We need to improve the examples

bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

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We need to improve the examples #40

Closed mwalzer closed 4 years ago

mwalzer commented 4 years ago

Is it Characteristics[data file] (PXD000612) or Comment[data file] (NCI60)?
Also using 'sample n' for a Source name is misleading if there is a Sample column (and if there is not, too).
What keeps us from using/adapting the Labeled extracts column?

mwalzer commented 4 years ago

If I understood correctly, the Source name should comprise all fractions (could we use Extractions from the original sdrf definition?).

timosachsenberg commented 4 years ago

Thanks for bringing this up. Had the same problem with one of the examples where it was not clear how to group all fractions corresponding to the same biological replicate.

ypriverol commented 4 years ago

@mwalzer thanks for reporting this. Here I have fixed some of the examples https://github.com/bigbio/proteomics-metadata-standard/pull/62