Querying Pathway/Genome Databases

There are several approaches to writing programs that query PGDBs:

• Write a program that uses an API (application program interface) to dynamically query and/or edit a PGDB while it resides within Pathway Tools. Such programs can be written in Python, Perl, Java, and Common Lisp.

• Export a PGDB to a set of flat files, and:
  • Use Perl or another language to parse the data in those flat files directly
  • Use BioWarehouse to load the flat files into another database management system (DBMS), such as a relational DBMS, and query them there using SQL.

The next section describes the API options in more detail.

The Pathway Tools API

Please read the Pathway Tools API document to get an overview of how to access Pathway Tools programmatically.

Pathway Tools is written in Common Lisp, so the most powerful and recommended way to interact with Pathway Tools is via the Common Lisp API. For programmers who are not familiar with Common Lisp, a more limited set of functionality is available using Perl or Java.

• Querying PGDBs in Lisp
  • Introduction to writing PGDB queries in Common Lisp
  • Example Pathway Tools queries in Common Lisp
  • Library of Pathway Tools Lisp functions
  • General Information on the Common Lisp Language
    • BioLisp -- Lisp tools for Bioinformatics
    • The Association of Lisp Users
    • Common Lisp the Language (a reference manual for Common Lisp)
    • Information about the Loop macro (very handy for writing queries)
    • The Pathway Tools are implemented using Allegro Common Lisp (ACL), which is produced by Franz Inc. You can obtain additional Lisp licenses or ACL documentation from Franz.
    • Useful ACL Debugger commands
    • Other Lisp information:
      • An online Lisp tutorial
      • Basic Lisp Techniques, by David J. Cooper, Jr.
      • Lisp resources on the Web
      • Recommended book for learning Lisp: "ANSI Common Lisp" by Paul Graham, Prentice Hall, 1996, ISBN 0-13-370875-6.
      • Paul Graham's article on the competitive advantage Lisp provided in launching an E-commerce company
      • Finding Lisp: A Common Lisp resource for newbies by Dave Roberts

• Querying PGDBs in Perl
  • The PerlCyc API (Unix only)
  • Some PerlCyc Example Queries

• Querying PGDBs in Java
  • The JavaCyc API (Unix only)
  • A JavaCyc Example Query
  • Cyclone -- a package for mapping PGDB data to native Java objects and relational databases

• Querying PGDBs in Python
  • The Python API

• Information common to the Lisp, Perl and Java APIs
  • GFP -- the Generic Frame Protocol -- is the API for querying the object database underlying Pathway Tools DBs. The documentation below describes the Lisp interface, but translations also exist for Perl and Java.
    • Short introduction to GFP
    • The full GFP specification
  • Classes from the Pathway Tools schema that are most commonly used in queries
  • Information on the Ocelot Object Database
    • The Ocelot User's Guide.
    • The GKB Editor manual. Start with the section on the Frame Editor.