Supporting the Mapping Integration workflow
- Dominant language
- Scala
- Stars
- 37
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
The mapping Integration (as opposed to QC #333) workflow is about effective integration of new mappings into an ontology while maintaining consistency. The goal is to be able to rapidly slurp up existing mappings (almost) without the need of human review
### Workflow:
- Input Ontology O (e.g. Mondo)
- Input M:
- Merged set of mappings:
- Internal (existing, verified mappings):
- Reviewed: 0.99 %
- Not reviewed 0.95 %
- External (OAK lexmatch, existing mapping sets)
- Confidence on a case by case basis, configured as part of mapping commons
- PT=sssom-py:ptable(M)
- {best-guess.sssom.tsv, results.json, |cluster-X.png|, |cluster-X.md}, =boomer(PT, O)
- EDIT: I thought we would do a proper human review of questionable clusters here, but maybe we leave this to #333 instead to make this workflow more scalable
- difference.sssom.tsv = sssom-py:diff(M, best-guess.sssom.tsv)
- Cursory human review of difference.sssom.tsv (eyeballing), no semapv:MappingReview justification added. Links from SSSOM file to related cluster facilitates to effectively review using a nice image (this could be an app one day).
- Rejected mappings from the difference.sssom.tsv should be recorded in a "negative.sssom.tsv" mapping file by the curators
### New boomer requirements
- [ ] Output best-guess.sssom.tsv should be sssom #47 and also include a notion of mapping confidence (I didn't get 100% how cluster and mapping confidence should relate in our meeting, but I think you did) and a link to the associated mapping cluster. If there is other metadata you think that can help with the review, you can add it into the comment section.
- [ ] Most of the stuff in #333
### Comments:
- "low prior property mapping will be rejected in a high probability clique" (@cmungall)
- boomer does not necessarily create a globally coherent outcome model (@balhoff)
Contributor guide
No contributing guide indexed for this repository
Research direction
The issue names no files, tests, or entry points, so begin by locating the boomer workflow and the implementation of its output generation. Use the listed mapping workflow and new boomer requirements as the acceptance criteria, including SSSOM output with mapping confidence and a link to the associated cluster, while checking issue #333 for related scope.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- scala
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100