owlcollab / owlcollab/owltools
Add ontology trimming option to owlsim
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- Dominant language
- Java
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- 115
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Description
From cmung...@gmail.com on July 10, 2013 19:05:51
Add an option or command to remove any classes that have no (inferred) instances.
This can be done in owltools at the moment, but requires a few steps. E.g. you can make a GAF from the annotations and use --extract-ontology-subset-by-gaf, but this is not convenient.
This would be particularly useful for pre-calculations of the allxall attribute matrix
Original issue: http://code.google.com/p/owltools/issues/detail?id=72
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the existing owltools --extract-ontology-subset-by-gaf command and the steps needed to create a GAF from annotations. Determine where an option or command for removing classes without inferred instances belongs. Done means the trimming operation is available directly and supports the allxall pre-calculation use case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100