template for requesting addition of a new species

[petrelharp]

This would be a way for someone to compile the relevant information for adding a new species without doing the coding.

[codecov]

Codecov Report

Merging #772 (8026455) into main (e88fb3d) will not change coverage.
The diff coverage is n/a.

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  Coverage   99.62%   99.62%           
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  Files          34       34           
  Lines        2413     2413           
  Branches      298      298           
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  Hits         2404     2404           
  Misses          4        4           
  Partials        5        5           

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[grahamgower]

LGTM. Maybe we don't need the chromosome list though?

[grahamgower]

These are coming from ensembl now, so this isn't strictly necessary, right?

[jeromekelleher]

Speaking of which, the Ensembl ID is a necessary bit of info.

[jeromekelleher]

LGTM, but we should give more info on how to get the Ensembl ID, etc.

[jeromekelleher]

Speaking of which, the Ensembl ID is a necessary bit of info.

[jeromekelleher]

Or Hapmap? Don't want to people to convert to CSV if it's already in the right format.

[petrelharp]

Speaking of which, the Ensembl ID is a necessary bit of info.

Hm. So, here's the species that are apparently available on ensembl:

• mostly mammals
• "metazoa"
• plants
• fungi
• protists
• bacteria

I think that's all? I can't find a list of ensembl sites.

And, what do we do about species not in Ensembl (e.g., there are no Mimulus, looks like)? Do we say that we're only for species with annotations uploaded to Ensembl? Any idea how difficult getting a new species on there is?

[jeromekelleher]

I guess we could put the data files in by hand for species that aren't in Ensembl. We'd have to introduce some level of QC then, though.

Any idea how difficult getting a new species on there is?

No - can't imagine it's a quick process though, by the time the data gets into a release.

[petrelharp]

I guess we could put the data files in by hand for species that aren't in Ensembl. We'd have to introduce some level of QC then, though.

Can we do this currently or would this require a lot of changes to the infrastructure? In other words, is this something we want to allow in the "adding to the zoo" workshop?

[petrelharp]

Ok, I've updated this - I think it's OK now, unless we think we will never want to support non-Ensembl species.

[petrelharp]

More Ensembl info: from this page

Ensembl does not produce genome assemblies, instead we provide annotation on genome assemblies that have been deposited into the INSDC (GenBank, ENA, DDBJ) and are publicly available. We select species to annotate on a case-by-case basis ...

[jeromekelleher]

Can we do this currently or would this require a lot of changes to the infrastructure? In other words, is this something we want to allow in the "adding to the zoo" workshop?

No, probably not. I think we should focus on Ensembl species for the workshop.

[jeromekelleher]

LGTM!