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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Go annotation #767

Closed TomConlin closed 5 years ago

TomConlin commented 5 years ago

addresses #766

refactor column headers etc add s couple of new species types(mould & fungi) bump date for monarch archive change 

'<gene> <has_synonym> "prot_curie" .'

to 

 '<gene> <same _as> <prot_curie> .'

(open to alternative associations)

kshefchek commented 5 years ago 
    > '<gene> <same _as> <prot_curie> .'

I don't mind the simplification but we probably should align each source with this change. In other sources we use 'has gene product' to link proteins to genes. So if we half commit to gene-protein equivalence we'll end up with has gene product cycles.

TomConlin commented 5 years ago

I like 'has gene product' much better than 'same_as'
which a grabbed base on being proximally the closest thing to has_synonym in the model class.

changed locally.

... and matching on generic curie pattern broke in the full load because it came across a curie it does not know how to expand (BEST:GH05075). Changing it to only match UniProtKB curies