Bioperl-guts: FASTA/BLAST DTD request [was Re: Response/Hit fields RE: DB work, request to Aaron M. RE: Bioperl- guts: REMINDER: ISMB sig n-ups (fwd)]

Ewan Birney birney@sanger.ac.uk
Wed, 25 Aug 1999 16:34:48 +0100 (BST)


On Tue, 24 Aug 1999, Aaron J Mackey wrote:

> 
> Well here's where I try to pull in the XML folks to help us both out.
> I've stalled a bit in finalizing the data structure because of some work I
> was made aware of to create a FASTA DTD (Catherine Letondal at the Pasteur
> Institute, http://www-alt.pasteur.fr/~letondal/XML/).  There is also a
> BLAST DTD (http://workingobjects.com/blastxml/), although having looked at
> both, they're not complete (although the average user's idea of complete
> is probably not as broad as my idea of complete).


EEk. Check out www.bioxml.org/Projects/ and www.bioxml.org/Projects/Game. 
This has a single DTD which is applicable to both Fasta and Blast (the
part starts at computational_analysis). GAME is suzi lewis' exchange
format between berkeley drosophila genome project and celera and they are
quite fixed to it for the big things. 


Check it out and telll me what you think about how sensible it is wrt to
catherine's stuff. 


Boy - XML DTD expansions already...



 > 
> Regardless, I'm (going to be) working with Catherine on the FASTA DTD and
> integrating it into the FASTA package, in coordination with the
> Bio::Search::* modules.  As a result, data structures may change to
> reflect insight found from the construction of a reasonable DTD.
> 
> -Aaron
> 
> On Tue, 24 Aug 1999, Otillar, Robert {BIOI~Palo Alto} wrote:
> 
> > Thanks Aaron.
> > 	A breakdown would be helpful if it is available.
> > 	I think that would keep me from assuming unintended things from the
> > code-specifics.
> > Thanks,
> > 	Bobby O
> > 
> > -----Original Message-----
> > From: Aaron J Mackey [mailto:ajm6q@virginia.edu]
> > Sent: Tuesday, August 24, 1999 10:51 AM
> > To: Otillar, Robert {BIOI~Palo Alto}
> > Cc: Ewan Birney; bioperl guts
> > Subject: Re: DB work, request to Aaron M. RE: Bioperl-guts: REMINDER:
> > ISMB sig n-ups (fwd)
> > 
> > 
> > 
> > The latest FASTA code is available on the bioperl-live cvs branch -
> > consider it pre-alpha, to be sure.  From the Bio/Search/Processor/Fasta.pm
> > module you can see all the fields I'm setting (get ready for a big
> > regexp-induced headache when you do).  Let me know if you have any
> > questions about what you're seeing.
> > 
> > BTW, when you say Smith-Waterman, do you mean ssearch?  If so, ssearch
> > parsing will be elementary after FASTA, since they use the same
> > output/formatting code base.
> > 
> > If necessary, I can post an entire breakdown of available fields from the
> > Response/Hit objects (but you said a perl data structure would be
> > sufficient).
> > 
> > Best,
> > 
> > -Aaron
> > 
> > On Tue, 24 Aug 1999, Otillar, Robert {BIOI~Palo Alto} wrote:
> > 
> > > 
> > > 	Perl DBI database with oracle, MS access, and CSV is underway for
> > > simple sequence-like and alignment-like data.
> > > 	A schema/plan for Aaron M's HTTP Request/Response model for analysis
> > > services would be helpful to me. 
> > > 		Even preliminary/pre-alpha perl data-structure for these on
> > > FASTA, BLAST, PSI-BLAST, and/or Smith-Waterman would be a nice. I would
> > like
> > > to remain consistent with how AM plans to represent these objects.
> > > 	I will put up a proposal/request-for-suggestions after I've worked
> > > with this a bit more, preferrably after some response from AM with info on
> > > his objects. 
> > > 
> > > Thanks,
> > > 	Bobby O
> > > 
> > > -----Original Message-----
> > > From: Ewan Birney [mailto:birney@sanger.ac.uk]
> > > Sent: Tuesday, August 24, 1999 7:47 AM
> > > To: bioperl guts
> > > Subject: Bioperl-guts: REMINDER: ISMB sign-ups (fwd)
> > > 
> > > 
> > > 
> > > Just to remind people who signed up as developers at ISMB... we will be
> > > expecting code (or at the very least, excuses) from you this fall, so I
> > > hope you are going to be working away at figuring out how you want to
> > > contribute.
> > > 
> > > Chris has put up a status page at 
> > > 
> > > http://bio.perl.org/Core/status.html
> > > 
> > > To remind you in this email, this is what you said you would do:
> > > 
> > > aaron - lead the 0.5.2 bug fix release
> > > 	get the new simsearch agent/processor/result system working for
> > > 	fasta
> > > stevec - do psi blast support in the current blast system
> > > wolfgang - do swissprot AnnSeqIO support and taxonomy
> > > ralf - publication object
> > > Adam moore + Keith Neil - figure out XML support
> > > Bobby O - figure out database persistence
> > > Kris Boulez - The bioperl cookbook
> > > george hartzell - lead the alignment discussion.
> > > 
> > > 
> > > I *am* looking forward to people just committing code and also making
> > > proposals on the list for the more complex stuff. Get stuck in.
> > > 
> > > (BTW - I am serious about flying over and standing over you in person to
> > > make you do stuff!).
> > > 
> > > 
> > > 
> > > Ewan Birney
> > > <birney@sanger.ac.uk>
> > > http://www.sanger.ac.uk/Users/birney/
> > > 
> > > 
> > > 
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> > 
> 
> -- 
>  o ~   ~   ~   ~   ~   ~  o
> / Aaron J Mackey           \
> \  Dr. Pearson Laboratory  / 
>  \ University of Virginia  \     
>  /  (804) 924-2821          \
>  \  amackey@virginia.edu    /
>   o ~   ~   ~   ~   ~   ~  o
> 
> 
> 
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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