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#197 Store all evidence in Chado using ECO term IDs not names

eventually
open
nobody
None
3
2014-12-19
2013-07-01
Kim Rutherford
No

Currently we use ECO term IDs sometimes but for GO we use the GO evidence name (like "Inferred from Mutant Phenotype").

For FYPO there are still a few missing ECO terms: [curation-tasks:#192]

Related

Curation tasks: #192

Discussion

  • Kim Rutherford

    Kim Rutherford - 2013-07-01

    We need to load ECO too.

    And maybe add a DB level constraint (if possible) on the feature_cvtermprop table so that rows the type "evidence" must have a value from the ECO cvterm.

     

  • Kim Rutherford

    Kim Rutherford - 2013-07-08

    Currently we use ECO term IDs

    Sorry I got that wrong. We consistently use the name of the evidence in Chado. We use either GO evidence names or ECO term names.

     

  • Valerie Wood

    Valerie Wood - 2013-09-10
    • Priority: 5 --> 3
     

  • Kim Rutherford

    Kim Rutherford - 2014-10-23

    Midori has made a mapping file:
    pombe-embl/chado_load_mappings/ECO_evidence_mapping.txt

    We should use that to map evidence names from flat file to ECO term IDs when storing each annotation in Chado.

     

  • Antonia Lock

    Antonia Lock - 2014-12-19

    ECO:0001098 'microscopy evidence'

     

  • Midori Harris

    Midori Harris - 2014-12-19

    ECO:0001098 been in the mapping file for a while now.

     

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