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Update envo-edit.owl #759

Merged
merged 4 commits into from
Apr 26, 2019
Merged

Update envo-edit.owl #759

merged 4 commits into from
Apr 26, 2019

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rduerr
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@rduerr rduerr commented Apr 25, 2019

for #739 - Adding two subtypes of tundra (alpine and polar). Please verify that I got the numbering correctly!

@pbuttigieg pbuttigieg self-requested a review April 26, 2019 15:20
@pbuttigieg pbuttigieg self-assigned this Apr 26, 2019
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  • Moved tundra climatic condition out of the polar hierarchy, as tundra conditions can be elevation induced.
  • Created ecosystem classes to match areas759
  • Re-axiomatised qualities to match polar/tundra revision above
  • Adjusted labels to reflect that we're talking about sites/areas.
  • Minor tweaks to definitions.
  • Mapped tundra ecosystem to http://sweetontology.net/realmCryo/Tundra, but see Footnote 1

See also, ENVO:alpine tundra ecosystem, which is mapped to the SWEET:AlpineTundra SWEET class (FN 1).

Footnotes

1

Somethings not quite right with the SWEET Tundra class, one of its subclass axioms is mangled:
image
Further, it's hard to say from its placement under SWEET:Land whether SWEET is referring to the an area of tundra or the ecosystem itself. It probably doesn't distinguish between the two, so I'm mapping to both.

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Conflicts have been detected, as another branch was active and merged before this one was attended to. Will resolve these soon.

@pbuttigieg pbuttigieg mentioned this pull request Apr 26, 2019
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The conflicts seem pretty innocuous, just line number issues:
image

I ported some string-based ORCIDs to IRIs en passant. More of that later.

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Looks good overall - I made changes as reported in the discussion.

@@ -26,7 +26,7 @@ Import(<http://purl.obolibrary.org/obo/envo/imports/uberon_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/chebi_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/iao_import.owl>)
Annotation(<http://purl.org/dc/elements/1.1/creator> "http://orcid.org/0000-0002-4366-3088")
Annotation(<http://purl.org/dc/elements/1.1/creator> <http://orcid.org/0000-0002-4366-3088>)
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While fixing the nanocrediting APs in this PR, I've made a bunch of substitutions of old ORCIDs rendered as strings with IRIs. More to be done here in other PRs.

@@ -2942,6 +2942,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001621>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001622>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001623>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001624>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001625>))
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This, and the accompanying stanzas in the Class section, was what was causing the conflict.

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_00000112> "envoPolar")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000112> "tundra"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000112> "area of tundra"^^xsd:string)
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Making more explicit that some classes are site-based. I added ecosystem equivalents as described in this PR's discussion.

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