owlcollab / owlcollab/owltools
Conversion from OBO to OWL Functional creates invalid IRIs
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- Dominant language
- Java
- Stars
- 115
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- 34
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Description
Hi!
When converting from OBO to OWL Functional, some prefixed identifiers are expanded without proper escaping, creating the invalid IRIs.
Example:
- Download
ecocore.obo - Run
owltools ecocore.obo -o -f ofn ecocore.ofn
The resulting file will contain invalid IRIs such as:
http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso
(this is also an obvious roundtrip issue but as far as this goes I'm only concerned about the syntax right now).
Related issues:
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Research direction
Reproduce the issue with the linked ecocore.obo file using the owltools ecocore.obo -o -f ofn ecocore.ofn command. Inspect the OBO-to-OWL Functional conversion path and verify that the generated output contains syntactically valid IRIs instead of concatenating two full IRIs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100