INCATools / INCATools/semantic-sql

Handling KEGG Prefixes with Identical URI Resolution

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Python
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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

Open the contributing 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

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