From f871f4da5b1da17bbd342ce51696f3c1c80d0368 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Tue, 2 Jun 2026 12:40:51 -0400 Subject: [PATCH] fix(content): correct alkaphilic label spelling (#470) and NaCl delta high range bound (#471) Two pure-data corrections, made in the Google Sheet (SoT) and rebuilt: - METPO:1003002/1003004/1003005 labels `alkaphilic` -> `alkaliphilic` (the exact synonyms already had the correct spelling). - METPO:1000482 NaCl delta high: moved `8` from range_max to range_min so it agrees with the `xsd:decimal[>= 8]` equivalent_class_formula (a lower bound). Fixes #470, #471. Co-Authored-By: Claude Opus 4.8 --- metpo-base.json | 8 ++++---- metpo-base.obo | 8 ++++---- metpo-base.owl | 8 ++++---- metpo-full.json | 8 ++++---- metpo-full.obo | 8 ++++---- metpo-full.owl | 8 ++++---- metpo.json | 8 ++++---- metpo.obo | 8 ++++---- metpo.owl | 8 ++++---- src/ontology/components/metpo_sheet.owl | 14 +++++++------- src/templates/metpo_sheet.tsv | 8 ++++---- src/templates/stubs.tsv | 6 +++--- 12 files changed, 50 insertions(+), 50 deletions(-) diff --git a/metpo-base.json b/metpo-base.json index 893d6e82..245bf71a 100644 --- a/metpo-base.json +++ b/metpo-base.json @@ -14483,7 +14483,7 @@ "pred" : "http://qudt.org/schema/qudt/ucumCode", "val" : "%" }, { - "pred" : "https://w3id.org/metpo/range_max", + "pred" : "https://w3id.org/metpo/range_min", "val" : "8" } ] } @@ -21321,7 +21321,7 @@ } }, { "id" : "https://w3id.org/metpo/1003002", - "lbl" : "alkaphilic", + "lbl" : "alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21404,7 +21404,7 @@ } }, { "id" : "https://w3id.org/metpo/1003004", - "lbl" : "obligately alkaphilic", + "lbl" : "obligately alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21445,7 +21445,7 @@ } }, { "id" : "https://w3id.org/metpo/1003005", - "lbl" : "facultatively alkaphilic", + "lbl" : "facultatively alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { diff --git a/metpo-base.obo b/metpo-base.obo index e186eb10..63da2774 100644 --- a/metpo-base.obo +++ b/metpo-base.obo @@ -7539,7 +7539,7 @@ id: metpo:1000482 name: NaCl delta high synonym: "Nad_>8" RELATED [] {IAO:0000119="https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv"} is_a: metpo:1000335 ! NaCl delta -property_value: metpo:range_max "8" xsd:string +property_value: metpo:range_min "8" xsd:string property_value: qudt:ucumCode "%" xsd:string [Term] @@ -9927,7 +9927,7 @@ property_value: IAO:0000117 "Anthea Guo" xsd:string [Term] id: metpo:1003002 -name: alkaphilic +name: alkaliphilic def: "A pH growth preference in which an organism grows optimally at pH values above 9." [] {IAO:0000119="OMP:0005009", IAO:0000119="MICRO:0001549", IAO:0000119="OMP:0005010", IAO:0000119="ENVO:00002022", IAO:0000119="OMP:0005011"} synonym: "alkaliphile" EXACT [] synonym: "alkaliphilic" EXACT [] @@ -9946,7 +9946,7 @@ is_a: metpo:1003000 ! pH growth preference [Term] id: metpo:1003004 -name: obligately alkaphilic +name: obligately alkaliphilic def: "A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH." [] {IAO:0000119="OMP:0007947", IAO:0000119="ENVO:00002022", IAO:0000119="MICRO:0001565", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "obligate alkaliphile" EXACT [] synonym: "obligate alkaphilic" EXACT [] @@ -9956,7 +9956,7 @@ property_value: IAO:0000117 "Luke Wang" xsd:string [Term] id: metpo:1003005 -name: facultatively alkaphilic +name: facultatively alkaliphilic def: "A pH growth preference in which an organism can grow at alkaline pH but does not require it." [] {IAO:0000119="MICRO:0001558", IAO:0000119="OMP:0005009", IAO:0000119="OMP:0007947", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "facultative alkaliphile" EXACT [] synonym: "facultative alkaphilic" EXACT [] diff --git a/metpo-base.owl b/metpo-base.owl index e312894b..efbd8428 100644 --- a/metpo-base.owl +++ b/metpo-base.owl @@ -15539,7 +15539,7 @@ % Nad_>8 NaCl delta high - 8 + 8 @@ -21461,7 +21461,7 @@ alkaliphilic alkalophile alkalophilic - alkaphilic + alkaliphilic @@ -21514,7 +21514,7 @@ obligate alkaliphile obligate alkaphilic obligately alkaliphilic - obligately alkaphilic + obligately alkaliphilic @@ -21537,7 +21537,7 @@ facultative alkaliphile facultative alkaphilic facultatively alkaliphilic - facultatively alkaphilic + facultatively alkaliphilic diff --git a/metpo-full.json b/metpo-full.json index a996c28e..a2b82184 100644 --- a/metpo-full.json +++ b/metpo-full.json @@ -14481,7 +14481,7 @@ "pred" : "http://qudt.org/schema/qudt/ucumCode", "val" : "%" }, { - "pred" : "https://w3id.org/metpo/range_max", + "pred" : "https://w3id.org/metpo/range_min", "val" : "8" } ] } @@ -21319,7 +21319,7 @@ } }, { "id" : "https://w3id.org/metpo/1003002", - "lbl" : "alkaphilic", + "lbl" : "alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21402,7 +21402,7 @@ } }, { "id" : "https://w3id.org/metpo/1003004", - "lbl" : "obligately alkaphilic", + "lbl" : "obligately alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21443,7 +21443,7 @@ } }, { "id" : "https://w3id.org/metpo/1003005", - "lbl" : "facultatively alkaphilic", + "lbl" : "facultatively alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { diff --git a/metpo-full.obo b/metpo-full.obo index 97f7e761..3d906ff8 100644 --- a/metpo-full.obo +++ b/metpo-full.obo @@ -7538,7 +7538,7 @@ id: metpo:1000482 name: NaCl delta high synonym: "Nad_>8" RELATED [] {IAO:0000119="https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv"} is_a: metpo:1000335 ! NaCl delta -property_value: metpo:range_max "8" xsd:string +property_value: metpo:range_min "8" xsd:string property_value: qudt:ucumCode "%" xsd:string [Term] @@ -9926,7 +9926,7 @@ property_value: IAO:0000117 "Anthea Guo" xsd:string [Term] id: metpo:1003002 -name: alkaphilic +name: alkaliphilic def: "A pH growth preference in which an organism grows optimally at pH values above 9." [] {IAO:0000119="OMP:0005009", IAO:0000119="MICRO:0001549", IAO:0000119="OMP:0005010", IAO:0000119="ENVO:00002022", IAO:0000119="OMP:0005011"} synonym: "alkaliphile" EXACT [] synonym: "alkaliphilic" EXACT [] @@ -9945,7 +9945,7 @@ is_a: metpo:1003000 ! pH growth preference [Term] id: metpo:1003004 -name: obligately alkaphilic +name: obligately alkaliphilic def: "A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH." [] {IAO:0000119="OMP:0007947", IAO:0000119="ENVO:00002022", IAO:0000119="MICRO:0001565", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "obligate alkaliphile" EXACT [] synonym: "obligate alkaphilic" EXACT [] @@ -9955,7 +9955,7 @@ property_value: IAO:0000117 "Luke Wang" xsd:string [Term] id: metpo:1003005 -name: facultatively alkaphilic +name: facultatively alkaliphilic def: "A pH growth preference in which an organism can grow at alkaline pH but does not require it." [] {IAO:0000119="MICRO:0001558", IAO:0000119="OMP:0005009", IAO:0000119="OMP:0007947", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "facultative alkaliphile" EXACT [] synonym: "facultative alkaphilic" EXACT [] diff --git a/metpo-full.owl b/metpo-full.owl index 1333c94b..8668138f 100644 --- a/metpo-full.owl +++ b/metpo-full.owl @@ -15549,7 +15549,7 @@ % Nad_>8 NaCl delta high - 8 + 8 @@ -21471,7 +21471,7 @@ alkaliphilic alkalophile alkalophilic - alkaphilic + alkaliphilic @@ -21524,7 +21524,7 @@ obligate alkaliphile obligate alkaphilic obligately alkaliphilic - obligately alkaphilic + obligately alkaliphilic @@ -21547,7 +21547,7 @@ facultative alkaliphile facultative alkaphilic facultatively alkaliphilic - facultatively alkaphilic + facultatively alkaliphilic diff --git a/metpo.json b/metpo.json index 99813f05..e5f08713 100644 --- a/metpo.json +++ b/metpo.json @@ -14481,7 +14481,7 @@ "pred" : "http://qudt.org/schema/qudt/ucumCode", "val" : "%" }, { - "pred" : "https://w3id.org/metpo/range_max", + "pred" : "https://w3id.org/metpo/range_min", "val" : "8" } ] } @@ -21319,7 +21319,7 @@ } }, { "id" : "https://w3id.org/metpo/1003002", - "lbl" : "alkaphilic", + "lbl" : "alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21402,7 +21402,7 @@ } }, { "id" : "https://w3id.org/metpo/1003004", - "lbl" : "obligately alkaphilic", + "lbl" : "obligately alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { @@ -21443,7 +21443,7 @@ } }, { "id" : "https://w3id.org/metpo/1003005", - "lbl" : "facultatively alkaphilic", + "lbl" : "facultatively alkaliphilic", "type" : "CLASS", "meta" : { "definition" : { diff --git a/metpo.obo b/metpo.obo index b7246efa..9af46e27 100644 --- a/metpo.obo +++ b/metpo.obo @@ -7538,7 +7538,7 @@ id: metpo:1000482 name: NaCl delta high synonym: "Nad_>8" RELATED [] {IAO:0000119="https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv"} is_a: metpo:1000335 ! NaCl delta -property_value: metpo:range_max "8" xsd:string +property_value: metpo:range_min "8" xsd:string property_value: qudt:ucumCode "%" xsd:string [Term] @@ -9926,7 +9926,7 @@ property_value: IAO:0000117 "Anthea Guo" xsd:string [Term] id: metpo:1003002 -name: alkaphilic +name: alkaliphilic def: "A pH growth preference in which an organism grows optimally at pH values above 9." [] {IAO:0000119="OMP:0005009", IAO:0000119="MICRO:0001549", IAO:0000119="OMP:0005010", IAO:0000119="ENVO:00002022", IAO:0000119="OMP:0005011"} synonym: "alkaliphile" EXACT [] synonym: "alkaliphilic" EXACT [] @@ -9945,7 +9945,7 @@ is_a: metpo:1003000 ! pH growth preference [Term] id: metpo:1003004 -name: obligately alkaphilic +name: obligately alkaliphilic def: "A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH." [] {IAO:0000119="OMP:0007947", IAO:0000119="ENVO:00002022", IAO:0000119="MICRO:0001565", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "obligate alkaliphile" EXACT [] synonym: "obligate alkaphilic" EXACT [] @@ -9955,7 +9955,7 @@ property_value: IAO:0000117 "Luke Wang" xsd:string [Term] id: metpo:1003005 -name: facultatively alkaphilic +name: facultatively alkaliphilic def: "A pH growth preference in which an organism can grow at alkaline pH but does not require it." [] {IAO:0000119="MICRO:0001558", IAO:0000119="OMP:0005009", IAO:0000119="OMP:0007947", IAO:0000119="OMP:0005011", IAO:0000119="OMP:0007771"} synonym: "facultative alkaliphile" EXACT [] synonym: "facultative alkaphilic" EXACT [] diff --git a/metpo.owl b/metpo.owl index 6064d70a..53712450 100644 --- a/metpo.owl +++ b/metpo.owl @@ -15549,7 +15549,7 @@ % Nad_>8 NaCl delta high - 8 + 8 @@ -21471,7 +21471,7 @@ alkaliphilic alkalophile alkalophilic - alkaphilic + alkaliphilic @@ -21524,7 +21524,7 @@ obligate alkaliphile obligate alkaphilic obligately alkaliphilic - obligately alkaphilic + obligately alkaliphilic @@ -21547,7 +21547,7 @@ facultative alkaliphile facultative alkaphilic facultatively alkaliphilic - facultatively alkaphilic + facultatively alkaliphilic diff --git a/src/ontology/components/metpo_sheet.owl b/src/ontology/components/metpo_sheet.owl index be8d9304..cd38c3cc 100644 --- a/src/ontology/components/metpo_sheet.owl +++ b/src/ontology/components/metpo_sheet.owl @@ -10303,7 +10303,7 @@ SubClassOf( ) AnnotationAssertion( "%") AnnotationAssertion(Annotation( ) "Nad_>8") AnnotationAssertion(rdfs:label "NaCl delta high") -AnnotationAssertion( "8") +AnnotationAssertion( "8") EquivalentClasses( ObjectIntersectionOf( DataSomeValuesFrom( DatatypeRestriction(xsd:decimal xsd:minInclusive "8"^^xsd:decimal)))) SubClassOf( ) @@ -12703,14 +12703,14 @@ AnnotationAssertion( "neutrophilic") SubClassOf( ) -# Class: (alkaphilic) +# Class: (alkaliphilic) AnnotationAssertion(Annotation( ) Annotation( ) Annotation( ) Annotation( ) Annotation( ) "A pH growth preference in which an organism grows optimally at pH values above 9.") AnnotationAssertion( "alkaliphile") AnnotationAssertion( "alkaliphilic") AnnotationAssertion( "alkalophile") AnnotationAssertion( "alkalophilic") -AnnotationAssertion(rdfs:label "alkaphilic") +AnnotationAssertion(rdfs:label "alkaliphilic") SubClassOf( ) # Class: (acidophilic) @@ -12722,23 +12722,23 @@ AnnotationAssertion(Annotation( "acidophilic") SubClassOf( ) -# Class: (obligately alkaphilic) +# Class: (obligately alkaliphilic) AnnotationAssertion(Annotation( ) Annotation( ) Annotation( ) Annotation( ) Annotation( ) "A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH.") AnnotationAssertion( "Luke Wang") AnnotationAssertion( "obligate alkaliphile") AnnotationAssertion( "obligate alkaphilic") AnnotationAssertion( "obligately alkaliphilic") -AnnotationAssertion(rdfs:label "obligately alkaphilic") +AnnotationAssertion(rdfs:label "obligately alkaliphilic") SubClassOf( ) -# Class: (facultatively alkaphilic) +# Class: (facultatively alkaliphilic) AnnotationAssertion(Annotation( ) Annotation( ) Annotation( ) Annotation( ) Annotation( ) "A pH growth preference in which an organism can grow at alkaline pH but does not require it.") AnnotationAssertion( "facultative alkaliphile") AnnotationAssertion( "facultative alkaphilic") AnnotationAssertion( "facultatively alkaliphilic") -AnnotationAssertion(rdfs:label "facultatively alkaphilic") +AnnotationAssertion(rdfs:label "facultatively alkaliphilic") SubClassOf( ) # Class: (obligately acidophilic) diff --git a/src/templates/metpo_sheet.tsv b/src/templates/metpo_sheet.tsv index d89af553..d639eacf 100644 --- a/src/templates/metpo_sheet.tsv +++ b/src/templates/metpo_sheet.tsv @@ -59,7 +59,7 @@ METPO:1000478 pH delta high owl:Class pH delta pHd_5_9 https://ordar. METPO:1000479 NaCl delta low owl:Class NaCl delta Nad_<=1 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv % 1 'NaCl delta' and 'METPO:2000071' some xsd:decimal[<= 1] METPO:1000480 NaCl delta mid1 owl:Class NaCl delta Nad_1_3 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv % 1 3 'NaCl delta' and 'METPO:2000071' some xsd:decimal[>= 1, <= 3] METPO:1000481 NaCl delta mid2 owl:Class NaCl delta Nad_3_8 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv % 3 8 'NaCl delta' and 'METPO:2000071' some xsd:decimal[>= 3, <= 8] -METPO:1000482 NaCl delta high owl:Class NaCl delta Nad_>8 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv % 8 'NaCl delta' and 'METPO:2000071' some xsd:decimal[>= 8] +METPO:1000482 NaCl delta high owl:Class NaCl delta Nad_>8 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv % 8 'NaCl delta' and 'METPO:2000071' some xsd:decimal[>= 8] METPO:1000483 temperature delta very low owl:Class temperature delta Td_1_5 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv Cel 1 5 'temperature delta' and 'METPO:2000071' some xsd:decimal[>= 1, <= 5] METPO:1000484 temperature delta low owl:Class temperature delta Td_5_10 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv Cel 5 10 'temperature delta' and 'METPO:2000071' some xsd:decimal[>= 5, <= 10] METPO:1000485 temperature delta mid1 owl:Class temperature delta Td_10_20 https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv Cel 10 20 'temperature delta' and 'METPO:2000071' some xsd:decimal[>= 10, <= 20] @@ -212,10 +212,10 @@ METPO:1002005 Fermentation owl:Class respiration A respiration that generates en 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 -METPO:1003002 alkaphilic owl:Class pH growth preference A pH growth preference in which an organism grows optimally at pH values above 9. ENVO:00002022|MICRO:0001549|OMP:0005009|OMP:0005010|OMP:0005011 alkaliphilic|alkaliphile|alkalophilic|alkalophile +METPO:1003002 alkaliphilic owl:Class pH growth preference A pH growth preference in which an organism grows optimally at pH values above 9. ENVO:00002022|MICRO:0001549|OMP:0005009|OMP:0005010|OMP:0005011 alkaliphilic|alkaliphile|alkalophilic|alkalophile METPO:1003003 acidophilic owl:Class pH growth preference A pH growth preference in which an organism grows optimally at pH values below 5. MICRO:0001549|OMP:0005009|OMP:0005010|OMP:0005011|OMP:0007945 acidophile|acidophil acidophilic https://metatraits.embl.de/ -METPO:1003004 obligately alkaphilic owl:Class pH growth preference A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH. ENVO:00002022|MICRO:0001565|OMP:0005011|OMP:0007771|OMP:0007947 Luke Wang obligate alkaliphile|obligately alkaliphilic|obligate alkaphilic -METPO:1003005 facultatively alkaphilic owl:Class pH growth preference A pH growth preference in which an organism can grow at alkaline pH but does not require it. MICRO:0001558|OMP:0005009|OMP:0005011|OMP:0007771|OMP:0007947 facultative alkaliphile|facultatively alkaliphilic|facultative alkaphilic +METPO:1003004 obligately alkaliphilic owl:Class pH growth preference A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH. ENVO:00002022|MICRO:0001565|OMP:0005011|OMP:0007771|OMP:0007947 Luke Wang obligate alkaliphile|obligately alkaliphilic|obligate alkaphilic +METPO:1003005 facultatively alkaliphilic owl:Class pH growth preference A pH growth preference in which an organism can grow at alkaline pH but does not require it. MICRO:0001558|OMP:0005009|OMP:0005011|OMP:0007771|OMP:0007947 facultative alkaliphile|facultatively alkaliphilic|facultative alkaphilic METPO:1003006 obligately acidophilic owl:Class pH growth preference A pH growth preference characterized by the requirement for acidic environments (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values. MICRO:0001566 Anthea Guo|Jed Dongjin Kim-Ozaeta obligate acidophile|obligately acidophilic METPO:1003007 facultatively acidophilic owl:Class pH growth preference A pH growth preference characterized by optimal growth in acidic environments (pH below 5.5) with the capacity to also grow at near-neutral pH values. MICRO:0001557|OMP:0005009|OMP:0005010|OMP:0007009|OMP:0007945 Anthea Guo|Jed Dongjin Kim-Ozaeta facultative acidophile|facultatively acidophilic METPO:1003008 acidotolerant owl:Class pH growth preference A pH growth preference characterized by the ability to tolerate acidic environments (typically pH below 5.5) while maintaining optimal growth near neutral pH. MICRO:0001555 Anthea Guo|Jed Dongjin Kim-Ozaeta aciduric diff --git a/src/templates/stubs.tsv b/src/templates/stubs.tsv index 40f0f074..321589eb 100644 --- a/src/templates/stubs.tsv +++ b/src/templates/stubs.tsv @@ -212,10 +212,10 @@ METPO:1002005 Fermentation owl:Class METPO:1002006 Syntrophy owl:Class METPO:1003000 pH growth preference owl:Class METPO:1003001 neutrophilic owl:Class -METPO:1003002 alkaphilic owl:Class +METPO:1003002 alkaliphilic owl:Class METPO:1003003 acidophilic owl:Class -METPO:1003004 obligately alkaphilic owl:Class -METPO:1003005 facultatively alkaphilic owl:Class +METPO:1003004 obligately alkaliphilic owl:Class +METPO:1003005 facultatively alkaliphilic owl:Class METPO:1003006 obligately acidophilic owl:Class METPO:1003007 facultatively acidophilic owl:Class METPO:1003008 acidotolerant owl:Class