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Editing "landfill" and "piece of plastic", addressing issue #1106 #1107

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merged 7 commits into from
May 7, 2021
Merged

Editing "landfill" and "piece of plastic", addressing issue #1106 #1107

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6a8f2d1
editing landfill and piece of plastic, adressing issue #1106
iwilkie May 3, 2021
4c13d5c
added multilingual interpretations to landfill
iwilkie May 3, 2021
a42af01
moved multilingual interpretations into exact synonyms, corresponding…
iwilkie May 4, 2021
bf71dda
responding to review, corresponding to #1106
iwilkie May 5, 2021
5e57911
Merge branch 'master' into issue-1106
iwilkie May 7, 2021
8349563
Moved the FTT annotations to the class level, specified language on a…
iwilkie May 7, 2021
36f50b6
changed the definition of landfill, changed the parent class to depre…
iwilkie May 7, 2021
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22 changes: 17 additions & 5 deletions src/envo/envo-edit.owl
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Expand Up @@ -11827,13 +11827,18 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000532> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/ENVO_00000533> (landfill)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000533> "A site at which refuse is dumped, normally filling a natural or artificial depression."^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000533> "FTT:621"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000533> "FTT:624"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000533> "https://en.wikipedia.org/wiki/Landfill"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://doi.org/10.1177%2F0734242X0202000209>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Landfill>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FTT:621"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FTT:624"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000533> "An anthropogenic contamination feature which is used for solid waste disposal, filling a natural or artificial depression"^^xsd:string)
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@pbuttigieg I see there are a lot of pre-existing annotations on this term

  • annotation on definition: hasDbXref MA:ma;
  • general annotations: hasDbXref FTT:621, hasDbXref FTT:624, hasDbXref https://en.wikipedia.org/wiki/Landfill
  • annotation on has_related_synonym disposal site: hasDbXref ADL:FTT

Would you know what the letter codes stand for?
Should the wikipedia source (and the general annotation letter codes) be moved to be annotations on the definition?

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MA:ma was an attribution to Micheal Ashburner, who created most of ENVO's early terms.

FFT is the Feature Type Thesaurus, and ADL is the Alexandra Digital Library. These are legacy annotations from ENVO's early days, but likely still valid.

Should the wikipedia source (and the general annotation letter codes) be moved to be annotations on the definition?

Yes, sure.

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An anthropogenic contamination feature

Not really happy with this superclass, but it should be fine for now.

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MA:ma was an attribution to Micheal Ashburner, who created most of ENVO's early terms.
FFT is the Feature Type Thesaurus, and ADL is the Alexandra Digital Library. These are legacy annotations from ENVO's early days, but likely still valid.

Thanks for the clarification @pbuttigieg - Would you know if there a document or similar explaining those for ENVO users in general?

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I would like to have SSSOM files for all our mapped sources (made a ticket for myself here #1129) -- this would make it explicit in the header what the sources are, what the URI expansion is, when the mapping was made.

On the FTT mappings, I made a separate ticket: #1130.

AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_00000533> <https://orcid.org/0000-0002-2996-719X>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_00000533> <https://orcid.org/0000-0002-8166-0486>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_00000533> <https://orcid.org/0000-0003-1072-8081>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "Deponie"@de)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "discarica"@it)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "garbage dump")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "rubbish dump")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "vertedero"@es)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "垃圾掩埋場"@zh)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ADL:FTT"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000533> "disposal site"^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_00000533> "envoPlastics"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000533> "landfill"^^xsd:string)
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Yes, more clear superclassing

SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000533> <http://purl.obolibrary.org/obo/ENVO_00002204>)

Expand Down Expand Up @@ -25615,7 +25620,14 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000775> ObjectSomeValuesFrom(<

# Class: <http://purl.obolibrary.org/obo/ENVO_01000776> (piece of plastic)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000776> "An abiotic mesoscopic physical object which is primarily composed of plastic.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000776> "A mass of solid material which is primarily composed of plastic."@en)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_01000776> <https://orcid.org/0000-0002-2996-719X>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_01000776> <https://orcid.org/0000-0002-8166-0486>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_01000776> <https://orcid.org/0000-0003-1072-8081>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000776> "Plastikstück"@de)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000776> "pedazo de plástico"@es)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000776> "pezzo di plastica"@it)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01000776> "envoPlastics"@es)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000776> "piece of plastic"@en)
EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_01000776> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_01001687> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> <http://purl.obolibrary.org/obo/ENVO_01000404>)))

Expand Down