[XMLPipeDB-developer] minimum for a species profile and yeast

[Dahlquist, K. D. <kda...@lm...>]

Hi,

Here is the minimum for a new species profile:

1.  In Systems table, Species field of OrderedLocusNames record needs to read |<Genus species>|

It is currently being left blank with just two bars ||

2.  In Systems table, Link field of OrderedLocusNames record needs to have the appropriate URL query added where the ~ character refers to the ID to be inserted.  For example, it should be for Vibrio: "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=~"  

3.  For yeast, the SGD table has the fields ID, Symbol, ORF, Species, Date, Remarks instead of just ID, Date, and Remarks for a normal OrderedLocusNames table.

The ID is the Primary SGD ID of the form S#########.

The Symbol is the standard name or gene symbol, like CIN5, but it can also be a duplicate of the ORF or systematic name.

The ORF is the systematic name, Y[A-O][R/L]###[W/C] and sometimes -A or -B.  I didn't see any -C, but there always might be one.

When dealing with yeast, we will probably have the issues we did with TAIR because it already exists in the Systems table and it is being made twice, essentially with the OrderedLocusNames.

Cheers,
Kam