[Open-bio-l] RE: Schema for genes & features & mappings to assemblies

[Elia Stupka]

> 2) There is going to be a new schema in Ensembl which may be worth
> looking at (Ewan, do you have a pointer to DDL or even an ERD?).

Hi Hilmar, we produced a clickable ERD of the new schema, it's at:

http://www.fugu-sg.org/docs/intro/db_structure2.html

> GGB can run off any schema for which one writes an adaptor for

I think this is valid for other projects as well. Most of them split
adaptors, so in theory you could write an adaptor for making ensembl genes
out of somebodys-crazy-flat-file and things would work...

> mapped entities with a sequence; i.e., in order to obtain a feature's
> sequence you need to specify the feature /and/ the assembly (assuming
> you have a mapping for that assembly); this means a gene's CDS
> sequence is going to be different from one assembly to another. The
> open question is whether or not you still need a fixed sequence for
> that feature (e.g., in order to map it). Does this make some sense or
> sound like a stupid idea?

Actually sounds like if you don't want to go through a lot of headaches I
must admit a few hundred tiny bugs associated with doing the above have
been progressively squashed in ensembl, and I don't wish on anybody to go
again through coordinate conversions, sticky exons, negative strands and
off by one errors...

> and exit gracefully if it's nested and you can't handle that. The
> impact of not allowing something that some people need (or want)
> appears to be worse to me.

There seems to be a consensus that since some like the idea of having them
it could be better to allow for them and just "exit gracefully" or other
simlar mechanisms, if you can't be bothered about nested
assemblies... what do you say Ewan?

Still I do not wish the headaches to anybody, though doing it cleanly from
scratch with the knowledge of what is to come might be a lot easier then
it was the first time off in ensembl...

Elia

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