Thomas,
one obvious possibility is to look at NCBI's ASN.1 object model on handling
bibliographic data. This has proven useful and, in addition, is available
in XML format.
Uwe
Thomas Down <[EMAIL PROTECTED]>@biojava.org on 10/16/2001 04:44:21 PM
Sent by: [EMAIL PROTECTED]
To: Ron Kuhn <[EMAIL PROTECTED]>
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.
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