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Key Pathway Tools Classes

Key Pathway Tools Classes

Most queries to Pathway Tools databases iterate through one or more classes of frames to select frames of interest. These classes and their slots (attributes) are described in more detail in Appendix A of the Pathway Tools User Guide, which is supplied as part of the Pathway Tools software distribution.

The most likely frames that users will want to query are as follows. Note that for most classes, the frame ID is a symbol with mixed case. Because Lisp converts symbols to uppercase unless they are quoted using vertical bars. Therefore, in queries, classes would be written as '|Genes| The key classes are:

  • Genes
  • Proteins
  • Polypeptides (a subclass of Proteins)
  • Protein-Complexes (a subclass of Proteins)
  • Pathways
  • Reactions
  • Compounds
  • Enzymatic-Reactions
  • Transcription-Units
  • Promoters
  • Regulation
Pathway Tools DBs contain many additional classes that can be used to create more specialized queries. To browse the class hierarchy above any object, click on the "Superclasses" field displayed for that object with the Pathway Tools Navigator.