[Bioperl-l] Pathway tools output parser

Jim Hu jimhu at tamu.edu
Fri Feb 16 00:20:09 EST 2007


Hi Chris,

I need to check the list more often!  I never got an answer here, but  
Eric Just pointed out a perl api at TAIR that's linked from the  
BioCyc site.  I've used the lisp parser functions from that to move  
the data to a perl array of arrays, and I'm working on creating  
object classes for BioCyc objects, starting with genes and products.

I need to look at the appropriate ways to link this up to the  
existing codebase for interconverting to Chado and other BioPerl data  
types.

Jim
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


On Feb 7, 2007, at 12:07 AM, Chris Mungall wrote:

>
> Hi Jim
>
> Did you ever get an answer to this? I'm interested in storing  
> pathway data
> in Chado & I remember enough lisp to get it into something perl- 
> manageable
> like XML
>
> On Thu, 25 Jan 2007, Jim Hu wrote:
>
>> Is there a module to parse the lisp object files from Peter Karp's
>> Pathway Tools?   I need a parser to convert the gene and protein
>> objects in EcoCyc releases into something that can be imported into
>> Chado.
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>



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