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Reparent Fermentation under metabolism, not respiration (#472) #478

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4 changes: 2 additions & 2 deletions metpo-base.json
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Expand Up @@ -20775,7 +20775,7 @@
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"val" : "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
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}, {
"sub" : "https://w3id.org/metpo/1002005",
"pred" : "is_a",
"obj" : "https://w3id.org/metpo/1000800"
"obj" : "https://w3id.org/metpo/1000060"
}, {
"sub" : "https://w3id.org/metpo/1002006",
"pred" : "is_a",
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4 changes: 2 additions & 2 deletions metpo-base.obo
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Expand Up @@ -9657,10 +9657,10 @@ is_a: metpo:1000060 ! metabolism
[Term]
id: metpo:1002005
name: Fermentation
def: "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
def: "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://github.com/jmadin/bacteria_archaea_traits"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://metatraits.embl.de/"}
is_a: metpo:1000800 ! respiration
is_a: metpo:1000060 ! metabolism
property_value: IAO:0000117 "Luke Wang" xsd:string

[Term]
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6 changes: 3 additions & 3 deletions metpo-base.owl
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Expand Up @@ -20996,16 +20996,16 @@
<!-- https://w3id.org/metpo/1002005 -->

<owl:Class rdf:about="https://w3id.org/metpo/1002005">
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000800"/>
<obo:IAO_0000115>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000060"/>
<obo:IAO_0000115>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<obo:IAO_0000117>Luke Wang</obo:IAO_0000117>
<oboInOwl:hasRelatedSynonym>fermentation</oboInOwl:hasRelatedSynonym>
<rdfs:label>Fermentation</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="https://w3id.org/metpo/1002005"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<owl:annotatedTarget>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/GO_0006113"/>
</owl:Axiom>
<owl:Axiom>
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4 changes: 2 additions & 2 deletions metpo-full.json
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Expand Up @@ -20773,7 +20773,7 @@
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"val" : "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
Expand Down Expand Up @@ -31059,7 +31059,7 @@
}, {
"sub" : "https://w3id.org/metpo/1002005",
"pred" : "is_a",
"obj" : "https://w3id.org/metpo/1000800"
"obj" : "https://w3id.org/metpo/1000060"
}, {
"sub" : "https://w3id.org/metpo/1002006",
"pred" : "is_a",
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4 changes: 2 additions & 2 deletions metpo-full.obo
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Expand Up @@ -9656,10 +9656,10 @@ is_a: metpo:1000060 ! metabolism
[Term]
id: metpo:1002005
name: Fermentation
def: "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
def: "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://github.com/jmadin/bacteria_archaea_traits"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://metatraits.embl.de/"}
is_a: metpo:1000800 ! respiration
is_a: metpo:1000060 ! metabolism
property_value: IAO:0000117 "Luke Wang" xsd:string

[Term]
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6 changes: 3 additions & 3 deletions metpo-full.owl
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Expand Up @@ -21006,16 +21006,16 @@
<!-- https://w3id.org/metpo/1002005 -->

<owl:Class rdf:about="https://w3id.org/metpo/1002005">
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000800"/>
<obo:IAO_0000115>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000060"/>
<obo:IAO_0000115>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<obo:IAO_0000117>Luke Wang</obo:IAO_0000117>
<oboInOwl:hasRelatedSynonym>fermentation</oboInOwl:hasRelatedSynonym>
<rdfs:label>Fermentation</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="https://w3id.org/metpo/1002005"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<owl:annotatedTarget>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/GO_0006113"/>
</owl:Axiom>
<owl:Axiom>
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4 changes: 2 additions & 2 deletions metpo.json
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Expand Up @@ -20773,7 +20773,7 @@
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"val" : "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000119",
Expand Down Expand Up @@ -31059,7 +31059,7 @@
}, {
"sub" : "https://w3id.org/metpo/1002005",
"pred" : "is_a",
"obj" : "https://w3id.org/metpo/1000800"
"obj" : "https://w3id.org/metpo/1000060"
}, {
"sub" : "https://w3id.org/metpo/1002006",
"pred" : "is_a",
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4 changes: 2 additions & 2 deletions metpo.obo
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Expand Up @@ -9656,10 +9656,10 @@ is_a: metpo:1000060 ! metabolism
[Term]
id: metpo:1002005
name: Fermentation
def: "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
def: "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors." [] {IAO:0000119="GO:0006113"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://github.com/jmadin/bacteria_archaea_traits"}
synonym: "fermentation" RELATED [] {IAO:0000119="https://metatraits.embl.de/"}
is_a: metpo:1000800 ! respiration
is_a: metpo:1000060 ! metabolism
property_value: IAO:0000117 "Luke Wang" xsd:string

[Term]
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6 changes: 3 additions & 3 deletions metpo.owl
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Expand Up @@ -21006,16 +21006,16 @@
<!-- https://w3id.org/metpo/1002005 -->

<owl:Class rdf:about="https://w3id.org/metpo/1002005">
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000800"/>
<obo:IAO_0000115>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<rdfs:subClassOf rdf:resource="https://w3id.org/metpo/1000060"/>
<obo:IAO_0000115>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</obo:IAO_0000115>
<obo:IAO_0000117>Luke Wang</obo:IAO_0000117>
<oboInOwl:hasRelatedSynonym>fermentation</oboInOwl:hasRelatedSynonym>
<rdfs:label>Fermentation</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="https://w3id.org/metpo/1002005"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<owl:annotatedTarget>A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/GO_0006113"/>
</owl:Axiom>
<owl:Axiom>
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4 changes: 2 additions & 2 deletions src/ontology/components/metpo_sheet.owl
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Expand Up @@ -12434,12 +12434,12 @@ SubClassOf(<https://w3id.org/metpo/1002003> <https://w3id.org/metpo/1000060>)

# Class: <https://w3id.org/metpo/1002005> (Fermentation)

AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/GO_0006113>) <http://purl.obolibrary.org/obo/IAO_0000115> <https://w3id.org/metpo/1002005> "A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.")
AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> <http://purl.obolibrary.org/obo/GO_0006113>) <http://purl.obolibrary.org/obo/IAO_0000115> <https://w3id.org/metpo/1002005> "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <https://w3id.org/metpo/1002005> "Luke Wang")
AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> <https://github.com/jmadin/bacteria_archaea_traits>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <https://w3id.org/metpo/1002005> "fermentation")
AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> <https://metatraits.embl.de/>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <https://w3id.org/metpo/1002005> "fermentation")
AnnotationAssertion(rdfs:label <https://w3id.org/metpo/1002005> "Fermentation")
SubClassOf(<https://w3id.org/metpo/1002005> <https://w3id.org/metpo/1000800>)
SubClassOf(<https://w3id.org/metpo/1002005> <https://w3id.org/metpo/1000060>)

# Class: <https://w3id.org/metpo/1002006> (Syntrophy)

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2 changes: 1 addition & 1 deletion src/templates/metpo_sheet.tsv
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Expand Up @@ -208,7 +208,7 @@ METPO:1001104 biosafety level 3 owl:Class biosafety level A biosafety level that
METPO:1001105 biosafety level 4 owl:Class biosafety level A biosafety level that pose extreme risk of life-threatening disease through aerosol transmission with no available treatment. 4 https://bacdive.dsmz.de/
METPO:1001106 biosafety level 5 owl:Class biosafety level A biosafety level that is proposed as a classification beyond BSL-4 for hypothetical biological agents requiring enhanced containment. 5 https://bacdive.dsmz.de/
METPO:1002003 Cable bacteria metabolism owl:Class metabolism A metabolism in which electrons are transferred over centimeter-scale distances through multicellular filaments.
METPO:1002005 Fermentation owl:Class respiration A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors. GO:0006113 Luke Wang fermentation https://github.com/jmadin/bacteria_archaea_traits fermentation https://metatraits.embl.de/
METPO:1002005 Fermentation owl:Class metabolism A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors. GO:0006113 Luke Wang fermentation https://github.com/jmadin/bacteria_archaea_traits fermentation https://metatraits.embl.de/
METPO:1002006 Syntrophy owl:Class metabolism A metabolism in which the metabolism of one species is thermodynamically dependent on the removal of its products by another species. Jed Dongjin Kim-Ozaeta
METPO:1003000 pH growth preference owl:Class phenotype A phenotype that describes how the rate and extent of population growth are affected by environmental pH. OMP:0005008 pH growth https://metatraits.embl.de/
METPO:1003001 neutrophilic owl:Class pH growth preference A pH growth preference characterized by optimal growth at near-neutral pH values, typically between pH 6.5 and 7.5. PATO:0070046|OMP:0005010 Anthea Guo neutrophile|neutralophile|neutralophilic
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