INCATools / INCATools/semantic-sql
Handling KEGG Prefixes with Identical URI Resolution
- Dominant language
- Python
- Stars
- 69
- Forks
- 7
- Avg merge
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- Merged PRs (30d)
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Description
### KEGG Ontology Prefix Handling
We are currently using two KEGG prefixes:
- **kegg.reaction** ([KEGG Reaction](https://bioregistry.io/registry/kegg.reaction))
- **kegg.pathway** ([KEGG Pathway](https://bioregistry.io/registry/kegg.pathway))
Both of these prefixes resolve to the same base URL: `https://www.kegg.jp/entry`. For example:
- [R00100](https://www.kegg.jp/entry/R00100)
- [rsk00410](https://www.kegg.jp/entry/rsk00410)
I have been manually editing the `prefix.csv` files in my semsql installation to handle prefixes that are not already defined for ontologies we are currently developing. However, I'm uncertain how best to handle the KEGG prefixes given their shared resolution.
Any suggestions or guidance on a robust solution for this issue would be greatly appreciated.
Contributor guide
Research direction
Start by inspecting the prefix.csv files and the prefix-resolution handling in the semsql installation. Determine how kegg.reaction and kegg.pathway should remain distinct while sharing https://www.kegg.jp/entry, then verify that both prefixes resolve correctly without manual edits.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, sql
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100