omicverse.metabol.fetch_hmdb_from_name

omicverse.metabol.fetch_hmdb_from_name#

omicverse.metabol.fetch_hmdb_from_name(name, *, cache=True, refresh=False)[source]#

Resolve a metabolite name → HMDB / KEGG / ChEBI / PubChem CID.

Uses the PubChem REST API in two hops:

  1. compound/name/<name>/cids/JSON → PubChem CID

  2. compound/cid/<cid>/xrefs/RegistryID/JSON → a long list of external registry IDs; we filter by regex to pick out the HMDB, KEGG-compound, and ChEBI identifiers.

PubChem is publicly-accessible, tolerant of synonyms, and gives HMDB/KEGG/ChEBI in a single call. No API key needed.

Parameters:

  • name (str) – Common name ("Glucose", "L-isoleucine", …). Case- insensitive; PubChem’s synonym index covers most aliases.

  • cache (bool (default: True)) – Cache under ~/.cache/omicverse/metabol/pubchem_xref_cache.json so repeat calls are free.

  • refresh (bool (default: False)) – Force a network round-trip even if the name is cached.

Returns:

Keys: hmdb, kegg, chebi, pubchem. Missing ID → "".

Return type:

dict[str, str]

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