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Merge pull request #36 from NFDI4Chem/34-Addition-reactions-MOP
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Addition of trimerization, cyclotrimerization & protein trimerization to MOP
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@rsc-ontologies
rsc-ontologies authored Feb 17, 2022
2 parents c196e84 + 1cc6d4d commit 3c84124
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89 changes: 58 additions & 31 deletions mop.obo
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
format-version: 1.2
data-version: releases/2014-09-03
data-version: releases/2022-02-01
synonymtypedef: FORMULA "FORMULA"
synonymtypedef: IUPAC_NAME "IUPAC NAME"
ontology: mop
property_value: http://purl.org/dc/elements/1.1/date "01:02:2022 11:15" xsd:string
property_value: http://purl.org/dc/elements/1.1/description "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "MOP" xsd:string
property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/
Expand Down Expand Up @@ -30,6 +31,11 @@ id: CHEBI:18379
name: nitrile
is_a: CHEBI:36357 ! polyatomic entity

[Term]
id: CHEBI:22221
name: acyl group
is_a: CHEBI:33247 ! organic group

[Term]
id: CHEBI:23367
name: molecular entity
Expand Down Expand Up @@ -111,6 +117,11 @@ id: CHEBI:33246
name: inorganic group
is_a: CHEBI:24433 ! group

[Term]
id: CHEBI:33247
name: organic group
is_a: CHEBI:24433 ! group

[Term]
id: CHEBI:33595
name: cyclic compound
Expand Down Expand Up @@ -186,6 +197,11 @@ synonym: "isotellurocyanato" EXACT IUPAC_NAME [IUPAC:]
synonym: "TeCN-" RELATED [IUPAC:]
is_a: CHEBI:36823 ! pseudohalo groups

[Term]
id: CHEBI:37838
name: carboacyl group
is_a: CHEBI:22221 ! acyl group

[Term]
id: CHEBI:37997
name: homopolymer
Expand Down Expand Up @@ -238,6 +254,11 @@ synonym: "NC-" RELATED [IUPAC:]
xref: MSDchem:CN "MSDchem"
is_a: CHEBI:36823 ! pseudohalo groups

[Term]
id: CHEBI:51100
name: sulfonyl groups
is_a: CHEBI:24433 ! group

[Term]
id: CHEBI:51142
name: amino groups
Expand All @@ -251,6 +272,7 @@ is_a: CHEBI:24433 ! group
[Term]
id: CHEBI:51870
name: boryl group
is_a: CHEBI:24433 ! group
is_a: CHEBI:33246 ! inorganic group

[Term]
Expand Down Expand Up @@ -329,16 +351,24 @@ name: acetylenic compound
is_a: CHEBI:36357 ! polyatomic entity

[Term]
id: CHEBI:51870
name: boryl group
is_a: CHEBI:24433
id: GO:0070206
name: protein trimerization
namespace: biological_process
def: "The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits." []
synonym: "protein trimer assembly" EXACT []
synonym: "protein trimer biosynthesis" EXACT []
synonym: "protein trimer biosynthetic process" EXACT []
synonym: "protein trimer formation" EXACT []
xref: GOC:hjd
is_a: MOP:0000715 ! trimerization
property_value: IAO:0000412 http://purl.obolibrary.org/obo/go/releases/2022-01-13/go.owl xsd:string

[Term]
id: MOP:0000000
name: borylation
def: "Formation of a covalent bond between a substrate and a boryl group (-BR'R')." [https://orcid.org/0000-0001-5985-7429]
is_a: MOP:0000801 ! formation of covalent bond with boron centre
relationship: BFO:0000057 CHEBI:51870 ! boryl group
relationship: BFO:0000057 CHEBI:51870 ! has_participant boryl group

[Term]
id: MOP:0000001
Expand Down Expand Up @@ -563,22 +593,7 @@ def: "Formation of a covalent bond between a substrate and a carboacyl group." [
synonym: "carboacylation" EXACT []
is_a: MOP:0000479 ! acylation
is_a: MOP:0000800 ! formation of covalent bond with carbon centre
relationship: BFO:0000057 CHEBI:37838

[Term]
id: CHEBI:37838
name: carboacyl group
is_a: CHEBI:22221 ! acyl group

[Term]
id: CHEBI:22221
name: acyl group
is_a: CHEBI:33247 ! organic group

[Term]
id: CHEBI:33247
name: organic group
is_a: CHEBI:24433
relationship: BFO:0000057 CHEBI:37838 ! has_participant carboacyl group

[Term]
id: MOP:0000029
Expand Down Expand Up @@ -4156,8 +4171,8 @@ name: acylation
def: "Formation of a covalent bond between a substrate and an acyl group." [RSC:xp]
comment: you probably want "carboacylation", MOP:0000028, here
synonym: "acylation" EXACT []
is_a: MOP:0000800 ! formation of covalent bond with group
relationship: BFO:0000057 CHEBI:22221
is_a: MOP:0000800 ! formation of covalent bond with carbon centre
relationship: BFO:0000057 CHEBI:22221 ! has_participant acyl group

[Term]
id: MOP:0000480
Expand Down Expand Up @@ -4631,13 +4646,8 @@ def: "Formation of a covalent bond between a substrate and a sulfonyl group." [R
synonym: "sulfonylation" EXACT []
is_a: MOP:0000798 ! formation of covalent bond with sulfur centre
intersection_of: MOP:0000798 ! formation of covalent bond with sulfur centre
intersection_of: BFO:0000057 CHEBI:51100
relationship: BFO:0000057 CHEBI:51100

[Term]
id: CHEBI:51100
name: sulfonyl groups
is_a: CHEBI:24433
intersection_of: BFO:0000057 CHEBI:51100 ! has_participant sulfonyl groups
relationship: BFO:0000057 CHEBI:51100 ! has_participant sulfonyl groups

[Term]
id: MOP:0000540
Expand Down Expand Up @@ -6050,7 +6060,7 @@ relationship: BFO:0000078 CHEBI:33641 ! has participant ceasing to exist olefin
[Term]
id: MOP:0000713
name: acetylene reduction
def: "Hydrogenation of an acetylene to an olefin."
def: "Hydrogenation of an acetylene to an olefin." []
is_a: MOP:0000589 ! hydrogenation

[Term]
Expand All @@ -6064,6 +6074,23 @@ relationship: BFO:0000057 CHEBI:52214 ! has_participant ligand
created_by: http://orcid.org/0000-0002-4378-6061
creation_date: 2021-11-03T09:13:45Z

[Term]
id: MOP:0000715
name: trimerization
def: "The formation of a trimer from three molecular subunits." [https://en.wiktionary.org/wiki/trimerization]
is_a: MOP:0000543 ! molecular process
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4378-6061
property_value: http://purl.org/dc/elements/1.1/date 2022-02-01T09:40:48Z xsd:dateTime

[Term]
id: MOP:0000716
name: cyclotrimerization
def: "The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures thereof). A metal catalyst is usually required for this type of reaction." [https://doi.org/10.1002/anie.200700802]
is_a: MOP:0000562 ! cycloaddition
is_a: MOP:0000715 ! trimerization
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4378-6061
property_value: http://purl.org/dc/elements/1.1/date 2022-02-01T09:48:59Z xsd:dateTime

[Term]
id: MOP:0000721
name: [3,3]-sigmatropic rearrangement
Expand Down
114 changes: 112 additions & 2 deletions mop.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mop.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mop/releases/2014-09-03/mop.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mop/releases/2022-02-01/mop.owl"/>
<dc:date>01:02:2022 11:15</dc:date>
<dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.</dc:description>
<dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MOP</dc:title>
<terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
Expand Down Expand Up @@ -46,6 +47,14 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
<rdfs:label xml:lang="en">imported from</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0100001 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
Expand All @@ -70,6 +79,36 @@



<!-- http://purl.org/dc/elements/1.1/creator -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>



<!-- http://purl.org/dc/elements/1.1/date -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>



<!-- http://purl.org/dc/elements/1.1/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>



<!-- http://purl.org/dc/elements/1.1/title -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>



<!-- http://purl.org/dc/terms/license -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>



<!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty">
Expand Down Expand Up @@ -130,6 +169,14 @@



<!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
<rdfs:label>has_obo_namespace</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym">
Expand All @@ -152,6 +199,12 @@



<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>



<!-- http://www.w3.org/2000/01/rdf-schema#comment -->

<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
Expand Down Expand Up @@ -1259,6 +1312,24 @@



<!-- http://purl.obolibrary.org/obo/GO_0070206 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0070206">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOP_0000715"/>
<obo:IAO_0000115>The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://purl.obolibrary.org/obo/go/releases/2022-01-13/go.owl</obo:IAO_0000412>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hjd</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>protein trimer assembly</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>protein trimer biosynthesis</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>protein trimer biosynthetic process</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>protein trimer formation</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
<oboInOwl:id>GO:0070206</oboInOwl:id>
<rdfs:label>protein trimerization</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MOP_0000000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOP_0000000">
Expand Down Expand Up @@ -15387,6 +15458,45 @@



<!-- http://purl.obolibrary.org/obo/MOP_0000715 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOP_0000715">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOP_0000543"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The formation of a trimer from three molecular subunits.</obo:IAO_0000115>
<dc:creator rdf:resource="http://orcid.org/0000-0002-4378-6061"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-02-01T09:40:48Z</dc:date>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MOP:0000715</oboInOwl:id>
<rdfs:label xml:lang="en">trimerization</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOP_0000715"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The formation of a trimer from three molecular subunits.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://en.wiktionary.org/wiki/trimerization</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/MOP_0000716 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOP_0000716">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOP_0000562"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOP_0000715"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures thereof). A metal catalyst is usually required for this type of reaction.</obo:IAO_0000115>
<dc:creator rdf:resource="http://orcid.org/0000-0002-4378-6061"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-02-01T09:48:59Z</dc:date>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MOP:0000716</oboInOwl:id>
<rdfs:label xml:lang="en">cyclotrimerization</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOP_0000716"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures thereof). A metal catalyst is usually required for this type of reaction.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.1002/anie.200700802</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/MOP_0000721 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOP_0000721">
Expand Down Expand Up @@ -67905,5 +68015,5 @@



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->

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