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reconsider name choices #158

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cbizon opened this issue Jun 26, 2023 · 3 comments
Open

reconsider name choices #158

cbizon opened this issue Jun 26, 2023 · 3 comments
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@cbizon
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cbizon commented Jun 26, 2023

At the moment we choose a preferred label by following the label of the preferred prefix. Eg. if we're looking at a chemical, we take pubchem's label. But sometimes this leads to ugly names. Perhaps we should find a way to choose a nicer name, e.g. NCATSTranslator/Feedback#259 (comment)

@gaurav
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gaurav commented Oct 18, 2023

@gaurav
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gaurav commented Dec 10, 2023

See NCATSTranslator/Feedback#568 for an example.

@gaurav
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gaurav commented Dec 13, 2023

At least some of our long names are coming from PUBCHEM.COMPOUND. For example, PUBCHEM.COMPOUND:3420 has equivalent identifiers:

      {
        "identifier": "PUBCHEM.COMPOUND:3420",
        "label": "4-Cyclohexyl-1-[2-[(2-methyl-1-propanoyloxypropoxy)-(4-phenylbutyl)phosphoryl]acetyl]pyrrolidine-2-carboxylic acid"
      },
      {
        "identifier": "CHEMBL.COMPOUND:CHEMBL4078476",
        "label": "CHEMBL4078476"
      },
      {
        "identifier": "CAS:1910773-95-3"
      },
      {
        "identifier": "HMDB:HMDB0252464",
        "label": "Fosenopril"
      },
      {
        "identifier": "INCHIKEY:BIDNLKIUORFRQP-UHFFFAOYSA-N"
      }

I think we should push PUBCHEM.COMPOUND below HMDB in the priority list.

@gaurav gaurav self-assigned this Jan 9, 2024
gaurav added a commit to TranslatorSRI/NodeNormalization that referenced this issue May 1, 2024
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