Uploaded image for project: 'PhenoTips'
  1. PT-3265

getTerm in HGNC vocabulary should match on exact input provided

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.3.2, 1.4-milestone-1
    • Component/s: vocabularies
    • Labels:
      None

      Description

      The HGNC vocabulary, getTerm is too "eager" to match its input. Sometimes inputs are ambiguous and it's better to not return a match at all than to choose one of many options.

      Example:

      getTerm("CAKUT (PAX2, EYA1, GATA3, KAL1, SALL1, SIX1, SIX5, SOX17, BMP7, CHD1L, DLX5, FREM2, HPSE2, RET, ROBO2, SIX2, UPK3A, HNF1B, BMP4, FOXC2)")

      matches on

      KAL1

      (among other things), a previous symbol for

      AMOS1

      and returns the term with the gene symbol

      AMOS1

      . This behaviour is obviously wrong and the return value should be null (no exact match found).

        Attachments

          Issue links

            Activity

              People

              • Assignee:
                alina alina
                Reporter:
                marta Marta Girdea
              • Votes:
                0 Vote for this issue
                Watchers:
                1 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: