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:
The next section explores these options in more detail.
- Write a program that uses an API (application program
interface) to dynamically query a PGDB while it resides within Pathway
Tools. Such programs can be written in:
- The Common Lisp language
- The Perl language (using the PerlCyc API -- see below)
- The Java language (using the JavaCyc API -- see below)
- 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 Pathway Tools API
Please read the Pathway Tools
API document to get an overview of how to access Pathway Tools programmatically.
API-Based Queries to Pathway/Genome Databases
- Querying PGDBs in Lisp
- Querying PGDBs in Perl
- Querying PGDBs in Java
- Information common to the Lisp and Perl APIs
- GFP -- the Generic Frame Protocol -- is the API for querying Pathway Tools DBs, both
in Lisp and in Perl
- Classes from the Pathway Tools schema
that are most commonly used in queries
- Information on the Ocelot Object Database
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
aic-export/ecocyc directory, such
as in directory
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.