Version: 1.4 (4/29/09)
Contact: feedback@pharmkgb.org

In this directory, you will find simple client programs to access web services
on PharmGKB.  These clients are primarily meant as examples.  They require the
SOAP::Lite module, available from CPAN.

  search.pl - free-text search of PharmGKB
      usage: search <text>
      % perl search.pl CYP2D6


  specialSearch.pl - special searches, corresponding to the PharmGKB home page
      usage: specialSearch <searchType (integer)>

      where search type is one of:

       0  Genes with pharmacokinetic significance
       1  Genes with pharmacodynamic significance
       2  Genes with PharmGKB variant data
       3  Genes with PK variants
       4  Genes with PD variants
       5  Drugs with supporting information
       6  Diseases with supporting information
       7  Phenotype datasets
       8  Pathways with PGx significance
       9  Annotated publications describing relationships
          among genes, drugs and diseases
      10  Literature annotations, pathways and phenotype datasets
          annotated with pharmacokinetics
      11  Literature annotations, pathways and phenotype datasets
          annotated with pharmacodynamics
      12  Literature annotations and phenotype datasets
          annotated with clinical outcome

      % perl specialSearch.pl 0


  drugs.pl - PharmGKB drug information, by PharmGKB accession ID
      usage: drugs.pl <PharmGKB id>
      % perl drugs.pl PA451906


  diseases.pl - PharmGKB disease information, by PharmGKB accession ID
      usage: diseases.pl <PharmGKB id>
      % perl diseases.pl PA443425


  genes.pl - PharmGKB gene information, by PharmGKB accession ID
      usage: genes.pl <PharmGKB id>
      % perl genes.pl PA267


  publications.pl - PharmGKB publication and annotation information, by PharmGKB accession ID
      usage: publications.pl <PharmGKB id>
      % perl publications.pl PA133822615


  variants.pl - PharmGKB variant summary report, by chromosome and GoldenPath position
      usage: variants.pl <chromosome> <Golden Path position>
      % perl variants.pl 5 148185934


  getXrefs.pl - get PharmGKB data cross-referenced to external databases
      usage: getXrefs <chromosome> <gp_position>
      % perl getXrefs.pl 10 96692037


  getXrefsByRsId.pl - get PharmGKB data cross-referenced to external databases, by dbSNP rsID
      usage: getXrefsByRsId <rsid>
      % perl getXrefsByRsId.pl rs1648700


  getXrefsByGeneSymbol.pl - get PharmGKB data cross-referenced to external databases, by gene symbol
      usage: getXrefsByGeneSymbol <gene symbol>
      % perl getXrefsByGeneSymbol.pl ABCB1


(Note: some versions of SOAP::Lite have a bug in the way that they deal
with boolean values; see the SOAP::Lite documentation for details.)




CHANGE LOG
----------
  1.4:
    - search.pl no longer supports flags
    - improved error messages

  1.3:
    - add variants

  1.2:
    - add drugs, diseases, genes, and publications

  1.1:
    - add specialSearch operation for PharmGKB homepage searches

  1.0.1:
    - make www.pharmgkb.org the default
    - use explicit types for booleans
    - use strict;

  1.0:
    - original release