Querying Pathway/Genome Databases

This page summarizes approaches to querying information in Pathway/Genome Databases (PGDBs) maintained by Pathway Tools. Although the Pathway/Genome Navigator graphical user interface provides a number of fixed queries, those queries are of limited complexity. To write more comprehensive and sophisticated queries, the user will need to perform some amount of programming.

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,Java or Python.

API-Based Queries to Pathway/Genome Databases

• 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, Java and Python 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.

Querying Flat File Pathway/Genome Databases

In some cases, the flat file versions of a PGDB will be present in your Pathway Tools distribution under the directories for each organism that are in the aic-export/ecocyc directory, such as in directory aic-export/ecocyc/metacyc/released/data/.

However, you can also generate flat file versions of any PGDB by invoking the Pathway/Genome Navigator command Special / Misc / File Export / Dump KB to flat files.

The format of Pathway Tools flat files is described in detail in this Web page. The meaning of the fields in the flat files is described in Appendix I of the first volume of the Pathway Tools User's Guide.