SDRF definition for metabolomics and affinity proteomics

[ypriverol]

We should have a prototype of an SDRF definition for metabolomics data. EPMA will work with SDRF for the standard metadata for samples for proteomics and metabolomics, and in principle, the file format MUST be required for each submission.

In addition, the format MUST support affinity proteomics data because EPMA will support this type of submission. The corresponding validator must be updated for both use cases.

[javizca]

It is too early to say, but I think that it will be difficult in practice to make the format mandatory. This needs to be checked with the EGA team but my understanding is that every Consortium producing sensitive data have their own metadata format (as it usually happens). And also, very few people curate the datasets appropriately, unless the EGA team is "paid" to do it. I had this conversation with EGA Barcelona just before Christmas, in the context of the grant application we are working in.

As a possible idea, what could be made mandatory in a first stage is some kind of file including the experimental design information, even if it is not the same one. Again, to be discussed in detail, and also to learn from the experiences of the EGA team.

[ypriverol]

We do have an standard file format for sample metadata different to other consortiums. We can discuss this in person but we can't allow submissions without sample metadata because we will be repeating the same mistakes that PRIDE/ProteomeXchange made 10 years ago.

The format must be extended to support both types of experiments, and we should aim to make them mandatory. BTW, sample metadata is mandatory in EGA. The way the sample metadata is captured is in different file formats, but it is indeed mandatory. Also metaboligths require sample metadata.

Related with issue #9