Update databases with additional taxon ids for v3 and v4

warelab / gramene-ebeye

REST endpoint to furnish the Gramene ensembl site with search results

MIT License

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Update databases with additional taxon ids for v3 and v4 #13

Closed mycrobe closed 8 years ago

mycrobe commented 8 years ago

Proposed data hack to remove code hacks:

Create two child taxon nodes underneath maize, one for v3 and one for v4. Suggested taxon ids are 45770003 and 45770004, with species names Zea mays v3 and Zea mays v4.
Modify the two maps entries with the new taxon_ids.
Change the taxon_ids for all maize genes as appropriate.

This way, the v3 and v4 maize genomes can be visible and searchable in search.gramene.org (or another copy of it—maizev4search.gramene.org?)

ajo2995 commented 8 years ago

The changes to maps and taxonomy were done by hand. Genes docs were updated by script. This also let us to fix the inconsistent bins (based on taxon_id instead of the system_name hack). The only place where taxon_id was not updated is in the gene trees. This will be dealt with in another issue