[Biojava-l] Questions

[Ewan Birney]

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:td2@sanger.ac.uk]
> Sent: Tuesday, October 16, 2001 10:44 AM
> To: Ron Kuhn
> Cc: biojava-l@biojava.org
> 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.                                       
>        
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