Merge pull request #704 from EnvironmentOntology/ntr-frost-heaving

added frost heaving process and contextual semantics as well as envoNceas subset

src/envo/Makefile

@@ -267,6 +267,12 @@ GO.xrf_abbs: envo-edit.owl
 # These all depend on envo-basic, which is the whole ontology (ie all classes), minus non-basic axioms (e.g. complex owl axioms, some relations)
 
 # Update to use full ENVO graph, as other ontology terms may be included
+
+subsets/envoNceas.owl: subsets/envo-basic.obo
+	owltools $< --extract-ontology-subset --fill-gaps --subset envoNceas --iri $(OBO)/envo/$@ -o $@
+subsets/envoNceas.obo: subsets/envoNceas.owl
+	owltools $< -o -f obo $@
+
 subsets/envoMeo.owl: subsets/envo-basic.obo
 	owltools $< --extract-ontology-subset --fill-gaps --subset envoMeo --iri $(OBO)/envo/$@ -o $@
 subsets/envoMeo.obo: subsets/envoMeo.owl

src/envo/envo-edit.owl

@@ -2918,6 +2918,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001564>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001565>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001566>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001567>))
+Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001568>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_02000000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_02000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_02000002>))
@@ -3191,6 +3192,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03000119>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03000120>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03000121>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_04000000>))
+Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_04000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_08000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_08000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_1000745>))
@@ -10801,14 +10803,15 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000488> ObjectSomeValuesFrom(<
 
 # Class: <http://purl.obolibrary.org/obo/ENVO_00000489> (palsa)
 
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Palsa"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000489> "An elevation which is formed as the result of a perennial ice lens forming under soil, pushing a roughly oval portion land surface upwards."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Palsa"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000489> "A frost heave which is formed as the result of a perennial ice lens forming under soil, pushing a roughly oval portion land surface upwards."^^xsd:string)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000489> "palsa bog"^^xsd:string)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000489> "palsamoor")
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00000489> "Palsas typically occur in areas with discontinuous permafrost, frequently peat bogs. A palsa consists, similarly to a pingo, of an ice core and overlying soil materials, in case of a palsa usually boggy soil. Palsas are characteristically found in areas with discontinuous permafrost and in such areas bay be the only reliable surface evidence of permafrost. A palsa needs large quantities of water for the formation of its ice core (i.e. ice lens), which is why they frequently emerge from and are bound by boggy soils, which can store enormous quantities of water in their pores. Palsas develop particularly in moorlands and are therefore also named palsamoors.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000489> "palsa"^^xsd:string)
-SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000489> <http://purl.obolibrary.org/obo/ENVO_00000176>)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000489> <http://purl.obolibrary.org/obo/ENVO_01001568>)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000489> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_01001209> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_00000134>))))
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000489> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_01000279> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002219> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_00000134> <http://purl.obolibrary.org/obo/ENVO_00001998>)))))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000489> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002354> <http://purl.obolibrary.org/obo/ENVO_04000001>))
 
 # Class: <http://purl.obolibrary.org/obo/ENVO_00000490> (consequent stream)
 
@@ -32612,6 +32615,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://orcid.org/0000-0003-4808-4736") rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001538> "Permafrost hummocks are often found in uniformly spaced large groups. Hummocks can form in areas of permafrost or seasonally frozen ground, and are one of the most common surface features of the Arctic.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001538> "frost-formed hummock"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001538> <http://purl.obolibrary.org/obo/ENVO_00000516>)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001538> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002354> <http://purl.obolibrary.org/obo/ENVO_04000001>))
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001538> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_00000134> <http://purl.obolibrary.org/obo/ENVO_00001998>)))
 
 # Class: <http://purl.obolibrary.org/obo/ENVO_01001539> (branched valley glacier)
@@ -32826,6 +32830,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001558> <http://purl.obolibrar
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://nsidc.org/cryosphere/glossary?keys=cryopeg") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001559> "A layer which is composed of ground that 1) remains unfrozen due to increased solute concentration and 2) is present within a mass of permafrost.")
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_01001559> <http://orcid.org/0000-0003-1264-1166>)
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_01001559> "2019-03-01T23:23:15Z"^^xsd:dateTime)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001559> "envoNceas")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001559> "envoPolar")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001559> "cryopeg"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001559> <http://purl.obolibrary.org/obo/ENVO_01000281>)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001559> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/ENVO_00000134>))
@@ -32913,6 +32919,18 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSyno
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001567> "protected area"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001567> <http://purl.obolibrary.org/obo/ENVO_01000408>)
 
+# Class: <http://purl.obolibrary.org/obo/ENVO_01001568> (frost heave)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Frost_heaving") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001568> "An elevation which is formed as an ice mass forms under soil, resulting in upwards deformation of the land surface.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <http://purl.obolibrary.org/obo/ENVO_01001568> "http://orcid.org/0000-0002-4366-3088"^^xsd:string)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/ENVO_01001568> "2019-03-04T23:07:57Z"^^xsd:dateTime)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01001568> "frost heaving")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001568> "envoNceas")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001568> "envoPolar")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001568> "frost heave"@en)
+EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_01001568> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_00000176> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002354> <http://purl.obolibrary.org/obo/ENVO_04000001>)))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001568> <http://purl.obolibrary.org/obo/ENVO_00000176>)
+
 # Class: <http://purl.obolibrary.org/obo/ENVO_02000000> (hypodermic needle)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GEMINA:ag"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Hypodermic_needle"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000000> "A hypodermic needle is a medical instrument made from a hollow needle. It is commonly used with a syringe to inject substances into the body of an organism."^^xsd:string)
@@ -35595,11 +35613,26 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03000121> ObjectSomeValuesFrom(<
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.merriam-webster.com/dictionary/adfreezing") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_04000000> "Adfreezing is a freezing process during which two objects adhere to each other via ice.")
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_04000000> <http://orcid.org/0000-0003-1264-1166>)
 AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_04000000> "2019-03-04T18:47:34Z"^^xsd:dateTime)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_04000000> "envoNceas")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_04000000> "envoPolar")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_04000000> "adfreezing"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000000> <http://purl.obolibrary.org/obo/ENVO_01001548>)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002234> <http://purl.obolibrary.org/obo/ENVO_01001125>))
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002234> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000030> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002170> <http://purl.obolibrary.org/obo/BFO_0000030>))))
 
+# Class: <http://purl.obolibrary.org/obo/ENVO_04000001> (frost heaving process)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Frost_heaving") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_04000001> "Frost heaving is a process during which an upwards swelling of soil occurs due to freezing conditions caused by an increasing presence of ice as it grows towards the surface.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_04000001> <http://orcid.org/0000-0003-1264-1166>)
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_04000001> "2019-03-04T20:17:35Z"^^xsd:dateTime)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_04000001> "envoNceas")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_04000001> "envoPolar")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_04000001> "frost heaving process"@en)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000001> <http://purl.obolibrary.org/obo/ENVO_03000010>)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_01001549>))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/ENVO_01000324>))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_04000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_00000134> <http://purl.obolibrary.org/obo/ENVO_00001998>)))
+
 # Class: <http://purl.obolibrary.org/obo/ENVO_08000001> (axilla skin environment)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:TermGenie"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_08000001> "An environment that is determined by an axilla skin."^^xsd:string)