TranslatorSRI / NodeNormalization

Service that produces Translator compliant nodes given a curie
MIT License
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Sort chemical labels in the configured prefix order #260

Closed gaurav closed 1 month ago

gaurav commented 2 months ago

This PR updates NodeNorm so that it behaves the same way as Babel v1.5.0 when dealing with synonyms: for certain Biolink classes (in this case, biolink:ChemicalEntity), we boost certain prefixes to the front of the list when choosing a preferred label. In all other cases we use the first non-empty label as usual.

As of this PR, the preferred_name_boost_prefixes in both Babel v1.5.0 (and therefore in the current NameRes) and in NodeNorm are:

"preferred_name_boost_prefixes": {
  "biolink:ChemicalEntity": [
    "DRUGBANK",
    "GTOPDB",
    "DrugCentral",
    "CHEMBL.COMPOUND",
    "RXCUI",
    "CHEBI",
    "HMDB",
    "PUBCHEM.COMPOUND"
  ]
}