Bioperl: trying XML in biology...
David J. States
states@gpc.wustl.edu
Wed, 4 Aug 1999 10:02:21 -0500
Lincoln,
Have you written a DTD for the XML generated by the boulder I/O converter?
The natural tendency in the biological sciences has been to do things from
the bottom. Lots of independent solutions proposed and a few winners
eventually sorting themselves out. bioXML certainly seems to be following
this tradition with BSML, BIOML, GAMES, and the recent Institute Pasteur
examples. In addition, there are the "natural" mappings for GenBank, EMBL,
PDB, and NCBI ASN.1. Any suggestions on how this might all be brought
together? Or should bioXML be a testing ground for the XSL work on
translating XML to XML?
David
----
David J. States, M.D., Ph.D.
Associate Professor and Director
Institute for Biomedical Computing
Washington University in St. Louis
700 S. Euclid Ave.
St. Louis, MO 63110
tel: 314 362 2134
fax: 314 362 0234
email: states@ibc.wustl.edu
On Tuesday, August 03, 1999 11:17 AM, Lincoln Stein [SMTP:lstein@cshl.org]
wrote:
> I've just put together an xml2boulder converter (65 lines of code).
> Here's what's nice about it.
>
> Say you have an XML file that looks like this (real life example):
>
> <contig>
> <acc>NT_001817</acc>
> <name>Hs1_1938</name>
> <chr>1</chr>
> <labs>SC</labs>
> <partslist>
> <part>
> <cpos1>0</cpos1>
> <cpos2>41014</cpos2>
> <acc>AL049198</acc>
> <seqlen>41015</seqlen>
> <clone>590K14</clone>
> <ctype>pac</ctype>
> </part>
> <part>
> <cpos1>40915</cpos1>
> <cpos2>125326</cpos2>
> <acc>AL033533</acc>
> <seqlen>84412</seqlen>
> <clone>973M2</clone>
> </part>
> </contig>
>
> Then after converting it into boulder format, you can access the bits
> and pieces as methods, like so:
>
> $xml = Boulder::XML->new($xmlfile);
> $chromosome = $xml->chr;
> @parts = $xml->partslist->parts;
> for my $part (@parts) {
> my $accession = $part->acc;
> }
>
> I haven't written the corresponding boulder2xml converter, but if
> people are interested, I'll send out what I've got now for beta
> testing and experimentation.
>
> Lincoln
>
> Catherine Letondal writes:
> >
> > Hi,
> >
> > We have made some tries in XML here at Pasteur (thanks to an XML course
> > by S. Bortzmeyer).
> >
> > The main idea is to first convince authors of biologicial software how
XML
> > makes it easy to parse a program's output, and that producing
> > XML output is easy as well (well, as long as you are the author of the
code).
> >
> > That's why this page: http://www-alt.pasteur.fr/~letondal/XML/
> > shows examples of softs developped locally at Pasteur, to which we have
> > added an '-x' option in order to have them produce an XML output (CDS,
satellites).
> >
> > It shows also an XMLized fasta output with a parser, just to show
> > that a parser in XML is very easy to write, and how it could lower the
> > difficulty of parsing this kind of texts.
> >
> > We have also tried to see what a genbank entry would be like in XML.
This is
> > naive of course, for only the authors of databanks may decide about
this format, but
> > these are mainly examples. P. Bouige has also written a converter from
> > Genbank to XML, that works with the DTD we have set up.
> >
> > We have made also simple examples of more general objects, like Phylip
trees,
> > but I guess that such kinds of objects will be discussed at the Bioperl
> > workshop.
> >
> >
> > --
> > Catherine Letondal -- letondal@pasteur.fr -- +33 (1) 40 61 31 91
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>
> --
> ========================================================================
> Lincoln D. Stein Cold Spring Harbor Laboratory
> lstein@cshl.org Cold Spring
Harbor, NY
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