From d27e5b7c29a7985b3312c697cf1cc7a9e7f677b3 Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 16 Nov 2022 13:36:37 -0800 Subject: [PATCH 1/4] Fixing hash-relations, fixes #1380. - http://purl.obolibrary.org/obo/envo#has_condition was unused, so removed - http://purl.obolibrary.org/obo/envo#has_increased_levels_of is replaced by a new ENVO ID Note that in general we should not be minting relations in ENVO, but creating a design pattern to handle this may be a longer term project, and this PR is a first step towards such a solution Fixes #1380 --- src/envo/envo-edit.owl | 159 +++++++++++++++++++++-------------------- 1 file changed, 80 insertions(+), 79 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 45641e78..c5e66e00 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -42,11 +42,14 @@ Annotation( "http://environmentontology.org/ Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -4196,6 +4199,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -4259,8 +4263,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -4620,6 +4622,14 @@ AnnotationAssertion(rdfs:label "p AnnotationAssertion( "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity."@en) AnnotationAssertion(rdfs:label "derives from part of"@en) +# Object Property: (has increased levels of) + +AnnotationAssertion( "A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities.") +AnnotationAssertion(rdfs:comment "This relation is present in ENVO to support compositional classes such as \"X-enriched soil\". These will later be formalized, and a different relation from RO may be chosen.") +AnnotationAssertion(rdfs:label "has increased levels of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + # Object Property: (results in transformation into) AnnotationAssertion(rdfs:label "results in transformation into") @@ -4673,15 +4683,6 @@ AnnotationAssertion(rdfs:label "surr AnnotationAssertion(rdfs:label "has habitat") -# Object Property: (has_condition) - -AnnotationAssertion( "2013-05-08T07:33:05Z"^^xsd:string) -AnnotationAssertion( "ENVO"^^xsd:string) -AnnotationAssertion( "has_condition"^^xsd:string) -AnnotationAssertion(rdfs:comment "Experimental relation used in EnvO. A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional."^^xsd:string) -AnnotationAssertion(rdfs:label "has_condition"^^xsd:string) -InverseFunctionalObjectProperty() - ############################ @@ -8775,8 +8776,8 @@ AnnotationAssertion(Annotation( "freshwater wetland ecosystem"^^xsd:string) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))) SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) # Class: (abyssal plain) @@ -13074,8 +13075,8 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "waste water"^^xsd:string) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (obsolete food product) @@ -13194,8 +13195,8 @@ AnnotationAssertion( "The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.") AnnotationAssertion(rdfs:label "saline water"^^xsd:string) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (fresh water) @@ -13731,14 +13732,14 @@ SubClassOf( "Sediment which has increased levels of one or more chemical compounds.") AnnotationAssertion(rdfs:label "chemically enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (petroleum enriched sediment) AnnotationAssertion( "Organically enriched sediment which has increased levels of petroleum.") AnnotationAssertion(rdfs:label "petroleum enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (contaminated soil) @@ -13749,14 +13750,14 @@ AnnotationAssertion( "\"contaminant\" is more of a disposition - any material entity can be a contaminant in particular circumstances."^^xsd:string) AnnotationAssertion(rdfs:label "contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( ))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( ))))) # Class: (creosote contaminated soil) AnnotationAssertion( "Soil which has elevated concentrations of creosote.") AnnotationAssertion(rdfs:label "creosote contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sea sand) @@ -13796,7 +13797,7 @@ SubClassOf( "Mud which has elevated concentrations of arsenic.") AnnotationAssertion(rdfs:label "arsenic-rich mud"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (bioreactor) @@ -13910,7 +13911,7 @@ SubClassOf( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00002136"^^xsd:string) AnnotationAssertion(rdfs:label "arsenate treated wood"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (brackish estuary) @@ -13985,14 +13986,14 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion( "Soil which has elevated concentrations of chromate.") AnnotationAssertion(rdfs:label "chromate contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (xylene contaminated soil) AnnotationAssertion( "Soil which has elevated concentrations of xylene.") AnnotationAssertion(rdfs:label "xylene contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (coal mine lake sediment) @@ -14241,7 +14242,7 @@ SubClassOf( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00002177"^^xsd:string) AnnotationAssertion(rdfs:label "1,4-dioxane contaminated sludge"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (iron-reducing zone of petroleum contaminated sediment) @@ -14263,7 +14264,7 @@ SubClassOf( "Organically enriched sediment which has increased levels of naphthalene.") AnnotationAssertion(rdfs:label "naphthalene enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (neutral hot spring) @@ -14277,7 +14278,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion( "Organically enriched sediment which has increased levels of nitrobenzene.") AnnotationAssertion(rdfs:label "nitrobenzene enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (oil tank) @@ -14316,9 +14317,9 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00002186"^^xsd:string) AnnotationAssertion(rdfs:label "contaminated water"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (obsolete milk formula) @@ -14448,14 +14449,14 @@ SubClassOf( "Chemically-enriched sediment which has increased levels of organic compounds.") AnnotationAssertion(rdfs:label "organically enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (inorganically enriched sediment) AnnotationAssertion( "Chemically-enriched sediment which has increased levels of inorganic compounds.") AnnotationAssertion(rdfs:label "inorganically enriched sediment"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (anthropogenic contamination feature) @@ -14624,7 +14625,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion(Annotation( "MA:ma"^^xsd:string) "Water with a high nutrient level."^^xsd:string) AnnotationAssertion(rdfs:label "eutrophic water"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (mesotrophic water) @@ -15159,7 +15160,7 @@ SubClassOf( "Soil which has elevated concentrations of oil.") AnnotationAssertion(rdfs:label "oil contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (warm seep) @@ -16008,14 +16009,14 @@ AnnotationAssertion(owl:deprecated "Soil which has elevated concentrations of metals.") AnnotationAssertion(rdfs:label "metal contaminated soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (enriched soil) AnnotationAssertion( "A portion of enriched soil is a portion of soil with elevated levels of some material entity."^^xsd:string) AnnotationAssertion(rdfs:comment "This could be demoted to an inferred class if issues with double inheritance arise.") AnnotationAssertion(rdfs:label "enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (sarcosine enriched soil) @@ -16024,7 +16025,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003083"^^xsd:string) AnnotationAssertion(rdfs:label "sarcosine enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (trimethylamine enriched soil) @@ -16033,7 +16034,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003084"^^xsd:string) AnnotationAssertion(rdfs:label "trimethylamine enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (skatole enriched soil) @@ -16042,7 +16043,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003085"^^xsd:string) AnnotationAssertion(rdfs:label "skatole enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (ethanol enriched soil) @@ -16050,7 +16051,7 @@ SubClassOf( "A portion of ethanol enriched soil is a portion of soil with elevated levels of ethanol."^^xsd:string) AnnotationAssertion(rdfs:label "ethanol enriched soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (acetamide enriched soil) @@ -16058,7 +16059,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003087"^^xsd:string) AnnotationAssertion(rdfs:label "acetamide enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (pantothenate enriched soil) @@ -16067,7 +16068,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003088"^^xsd:string) AnnotationAssertion(rdfs:label "pantothenate enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (testosterone enriched soil) @@ -16076,7 +16077,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003089"^^xsd:string) AnnotationAssertion(rdfs:label "testosterone enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (kynurenate enriched soil) @@ -16085,7 +16086,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003090"^^xsd:string) AnnotationAssertion(rdfs:label "kynurenate enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (threonine enriched soil) @@ -16094,7 +16095,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003091"^^xsd:string) AnnotationAssertion(rdfs:label "threonine enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (salicylate enriched soil) @@ -16103,14 +16104,14 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003092"^^xsd:string) AnnotationAssertion(rdfs:label "salicylate enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (poly-beta-hydroxybutyrate enriched soil) AnnotationAssertion( "A portion of poly-beta-hydroxybutyrate enriched soil is a portion of soil with elevated levels of poly-beta-hydroxybutyrate."^^xsd:string) AnnotationAssertion(rdfs:label "poly-beta-hydroxybutyrate enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (L-(+)-tartrate enriched soil) @@ -16127,7 +16128,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00003095"^^xsd:string) AnnotationAssertion(rdfs:label "quinate enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (tap water) @@ -16540,7 +16541,7 @@ AnnotationAssertion(owl:deprecated "Soil which has increased levels of chalk."@en) AnnotationAssertion(rdfs:label "chalk soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (obsolete fermented soybean product) @@ -16890,7 +16891,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00005753"^^xsd:string) AnnotationAssertion(rdfs:label "urea enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (fertilized soil) @@ -16957,7 +16958,7 @@ AnnotationAssertion( "ENVO"^^xsd:string) AnnotationAssertion( "ENVO:00005762"^^xsd:string) AnnotationAssertion(rdfs:label "chloropicrin enriched soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (humus-rich acidic ash soil) @@ -16965,9 +16966,9 @@ SubClassOf( "Soil which 1) has increased levels of humus, 2) has low pH levels, 3) has increased levels of mineral ash."@en) AnnotationAssertion(rdfs:label "humus-rich acidic ash soil"^^xsd:string) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (pond soil) @@ -17055,15 +17056,15 @@ AnnotationAssertion( "salty soil"^^xsd:string) AnnotationAssertion(rdfs:label "salt contaminated soil"^^xsd:string) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (peaty paddy field soil) AnnotationAssertion( "Paddy field soil which has increased levels of peat."@en) AnnotationAssertion(rdfs:label "peaty paddy field soil"^^xsd:string) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (steppe soil) @@ -22074,7 +22075,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion( "A haline environment is an environment in which entities are exposed to high concentrations of salt, typically above 2 molar.") AnnotationAssertion(rdfs:label "haline environment") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (cultivated environment) @@ -22227,8 +22228,8 @@ AnnotationAssertion( "https://en.wikipedia.org/wiki/Deep_chlorophyll_maximum") rdfs:comment "The DCM may or may not indicate greater abundance of photosynthetic, chlorophyll-bearing cells, as shade-adapted cells may have a greater chlorophyll to biomass ration than surface variants. Further, some DCMs may be formed by the sinking of cells from surface zones or the subduction of surface waters, rather than through biotic, community-level processess.") AnnotationAssertion(rdfs:label "deep chlorophyll maximum layer") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (strand swamp) @@ -23090,7 +23091,7 @@ AnnotationAssertion( "Logical definition will be created pending import of \"carbon nanotube\" from CHEBI"^^xsd:string) AnnotationAssertion(rdfs:label "carbon nanotube enriched soil") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (area of rocky shore) @@ -24125,7 +24126,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "ozone layer"@en) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (atmospheric layer) @@ -25202,9 +25203,9 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion( "Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.") AnnotationAssertion(rdfs:label "contaminated air"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (earthquake) @@ -25404,7 +25405,7 @@ AnnotationAssertion( "\"Mudflows are often called mudslides, a term applied indiscriminately by the mass media to a variety of mass wasting events. Mudflows often start as slides, becoming flows as water is entrained along the flow path; such events are often called flow slides.\" https://en.wikipedia.org/wiki/Mudflow") AnnotationAssertion(rdfs:label "mudflow"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf( )))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf( )))))) # Class: (debris flow) @@ -25423,7 +25424,7 @@ AnnotationAssertion(Annotation( "environmental_hazards") AnnotationAssertion(rdfs:label "lahar"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( ))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( ))))) SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) # Class: (sturzstrom) @@ -26590,8 +26591,8 @@ SubClassOf( "Air which has increased levels of water vapour.") AnnotationAssertion(rdfs:label "humid air"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (water vapour saturated air) @@ -28355,7 +28356,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "non-saline environment"@en) SubClassOf( ) SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) # Class: (groundwater) @@ -28670,8 +28671,8 @@ AnnotationAssertion( "The United States Geological Survey classifies slightly saline water as having around 1,000 to 3,000 ppm (0.1–0.3%) of dissolved salts.") AnnotationAssertion(rdfs:label "slightly saline water"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (moderately saline water) @@ -28684,8 +28685,8 @@ AnnotationAssertion( "The United States Geological Survey classifies moderately saline water as having around 3,000 to 10,000 ppm (0.3–1%) of dissolved salts.") AnnotationAssertion(rdfs:label "moderately saline water"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (highly saline water) @@ -28698,8 +28699,8 @@ AnnotationAssertion( "The United States Geological Survey classifies highly saline water as having around 10,000 to 35,000 ppm (1–3.5%) of dissolved salts.") AnnotationAssertion(rdfs:label "highly saline water"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (saline environment) @@ -28708,10 +28709,10 @@ AnnotationAssertion(Annotation( "envoEmpo") AnnotationAssertion(rdfs:comment "The thresholds for \"significant\" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request.") AnnotationAssertion(rdfs:label "saline environment"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) # Class: (fungi-associated environment) @@ -28854,7 +28855,7 @@ AnnotationAssertion(Annotation( "envoEmpo") AnnotationAssertion( "envoOmics") AnnotationAssertion(rdfs:label "non-saline aerosol environment"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))))) SubClassOf( ) # Class: (environment associated with an animal part or small animal) @@ -30546,9 +30547,9 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Kerogen") "Kerogen which is enriched in sulfur compounds, has a hydrogen to carbon ratio under 1.25, an oxygen to carbon ratio between 0.03 and 0.18, derives into mixtures of hydrocarbon gas and oil, and derives from marine organic materials (primarily lipids) which are formed in reducing environments.") AnnotationAssertion(rdfs:label "planktonic kerogen"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ))) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (sulfrous kerogen) @@ -38493,7 +38494,7 @@ AnnotationAssertion( "Pollutants may be material or immaterial (e.g. heat energy)") AnnotationAssertion(rdfs:label "environmental pollution") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) # Class: (air pollution) @@ -38534,7 +38535,7 @@ AnnotationAssertion( "envoPolar") AnnotationAssertion(rdfs:label "plastic pollution") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) # Class: (environmental monitoring) @@ -38567,7 +38568,7 @@ AnnotationAssertion(rdfs:label "u EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))))) # Class: (neve) @@ -44082,7 +44083,7 @@ Uses undesirability standard, compared to polluted river's ecological impact sta AnnotationAssertion( ) AnnotationAssertion( "2021-04-05T16:38:47.162Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "chemically contaminated sediment"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ) # Class: (cooling water) @@ -44228,7 +44229,7 @@ AnnotationAssertion( AnnotationAssertion(rdfs:comment "The contaminants may cause adverse changes in the ecosystems associated with it."@en) AnnotationAssertion(rdfs:label "polluted river"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) # Class: (saprolite) @@ -46023,7 +46024,7 @@ AnnotationAssertion( "https://sis.agr.gc.ca/cansis/glossary/t/index.html") Annotation( "https://www.fao.org/fishery/docs/CDrom/FAO_Training/FAO_Training/General/x6706e/x6706e06.htm") Annotation(rdfs:comment "USDA textural classes of soils") rdfs:comment "Some authorities consider sandy loam to be a soil composed of 50-70% sand, 0-50% silt, and 0-20% clay. Others, a soil material that contains either 20% or less clay, with a percentage of silt plus twice the percentage of clay that exceeds 30, and 52% or more sand; or less than 7% clay, less than 50% silt, and between 43% and 52% sand."@en) AnnotationAssertion(rdfs:label "sandy loam"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (silty loam) @@ -46035,7 +46036,7 @@ AnnotationAssertion(Annotation( "USDA textural classes of soils") AnnotationAssertion(rdfs:label "silty loam"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sandy clay loam) @@ -46046,7 +46047,7 @@ AnnotationAssertion( "https://sis.agr.gc.ca/cansis/glossary/t/index.html") rdfs:comment "Some authorities consider sandy clay loam to be a soil composed of 45-80% sand, 0-28% silt, and 20-35% clay."@en) AnnotationAssertion(rdfs:label "sandy clay loam"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (clay loam) @@ -46058,7 +46059,7 @@ AnnotationAssertion( "https://sis.agr.gc.ca/cansis/glossary/t/index.html") Annotation(rdfs:comment "USDA textural classes of soils") rdfs:comment "Some authorities consider clay loam to be a soil composed of 20-45% sand, 15-52% silt, and 27 to 40% clay."@en) AnnotationAssertion(rdfs:label "clay loam"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (silty clay loam) @@ -46069,7 +46070,7 @@ AnnotationAssertion( "https://www.fao.org/fishery/docs/CDrom/FAO_Training/FAO_Training/General/x6706e/x6706e06.htm") Annotation(rdfs:comment "USDA textural classes of soils") rdfs:comment "Some authorities consider silty clay loam to be a soil composed of 0-20% of sand, 40-73 of silt and 27-40% of clay."@en) AnnotationAssertion(rdfs:label "silty clay loam"@en) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (sandy clay) From 078eb8a19ab1ec8980ddda8551b5d606056e0fb6 Mon Sep 17 00:00:00 2001 From: cmungall Date: Wed, 16 Nov 2022 14:02:59 -0800 Subject: [PATCH 2/4] Adding DP --- src/envo/patterns/increased_levels.yaml | 38 +++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 src/envo/patterns/increased_levels.yaml diff --git a/src/envo/patterns/increased_levels.yaml b/src/envo/patterns/increased_levels.yaml new file mode 100644 index 00000000..e527bc35 --- /dev/null +++ b/src/envo/patterns/increased_levels.yaml @@ -0,0 +1,38 @@ +pattern_name: envo-p/patterns/increased_levels +classes: + material entity: BFO:0000040 + +relations: + has increased levels of: ENVO:02000200 + +vars: + whole: "'material entity'" + part: "'material entity'" + +name: + text: "%s-enriched %s" + vars: + - part + - whole + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +annotations: + - annotationProperty: exact_synonym + text: "%s enriched %s" + vars: + - part + - whole + +def: + text: "A %s which has elevated levels of %s." + vars: + - part + - whole + +equivalentTo: + text: "%s and 'has increased levels of' some %s" + vars: + - whole + - part From 06e23c18636e71bd142a829d1953bc9949a961cb Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 5 Dec 2022 12:06:04 -0500 Subject: [PATCH 3/4] closes #1367 ? --- src/envo/envo-edit.owl | 49 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 45641e78..9ad63112 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3984,6 +3984,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44772,6 +44776,51 @@ AnnotationAssertion( "greenhouse"@en) SubClassOf( ) +# Class: (alcohol fermentation pit) + +AnnotationAssertion( "A fermentation pit which is constructed to facilitate the fermentation of alcoholic substances.") +AnnotationAssertion( "https://orcid.org/0000-0001-9076-6066") +AnnotationAssertion( "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion( "https://orcid.org/0000-0002-4366-3088") +AnnotationAssertion( "2021-08-09T15:00:00.000Z") +AnnotationAssertion(rdfs:comment "Definition from 2021-08-05 call with Buttigieg, Duncan and Miller") +AnnotationAssertion(rdfs:label "alcohol fermentation pit") +SubClassOf( ) + +# Class: (clay fermentation pit) + +AnnotationAssertion( "A fermentation pit which is constructed from clay.") +AnnotationAssertion( "https://orcid.org/0000-0001-9076-6066") +AnnotationAssertion( "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion( "https://orcid.org/0000-0002-4366-3088") +AnnotationAssertion( "2021-08-09T15:00:00.000Z") +AnnotationAssertion(rdfs:comment "Definition from 2021-08-05 call with Buttigieg, Duncan and Miller") +AnnotationAssertion(rdfs:label "clay fermentation pit") +SubClassOf( ) + +# Class: (artificial pond) + +AnnotationAssertion( "A pond which has been constructed by humans or their technologies.") +AnnotationAssertion( "https://orcid.org/0000-0001-9076-6066") +AnnotationAssertion( "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion( "https://orcid.org/0000-0002-4366-3088") +AnnotationAssertion( "2021-08-09T15:00:00.000Z") +AnnotationAssertion(rdfs:comment "Definition from 2021-08-05 call with Buttigieg, Duncan and Miller") +AnnotationAssertion(rdfs:label "artificial pond") +SubClassOf( ) + +# Class: (artificial satellite) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Satellite") "A human construction that has intentionally been placed into orbit.") +AnnotationAssertion( "https://orcid.org/0000-0001-9076-6066") +AnnotationAssertion( "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion( "https://orcid.org/0000-0002-4366-3088") +AnnotationAssertion( "2021-08-09T15:00:00.000Z") +AnnotationAssertion(rdfs:comment "Definition from 2021-08-05 call with Buttigieg, Duncan and Miller") +AnnotationAssertion(rdfs:comment "Not to be confused with a natural satellite like the earth's moon (https://en.wikipedia.org/wiki/Natural_satellite)") +AnnotationAssertion(rdfs:label "artificial satellite") +SubClassOf( ) + # Class: (adfreezing) AnnotationAssertion(Annotation( "https://www.merriam-webster.com/dictionary/adfreezing") "Adfreezing is a freezing process during which two objects adhere to each other via ice.") From b04f9d9ec36b878f2fa31446733a1725971b0dc7 Mon Sep 17 00:00:00 2001 From: cmungall Date: Tue, 21 Mar 2023 17:58:12 -0700 Subject: [PATCH 4/4] Relax logical definition of water ice, liquid water=>water. Fixes #1410 --- src/envo/envo-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 4e416145..605154cc 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -21720,7 +21720,7 @@ In permafrost regions, ice may occupy voids in soils and rocks and may develop i In nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze.") AnnotationAssertion(rdfs:label "water ice"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( )))