Version 1.1 requirements and improvements

[ypriverol]

Dear all @bigbio/collaborators :

Long time since our last discussions in the repo about SDRF structure. First some updates:

• The format has been submitted to HUPO-PSI revision process.
• @compomics team is now developing an annotator tool to enable the annotation of SDRF files.
• PRIDE database is getting more and more submissions with the corresponding SDRF.
• Our team has been working in the validator and now is more stable and enables validation of ontology terms.
• Help page has been created using readthedocs

While we should continue working in the first version of the format (mainly in the tooling ecosystem around it), major discussions has been going about future use cases, and changes in the current version. In HUPO-PSI we had a couple of discussions about new use cases for the format and changes:

Minor issues:

• Formalization of how DIA data should be annotated. While we have already datasets annotated for DIA data, in the specification no references to this particular use case.
• Better formalization of metaproteomics. We already have multiple datasets for metaproteomics annotated in the repo, while no normalization in the specification has been done. Probably the input from the metaproteomics community.

Major issues:

• Metabolomics: We got a lot of attention and interest to make SDRF compatible with metabolomics. @nilshoffmann is interested to work on this particular topic. @mwang87 we started this topic in the first release of SDRF but never finish. I think now that we have more people interested, it would be nice to push forward.

• Major changes on the structure: Some developers and users has been complaining that the SDRF do not contain information about the version of the format, or description of the dataset etc. We should work (in version 1.1) to increase the information about the format, and the study withing the SDRF format. Future issues will be describing the proposal.

• Single Cell: We have got a lot of interest around how to represent Single-cell data into SDRF. I think @lgatto if you are interested we can collaborate on this issue to move the representation of single cell in SDRF. We had some previous work in transcriptomics that can give us some light around how to do it SDRF transcriptomics Single-Cell.

Please let me know your opinion and if you are interested in other particular topics for version 1.1.