RaMP: process of x-bte annotation + adding to BTE

[colleenXu]

Opening an issue here to better track the status of this effort. In the future, when data resources reach the x-bte annotation part, we'll want to open an issue in this repo for tracking.

Previous discussion in biothings/pending.api#69, with the currently-relevant comments starting biothings/pending.api#69 (comment)

Related to post-processing and JQ-related work, which is described in biothings/pending.api#69 (comment) and #489 (comment)

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I'm writing x-bte annotation in my fork: https://github.com/colleenXu/RaMP-Client/blob/x-bte-annotation/libs/features/ramp/ramp-api/src/assets/data/ramp_openapi_with_extensions.yml

That file is registered https://smart-api.info/registry?q=ac9c2ad11c5c442a1a1271223468ced1

[colleenXu]

Discussion topics:

1: current BTE has buggy behavior when parsing the output of this API: see here, and here. I therefore suggest NOT "fully deploying" this as a KP used by BTE and others (by adding to BTE's config list) until this has been addressed

• It's difficult to write all the possible x-bte annotation because the bugs interfere with successful testing
• I anticipate that BTE could handle this better with the JQ-related features (two main issues) or a custom api-response-transform (current handling method). So I suggest getting the JQ-related features working first...

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2: writing up all the possible x-bte annotation (depends on 1)

• ask the RaMP team: what is going on with the chemical/metabolite + gene namespaces? Ideally, we want to query for/retrieve as many entities as possible without getting "duplicates".
  • right now, I'm assuming HMDB and entrez/NCBIGene are the only namespaces needed.
    • Other chem namespaces returned in responses are CAS, chebi, kegg, pubchem.
    • Other gene namespaces are ensembl, uniprot, hmdb
  • an old note: for example, these equivalent IDs for glutamic acid retrieve the same data: PUBCHEM:33032,CHEBI:16015,HMDB:HMDB0000148,KEGG:C00025
• Also ask RaMP team or search: what are the sources for the MetaEdges/operations? If the answer isn't simple or RaMP is the source, we can set RaMP as the primary source when we add it to the config list (noted here)
• /pathways-from-analytes: based on old notes starting here
  • hmdbChem - reactPathway (already written)
  • hmdbChem - wikiPathway
  • hmdbChem - keggPathway
  • entrezGene - reactPathway (already written)
  • entrezGene - wikiPathway
  • entrezGene - keggPathway
• /analytes-from-pathways: based on Andrew's notes here
  • reactPathway - hmdbChem
  • reactPathway - entrezGene
  • wikiPathway - hmdbChem
  • wikiPathway - entrezGene
• /common-reaction-analytes: based on old notes here. I'm not clear on what this data is representing: provide gene -> chem (gene2met) and chem -> gene (met2gene) that are involved in the same reaction? what reaction/pathway they're both in isn't provided
  • hmdbChem - entrezGene
  • entrezGene - hmdbChem

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3: discussing with the RaMP team: what SmartAPI yaml file to have x-bte annotations on and register in the SmartAPI registry (including what repo).

• This probably involves removing the current SmartAPI registrations: older (alpha-version??) version, and my current (forked) version
• previously noted here

[colleenXu]

Updated notes:

• RaMP's github repo has 3 SmartAPI yamls: https://github.com/search?q=repo%3Ancats%2FRaMP-Client%20openapi&type=code
  • my old notes are that this one appears to be used by https://rampdb.nih.gov/api but I'm still not sure
• I've updated my fork's master and x-bte-annotation branches to reflect updates made upstream in late April / early May
• I previously thought the ontologies-from-metabolites / metabolites-from-ontologies were interesting, but couldn't be annotated because the ontologies weren't IDs. My notes are here

[colleenXu]

Found some info on ID namespaces available: https://github.com/ncats/RaMP-DB?tab=readme-ov-file#important-notes