[Open-bio-l] Re: [GMOD-devel] What is the clear distinction between a feature and a bioentry

[Elia Stupka]

> Bioentry vs. Feature: we decided that everything that
> - lives in a namespace (biodatabase), and
> - has a stable accession and/or ID, and
> - has a sequence (physically in the database or not)
> shall be a Bioentry. Features shall be essentially lightweight objects.

Just wondering, wouldn't you want to treat a unigene cluster as a bioentry
even though it doesn't have a real sequence, but is just a collection of
sequences? We allow bioentries not to have sequences, and I like that...

> 1) As much as possible, Bioentries will be mapped down to chromosomes,
even if the
>datasource only gives the coordinates to contigs. (I think this also aligns
it better with Lincoln's >DB:GFF view.) Contigs will be retained in the
database though, in case they are needed at some >time as an entry point.

just wondering again, we are not saying all bioentries need to be located on
a genome, are we? I am just trying to make sure we keep it generic and able
to deal with much more than genome annotations...

> 2) According to the definition given above, Genes, transcripts, and
proteins, will all go into >Bioentry. Exons will be features (and therefore
not directly mapped to chromosomes).

Genes as such don't have sequences, only their transcripts do, so it
wouldn't fit the definition, unless you allow bioentries without sequences

Elia