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VirtualFlyBrain / VFB_json_schema

VFB json schema spec + code for rolling queries producing VFB json schema + related integration tests
Apache License 2.0
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Publications and Synonyms #13

Open dosumis opened 5 years ago

dosumis commented 5 years ago

What part of the schema is being reviewed?

pub_syn pub_def pubs

What is the intended usage/context of this part_of the schema?

Population of publications for TermInfo. Publications associated with synonyms are treated separately from those associated with defs or simply attached to the term.

Questions for reviewers

If the answer to any question is no, please suggest improvements.

  1. Are the names of properties intuitive and consistent?
  2. Does the structure work to capture relationships between elements?
  3. Is the internal documentation (description field content) sufficient?
  4. Does this list of required fields make sense?
  5. Is there any content missing?
dosumis commented 5 years ago

pub_syn illustrates the current schema. pub_def re-uses the pub subschema you can see here

"pub_syn": [
    {
      "pub": {
        "DOI": "",
        "core": {
          "types": [
            "Individual",
            "pub"
          ],
          "iri": "http://flybase.org/reports/FBrf0064793",
          "short_form": "FBrf0064793",
          "label": "Bate, 1993, Bate, Martinez Arias, 1993: 1013--1090"
        },
        "PubMed": "",
        "FlyBase": "FBrf0064793"
      },
      "synonym": {
        "label": "A1-7 DA1",
        "type": "None",
        "scope": "hasExactSynonym"
      }
    }

In pub_syn, one pub is associated with one synonym, so if the same synonym is linked to multiple pubs, there will be multiple entries for the same synonym, and vice-versa.

Note - This assumed links to pubMed, FlyBase etc remain on the Pub node, rather than being expanded into Xrefs. I've done some preliminary work to support the latter, but if I do move to this then I'm not sure it will be possible to support grouping xrefs under each pub given the Cypher-only approach. The result would be an even more flattened schema with the same pubs and synonyms appearing multiple times, each time with a different Xref.