Thomas Down wrote:
> [snip] > > Would this return the feature as some sort of generic gene.id feature? My > > growing concern is that for each file/db/SQL format we are adding features with > > their original names rather than some defined BioJava enforced named feature. I > > noticed a dtd for features. Unfortunately, I don't know much about XML besides > > the simple things. Could we make something like gene_id, accession_no, etc... > > ? By using these set names, you don't have to know what a gene_id tag is for > > EMBL, genbank, SQL,....... > > > > Or have I missed this ability in BioJava somehow? > > No, your concern is quite justified. It is, indeed, necessary to > have some specialized knowledge about a particular data source before > you can really make use of the tag-value data present in the > Annotation bundles. > > I think a set of `common' key names would be a big help, and I'd welcome > any proposals for what should be in here (the standard set of feature > types and qualifiers from EMBL might be a good starting point, but > probably not a complete solution). I'd also like to be able to introspect, > for a given database, what properties I should expect to find on features. > The AnnotationType objects, written recently by Matthew, ought to be one > part of the puzzle. > > Even before this problem is solved, the filter-all-features-in-a-database > operator still seems to me to be useful -- and I can't see any way in > which it should make improved standardization and `introspectability' harder > in the future. Or am I missing something? > > Thomas. Well after looking around I did find something that would make me happy and possibly others. A common interface has been worked out for EMBL/GenBank/DDBJ flat file formats in use with CORBA servers <http://corba.ebi.ac.uk/EMBL_embl.html>. I didn't find anything in biocorba or Biocorba folders and I don't know what BioFetch is for. So my guess is, this hasn't been touched here (in BioJava). I think it would be a good option. If I every have time away from the bench or my class homework, I could work on it. Marc _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
