Dear community,
Since openBIS version 20.10.2, we can provide a metadata.json file that goes with the data upload documented here: openBIS | Data upload via dropbox. I was wondering if anyone has experience providing metadata related to an RNA-seq file. Specifically, I want to know if you have:
-Convert MAGE-TAB to JSON
-Upload the JSON file with the RNA-seq
Any tips are highly appreciated.
I will use the opportunity to wish you all happy holidays!
Dear Thiago,
As far as I know we do not have a fixed implementation of RNA-seq related structures in openBIS.
Also the sequencing core facilities that use openBIS have mainly standards on raw data for FASTQ production only.
But I think I can imagine your use case… Once you have defined data structures for RNA-seq (experiment, sample, count table, analysis etc), if you have also json description of them (from eg sequencing facility or from SRA) then in theory you can go this way as you suggest: upload it into dropbox with the dataset and have the metadata filled in. Some tests would be needed for your specific formats, but once it works, it can be potentially part of an automated data registration.
As for MAGE-TAB, it is a tabular format, so a converter to json would be needed indeed.
Perhaps this gives some hints, but have never needed or tried it, so do not have hands-on experience:
https://isatools.readthedocs.io/en/latest/index.html
https://github.com/ISA-tools/isa-rest-service/issues/10
Overall, the idea sounds interesting and feasible to me, but would need implementation work…
all the best,
Michal
Hi Michal,
Thank you for your detailed comment (and sorry about the delayed answer, I was on leave). I will discuss the considerations and feedback here in case we make any progress on this end.
All the best,
Thiago
Good luck Thiago, and if you will have some solutions or implementations I’ll be curious to learn!