Comments (4)
brynnz22
commented on September 13, 2024
1
Its done, its just in review with requested changes that I need to do.
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kheal
commented on September 13, 2024
These metadata changes will be in alignment with the Berkeley schema
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brynnz22
commented on September 13, 2024
editing to create smaller subtasks of what is left to do. Most of the lipidomics has been designed and written, what is left to do is:
- Add functionality for processed data to lipidomics metadata gen script
- Add functionality for
MaterialProcessingfunctionality to lipidomics metadata gen script - Add documentation to lipidomics metadata gen script
- Add optional parameter functionality if biosamples already exist or will need to be created for lipidomics metadata gen script.
Can create issues for these as needed.
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mslarae13
commented on September 13, 2024
@brynnz22 can we move this meta-issue into in progress if it has sub-issues that you'll be adding and are still in progress? Or is there a task for this that is in review or ready to close?
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Related Issues (20)
- Add lipid workflow as a test to corems
- Develop database interface base class for flexible database linking
- Develop MetabRef-specific database interface
- Apply properties to ChromaPeak attributes HOT 1
- Harmonize GC and LC spectral library creation and interfacing with MetabRef HOT 1
- Add private attributes and associated properties to LCMSMassFeatures class to lcms_dev on CoreMS HOT 3
- Add functionality for parameter import/export using a tmol file HOT 1
- Modify peak picking parameters to call by relative abundance (not absolute value) HOT 1
- Remove api token path parameter and usage from LCMSBase object HOT 1
- Remove `to_json` method from `LCMSParameters` in `encapsulation/factory/parameters` module to `encapsulation/output/parameter_to_json` and adjust usage throughout. HOT 1
- Add lipidomics-specific exporter to lcms_dev on CoreMS
- Format lcms_dev branch according to PEP8 guidelines
- Re-render documentation on lcms_dev branch on CoreMS
- Merge lcms_dev into main branch of CoreMS
- Modify metadata generation scripts for GC-MS Metabolomics workflow to berkeley-schema-fy24 HOT 2
- Generate updated metadata and upload HOT 1
- Load Configuration and Calibration objects for berkeley-schema implementation HOT 1
- Add DatabaseInterface module and classes for pulling and organizing spectra from MetabRef HOT 1
- Upgrade wdl to version 1.0 HOT 1
- Add CI/CD to test wdl validity HOT 1
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