cancervariants / cancervariants/therapy-normalization

Handle wrongly-excluded ChemIDplus records

Open
#86 0 comments 0 reactions 0 assignees View on GitHub
bug ChemIDplus data-cleaning
Dominant language
Python
Stars
15
Forks
3
PR merge metrics
No merged PRs in 30d

Description

Our current filtering strategy to get relevant ChemIDplus records (checking for nomenclature tags) removes some entries that our NCIt data links to. So, we want to be able to opt-in records pointed to by NCIt. We need some combo of the following:
* NCIt should be able to tell us which ChemIDplus records are missing (or at least build a list of all referenced ChemIDplus records).
* When performing a normal ChemIDplus load, it should be able to reference an existing allow-list to rule-in records that it would otherwise exclude.
* ChemIDplus should probably be able to perform a run that only adds in allow-listed records, rather than reimporting the entire source.
* We need to think about how this would work if users import both sources at once, or if they import one and then the other later.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by tracing the existing ChemIDplus filtering and NCIt loading workflows described in the issue, including how each source is imported separately or together. Define the allow-list flow, missing-record discovery, and import-order behavior; the work is done when linked ChemIDplus records can be included without reimporting the full source and both import sequences are supported.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, data
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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