Coming to consensus on germline database website + backend design

[w.lees]

@mikhail.shugay

Another important aspect of storing the germline sequences is the germline itself. It would be ideal if each sequence can be traced directly to corresponding genome contig, i.e. genome assembly ID and genomic coordinates (e.g. in GTF format). There are many tasks where this is quite important such as looking at genomic features shaping V-J recombination. I haven’t found anything related in the schema linked in original post. Have you considered adding this feature?

The schema started off as the minimum subset of information required by germline parsers but has grown into a schema definition for the whole germline set. I’ll be adding traceability to the germline this weekend, along with other related items suggested by @werner.muller. I would be grateful of further advice from you and others about what is required in the way of evidence and metadata, though, because I feel I understand what is required by parsers quite well, but am less confident about this area. Please feel free to contribute to the standardization thread

William

[sdwfrost]

Dear @cswarth

Would you mind putting your Jinja2 templates up somewhere? I’m working on some similar problems (with a real time HIV surveillance system, modelled from NextStrain, HIVtrace and Microreact), and it would be great to share code for more generic components.

Best
Simon

[cswarth]

Simon, Our prototype jinja templates are in the igdbweb repo on github,
https://github.com/cswarth/igdbweb/tree/master/igdbweb/templates

These really are crude prototypes. You’ll see some non-functional display elements like breadcrumbs that I’m in the process of replacing with real Flask code.
Flask and Frozen-Flask works like a dream.

– Chris