Comments (2)
dustine32
commented on June 22, 2024
I finished model.translate() to the point where it will create annotons from GPAD lines using the same logic from ontobio/rdfgen, though (except for extensions) similar to Paul's rules.
One issue I dealt with was retrieving the aspect from the term since the existing logic (stolen from rdfgen) needed this. Since GPAD doesn't contain this aspect column like GAF does, GPAD could not be translated directly in ontobio/rdfgen. For now, I created a PR in ontobio for getting the GO aspect from a term. This PR's same code is currently in gocamgen but I'll remove it once the PR is merged and the ontobio package gets updated.
A TODO in rdfgen is to utilize the GPAD relation field, but this can be discussed when further defining translation rules and then implemented either here or in ontobio.
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dustine32
commented on June 22, 2024
Since the PR has been incorporated into ontobio 1.7.0, a couple more things before closing this:
- Update
ontobioin requirements.txt to 1.7.0 - Remove redundant
go_aspectcode from gocamgen.
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Related Issues (20)
- Update extension validation rules TSV
- Update extension validation rules for acts_o_population_of HOT 3
- Create test files for additional annotation metadata HOT 31
- No extension is an island HOT 4
- Resolve Shex failures in MGI annotations due to invalid identifiers for binding input HOT 38
- add taxon metadata for each model HOT 5
- Create test files for WB import HOT 12
- Write translated models out in N-Quads format HOT 1
- Proteoforms shouldn't be split into separate models HOT 14
- Handle pipe-separation in translation of with/from field HOT 1
- Handling interacting taxon data
- Add date and contributor to ALL annotation individuals? Not just evidence and Axiom? HOT 4
- Emit comment in annotation properties HOT 1
- Collapse comma-delimited objects of chain relations
- Add providedBy to all individuals HOT 2
- Add gene symbol to model title HOT 14
- Param to set modelstate HOT 1
- Comment missing some text from the GPAD HOT 1
- Set import model states to production so annotations are in GPAD outputs from dev HOT 5
- Processing annotation contributors for multiple GPAD lines with single annotation id HOT 5
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