Querying Pathway/Genome DatabasesThis 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 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 Flat File Pathway/Genome DatabasesIn 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
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.
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