phase 3: add association property to /meta_knowledge_graph responses

[colleenXu]

With TRAPI 1.4, tools can specify the "type of association" in their /meta_knowledge_graph endpoint responses (edges section). This property isn't being made required, and I'm not aware of a Translator-wide push to add it to as many MetaEdges as possible.

• timing: see if SRI team asks for a specific implementation date. This is likely related to their reasoner-validator
• priority: lowest priority
• responsible dev: me + another dev

This addition to the /meta_knowledge_graph MetaEdge info is buried in the MetaEdge qualifier change, which is bullet 4 of the changelog:

In MetaKnowledgeGraph component, added MetaEdge.qualifiers as list of new MetaQualifier types https://github.com/NCATSTranslator/ReasonerAPI/pull/387/files

        association:
          description: >-
            The Biolink association type (entity) that this edge represents.
            Associations are classes in Biolink
            that represent a relationship between two entities.
            For example, the association 'gene interacts with gene'
            is represented by the Biolink class,
            'biolink:GeneToGeneAssociation'.  If association
            is filled out, then the testing harness can
            help validate that the qualifiers are being used
            correctly.
          example: 'biolink:ChemicalToGeneAssociation'
          $ref: '#/components/schemas/BiolinkEntity'

This involves:

• add association annotation to x-bte operations (edit SmartAPI yamls)
  • unsure how many we want to do, and whether we'll find corresponding Associations that fit them in the biolink-model
• make sure BTE advertises the association info from the x-bte operations in its "KP"

But there's something I'm unsure of:

• do we want BTE to advertise association info in its "ARA" /meta_knowledge_graph response? Would that mean ingesting association info from TRAPI KP MetaEdges?
• so what if x-bte operations or TRAPI KP MetaEdges with the same S-P-O combo have different values for association? This is a hypothetical (not sure if this can actually happen)...

[rjawesome]

Where would the association be found for TRAPI apis?

[colleenXu]

@rjawesome The TRAPI KPs that we use may provide the association property in their /meta_knowledge_graph responses (edges section, on none/some/all of their edge objects).

However, I suggest working on another issue instead.

This one is very low priority and optional. I have edited the opening post to make this clearer and add some detail. This issue also involves getting certain pieces into place first, like x-bte annotation or TRAPI KPs with this in their /meta_knowledge_graph responses. And checking how current /meta_knowledge_graph response generation works and whether that needs tweaking.

[colleenXu]

Update notes:

• TRAPI 1.4 may still change. When those changes happen, they should be on this branch and documented in this branch's changelog

Note: in the TRAPI spec, association will inherit the BiolinkEntity schema and should be type:string, not type:object. It also would be better if TRAPI changelog more clearly stated that this is a thing...

[colleenXu]

I've posed the "unsure" questions in the opening post and the "TRAPI spec" commentary from the previous post to the TRAPI team here NCATSTranslator/ReasonerAPI#426

edit:

• minor update: my comment on type:string vs type:object has been resolved by a PR merged into the 1.4 branch of TRAPI. It's type:string (a biolink CURIE).

[colleenXu]

Note that COHD's dev instance seems to be on TRAPI 1.4 (we can access it through the registration we currently use, but they also registered a separate yaml for TRAPI 1.4). BUT I didn't see any association property provided on the MetaEdges of its /meta_knowledge_graph response...

From my post here: #597 (comment)

[colleenXu]

Going to move this to "on-hold" since it seems to be a pretty low-priority issue.

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Right now, our ARA /meta_knowledge_graph response doesn't have any "association" values.

Based on a quick check, TRAPI 1.4 instance meta_knowledge_graphs for COHD, CHP, and Automat KPs (pharos, hetio) don't have "association" values.

So it's unclear if our /meta_knowledge_graph response for our ARA should have any "association" values inherited from our TRAPI KPs.

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I haven't added any x-bte annotation for this property, and I haven't really been asked to.