[Biophp-dev] Updates

Greg Tyrelle biophp-dev@bioinformatics.org
Fri, 6 Jun 2003 12:15:45 +1000

*** S Clark wrote: 
  |The updates to esearch, esummary, and the generic xml parser should all
  |be on CVS tomorrow morning (US West Coast time) along with HOPEFULLY a 
  |functioning NCBI BLAST set of code.

Hey Sean, Nico, Serge et al.

Sean: I've checked out the changes to the ESearch, ESummary and
generic xml parsers modules. I will hopefully have some time to test
the updates to the modules in the next few days.

I would also like to upgrade the pubmed module I wrote for my site
(nodalpoint.org) to work with the new EUtils classes. Hopefully this
should provide some more testing.

Also there have been some announcements from NCBI that may effect
these classes (you may have seen them):

"ESummary XML will be modified the first week in June to accommodate a
number of changes in PubMed"

I don't know how this will effect the ESummary parser but I can
investigate if you like ?

"To provide more efficient processing NCBI has created a new domain
for EUtilities, http://eutils.ncbi.nlm.nih.gov/entrez/eutils"

I noticed the host name hasn't been updated in the latest cvs
check-ins. But the test cases still seem to work with the old host name

Further issues on testing: The ESearch interface returns various
errors that are not currently handled by the ESearch classes. For
example a search for "asdfg and cancer" will return the following
chunk of XML in the result:


Any thoughts on how to handle these cases ? Also any thoughts on unit
testing these classes ? Are there any frame works available for PHP ?

Have any decisions been made about code standards for BioPHP (PEAR) ?
I'd be happy to submit patches to the EUtils class to bring them up to
what ever code standards are decided upon ?

Further more I will be attending BOSC/ISMB [1/2] in Brisbane in
June/July. I will be giving a short talk at BOSC on a few topics (My
PhD research, nodalpoint.org, debian and bioinformatics). Since BOSC
is *the* open-source bioinformatics conference I would be happy to
mention the BioPHP project in the talk too.

My question is would everyone else be happy with this ? 

My intention is simply to give BioPHP some publicity in the
open-source bioinforamtics world. No to steal the lime light :)

Lastly, does the presence of a genephp directory in cvs imply that
these two code bases will be merged ? And I notice that the GenePHP
website is now advertising itself as BioPHP but pointing to the
GenePHP source ? 

My question is: Which is the official BioPHP site ?

Sorry for the long email and keep up the good work :)


[1] http://www.iscb.org/ismb2003/index.shtml
[2] http://www.open-bio.org/bosc2003/
Greg Tyrelle  (http://www.kinglab.unsw.edu.au/~greg)

"Logic only gives man what he needs, 
 magic gives man what he wants" - Tom Robbins