Don Gilbert said:
>
> Pankaj,
>
> Here is an experiment for you. Take your template_gene_page_entry and go
> look at other MODs standard gene pages. See what you have that others
> do (maybe labelled differently), and mark those fields in your
> template somehow as common (asterisk, color-coded, ..).
>> http://ascus.plbr.cornell.edu/~gramene/gene/template_gene_page_entry.html.
>
I will do that.
> Do the other MOD common fields have labels that
> might be more general use for an average biologist?
> (e.g. I'm not sure what 'Systematic ORF name' is for a gene, even
> though SGD also uses it. Would plain 'Name' be as informative?).
>
I guess at some point it will be a problem if not included, because a gene
is named with some authentic label like cam1, atpA etc. only when the real
functional info is available, whereas with so many genomes getting
sequenced, every gene has a (locus) identifier (systematic name) in the
genome assembly. Its kind of an accession. So quite often this gene is
addressed by its identifier in the literature and that is what the users
may be searching for.
SGD calls it systematic identifier, TAIR calls it Locus id and at some
point rice may use it too as we have recommended its use.
> You include GO parts beyond term: evidence, etc. Some MODs do,
> others don't. Is this an issue for us (e.g. basic info versus detailed)?
>
We can get rid of the extended info, but I think when the alleles are
included in curation, then the main curation will be of alleles with
details. On the gene page it may just be summary of info ported from
allele associations. Reason being an allele may not have an activity which
another allele of the same gene may have, because of mutation/knockout
etc. So in a nutshell Gene can have all the possible associations and
features but not an allele.
> 'Location/Map' parts could be separated out of the general gene
> info block, but does it make more sense to keep with it?
You are right for db purposes this info comes from a separate table.
> -- Don
>
--
Pankaj Jaiswal
Gramene Database
www.gramene.org
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