Create / produce additional GOlr fields to support default relation change

[kltm]

There are fields in GOlr, like regulates_transitivity_graph_json, which seem to have been created after the initial switch from isa_partof to regulates and have no isa_partof analog. The schema will have to be extended and those would need to be added to the loader.

This is a spinoff from #620

[kltm]

Explicit metadata "regulates" fields: regulates_closure regulates_closure_label regulates_transitivity_graph_json

The last one is the problematic one. It is defined in only: neo-config.yaml and ont-config.yaml

[kltm]

As a technical "huh" note, given how we do this, we could be done this in the (relative) snap of the fingers if we forgive ourselves the field id "regulates_..." and just redefine it using the relation set we want.

  - id: regulates_transitivity_graph_json
    description: "JSON blob form of the local relation transitivity graph. Uses various relations (including regulates, occurs in, capable_of)."
    display_name: Regulates transitivity graph (JSON)
    type: string
    property:
      - "getLineageShuntGraphJSON"
      - "BFO:0000050"
      - "BFO:0000066"
      - "RO:0002211"
      - "RO:0002212"
      - "RO:0002213"
      - "RO:0002215"
      - "RO:0002216"
    indexed: false

[kltm]

Noting that topology_graph_json is defined as the regulates set of relations. Hm. I'm not sure what exactly that will have consequences for or if there will be an incompatibility. It's possible that that might have to be factored out with a set of two new fields mirroring the transitivity fields.

Similarly, I wonder what is loaded into "neighborhood_.." fields, as they are not exposed at all in the metadata and would required some owltools exploration. I don't believe they're used outside of a single minor sub-display on ontology pages that probably wouldn't be missed even if something did break, so will forge ahead ignoring that for now.

[kltm]

Should now have index building image with geneontology/golr-autoindex:f815e3e9004f96493f29a80a73526c91c2a4c25d_2021-10-01T162208_issue-620-change-default-closure Will test after release.

[kltm]

Bad SOP for docker build; updated and retrying.

[kltm]

I believe that this is now generally working. New tickets will be refinement or bug fixes.