dgidb / dgidb-v5

Providing interactions between drugs and genes sourced from a variety of publications and knowledgebases
https://dgidb.org
MIT License
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Interaction types docs page/db structure #211

Closed jsstevenson closed 1 year ago

jsstevenson commented 2 years ago

For reference, this is the v4 page: https://www.dgidb.org/interaction_types. For v5, this section is blank, and needs to be rebuilt.

One additional pitch: The HTML for the "reference" column in the above table is stored in the DB as HTML snippets. Take these three DB seeds:

  {
    type: 'chaperone',
    directionality: 0,
    definition: 'Pharmacological chaperone interactions occur when substrates or modulators directly bind to a partially folded biosynthetic intermediate to stabilise the protein and allow it to complete the folding process to yield a functional protein.',
    reference: '<a href="http://www.ncbi.nlm.nih.gov/pubmed/17597553">pubmed:17597553</a>'
  },
  {
    type: 'stimulator',
    directionality: 0,
    definition: 'In a stimulator interaction, the drug directly or indirectly affects its target, stimulating a physiological response.',
    reference: 'DrugBank examples: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23318685">pubmed:23318685</a> <a href="http://www.ncbi.nlm.nih.gov/pubmed/17148649">pubmed:17148649</a> <a href="http://www.ncbi.nlm.nih.gov/pubmed/15955613">pubmed:15955613</a>'
  },
  {
    type: 'modulator',
    directionality: nil,
    definition: 'In modulator interactions, the drug regulates or changes the activity of its target. In contrast to allosteric modulators, this interaction type may not involve any direct binding to the target.',
    reference: "Modulators. Segen's Medical Dictionary. (2011). <a href=\"http://medical-dictionary.thefreedictionary.com/modulators\">Retrieved online</a> October 9 2015."
  },

Here, reference is doing a bunch of different things. It'd be nice if, instead, we could break them up (examples as a different column?) and provide more structured columns in the DB table (eg "Link Name" and "Link URL" rather than an html component).

github-actions[bot] commented 1 year ago

Closed by #272.