Enable gene function search on GO terms #1465
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TODO: add mapping file to NERSC CFS
naglepuff
changed the title
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BEFORE MERGE: Update the down-revision of the migration introduced here. (#1471 has been merged an includes a migration) |
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Fix #1388
Changes
Data Model
New tables:
go_term_textandgo_term_to_pfam_entryto model GO terms and how they map to PFAM entries. A new migration has been added to create the tables.Ingest
Ingest GO terms by iterating over the "nodes" in the graph defined by: http://current.geneontology.org/ontology/go-basic.json
Ingest PFAM entry to GO term mapping using a file derived from: current.geneontology.org/ontology/external2go/pfam2go
API
New endpoint for text search of GO terms.
Query
New logic that transforms conditions using GO terms to their associated PFAM entries.
UI
New facet for GO has been added.
Testing
To test, you'll have to have to run a local ingest. Make sure you obtain the new file added to NERSC:
.../data/ingest/go/pfam_go_mappings.txt.Verify ingest populates the
go_term_textandgo_term_to_pfam_entrytables, and searching on GO terms works through the UI. That is, make sure searching for GO terms works using the new endpoint, and make sure you get the results you'd expect when searching using this facet. Pick some PFAM value from thegene_functiontable, use the new mapping table to find associated GO terms, and use those for testing. For example, GO:0004930 maps to PF00001