[BioSQL-l] Fwd: error on insert new sequences from GenBank: no annotations saved in BioSQL database
Chris Fields
cjfields at uiuc.edu
Mon Mar 3 04:36:56 UTC 2008
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
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