Link MetaCyc pathways to reactions

[y1zhou]

Unsure of the difference between reactions.dat and #reactions.dat#.

• Additional information in reactions.dat #8
• Use pathways.dat to create annotation on Pathway nodes.
  • UNIQUE-ID are identifiers of the pathways, i.e. the BioCyc ID.
  • CITATIONS can have multiple entries and point to pubs.dat or Pathway Tools evidence ontology.
  • Parse links in the COMMENT field #11
  • IN-PATHWAY points to SuperPathway nodes. Seems to be the same with SUPER-PATHWAYS. Similarly for super pathways there's an SUB-PATHWAY attribute.
  • PATHWAY-LINKS are tuples with the first element being metabolites in the pathway, and other elements being IDs of other pathways.
  • PREDECESSORS connects reactions in the pathway. 2nd (and 3rd, etc.) element is the predecessor of the 1st element.
  • PRIMARY-PRODUCTS and PRIMARY-REACTANTS are beginning and ending metabolites.
  • REACTION-LAYOUT gives the primary metabolites and direction of each reaction.
  • REACTION-LIST enumerates the reaction IDs in the pathway.
  • SPECIES enumerates taxa known to possess this pathway.
  • SYNONYMS are names for the pathway.
  • TAXONOMIC-RANGE are the expected taxonomic range.
• classes.dat contains the common name for a lot of the frames and IDs used in pathways.dat. #13

[y1zhou]

In pathways.dat, documented keys include:

    UNIQUE-ID, TYPES, COMMON-NAME, CITATIONS, CLASS-INSTANCE-LINKS, COMMENT,
    CREDITS, DBLINKS, ENZYME-USE, HYPOTHETICAL-REACTIONS, IN-PATHWAY,
    NET-REACTION-EQUATION, PATHWAY-INTERACTIONS, PATHWAY-LINKS,
    POLYMERIZATION-LINKS, PREDECESSORS, PRIMARIES, REACTION-LAYOUT,
    REACTION-LIST, SPECIES, SUB-PATHWAYS, SUPER-PATHWAYS, SYNONYMS

All possible keys that appear in the file are:

    ABBREV-NAME, CHIMERIC?, CITATIONS, CLASS-INSTANCE-LINKS, COMMENT,
    COMMON-NAME, CREDITS, DBLINKS, ENGINEERED?, ENZRXNS, ENZYMES-NOT-USED,
    ENZYME-USE, EXPLANATION-CODE, HYPOTHETICAL-REACTIONS, IN-PATHWAY,
    INSTANCE-NAME-TEMPLATE, KEY-NON-REACTIONS, KEY-REACTIONS, PATHWAY-LINKS,
    PATHWAY-TRANSPORT-MAPPINGS, POLYMERIZATION-LINKS, PREDECESSORS,
    PRIMARIES, PRIMARY-PRODUCTS, PRIMARY-REACTANTS, RATE-LIMITING-STEP,
    REACTION-LAYOUT, REACTION-LIST, SCORE, SPECIES, SUB-PATHWAYS,
    SUPER-PATHWAYS, SYNONYMS, TAXONOMIC-RANGE, TYPES, UNIQUE-ID