sdsc-ordes / sdsc-ordes/modos-api
[Feature request]: metabolomics integration
Open
@cmdoret is already working on this.
Since Dec 4, 2024.
enhancement
- Dominant language
- Python
- Stars
- 2
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
Contact Details
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Description
These are the minimum features to efficiently embed mzTab (as standard format for exchange of metabolomics data) into MODOs:
- The metadata on samples and assays specified in the mzTab (MTD lines) should be available and queryable through the API. Having to download the full file (or files) and parse it externally to know what data is included kills any
- The API should include helpers to pull pandalized versions of the SML, SMF, SME, etc.
- There should be helpers to remove data that is associated with a specific sample_id (=set columns in SML and SMF to NaN). Think of a patient who decides to opt-out of a study,
- The mzTab file should definitely be stored within the object. How else can you ensure sync, slicing, etc of modo? I can't imagine there is no way of storing a text file into zarr arrays.
- There should be coherence in how sample metadata across different omics layers is represented. It should be user-friendly to obtain a single table with sample_id, patient_id, batch_id, all types of objects included, and their name id
Importance Level
High
Affected Components
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Technical Requirements
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Acceptance criteria
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