Align FASTQmetadata entity to SRA Run

[ericcrandall]

materialSamples in GEOME are allowed to have multiple Tissues, which can each have multiple FASTQmetadatas. Would it be possible to align this hierarchy to match what is in SRA like so?

GEOME == SRA
materialSample == BioSample
tissue == NA or possibly Experiment
FASTQmetadata == Run

The FASTQMetadata are an important aspect of what GEOME tracks, and a single sample or tissue could have multiple runs of the same data type (e.g. multiple runs of RAD data) or multiple runs of different data types (e.g. a coral sample could have its genome sequenced, and its microbiome metabarcoded).

[ericcrandall]

https://twitter.com/alx_sim/status/1321482133400178691

[jdeck88]

I think this request looks like a clarification of existing functionality in our documentation. That is, we want to draw out in our documentation especially the point that FASTQmetadata (in GEOME) == Run (in SRA). If that is the case, we can add this to our FAQ (https://docs.google.com/document/d/1tEFpclCyJ6aLnypmtdfdjLVhiWQ-rYhGqu5eGhq3s5s/edit) and user help (https://geome-db.org/docs/helpDocumentation.pdf). and then great if you can help with that text.... if there is a request for new features here then we should talk.

[ericcrandall]

My understanding from RJ is that when GEOME submits multiple runs for the same biosample, it re-submits the biosample entirely. The new feature I am requesting is the ability to submit multiple runs for the same Biosample in SRA. Can we discuss before or during the steering committee meeting?

From email of August 21:

Creating a 2nd fastq submission would be the best way too do this.

Unfortunately, I don’t think GEOME will create a 2nd run with SRA, but instead will re-submit the biosample. Submitting as a second run would be the correct way to do this.

RJ