On Tue, 16 Oct 2001, Ron Kuhn wrote: > Is BioPerl more mature or do they have the same issues? Should I look > elsewhere or should I do my own parser?
BioPerl is more mature but not 100% round-tripping the information for, in particular - swissprot. It is close. > Ron > > -----Original Message----- > From: Thomas Down [mailto:[EMAIL PROTECTED]] > Sent: Tuesday, October 16, 2001 10:44 AM > To: Ron Kuhn > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] Questions > > > On Tue, Oct 16, 2001 at 10:29:28AM -0400, Ron Kuhn wrote: > > Is there a forum related to the BIOJAVA software??? That is really where I > > should be posting this email. > > Yes, this mailing list is where most discussion happens. Please > post any questions/bug reports/suggestions/patches here. > > > I am trying to use your software to parse Genbank and SwissProt flat > files. > > I made 2 fixes (1 for each) and all seems to work fine. I am successfully > > parsing the files and interpretting sequences. My only problem is that the > > information about the references to the sequences should be heirarchical > (in > > SwissProt - the RP, RX, RA, RT and RL fields relate to a specific RN) but > > the object used to hold the reference information (Annotation) is NOT (XML > > is though). If multiple RNs exist and 0 or more RTs exist per RN, then how > > are we supposed to relate the RTs to the correct RN??? > > BioJava's currently not very good at handling the metadata associated > with sequence files -- any improvements would be welcome. > > When the Annotation objects were originally designed, there > was a general suggestion that they should be used as hierarchies > to model this kind of thing. So you could have a structure like: > > > Top-level annotation > | > | references > |----------------------> ArrayList > |------->Reference annotation > | | > | +----> journal > | +----> author > | +----> title > | > +-------> Another reference > > Actually, it might be even better to have a dedicated object > model for bibliographical references, but nobody has been particualary > enthusiastic about working on this. > > > Thomas. > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
