Relabel specified input/output terms to remove underscores

obi-ontology · Nov 22, 2024 · a0e030f · a0e030f
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Showing 15 changed files with 66 additions and 66 deletions.
diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
@@ -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>
 
 
@@ -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>
 
 
@@ -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>
 
 
@@ -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>
 
 

diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv
@@ -2,7 +2,7 @@ ontology ID	label	editor preferred term	has curation status	alternative term	def
 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 %
 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				

diff --git a/src/ontology/templates/antibody-purification.tsv b/src/ontology/templates/antibody-purification.tsv
@@ -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	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 %
 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