cytoscape / cytoscape/idmapper

metabolite support is incomplete and not implemented properly

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bug
Dominant language
Java
Stars
2
Forks
0
PR merge metrics
No merged PRs in 30d

Description

HMDB was added, but no other chem sources.
https://github.com/cytoscape/idmapper/blob/master/src/main/java/org/cytoscape/idmapper/MappingSource.java#L9

1. Should add other common chem sources
2. Should restrict "to" list to same type as "from" list, e.g., chem types or gene types, since mapping from HMDB to Ensembl (or vice versa) makes no sense and will always fail.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with src/main/java/org/cytoscape/idmapper/MappingSource.java and trace how its identifier sources populate the available from and to lists. Determine which common chemical sources are required and how source types are represented; done means those sources are supported and incompatible mappings, such as HMDB to Ensembl, cannot be selected.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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