Comments (4)
@cmungall can you just roughly jot down the method, e.g. something like:
- collect all mappings
- (unify to skos? or can the input be mix of skos and owl)
- generate individual ptables for each input table
- (how to provide global priors on mapping set level?)
- Or: merge everything first into one massive SSSOM file?
- run boomer
- Look at X (what is X) make a fix, run again
Thanks.
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- Generate OWL for each source
- can we flat
- should use subClassOf where appropriate (I think this only applies to ORDO - transform the part-ofs to is-a)
- Aggregate all mappings as SSSOM files
- Select subset of ontologies mappings for any given experiment (this may be simply everything to start with)
- Merge selected OWL ontologies using robot
- Fill a default confidence value for each SSSOM file
- we can iterate on more sophisticated strategies, just choose 0.8 as a default for now
- Extract a ptable from all selected SSSOM files.
- just use the default sssom-py method for now, no parameter tweaking
- eventually boomer will take sssom natively INCATools/boomer#47
- I don't think sssompy will make the prefixes table for boomer but this would be good functionality to have
- Feed the ptable and the merged ontology to boomer
- use defaults for now
- Explore output
- working on documenting this: INCATools/boomer#261
- but for now if you see a folder full of json and a md file, consider it a success
The input to boomer should be a ptable and the combined OWL files of all ontologies. We can iterate on methods to set priors but just to get started, something like 0.85/0.5/0.05/0.5.
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Something to look at: https://github.com/geneontology/go-rhea-boom/blob/master/Makefile
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This ticket is now a bit too general, I consider this done - we will replace this now moving forward by more specific issues
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Related Issues (17)
- Integrate other mapping sources (drop links)
- Prefix maps do not exist HOT 1
- Ingest Mondo mappings
- Ingest DO, ORDO, OMIM, NCIT mappings HOT 17
- Document ICD10 mapping sources HOT 3
- Ingest OMOP2OBO mappings HOT 3
- Build ingest pipeline for SNOMED-ICD10 mappings HOT 3
- Capturing confidence levels from the side of the registry
- Basic progress monitor for mappings HOT 3
- Include Meddra mappings from Open Targets
- Change default license HOT 1
- Review general mapping rules for diseases and phenotypes HOT 6
- Rules for disease mappings
- Add mapping sets to disease mapping commons
- Slurp Medgen HPO mappings HOT 1
- UMLS - HPO Mappings HOT 1
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