Bioperl: XML/BioPerl

Gunther Birznieks
Thu, 31 Dec 1998 09:41:29 -0500 (EST)

On Thu, 31 Dec 1998, Ewan Birney wrote:

> David,
> 	A very interesting read (as was gunther's comments on it).
> 	I think XML has a big part to play in serving up biological
> data in a more compatible form than hard-to-digest ASCII formats. XML
> fits very well with perl's 'just-do-it' philosohpy, and I suspect that
> any XML transport mechanisms will be first implemented in perl... so
> bioperl is a good place to start airing these sorts of ideas.

> 	a) that you start a web site pulling together all these links to
> other biological schemas and your own take on the problem
> 	c) Come up with some conrete proposals
Yes, just do it.  My belief is that too much time is spent by committee
designing things before actually testing them out on the real world.  It
would be nice to see some people do concrete (even if *beta* status) XML
implementations of their data interfaces.

Only after some real world experience is gathered through these initial
projects will a really nice standard result anyway. Otherwise its just a
bunch of people talking.  It's good to talk initially for some rough
guidelines, but implementation is necessary to test the waters.  

> For both a) and c) I can strongly encourage you to do this inside the 
> 'bioperl' web site and code base. I know I would be very supportive of it.
> You can get an account on and add pages to the web site via
> CVS (the web site is under cvs control). It will probably take a while
> to gather all the information and come up with proposals that enough
> people agree with to make them sensible, and once you have done that you
> can start trying to layout some serious pieces of code inside the bioperl
> code base. that's looking ahead 3-6 months probably at a minimum. 
Also, some initial implementations are necessary to help build momentum.
I know that if I see people actually providing an XML interface, I become
more excited about writing to XML.  As more people get used to the idea
of seeing XML interfaces, they will also be more apt to use XML.
Protocols like XML are typically very much a momementum thing. People need
to see people implementing something before other people start thinking
its cool.

I am just sick of HTML::Parser and having to say a prayer each morning
when I get into work that the HTML GUI has not changed on the sites I pull
data from. Just having a Web-enabled data abstraction standard like XML is
a world of improvement on my life as a programmer -- I don't care quite
yet that there isn't one standard XML markup for biology. I just care that
the display (HTML) finally gets decoupled from the dataset transport

> I know you are a busy man ;) so you might feel that it is better done
> by someone else. However, I think you seem interested and have already
> thought about the problem, and so I would encourage you to keep at it
> and try to make sense of what is already out there, followed by coming
> up with serious proposals.
I would encourage it as well.  If XML takes off, the first people to
produce Genome XML-based datasets will get kudos as helping pioneer that
portion of Bioperl...



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