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option to accept an URL with embedded Bioschemas #15

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egonw opened this issue May 10, 2023 · 0 comments
Open

option to accept an URL with embedded Bioschemas #15

egonw opened this issue May 10, 2023 · 0 comments
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enhancement New feature or request

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@egonw
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egonw commented May 10, 2023

A growing number of databases, including the ChEMBL database, use Bioschemas to make molecular entity info available in a (more) machine readable way. For example, https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL59/ will contain Bioschemas like:

    {
  "@context": "http://schema.org",
  "@type": "MolecularEntity",
  "identifier": "CHEMBL59",
  "url": "http://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL59/",
  "name": "DOPAMINE",
  "image": "https://www.ebi.ac.uk/chembl/api/data/image/CHEMBL59.svg",
  "molecularFormula": "C8H11NO2",
  "molecularWeight": 153.18,
  "monoisotopicMolecularWeight": 153.079,
  "inChI": "InChI=1S/C8H11NO2/c9-4-3-6-1-2-7(10)8(11)5-6/h1-2,5,10-11H,3-4,9H2",
  "inChIKey": "VYFYYTLLBUKUHU-UHFFFAOYSA-N",
  "smiles": [
    "NCCc1ccc(O)c(O)c1"
  ]
}

I can imagine an lwreg "URL" option for the registry which would take a URL, extract the SMILES from the Bioschemas, and register that SMILES.

@greglandrum greglandrum added the enhancement New feature or request label Jul 4, 2024
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