/2000/01/rdf-schema#label
Expand Down
126 changes: 4 additions & 122 deletions src/ontology/OntoFox_outputs/IAO_imports.owl
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Expand Up @@ -194,52 +194,6 @@



<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<obo:IAO_0000111 xml:lang="en">entity</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">entity</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000002 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
<obo:IAO_0000111 xml:lang="en">continuant</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">continuant</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
<obo:IAO_0000111 xml:lang="en">quality</obo:IAO_0000111>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">quality</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000020 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<obo:IAO_0000111 xml:lang="en">specifically dependent continuant</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">b is a specifically dependent continuant = Def. b is a continuant &amp; there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">specifically dependent continuant</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031"/>
Expand Down Expand Up @@ -300,18 +254,6 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000007 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000111 xml:lang="en">action specification</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A directive information entity that describes an action the bearer will take.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">action specification</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000009 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000009">
Expand All @@ -337,18 +279,6 @@ interpreted by or directly executed by a processing unit.</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/IAO_0000015 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
<obo:IAO_0000111 xml:lang="en">information carrier</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A quality of an information bearer that imparts the information content</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">information carrier</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
Expand Down Expand Up @@ -424,7 +354,7 @@ interpreted by or directly executed by a processing unit.</obo:IAO_0000115>
<!-- http://purl.obolibrary.org/obo/IAO_0000038 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000038">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000309"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000308"/>
<obo:IAO_0000111 xml:lang="en">graph</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
Expand Down Expand Up @@ -460,7 +390,7 @@ interpreted by or directly executed by a processing unit.</obo:IAO_0000115>
<!-- http://purl.obolibrary.org/obo/IAO_0000078 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000078">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">curation status specification</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
Expand Down Expand Up @@ -530,18 +460,6 @@ Example: The ISO document specifying what encompasses an XML document; The instr



<!-- http://purl.obolibrary.org/obo/IAO_0000102 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">data about an ontology part</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">Data about an ontology part is a data item about a part of an ontology, for example a term</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">data about an ontology part</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000104 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000104">
Expand Down Expand Up @@ -679,18 +597,6 @@ clustering algorithm.</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/IAO_0000309 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000309">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000308"/>
<obo:IAO_0000111 xml:lang="en">diagram</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A figure that expresses one or more propositions</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">diagram</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000310 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000310">
Expand Down Expand Up @@ -727,22 +633,10 @@ clustering algorithm.</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/IAO_0000400 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000400">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">cartesian spatial coordinate datum</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">cartesian spatial coordinate datum</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000401 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000401">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">one dimensional cartesian spatial coordinate datum</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
Expand Down Expand Up @@ -862,7 +756,7 @@ points together with a line.</obo:IAO_0000115>
<!-- http://purl.obolibrary.org/obo/IAO_0000579 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000579">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0020020"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">centrally registered identifier registry</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
Expand All @@ -883,18 +777,6 @@ points together with a line.</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/IAO_0020020 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0020020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">code set</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">code set</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0000011 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
Expand Down
12 changes: 0 additions & 12 deletions src/ontology/modules/data-sets.owl
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Expand Up @@ -92,12 +92,6 @@



<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000100 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000100"/>
Expand All @@ -114,12 +108,6 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003327">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>The output produced by a digital imaging technique, such as microscopy, MRI, or CT.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced.</obo:IAO_0000115>
<obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 &quot;William D. Duncan&quot;</obo:IAO_0000117>
Expand Down
6 changes: 3 additions & 3 deletions src/ontology/modules/devices.owl
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Expand Up @@ -9247,7 +9247,7 @@
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina HiSeq Series Instrument</rdfs:label>
<rdfs:label>Illumina HiSeq series instrument</rdfs:label>
</owl:Class>


Expand All @@ -9271,7 +9271,7 @@
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina NextSeq Series Instrument</rdfs:label>
<rdfs:label>Illumina NextSeq series instrument</rdfs:label>
</owl:Class>


Expand All @@ -9294,7 +9294,7 @@
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina NovaSeq Series Instrument</rdfs:label>
<rdfs:label>Illumina NovaSeq series instrument</rdfs:label>
</owl:Class>


Expand Down
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