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

iwilkie · 2021-05-03T11:12:39Z

This PR corresponds to issue #1106. We have edited "landfill" and "piece of plastic" to ensure that they follow the genus-differentia structure, added Mandarin, Italian, German and Spanish interpretations, and added them to the "envoPlastics" subset

We will add the axioms at a later date.

Thank you!

raissameyer

Hi @iwilkie. Thanks for the updates to "landfill" and "piece of plastic".

I think your revisions looks good. However, I was wondering how come you added the multilingual interpretations as has_related_synonym and not has_exact_synonym (as you had done for previous terms) - is there an additional layer of interpretation between the languages?

I also had one question for @pbuttigieg about the pre-existing annotations on the term "landfill", the answer to which we could consider before merging this PR.

raissameyer · 2021-05-04T07:51:09Z

src/envo/envo-edit.owl

@@ -11827,13 +11827,21 @@ 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(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://doi.org/10.1177%2F0734242X0202000209>) 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)


@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?

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.

An anthropogenic contamination feature

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

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?

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.

… to #1106

iwilkie · 2021-05-04T12:15:43Z

@raissameyer thanks for pointing that out, I just moved the multilingual interpretations so that they are now under has_exact_synonym.

pbuttigieg

Minor tweaks

pbuttigieg · 2021-05-04T15:18:50Z

src/envo/envo-edit.owl

@@ -11827,13 +11827,21 @@ 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(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://doi.org/10.1177%2F0734242X0202000209>) 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)


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.

pbuttigieg · 2021-05-04T15:19:32Z

src/envo/envo-edit.owl

@@ -11827,13 +11827,21 @@ 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(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://doi.org/10.1177%2F0734242X0202000209>) 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)


An anthropogenic contamination feature

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

iwilkie · 2021-05-05T08:47:24Z

@pbuttigieg thank you for the review, I have now moved the wikipedia reference and the letter code annotations as indicated by @raissameyer.

raissameyer

@iwilkie Looks good!

Any further comments from you @pbuttigieg?

cmungall

It looks like you are trying to move the mappings between the class and the external vocabulary term and turn them into provenance on the definition. I don't think should be done

in this case you are taking the definition of landfill
http://purl.obolibrary.org/obo/ENVO_00000533 and attributing the definition to FTT. This shouldn't be done as FTT was not used as a source of the definition.

DbXref annotations on the class are simply mappings (they may be poor mappings, as in the case of FTT)

A DbXref axiom annotation indicates source/provenance for that axiom

Apologies for the lack of guidelines here, I am remiss in trying to collate documentation across different ontologies, for now it may be useful to look at the GO gude
http://wiki.geneontology.org/index.php/Guidelines_for_GO_textual_definitions

raissameyer · 2021-05-07T05:26:04Z

Many thanks for the clarification @cmungall - we didn't realise those were mappings.

We'll reverse the recent changes of moving the FTT annotations on the definition.

Please let us know if the MA:ma annotation should be an annotation on the definition - as this is "an attribution to Micheal Ashburner", I would expect this annotation to acknowledge him as the definition source/provenance?

🆕 [EDIT: CM confirmed that MA:ma should not be class-level, but an annotation on the definition]

iwilkie · 2021-05-07T12:23:08Z

@cmungall and @raissameyer thank you for the comments. I have moved the FTT annotations back to how they were before, thank you for pointing that out.

… couple of the synonyms

…ssion

iwilkie · 2021-05-07T12:53:31Z

Based on some side conversations, we have moved "landfill" into "depression" and adjusted the definition accordingly.

pbuttigieg

@iwilkie looks good! @raissameyer feel free to merge.

pbuttigieg · 2021-05-07T12:59:42Z

src/envo/envo-edit.owl

@@ -11839,15 +11839,22 @@ 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(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> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000533> "A depression which contains objects and materials discarded by humans or their technologies."^^xsd:string)


Yes, more clear superclassing

pbuttigieg · 2021-05-07T13:05:07Z

The failing Travis check seems to be that usual ghost issue. Merging should be fine

iwilkie added 2 commits May 3, 2021 13:09

editing landfill and piece of plastic, adressing issue #1106

6a8f2d1

added multilingual interpretations to landfill

4c13d5c

iwilkie requested review from pbuttigieg and raissameyer May 3, 2021 11:16

iwilkie self-assigned this May 3, 2021

iwilkie added Modify term SDG Ontology Framework labels May 3, 2021

raissameyer reviewed May 4, 2021

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moved multilingual interpretations into exact synonyms, corresponding…

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… to #1106

pbuttigieg requested changes May 4, 2021

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responding to review, corresponding to #1106

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iwilkie requested review from pbuttigieg and raissameyer May 5, 2021 08:48

raissameyer approved these changes May 5, 2021

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cmungall requested changes May 6, 2021

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cmungall mentioned this pull request May 6, 2021

Review FTT mappings #1130

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raissameyer mentioned this pull request May 7, 2021

Editing "marine bed", "shoreline", "sea surface layer" - addressing #1122 #1125

Merged

Merge branch 'master' into issue-1106

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iwilkie added 2 commits May 7, 2021 14:31

Moved the FTT annotations to the class level, specified language on a…

8349563

… couple of the synonyms

changed the definition of landfill, changed the parent class to depre…

36f50b6

…ssion

pbuttigieg approved these changes May 7, 2021

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raissameyer merged commit f216119 into master May 7, 2021

pbuttigieg deleted the issue-1106 branch May 7, 2021 13:28

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Editing "piece of plastic" and "landfill" #1106

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

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

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