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Add fields for storing curator information #119

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gaurav opened this issue Nov 15, 2022 · 4 comments · Fixed by #125
Closed

Add fields for storing curator information #119

gaurav opened this issue Nov 15, 2022 · 4 comments · Fixed by #125

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@gaurav
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gaurav commented Nov 15, 2022

This is needed by Klados, and should only include the curator name and ORCID. Looking at some other ontologies, there are a number of ways in which this information is recorded:

I propose we add a contributors field as a list of strings to phyloreferences and map it to dc:contributor in JSON-LD. We would recommend that contributors should be recorded as a string in the format Name (orcid:1111-2222-3333-4444).

@hlapp
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hlapp commented Nov 16, 2022

@matentzn or @cmungall if either of you have any additional pointers or comments on where to look for ontology term curator attribution recommended practices for OBO, that'd be useful.

(FYI, in the OG issue documentation above, a phyloreference becomes a (defined) class in an ontology, so it's about documenting curators at the level of terms/classes.)

@matentzn
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Here is a nice issue that illustrates the chaos: information-artifact-ontology/ontology-metadata#60

If you cover all properties mentioned by this thread you are probably in a good place.

We are pushing hard (against plenty resistance) to standardise on dcterms:contributor orcid:123, but its a slow process.

dc:creator is found as well, always check the dcterms vs dc elements variants of IRIs if you want everything.

My two cents: dcterms:contributor plus orcid/ror/wikidata is the right way to go.

@gaurav
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gaurav commented Dec 1, 2022

@balhoff pointed out that Dublin Core recommends that creators and contributors are identified by URI if feasible, and suggested the following approach:

:phyloref0 dc:contributor <http://orcid.org/0000-0003-0587-0454> .
<http://orcid.org/0000-0003-0587-0454> foaf:name "Gaurav Vaidya"

This can be represented in JSON-LD in a pretty compact way by adding two additional terms to our JSON-LD context:

{
  "@context": {
    "contributors": {
      "@id": "http://purl.org/dc/terms/contributor",
      "@container": "@set"
    },
    "name": "http://xmlns.com/foaf/0.1/name"
  },

  "contributors": [{
    "@id": "http://orcid.org/0000-0003-0587-0454",
    "name": "Gaurav Vaidya"
  }, {
    "@id": "https://orcid.org/0000-0001-9107-0714",
    "name": "Hilmar Lapp"
  }]
}

A contributor without an ORCID could either be represented by a blank node with a foaf:name property (i.e. "contributors": [{ "name": "Albert Einstein" }]) or by just including their directly in the contributors list (i.e. "contributors": [ "Albert Einstein" ]).

@hlapp
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hlapp commented Dec 2, 2022

Sounds like a good plan to me, and I agree, the dcterms namespace properties should have a URI or object as value.

gaurav added a commit that referenced this issue Feb 1, 2023
gaurav added a commit that referenced this issue Feb 1, 2023
gaurav added a commit that referenced this issue Feb 1, 2023
gaurav added a commit that referenced this issue May 7, 2023
This PR adds curator information to the Phyx file as "contributors" with ORCIDs and names as described in #119 (comment). Closes #119.

I've also added a `.java-version` file to indicate that Java 15 should be used to run JPhyloRef, and pinned newick-js to v1.1.1 to avoid a bug (keesey/newick-js#4).
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3 participants