Update to Biolink 2.1.0

[colleenXu]

Translator has a compliance deadline of July 1st for "Biolink 2.0.2" for KPs/ARAs.

I'm not sure of all the code that needs to be changed, but this update probably involve changes to:

• https://github.com/biothings/biolink-model.js
• biomedical_id_resolver
  • https://github.com/biothings/biomedical_id_resolver.js/blob/master/src/config.ts
  • https://github.com/biothings/biomedical_id_resolver.js/blob/master/src/common/types.ts
• x-bte operations in registry files
  • in here: https://github.com/NCATS-Tangerine/translator-api-registry
  • in other github files - have to find them. May involve multiomics provider

---

What does an update mean?

• what do we do if our id resolution doesn't match with biolink model's id prefixes for that semantic type?
  • Happening to drug. How to handle this? Notice biolink definition, prefixes here
    • Could change some operations to drug (like drugcentral, drugbank based operations?) and leave others as small molecule
• ChemicalSubstance deprecated. We probably want to use SmallMolecule instead. However, there's various things to consider:
  • This is a "simple" fix. However, we know that ChemicalSubstances currently includes chemical mixtures (like racemic mixes, compounds, drugs?)...
  • Chemical entity looks right but....it encompasses chemicals + molecular entities (genes/proteins) so it would be too broad...EDIT: Chris Bizon has noticed this and is wondering about change
• registry-specific:
  • update some predicates in x-bte operations
  • Check node type/predicate: reactions fall under molecular activity, pathways under biological process
• Will multiomics / text-mining provider need to use different Biolink node types or predicates?
  • Treatment vs Procedure (given the mixin Chemical or drug or treatment for future queries?)
  • Exposure / Outcome mixins
  • predicates like "affects risk for" vs "positively correlated with". (negatively correlated with doesn't have a corresponding predicate yet.)

[colleenXu]

PRs to merge to move to v2.1.0:

[EDIT: 7/29 for biolink-model module fix]

BTE JS tool code updates (branch biolink_v2.1 for all):

• merge this for biolink v2.1.0 update biomedical_id_resolver.js#73
• merge for biolink v2.1 update bte_trapi_query_graph_handler#23
• merge for Biolink v2.1 code update biolink-model.js#17
• merge for Biolink v2.1 code updates #238

After code in BTE JS tools is updated/deployed:

Merge these PRs for registry files or contact Ryan Roper (multiomics provider) to merge PRs. All on branches named biolink_v2.1

• merge for biolink v2.1 updates NCATS-Tangerine/translator-api-registry#75
• don't merge until BTE is ready: changing spec for biolink v2.1 Hadlock-Lab/clinical_risk_kp#7
• don't merge until BTE is ready: updating to Biolink v2.1 Hadlock-Lab/multiomics_wellness_kp#7

[colleenXu]

@newgene @andrewsu check how BTE is loading the biolink model (which yaml).

If it's loading something older/cached, we will want it to get the latest biolink model yaml off of master when we do the update to v2.0.

[andrewsu]

@colleenXu I think you're right. In https://github.com/biothings/bte_trapi_query_graph_handler/blob/main/src/biolink.js#L9, looks like Biolink model is being loaded from this cached version https://github.com/biothings/bte_trapi_query_graph_handler/blob/main/src/biolink.json.

[colleenXu]

[UPDATE: this bug is fixed; there's another bug now...]

The Architecture call confirmed that we should move to v2.1.0.

@newgene to review BTE code to see where else we need to update. Notes for Chunlei below:

• It looks like the biolink-model module crashes soon after BTE is started. This seems to happen when trying to parse the biolink v2.1.0 json (converted from YAML). Please investigate this.

I encountered this error after:

• cd into packages and checking out the biolink v2.1.0 branches for query_graph_handler (biolinkv2.1-update) and biomedical_id_resolver (biolinkv2.1.0-updates-only).
• I then ran npm run compile, and then npm run debug. The error was hit soon after the run started (I hadn't sent a query yet).

The error messages I get are below:

[nodemon] starting `node src/server.js`
  bte:biothings-explorer-trapi:EdgeReverse BioLink-model class is initiated. +0ms
/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/object/entity_object.js:22
            this._id_prefixes = [...['UMLS'], ...idPrefixes];
                                                 ^

TypeError: idPrefixes is not iterable
    at Entity.set id_prefixes [as id_prefixes] (/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/object/entity_object.js:22:50)
    at new Entity (/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/object/entity_object.js:11:26)
    at BioLinkClassTree.addNewObjectToTree (/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/tree/class_tree.js:18:53)
    at /Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/tree/base_tree.js:31:63
    at Array.map (<anonymous>)
    at BioLinkClassTree.construct (/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/tree/base_tree.js:31:44)
    at BioLink.loadSync (/Users/jay/Desktop/bte-trapi-workspace/packages/biolink-model/built/index.js:28:34)
    at new BioLinkModel (/Users/jay/Desktop/bte-trapi-workspace/packages/@biothings-explorer/query_graph_handler/built/biolink.js:10:26)
    at Object.<anonymous> (/Users/jay/Desktop/bte-trapi-workspace/packages/@biothings-explorer/query_graph_handler/built/biolink.js:40:30)
    at Module._compile (internal/modules/cjs/loader.js:1063:30)

• See the linked PRs in my comment above. I have edits to the query graph handler (where the cached biolink model seems to be), ID resolver, and registry (smartapi files).

After discussion with @andrewsu, We want to map operations with ambiguous IDs (like MESH/UMLS) to SmallMolecule for now - even when that isn't always the most "accurate" semantic class for those IDs. This allows queries with SmallMolecule or ChemicalEntity to use those operations. [note: SEMMED api updates will use the new Biolink model version - see Sander for details]

See the deadline tracker here (probably need to be registered in ncats translator google permissions).

[colleenXu]

All PRs are merged; this update should be basically complete.

However, there may still be some tests/examples/README/saved-example-jsons that could be updated...

[colleenXu]

Closing issue:

I have reviewed tests/examples/README/saved-example-jsons in all the bte-trapi-workspace repos.

Note:

• I didn't update some tests (like in api-response-transform module) since tests were then breaking and seemed not easy to fix...
• the CHANGELOG of some repos is outdated