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Added spatio-temporal scale #1576

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Added spatio-temporal scale #1576

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5a94173
Added spatio-temporal scale
timalamenciak Dec 12, 2024
d6df28b
Removed scale under qualitative and added under PATO age and size
timalamenciak Dec 16, 2024
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98 changes: 97 additions & 1 deletion src/envo/envo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -4136,6 +4136,14 @@ Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03605007>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03605008>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03605009>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620000>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620010>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620011>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620012>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620013>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620014>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620015>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620016>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_03620017>))
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_04000002>))
Expand Down Expand Up @@ -4332,6 +4340,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000323>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000963>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001351>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001360>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001486>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001576>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001595>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001657>))
Expand Down Expand Up @@ -11159,9 +11168,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000424> <http://purl.obolibrar
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Ocean_floor>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000426> "A marine bed which lies below an ocean.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000426> "FTT:1020")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean bed")
AnnotationAssertion(Annotation(rdfs:comment "When \"ocean basin\" is used in a hydrological sense, then \"ocean basin floor\" is any floor under seawater. In ENVO, the class \"ocean basin\" is used in a geological sense, which does not include all areas of ocean floor.") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean basin floor")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ADL:FTT") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean floor feature")
AnnotationAssertion(Annotation(rdfs:comment "Seas are smaller than oceans and are usually located where the land and ocean meet. However, these two terms are often used interchangeably."@en) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "seafloor"@en)
AnnotationAssertion(Annotation(rdfs:comment "When \"ocean basin\" is used in a hydrological sense, then \"ocean basin floor\" is any floor under seawater. In ENVO, the class \"ocean basin\" is used in a geological sense, which does not include all areas of ocean floor.") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean basin floor")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean floor")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000426> <http://purl.obolibrary.org/obo/ENVO_01001378>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000426> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/ENVO_00002450>))
Expand Down Expand Up @@ -46308,6 +46317,86 @@ AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibra
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620000> "biogeographic realm"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620000> <http://purl.obolibrary.org/obo/ENVO_01000254>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620010> (landscape megascale age)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620010> "Chronological age which inheres in a bearer by virtue of that bearer existing for at least 1,000,000 years.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620010> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620010> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620010> "2024-12-16T14:35:15Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620010> "https://en.wikipedia.org/wiki/Scale_(geography)")
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I wouldn't use an xref here..

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620010> "landscape megascale age"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620010> <http://purl.obolibrary.org/obo/PATO_0001486>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620011> (landscape macroscale age)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620011> "Chronological age which inheres in a bearer by virtue of that bearer existing for between 10,000 and 1,000,000 years.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620011> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620011> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620011> "2024-12-16T14:35:25Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620011> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620011> "landscape macroscale age"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620011> <http://purl.obolibrary.org/obo/PATO_0001486>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620012> (landscape mesoscale age)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620012> "Chronological age which inheres in a bearer by virtue of that bearer existing for between 500 and 10,000 years.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620012> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620012> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620012> "2024-12-16T14:35:35Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620012> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620012> "landscape mesoscale age"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620012> <http://purl.obolibrary.org/obo/PATO_0001486>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620013> (landscape microscale age)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620013> "Chronological age which inheres in a bearer by virtue of that bearer existing for between1 and 500 years.")
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add space

AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620013> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620013> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620013> "2024-12-16T14:35:46Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620013> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620013> "landscape microscale age"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620013> <http://purl.obolibrary.org/obo/PATO_0001486>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620014> (landscape megascale size)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620014> "An area quality which inheres in a bearer by virtue of that bearer having an area greater than 10,000,000,000,000 square metres")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620014> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620014> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620014> "2024-12-16T14:43:20Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620014> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620014> "landscape megascale size"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620014> <http://purl.obolibrary.org/obo/PATO_0001323>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620015> (landscape macroscale size)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620015> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 10,000,000,000 and 10,000,000,000,000 square metres")
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10e10 is 100,000,000,000

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I prefer exponential notation, but is it even true that this is an accepted cutoff? Sources would be good

AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620015> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620015> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620015> "2024-12-16T14:43:33Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620015> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620015> "landscape macroscale size"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620015> <http://purl.obolibrary.org/obo/PATO_0001323>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620016> (landscape mesoscale size)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620016> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 1,000,000 and 10,000,000,000 square metres.")
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10e6 is and 10,000,000 and 10e10 is 100,000,000,000

AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620016> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620016> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620016> "2024-12-16T14:43:40Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620016> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620016> "landscape mesoscale size"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620016> <http://purl.obolibrary.org/obo/PATO_0001323>)

# Class: <http://purl.obolibrary.org/obo/ENVO_03620017> (landscape microscale size)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620017> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 0 and 1,000,000 square metres")
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10e6 is and 10,000,000

AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620017> "https://orcid.org/0000-0002-4366-3088")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620017> <https://orcid.org/0000-0002-1296-2528>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620017> "2024-12-16T14:43:48Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620017> "https://en.wikipedia.org/wiki/Scale_(geography)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03620017> "landscape microscale size"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03620017> <http://purl.obolibrary.org/obo/PATO_0001323>)

# Class: <http://purl.obolibrary.org/obo/ENVO_04000000> (adfreezing)

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.")
Expand Down Expand Up @@ -48367,6 +48456,12 @@ SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000967> <http://purl.obolibrary.

SubClassOf(<http://purl.obolibrary.org/obo/OBI_0000968> <http://purl.obolibrary.org/obo/ENVO_00003074>)

# Class: <http://purl.obolibrary.org/obo/PATO_0001486> (chronological age)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001486> "An age quality that exists by virtue of the time (years and months) that the bearer has existed.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001486> "chronological age")
SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001486> <http://purl.obolibrary.org/obo/PATO_0000011>)

Comment on lines +48459 to +48464
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Was this added manually or via a process like https://github.com/EnvironmentOntology/envo/wiki/Import-terms-from-other-ontologies?

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@timalamenciak this process is a bit involved, but it's worth knowing how to set up the docker container that runs all the robot tools etc.

If this is too much right now, don't worry - we can fix it later. Proceed like you are right now and create a new issue to patch up the import of chronological age

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This was added manually using Protege. I can look through the process shortly though and take another run at it.

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It takes some docker magic, but isn't that hard if you have the memory (around 16 GB for the container is usually enough, processing the CHEBI and NCBITaxon imports hog memory)

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Added PATO chronologic age import as issue #1587


############################
# Named Individuals
Expand Down Expand Up @@ -48903,6 +48998,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000111> "editor preferred term~editor preferred label")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000412> "imported from")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000424> "expand expression to")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0000068> "A quality of an entity that is descriptive or observational, typically not represented numerically.")
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Not sure what's happening here in the Named Individuals block - could you clarify?

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/RO_0001900> "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0001900> "temporal interpretation")
)
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