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cellannotation / cap-pipeline-config

Building ontology pipeline configurations for the Cell Annotation Platform
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Split Developmental_stage tag into multiple tags based on organisms #89

Closed ubyndr closed 1 year ago

ubyndr commented 1 year ago

Since we have contextual search integrated and David mention on people desire to see cell types of organisms other than humans, I think we should split up the following config into separated tags based on organisms;

  - classes:
      - UBERON:0000105
      - FBdv:00007012
      - WBls:0000075
      - ZFS:0100000
      - MmusDv:0000000
      - HsapDv:0000000
      - XAO:1000000
    label: Developmental_stage

What do you think about this change @dosumis , @evanbiederstedt and @bvarner-ebi ?

ghost commented 1 year ago

@ubyndr, can you clarify, are you suggesting that the input in the ORGANISM metadata field would filter the results in CELL_TYPE so that the cell types are based on the selected organism?

If so, that seems reasonable since it would prevent the following scenario, as an example:

User enters 'Homo sapiens' in ORGANISM User types "epidermal" in CELL_TYPE and sees search result 'epidermal cell (sensu Arthropda)' The user selects 'epidermal cell (sensu Arthropda)'

Since 'epidermal cell (sensu Arthropda)' should be restricted to arthropods, a combination of 'Homo sapiens' and 'epidermal cell (sensu Arthropda)' is a conflict.

ubyndr commented 1 year ago

@ubyndr, can you clarify, are you suggesting that the input in the ORGANISM metadata field would filter the results in CELL_TYPE so that the cell types are based on the selected organism?

If so, that seems reasonable since it would prevent the following scenario, as an example:

User enters 'Homo sapiens' in ORGANISM User types "epidermal" in CELL_TYPE and sees search result 'epidermal cell (sensu Arthropda)' The user selects 'epidermal cell (sensu Arthropda)'

Since 'epidermal cell (sensu Arthropda)' should be restricted to arthropods, a combination of 'Homo sapiens' and 'epidermal cell (sensu Arthropda)' is a conflict.

Yes, this is the reason. David wanted to filter out the cell types related with Drosophila when it is not selected. If we introduce separate tags for each organisms it would be easier to achieve this.