Metabolomics example

[mmattano]

Annotation of example studies for metabolics SDRF

[ypriverol]

@mmattano I have done the first review of the proposal, here are a couple of ideas:

• mzXML is in principle a raw file, like mzML or the Raw files. Then, it should be possible to add them as raw files.
• I see that you have the same sample, with 2 organism parts liver and plasma; unless you have a different raw file you should annotate the sample + data file relation into only one row of the file. Then you need to add two columns with two organism parts liver, plasma.
• Im wondering if we need to annotate for SDRF files the comment[metabolite assignment file], this looks like another file relation that should be annotated in the SDRF at least not in this way. We have tried to keep the SDRF as the relation between the Sample and the Data (Raw) files, not results involved. My question is what is that field for? Are this the metabolites quantified or the database used to perform the identification/quant process. ?

[mmattano]

@ypriverol I made some changes to the file to get closer to complying with the testing (I'll edit it more with the next upload) and to incorporate your comments. About them:

• I moved the mzXML to the raw file column. You're right to suggest putting it there, I originally reserved it for the instrument output files but that would be overkill
• There are different raw files for the each plasma and each liver sample. Is that ok and is that what you were asking? Let me know if I missed something
• I do agree that it's something that is not needed to purely connect the sample to the data, but it is something that is needed for further processing. So I'd say that it's ok to kick it out for a "pure" sample-data annotation, but that it would be good to have a link to that. what do you think?