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During the PR from @mmattano https://github.com/bigbio/proteomics-sample-metadata/pull/680 we detected multiple fields that we need to decide if they will be required, recommended or optional:
- `…
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- **Modality**: error
- **Exp. Type**: All
Protocols used in SDRF must be declared in IDF
..except of "standard" (or ArrayExpress) protocols (I guess)
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Hey,
so just to be sure and document it here. Veit mentioned this project to us for potential use in ProteoBench. We aim to parse parameter files into a common format (or at least parts of it).
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enryH updated
9 months ago
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### Context
In order to be able to process ArrayExpress platform experiments we need to migrate to a new API endpoint:
`The endpoint has changed from https://www.ebi.ac.uk/arrayexpress/xml/v3 to h…
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We need to make sure that the [examples on the website](https://hupo-psi.github.io/mzQC/examples/) are fully complaint with the official mzQC v1.0 specification.
Examples to update:
- [x] [Singl…
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My pipeline fails when using Lys-C as a digestion enzyme, ```NT=Lys-C;AC=MS:1001309 ``` or ```NT=Lys-C/P;AC=MS_1001310```. It works with trypsin ```NT=Trypsin;AC=MS_1001251```. My command is:
```
n…
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It would be better to not manually work with path strings but use the modern `pathlib` instead.
https://github.com/bigbio/sdrf-pipelines/blob/837af51f360e81d5b9b6b10a21698fc4c7a3c582/sdrf_pipelines…
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@Silvie menthioned that something went wrong with this experiment - it doesn't have inferred cell type information, so anatomogram shouldn't be displayed on the experiment page but it is there (empty)…
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We could also overwrite the experimental design generated from the SDRF but I don't know if that gets even more confusing.
Maybe in the long run we even deprecated the "--expdesign" parameter and req…
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@ypriverol Do you have a set of SDRF files for experiments of all different kinds of expected flavors?
If not we should systematically generate SDRF example files with all the different labelling t…