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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
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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>


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22 changes: 11 additions & 11 deletions src/ontology/obi-edit.owl
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Expand Up @@ -14,7 +14,7 @@
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<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/omo.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2024-11-13/omo.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.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"/>
Expand Down Expand Up @@ -679,16 +679,16 @@ https://sourceforge.net/tracker/?func=detail&amp;aid=3603413&amp;group_id=177891
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>has_specified_input</obo:IAO_0000111>
<obo:IAO_0000111>has specified input</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">see is_input_of example_of_usage</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The inverse property of is_specified_input_of</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">The inverse property of is specified input of</obo:IAO_0000115>
<obo:IAO_0000116>8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how &apos;has participant&apos; works.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Coutot</obo:IAO_0000117>
<rdfs:label xml:lang="en">has_specified_input</rdfs:label>
<rdfs:label xml:lang="en">has specified input</rdfs:label>
</owl:ObjectProperty>


Expand All @@ -714,13 +714,13 @@ https://sourceforge.net/tracker/?func=detail&amp;aid=3603413&amp;group_id=177891
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000295">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>is_specified_input_of</obo:IAO_0000111>
<obo:IAO_0000111>is specified input of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<rdfs:label xml:lang="en">is_specified_input_of</rdfs:label>
<rdfs:label xml:lang="en">is specified input of</rdfs:label>
</owl:ObjectProperty>


Expand Down Expand Up @@ -766,14 +766,14 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>has_specified_output</obo:IAO_0000111>
<obo:IAO_0000111>has specified output</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The inverse property of is_specified_output_of</obo:IAO_0000115>
<obo:IAO_0000115 xml:lang="en">The inverse property of is specified output of</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
<rdfs:label xml:lang="en">has_specified_output</rdfs:label>
<rdfs:label xml:lang="en">has specified output</rdfs:label>
</owl:ObjectProperty>


Expand Down Expand Up @@ -928,12 +928,12 @@ instance level relation [GOC:cjm]</obo:IAO_0000115>
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<obo:IAO_0000111>is_specified_output_of</obo:IAO_0000111>
<obo:IAO_0000111>is specified output of</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON:Bjoern Peters</obo:IAO_0000117>
<rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
<rdfs:label xml:lang="en">is specified output of</rdfs:label>
</owl:ObjectProperty>


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6 changes: 3 additions & 3 deletions src/ontology/templates/administration.tsv
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@@ -1,8 +1,8 @@
ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique objective associated axiom
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C %
ontology ID label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique objective associated axiom
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C %
OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe')))
OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum
OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has_specified_input' some 'pill')
OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has specified input' some 'pill')
OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe')))
OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe')))
OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth
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4 changes: 2 additions & 2 deletions src/ontology/templates/antibody-purification.tsv
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@@ -1,5 +1,5 @@
id rdfs label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent output
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C has_specified_output some %
id rdfs label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent output
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C 'has specified output' some %
OBI:0003616 antibody purification of MHC class I protein complex An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC protein complex MHC class I protein complex
OBI:0003617 antibody purification of human MHC class I protein complex An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC class I protein complex human MHC class I protein complex
OBI:0003618 antibody purification of HLA protein complex with A2 serotype An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of human MHC class I protein complex HLA protein complex with A2 serotype
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