Bioperl: re: fasta def line problem

Lincoln Stein
Fri, 28 Aug 1998 09:49:47 -0400

H'mmm.  BSML and BIOML seem to be taking two very different
approaches.  BIOML describes a high level data model for proteins,
nucleic acids, chromosomes, and taxa.  It's short and easy to

BSML ( is much more low-level
and detailed.  It looks like the union of the ASN.1, PIR, EMBL and
SwissProt schemas.  There's also a lot of stuff in BSML that has
nothing to do with data, but rather with data presentation, such as
scales, colors, line widths and patterns.  BSML's DTD is HUMUNGOUS.
On the plus side, the company has put together a working Windows98
browser that is actually pretty nice.

What is the status of BIOML?  Who's working on it?


Kenneth Geisshirt writes:
 > lstein> If there were a fast Perl-based XML parser, I'd vote for XML syntax.
 > lstein> Right now there's an interface to a C XML parser, but it is dog slow.
 > lstein> Has anyone looked at BSML (biological sequence markup language)?
 > Actually I was going to ask more or less the same question: has anyone
 > taken a look at bioml (biopolymer markup language) - the url is:
 > Kneth
 > -----------------------------------------------------------
 > Kenneth Geisshirt, M.Sc., Ph.D.     Computational Scientist 
 > Structural Bioinformatics               Tel:  +45 4516 2804
 > Advanced Technologies                   Fax:  +45 4516 2802
 >                  LOAD "",8,1
Lincoln D. Stein                           Cold Spring Harbor Laboratory			                  Cold Spring Harbor, NY
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