From 5b60effce0ac88ae87155e473f309c979c80b1e0 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Tue, 2 Jun 2026 12:45:44 -0400 Subject: [PATCH] fix(modeling): reparent Fermentation under metabolism, not respiration (#472) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit METPO:1002005 Fermentation was a child of `respiration` with a self-contradictory definition ("A respiration that … without using an external electron acceptor"). Fermentation is canonically distinct from respiration (cf. GO:0006113 vs GO:0009060). Reparented to `metabolism` (respiration's own parent, making Fermentation a sibling of respiration) and reworded the genus to match: "A metabolism in which energy is generated through the oxidation of organic compounds without using an external electron acceptor …". Edited in the Sheet (SoT) and rebuilt. Fixes #472. Co-Authored-By: Claude Opus 4.8 --- metpo-base.json | 4 ++-- metpo-base.obo | 4 ++-- metpo-base.owl | 6 +++--- metpo-full.json | 4 ++-- metpo-full.obo | 4 ++-- metpo-full.owl | 6 +++--- metpo.json | 4 ++-- metpo.obo | 4 ++-- metpo.owl | 6 +++--- src/ontology/components/metpo_sheet.owl | 4 ++-- src/templates/metpo_sheet.tsv | 2 +- 11 files changed, 24 insertions(+), 24 deletions(-) diff --git a/metpo-base.json b/metpo-base.json index 245bf71a..a49c61bb 100644 --- a/metpo-base.json +++ b/metpo-base.json @@ -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", @@ -31055,7 +31055,7 @@ }, { "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", diff --git a/metpo-base.obo b/metpo-base.obo index 63da2774..a0a19f4a 100644 --- a/metpo-base.obo +++ b/metpo-base.obo @@ -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] diff --git a/metpo-base.owl b/metpo-base.owl index efbd8428..3463b1e2 100644 --- a/metpo-base.owl +++ b/metpo-base.owl @@ -20996,8 +20996,8 @@ - - 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. + + 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. Luke Wang fermentation Fermentation @@ -21005,7 +21005,7 @@ - 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. + 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. diff --git a/metpo-full.json b/metpo-full.json index a2b82184..b14cb956 100644 --- a/metpo-full.json +++ b/metpo-full.json @@ -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", @@ -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", diff --git a/metpo-full.obo b/metpo-full.obo index 3d906ff8..fe29ee83 100644 --- a/metpo-full.obo +++ b/metpo-full.obo @@ -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] diff --git a/metpo-full.owl b/metpo-full.owl index 8668138f..7bc6248d 100644 --- a/metpo-full.owl +++ b/metpo-full.owl @@ -21006,8 +21006,8 @@ - - 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. + + 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. Luke Wang fermentation Fermentation @@ -21015,7 +21015,7 @@ - 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. + 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. diff --git a/metpo.json b/metpo.json index e5f08713..e768c462 100644 --- a/metpo.json +++ b/metpo.json @@ -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", @@ -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", diff --git a/metpo.obo b/metpo.obo index 9af46e27..fecc8d1c 100644 --- a/metpo.obo +++ b/metpo.obo @@ -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] diff --git a/metpo.owl b/metpo.owl index 53712450..999460cb 100644 --- a/metpo.owl +++ b/metpo.owl @@ -21006,8 +21006,8 @@ - - 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. + + 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. Luke Wang fermentation Fermentation @@ -21015,7 +21015,7 @@ - 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. + 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. diff --git a/src/ontology/components/metpo_sheet.owl b/src/ontology/components/metpo_sheet.owl index cd38c3cc..fc739b21 100644 --- a/src/ontology/components/metpo_sheet.owl +++ b/src/ontology/components/metpo_sheet.owl @@ -12434,12 +12434,12 @@ SubClassOf( ) # Class: (Fermentation) -AnnotationAssertion(Annotation( ) "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( ) "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( "Luke Wang") AnnotationAssertion(Annotation( ) "fermentation") AnnotationAssertion(Annotation( ) "fermentation") AnnotationAssertion(rdfs:label "Fermentation") -SubClassOf( ) +SubClassOf( ) # Class: (Syntrophy) diff --git a/src/templates/metpo_sheet.tsv b/src/templates/metpo_sheet.tsv index d639eacf..176f48d8 100644 --- a/src/templates/metpo_sheet.tsv +++ b/src/templates/metpo_sheet.tsv @@ -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