[BioSQL-l] Fwd: error on insert new sequences from GenBank: no annotations saved in BioSQL database

[Chris Fields]

On Mar 2, 2008, at 9:38 PM, Hilmar Lapp wrote:

> FYI, I used this to start a page on the recommended mapping of  
> sequence annotation to BioSQL:
>
> http://www.biosql.org/wiki/Annotation_Mapping
>
> Obviously, this is very rudimentary, but everyone is welcome to add  
> to it or comment with further questions. Also, one of the most  
> important questions, namely a consistent vocabulary for annotation  
> (qualifier) tags, isn't mentioned there (yet).
>
> 	-hilmar
>
>> ...
>> Maybe we need to hold some mini-hackathon to make the different
>> toolkits compatible in how they map annotation to the schema.
>> Obviously I don't know whether you have the latest Biojava setup
>> here, but I'll just comment how BioPerl/Bioperl-db would map this:

These are the ones I know of:

>> 'cross_references' - not sure where these would be coming from in
>> GenBank format; for EMBL this will map to the dbxref table

GenPept has DBSOURCE, so maybe from there?

>> 'data_file_division' - not sure what this is (same as DIVISION?)

Note sure about that one, but division sounds right.

>> 'MDAT' - not sure what this is

Modification Date, I think.  'MDAT' is a field name used for limits in  
Entrez searches:

	Field code: MDAT
	      name: Modification Date
	      desc: Date of last update
	     count: 4012
	Attributes: is_date,is_singletoken

chris