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bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
GNU General Public License v2.0
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Add Technology Type to each SDRF #506

Closed ypriverol closed 3 years ago

ypriverol commented 3 years ago

@daichengxin :

Can you add to each SDRF in my fork https://github.com/ypriverol/proteomics-metadata-standard the field

Technology Type with the value: proteomic profiling by mass spectrometer

like the project: PXD000288 https://github.com/ypriverol/proteomics-metadata-standard/blob/master/annotated-projects/PXD000288/PXD000288.sdrf.tsv

daichengxin commented 3 years ago

I have added @ypriverol . https://github.com/ypriverol/proteomics-metadata-standard/pull/2

levitsky commented 3 years ago

Why is this necessary? Are we adding a completely fixed value to every row in every SDRF-Proteomics file everywhere?

ypriverol commented 3 years ago

@levitsky the field is optional, but it is RECOMMENDED for compatibility with Transcriptomics data. EXample https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-9694/E-MTAB-9694.sdrf.txt The Technology Type is used to describe the omics technology.

Most of these issues and new improvements @levitsky is to make the SDRF more compatible with the existing transcriptomics datasets.