Reference Genome Database Requirements Discussion 2007 (Retired)

This is the place to discuss features and requirements for the Reference Genome Database being designed to replace the Google Spreadsheet system currently in use.

(here's one to get us started --chris):

Ensures consistent use of identifiers

Identifiers must unambiguously identify a single entry in a database.

Identifiers should conform to the following syntax:

 DBAuthority : LocalID

DBAuthority should be in the GO xrefs metadata list:

• http://www.geneontology.org/cgi-bin/xrefs.cgi

E.g.

 FB:FBgn0000001

Curators should not be expected to memorise identifiers, so a data entry system should allow them to enter symbols etc and have this resolved as an ID eg using some automatic lookup mechanism

Should allow loading of MOD reports

The database should allow MODs to submit their metrics via a tab-delimited file that can be automatically downloaded from their ftp site. The file should contain columns for the Reference gene, the organism's ortholog/orthologs, date genes have been completed and reference counts for total number of papers associated with a gene etc.

In the future we may want to add capability to determine when genes that have been completed but have new references associated with them.

References should be compiled in a central location, so once a paper is curated, it is somehow flagged that it has been done.

We need to decide whether we will allow individual users to modify the database a record at a time or whether the database should only be populated with files from each MOD.