From 1011f2df0a18708b618ed3ef395c8560c4606506 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 11 Sep 2023 12:31:21 -0400 Subject: [PATCH 1/6] #1456 SPARQL for misclassified biomes --- misclassified_biomes.Makefile | 4 ++++ misclassified_biomes.rq | 18 ++++++++++++++++++ misclassified_biomes.tsv | 33 +++++++++++++++++++++++++++++++++ 3 files changed, 55 insertions(+) create mode 100644 misclassified_biomes.Makefile create mode 100644 misclassified_biomes.rq create mode 100644 misclassified_biomes.tsv diff --git a/misclassified_biomes.Makefile b/misclassified_biomes.Makefile new file mode 100644 index 00000000..99245a03 --- /dev/null +++ b/misclassified_biomes.Makefile @@ -0,0 +1,4 @@ +misclassified_biomes.tsv: envo.owl misclassified_biomes.rq + robot query \ + --input $(word 1, $^) \ + --query $(word 2, $^) $@ \ No newline at end of file diff --git a/misclassified_biomes.rq b/misclassified_biomes.rq new file mode 100644 index 00000000..61d0addf --- /dev/null +++ b/misclassified_biomes.rq @@ -0,0 +1,18 @@ +PREFIX rdfs: +PREFIX ENVO: +PREFIX owl: +PREFIX nmdc: +select ?class_curie (str(?label) as ?label_str) +where { + { + ?c rdfs:label ?label . + filter(strends(?label, "biome")) + } minus { + ?c owl:deprecated true + } + minus { + ?c rdfs:subClassOf* ENVO:00000428 . + } + bind(concat("ENVO:", strafter(str(?c), "http://purl.obolibrary.org/obo/ENVO_")) as ?class_curie) +} +order by str(?label) \ No newline at end of file diff --git a/misclassified_biomes.tsv b/misclassified_biomes.tsv new file mode 100644 index 00000000..4dac661b --- /dev/null +++ b/misclassified_biomes.tsv @@ -0,0 +1,33 @@ +?class_curie ?lable_str +"ENVO:01000197" "broadleaf forest biome" +"ENVO:01000196" "coniferous forest biome" +"ENVO:01000245" "cropland biome" +"ENVO:01000179" "desert biome" +"ENVO:01000195" "flooded grassland biome" +"ENVO:01000174" "forest biome" +"ENVO:01000177" "grassland biome" +"ENVO:01000199" "mediterranean forest biome" +"ENVO:01000224" "mediterranean grassland biome" +"ENVO:01000198" "mixed forest biome" +"ENVO:01000185" "montane desert biome" +"ENVO:01000194" "montane grassland biome" +"ENVO:01000186" "polar desert biome" +"ENVO:01000250" "subpolar coniferous forest biome" +"ENVO:01000201" "subtropical broadleaf forest biome" +"ENVO:01000209" "subtropical coniferous forest biome" +"ENVO:01000184" "subtropical desert biome" +"ENVO:01000225" "subtropical dry broadleaf forest biome" +"ENVO:01000191" "subtropical grassland biome" +"ENVO:01000226" "subtropical moist broadleaf forest biome" +"ENVO:01000202" "temperate broadleaf forest biome" +"ENVO:01000211" "temperate coniferous forest biome" +"ENVO:01000182" "temperate desert biome" +"ENVO:01000193" "temperate grassland biome" +"ENVO:01000212" "temperate mixed forest biome" +"ENVO:01000200" "tropical broadleaf forest biome" +"ENVO:01000210" "tropical coniferous forest biome" +"ENVO:01000183" "tropical desert biome" +"ENVO:01000227" "tropical dry broadleaf forest biome" +"ENVO:01000192" "tropical grassland biome" +"ENVO:01001798" "tropical mixed forest biome" +"ENVO:01000228" "tropical moist broadleaf forest biome" From fc5e470b7da3d67d2bfb43752921e659bdc7d6d0 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 11 Sep 2023 16:42:34 -0400 Subject: [PATCH 2/6] better input and comments for misclassified_biomes.tsv target --- misclassified_biomes.Makefile | 6 ++++-- misclassified_biomes.tsv | 33 --------------------------------- 2 files changed, 4 insertions(+), 35 deletions(-) delete mode 100644 misclassified_biomes.tsv diff --git a/misclassified_biomes.Makefile b/misclassified_biomes.Makefile index 99245a03..6cb599ad 100644 --- a/misclassified_biomes.Makefile +++ b/misclassified_biomes.Makefile @@ -1,4 +1,6 @@ -misclassified_biomes.tsv: envo.owl misclassified_biomes.rq +# from src/envo, do `./run.sh make all` first + +misclassified_biomes.tsv: src/envo/envo.owl misclassified_biomes.rq robot query \ --input $(word 1, $^) \ - --query $(word 2, $^) $@ \ No newline at end of file + --query $(word 2, $^) $@ diff --git a/misclassified_biomes.tsv b/misclassified_biomes.tsv deleted file mode 100644 index 4dac661b..00000000 --- a/misclassified_biomes.tsv +++ /dev/null @@ -1,33 +0,0 @@ -?class_curie ?lable_str -"ENVO:01000197" "broadleaf forest biome" -"ENVO:01000196" "coniferous forest biome" -"ENVO:01000245" "cropland biome" -"ENVO:01000179" "desert biome" -"ENVO:01000195" "flooded grassland biome" -"ENVO:01000174" "forest biome" -"ENVO:01000177" "grassland biome" -"ENVO:01000199" "mediterranean forest biome" -"ENVO:01000224" "mediterranean grassland biome" -"ENVO:01000198" "mixed forest biome" -"ENVO:01000185" "montane desert biome" -"ENVO:01000194" "montane grassland biome" -"ENVO:01000186" "polar desert biome" -"ENVO:01000250" "subpolar coniferous forest biome" -"ENVO:01000201" "subtropical broadleaf forest biome" -"ENVO:01000209" "subtropical coniferous forest biome" -"ENVO:01000184" "subtropical desert biome" -"ENVO:01000225" "subtropical dry broadleaf forest biome" -"ENVO:01000191" "subtropical grassland biome" -"ENVO:01000226" "subtropical moist broadleaf forest biome" -"ENVO:01000202" "temperate broadleaf forest biome" -"ENVO:01000211" "temperate coniferous forest biome" -"ENVO:01000182" "temperate desert biome" -"ENVO:01000193" "temperate grassland biome" -"ENVO:01000212" "temperate mixed forest biome" -"ENVO:01000200" "tropical broadleaf forest biome" -"ENVO:01000210" "tropical coniferous forest biome" -"ENVO:01000183" "tropical desert biome" -"ENVO:01000227" "tropical dry broadleaf forest biome" -"ENVO:01000192" "tropical grassland biome" -"ENVO:01001798" "tropical mixed forest biome" -"ENVO:01000228" "tropical moist broadleaf forest biome" From 1f4de2cb953884c18d34988c96d4b352d5ee36ec Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 11 Sep 2023 16:48:06 -0400 Subject: [PATCH 3/6] #1458 more participates in some climactic ecosystem succession axioms --- misclassified_biomes.Makefile | 6 ------ misclassified_biomes.rq | 18 ------------------ src/envo/envo-edit.owl | 22 ++++++++++++++++++++++ 3 files changed, 22 insertions(+), 24 deletions(-) delete mode 100644 misclassified_biomes.Makefile delete mode 100644 misclassified_biomes.rq diff --git a/misclassified_biomes.Makefile b/misclassified_biomes.Makefile deleted file mode 100644 index 6cb599ad..00000000 --- a/misclassified_biomes.Makefile +++ /dev/null @@ -1,6 +0,0 @@ -# from src/envo, do `./run.sh make all` first - -misclassified_biomes.tsv: src/envo/envo.owl misclassified_biomes.rq - robot query \ - --input $(word 1, $^) \ - --query $(word 2, $^) $@ diff --git a/misclassified_biomes.rq b/misclassified_biomes.rq deleted file mode 100644 index 61d0addf..00000000 --- a/misclassified_biomes.rq +++ /dev/null @@ -1,18 +0,0 @@ -PREFIX rdfs: -PREFIX ENVO: -PREFIX owl: -PREFIX nmdc: -select ?class_curie (str(?label) as ?label_str) -where { - { - ?c rdfs:label ?label . - filter(strends(?label, "biome")) - } minus { - ?c owl:deprecated true - } - minus { - ?c rdfs:subClassOf* ENVO:00000428 . - } - bind(concat("ENVO:", strafter(str(?c), "http://purl.obolibrary.org/obo/ENVO_")) as ?class_curie) -} -order by str(?label) \ No newline at end of file diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 2ff7d929..64257b3a 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -20670,6 +20670,7 @@ AnnotationAssertion( "2013-04-07T14:26:46Z") AnnotationAssertion( "SPIRE:Savannah_or_grassland") AnnotationAssertion(rdfs:label "grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (savanna biome) @@ -20819,6 +20820,7 @@ AnnotationAssertion( "2013-04-07T14:29:48Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subtropical grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20829,6 +20831,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "tropical grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20839,6 +20842,7 @@ AnnotationAssertion( AnnotationAssertion( "prairie biome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "temperate grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20850,6 +20854,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition.") AnnotationAssertion(rdfs:label "montane grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20859,6 +20864,7 @@ AnnotationAssertion( "2013-04-07T14:29:48Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "flooded grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) @@ -20871,6 +20877,7 @@ AnnotationAssertion( "ENVO:01000196") AnnotationAssertion(rdfs:comment "Preliminary definition.") AnnotationAssertion(rdfs:label "coniferous forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (broadleaf forest biome) @@ -20890,6 +20897,7 @@ AnnotationAssertion( "2013-04-07T14:31:01Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "mixed forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (mediterranean forest biome) @@ -20899,6 +20907,7 @@ AnnotationAssertion( "2013-04-07T14:31:01Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "mediterranean forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20908,6 +20917,7 @@ AnnotationAssertion( "ORCID:0000-0002-4366-3088") AnnotationAssertion( "2013-04-07T14:32:28Z") AnnotationAssertion(rdfs:label "tropical broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20928,6 +20938,7 @@ AnnotationAssertion( "2013-04-07T14:32:28Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "temperate broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21001,6 +21012,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "subtropical coniferous forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21012,6 +21024,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "tropical coniferous forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21023,6 +21036,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "temperate coniferous forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21033,6 +21047,7 @@ AnnotationAssertion( "2013-04-07T14:39:30Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "temperate mixed forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21161,6 +21176,7 @@ AnnotationAssertion( "2013-04-19T11:42:48Z") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "mediterranean grassland biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21172,6 +21188,7 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subtropical dry broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (subtropical moist broadleaf forest biome) @@ -21181,6 +21198,7 @@ AnnotationAssertion( "2013-04-24T12:04:53Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subtropical moist broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (tropical dry broadleaf forest biome) @@ -21191,6 +21209,7 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "tropical dry broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (tropical moist broadleaf forest biome) @@ -21202,6 +21221,7 @@ AnnotationAssertion( "rainforest biome") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "tropical moist broadleaf forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (mediterranean savanna biome) @@ -21425,6 +21445,7 @@ AnnotationAssertion( "taiga") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subpolar coniferous forest biome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35965,6 +35986,7 @@ AnnotationAssertion( "2019-10-27T16:05:39Z"^^xsd:dateTime) AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "tropical mixed forest biome"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) From f96faf4018eeb95cc65230b88041d13887157841 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Fri, 22 Sep 2023 09:17:02 -0400 Subject: [PATCH 4/6] removed biome has qual axioms except in coniferous forest biomes --- src/envo/envo-edit.owl | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 9cfb4eb3..5e5b9f5b 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -20806,7 +20806,7 @@ AnnotationAssertion( "2013-04-07T14:29:48Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subtropical grassland biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20817,7 +20817,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "tropical grassland biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20828,7 +20828,7 @@ AnnotationAssertion( AnnotationAssertion( "prairie biome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "temperate grassland biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -20874,7 +20874,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "broadleaf forest biome") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (mixed forest biome) @@ -21010,7 +21009,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "tropical coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21033,7 +21032,7 @@ AnnotationAssertion( "2013-04-07T14:39:30Z") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "temperate mixed forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -35972,7 +35971,7 @@ AnnotationAssertion( "2019-10-27T16:05:39Z"^^xsd:dateTime) AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "tropical mixed forest biome"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) From 6d0f35fd4e0d66166f955c81d43ab49dc256c183 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Fri, 22 Sep 2023 09:22:24 -0400 Subject: [PATCH 5/6] removed has qual axioms from coniferous forest biomes causing asserted equivalent classes --- src/envo/envo-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 5e5b9f5b..329553a9 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -20997,7 +20997,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "subtropical coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21021,7 +21021,7 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "temperate coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21430,7 +21430,7 @@ AnnotationAssertion( "taiga") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subpolar coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) From b711bfe4abaaa6e6b8c4df1214275d380e272b17 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Fri, 22 Sep 2023 09:32:33 -0400 Subject: [PATCH 6/6] zero biome has property axioms --- src/envo/envo-edit.owl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 329553a9..900b2ce4 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -20997,7 +20997,6 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "subtropical coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21021,7 +21020,6 @@ AnnotationAssertion( AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:comment "Preliminary definition. The semantics and definitions of \"mediterranean\", \"subtropical\", \"tropical\", \"temperate\", \"polar\", and similar climate types may be transferred to an \"environmental condition\" class once the semantics of this class have been established.") AnnotationAssertion(rdfs:label "temperate coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -21430,7 +21428,6 @@ AnnotationAssertion( "taiga") AnnotationAssertion( "wwfBiome") AnnotationAssertion(rdfs:label "subpolar coniferous forest biome") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( ))