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Merge pull request #28729 from geneontology/issue-28550-merge
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Obsoleted GO:0106339; #28550.
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@raymond91125
raymond91125 authored Aug 21, 2024
2 parents 865a932 + 7c7ba9a commit b94758f
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34 changes: 17 additions & 17 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -337183,7 +337183,7 @@ synonym: "tRNA cytosine-2'-O-methyltransferase activity" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26018" xsd:anyURI
is_obsolete: true
consider: GO:0106059
consider: GO:0106339
consider: GO:0106340
created_by: ai
creation_date: 2010-10-11T01:05:47Z

Expand Down Expand Up @@ -441958,37 +441958,37 @@ creation_date: 2020-11-05T17:56:43Z

[Term]
id: GO:0106339
name: tRNA (cytidine(32)-2'-O)-methyltransferase activity
name: obsolete tRNA (cytidine(32)-2'-O)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:25404562, RHEA:42932]
def: "OBSOLETE. Catalysis of the reaction: cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:25404562]
comment: The reason for obsoletion is that this term is equivalent to tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity.
synonym: "tRNA (cytidine 32-2'-O)-methyltransferase activity" EXACT []
xref: EC:2.1.1.200 {source="skos:broadMatch"}
xref: EC:2.1.1.205 {source="skos:broadMatch"}
xref: MetaCyc:RXN-11866 {source="skos:exactMatch"}
xref: RHEA:42396 {source="skos:broadMatch"}
xref: RHEA:42932 {source="skos:exactMatch"}
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24771" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26018" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26086" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28550" xsd:anyURI
is_obsolete: true
replaced_by: GO:0106340
created_by: hjd
creation_date: 2020-11-05T22:48:53Z

[Term]
id: GO:0106340
name: tRNA (guanine(34)-2'-O)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine 34 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylguanosine 34 in tRNA." [PMID:25404562]
synonym: "tRNA (guanosine 34-2'-O)-methyltransferase activity" EXACT []
synonym: "tRNA (guanosine(34)-2'-O)-methyltransferase activity" EXACT []
xref: EC:2.1.1.205 {source="skos:broadMatch"}
xref: MetaCyc:RXN-11868 {source="skos:exactMatch"}
xref: RHEA:42396 {source="skos:broadMatch"}
name: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: cytidine(32)/guanosine(34) in tRNA + 2 S-adenosyl-L-methionine = 2'-O-methylcytidine(32)/2'-O-methylguanosine(34) in tRNA + 2 H+ + 2 S-adenosyl-L-homocysteine." [RHEA:42396]
synonym: "tRNA (cytidine 32-2'-O)-methyltransferase activity" NARROW []
synonym: "tRNA (cytidine(32)-2'-O)-methyltransferase activity" NARROW []
synonym: "tRNA (guanosine 34-2'-O)-methyltransferase activity" NARROW []
synonym: "tRNA (guanosine(34)-2'-O)-methyltransferase activity" NARROW []
xref: EC:2.1.1.205
xref: RHEA:42396
is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25257" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26085" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26086" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28550" xsd:anyURI
created_by: hjd
creation_date: 2020-11-05T22:52:49Z

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47 changes: 2 additions & 45 deletions src/ontology/imports/go-catalytic-activities-participants.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -175056,50 +175056,7 @@

<!-- http://purl.obolibrary.org/obo/GO_0106339 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0106339">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_15378"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_57856"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_59789"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_74269"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_74445"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_74495"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_82748"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0106339"/>



Expand Down Expand Up @@ -184748,5 +184705,5 @@



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->

79 changes: 19 additions & 60 deletions src/ontology/imports/go_taxon_constraints.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -33397,49 +33397,8 @@
<!-- http://purl.obolibrary.org/obo/GO_0106339 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0106339">
<rdfs:subClassOf rdf:nodeID="genid4497"/>
<rdfs:subClassOf rdf:nodeID="genid4500"/>
<owl:disjointWith rdf:nodeID="genid4503"/>
<obo:RO_0002161 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Class>
<owl:Class rdf:nodeID="genid4497">
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
<owl:Restriction rdf:nodeID="genid4500">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom>
<owl:Class>
<owl:complementOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction rdf:nodeID="genid4503">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Restriction>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0106339"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4497"/>
<oboInOwl:source>PMID:18068186</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0106339"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4500"/>
<oboInOwl:source>PMID:18068186</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0106339"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#disjointWith"/>
<owl:annotatedTarget rdf:nodeID="genid4503"/>
<oboInOwl:source>PMID:18068186</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0106339"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002161"/>
Expand Down Expand Up @@ -34684,27 +34643,27 @@
<!-- http://purl.obolibrary.org/obo/GO_0141133 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0141133">
<rdfs:subClassOf rdf:nodeID="genid4660"/>
<rdfs:subClassOf rdf:nodeID="genid4662"/>
<rdfs:subClassOf rdf:nodeID="genid4652"/>
<rdfs:subClassOf rdf:nodeID="genid4654"/>
</owl:Class>
<owl:Restriction rdf:nodeID="genid4660">
<owl:Restriction rdf:nodeID="genid4652">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
</owl:Restriction>
<owl:Restriction rdf:nodeID="genid4662">
<owl:Restriction rdf:nodeID="genid4654">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
</owl:Restriction>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141133"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4660"/>
<owl:annotatedTarget rdf:nodeID="genid4652"/>
<oboInOwl:source>PMID:24739148</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141133"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4662"/>
<owl:annotatedTarget rdf:nodeID="genid4654"/>
<oboInOwl:source>PMID:24739148</oboInOwl:source>
</owl:Axiom>

Expand Down Expand Up @@ -34732,27 +34691,27 @@
<!-- http://purl.obolibrary.org/obo/GO_0141153 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0141153">
<rdfs:subClassOf rdf:nodeID="genid4666"/>
<rdfs:subClassOf rdf:nodeID="genid4668"/>
<rdfs:subClassOf rdf:nodeID="genid4658"/>
<rdfs:subClassOf rdf:nodeID="genid4660"/>
</owl:Class>
<owl:Restriction rdf:nodeID="genid4666">
<owl:Restriction rdf:nodeID="genid4658">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Restriction>
<owl:Restriction rdf:nodeID="genid4668">
<owl:Restriction rdf:nodeID="genid4660">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2157"/>
</owl:Restriction>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141153"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4666"/>
<owl:annotatedTarget rdf:nodeID="genid4658"/>
<oboInOwl:source>PMID:15557260</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141153"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4668"/>
<owl:annotatedTarget rdf:nodeID="genid4660"/>
<oboInOwl:source>PMID:15557260</oboInOwl:source>
</owl:Axiom>

Expand All @@ -34761,27 +34720,27 @@
<!-- http://purl.obolibrary.org/obo/GO_0141169 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0141169">
<rdfs:subClassOf rdf:nodeID="genid4670"/>
<rdfs:subClassOf rdf:nodeID="genid4672"/>
<rdfs:subClassOf rdf:nodeID="genid4662"/>
<rdfs:subClassOf rdf:nodeID="genid4664"/>
</owl:Class>
<owl:Restriction rdf:nodeID="genid4670">
<owl:Restriction rdf:nodeID="genid4662">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
</owl:Restriction>
<owl:Restriction rdf:nodeID="genid4672">
<owl:Restriction rdf:nodeID="genid4664">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
</owl:Restriction>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141169"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4670"/>
<owl:annotatedTarget rdf:nodeID="genid4662"/>
<oboInOwl:source>PMID:31546611</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0141169"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:nodeID="genid4672"/>
<owl:annotatedTarget rdf:nodeID="genid4664"/>
<oboInOwl:source>PMID:31546611</oboInOwl:source>
</owl:Axiom>

Expand Down Expand Up @@ -37766,5 +37725,5 @@



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->

12 changes: 6 additions & 6 deletions src/taxon_constraints/never_in_taxon.ofn
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Original file line number Diff line number Diff line change
Expand Up @@ -372,7 +372,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0098769>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0098770>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0106036>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0106037>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0106339>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0106340>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0120020>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0120164>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0140223>))
Expand Down Expand Up @@ -3751,12 +3751,12 @@ DisjointClasses(<http://purl.obolibrary.org/obo/GO_0106037> ObjectSomeValuesFrom
DisjointClasses(<http://purl.obolibrary.org/obo/GO_0106037> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4896>))
DisjointClasses(<http://purl.obolibrary.org/obo/GO_0106037> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_4932>))

# Class: <http://purl.obolibrary.org/obo/GO_0106339> (<http://purl.obolibrary.org/obo/GO_0106339>)
# Class: <http://purl.obolibrary.org/obo/GO_0106340> (<http://purl.obolibrary.org/obo/GO_0106340>)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/RO_0002161> <http://purl.obolibrary.org/obo/GO_0106339> <http://purl.obolibrary.org/obo/NCBITaxon_2157>)
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106339> ObjectComplementOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2157>)))
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106339> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_2157>)))
DisjointClasses(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106339> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2157>))
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/RO_0002161> <http://purl.obolibrary.org/obo/GO_0106340> <http://purl.obolibrary.org/obo/NCBITaxon_2157>)
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106340> ObjectComplementOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2157>)))
SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106340> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> ObjectComplementOf(<http://purl.obolibrary.org/obo/NCBITaxon_2157>)))
DisjointClasses(Annotation(<http://www.geneontology.org/formats/oboInOwl#source> "PMID:18068186"^^xsd:string) <http://purl.obolibrary.org/obo/GO_0106340> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2157>))

# Class: <http://purl.obolibrary.org/obo/GO_0120020> (<http://purl.obolibrary.org/obo/GO_0120020>)

Expand Down
2 changes: 1 addition & 1 deletion src/taxon_constraints/never_in_taxon.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -574,7 +574,7 @@ GO:0003365 establishment of cell polarity involved in ameboidal cell migration N
GO:0090398 cellular senescence NCBITaxon:4751 Fungi
GO:0000365 mRNA trans splicing, via spliceosome NCBITaxon:4751 Fungi
GO:0016477 cell migration NCBITaxon:4890 Ascomycota
GO:0106339 tRNA (cytidine 32-2'-O)-methyltransferase activity NCBITaxon:2157 Archaea PMID:18068186
GO:0106340 tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase activity NCBITaxon:2157 Archaea PMID:18068186
GO:0035658 Piccolo NuA4 histone acetyltransferase complex NCBITaxon:4896 Schizosaccharomyces pombe PMID:37550452
GO:0002224 toll-like receptor signaling pathway NCBITaxon:7215 Drosophila PMID:30034391
GO:0017015 regulation of transforming growth factor beta receptor signaling pathway NCBITaxon:4751 Fungi
Expand Down
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