ebi-ait / ebi-ait/microbe-central

Check Metadata Fields in BioSamples

Open
#44 1 comment 0 reactions 0 assignees View on GitHub
Microbe
Dominant language
No language data
Stars
0
Forks
0
PR merge metrics
No merged PRs in 30d

Description

Two tasks here:

Correct existing metadata in BioSamples

Search for samples with similar issues in BioSamples

- [ ] '[broadleaf forest biome](https://www.google.com/url?q=https://www.ebi.ac.uk/biosamples/samples?text%3D%26filter%3Dattr%253Abroad-scale%2Benvironmental%2Bcontext%253Abroadleaf%2Bforest%2Bbiome&sa=D&source=docs&ust=1736874030090424&usg=AOvVaw2P0O0BFUMCdQapIYyC5oAQ)' as a 'local environment context' in Microbe samples - this is not right according to Tanja. Figure out the correct ontology term to put here.
- [x] Collection date showing 2023-05-72
- [x] [SAMEA115410272](https://www.ebi.ac.uk/biosamples/samples/SAMEA115410272) has 'preservation temperature' of 4C but 'freezing method' of Ultra Low Temperature Freezer.
- [x] [SAMEA115408689](https://www.ebi.ac.uk/biosamples/samples/SAMEA115408689) has duplicated values in each of freezing/preservation method and freezing/preservation temperature. (Low priority as this comes from some freezing methods and preservation methods being identical)
- [x] Some samples have "timepoint" instead of "time point"

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the unchecked BioSamples query for “broadleaf forest biome” and compare its value with the relevant ontology terms; the issue names no repository files or tests. Review similar Microbe samples for the same metadata problem. Done means the incorrect term is replaced with the agreed ontology term and comparable issues are identified.

Written by the indexing model from the issue text.

Assessment

Domain
databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.