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bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
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biological replicate should be a comment or a characteristics #267

Closed ypriverol closed 4 years ago

ypriverol commented 4 years ago

@levitsky @anjaf @daichengxin :

While technical replicate is annotated always as a comment, the biological replicate is annotated sometimes as comment other as characteristics. See example here https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD000288/sdrf.tsv

I think it should be a characteristic rather than a comment. Please provide feedback.

@levitsky when we arrive to a conclusion probably we will need to change the validator.

daichengxin commented 4 years ago

I prefer that technical replicate is a [comment] , while biological replicate is a [characteristic] . There are several reasons:

  1. Technical replicate refers to the number of times the mass spectrometer is run repeatedly on the same sample, more on the MS run level
  2. Individually, biological replicate is more like replication at the sample level . Right ??
anjaf commented 4 years ago

Yes, I agree. Everything regarding the sample (including biological replicate) should be characteristics, while attributes regarding the assay are comments.

levitsky commented 4 years ago

I agree. Should be characteristics[biological replicate].

What do you want to change in the validator about this? It doesn't know about biological replicates.

ypriverol commented 4 years ago

I think is the validator we should check that biological replicate is not provided as a comment.