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. 2011 Nov 17;40(Database issue):D761–D769. doi: 10.1093/nar/gkr1023

Table 1.

UniPathway classes and their attributes

UniPathway classes Mandatory attributes Optional attributes
UPC compound

  • A unique identifier (upcid)

  • A label, i.e. the common name used to build the controlled vocabulary

  • A list of synonyms

  • Information relating to 2D structure (formula, MW, InChI, 2D coordinates)

  • A chemical type (abstract, chemical)

  • Cross-references to chemical resources: KEGG, MetaCyc and ChEBI
UCR chemical reaction

  • A unique identifier (ucrid)

  • Left part compounds and their stoichiometry

  • Right part compounds and their stoichiometry

  • Cross-references to reaction resources: KEGG and Rhea
UER enzymatic reaction

  • A unique identifier (uerid)

  • A (ordered) list of UCR, representing either a single UCR or the serialization of several UCRs, and specifying a direction and stoichiometry for each UCR

  • A global chemical equation specifying input and output compound(s) and their stoichiometry

  • A subpathway (ULS) container

  • A set of alternate UERs (for cases where a single enzyme can catalyze two reactions differing only by their co-substrates, such as NADPH/NADH)

  • One or more EC numbers

  • Cross-references to other reaction resources: MetaCyc and Rhea

  • Bibliographic references (PubMed)

  • UniProtKB/Swiss-Prot, protein/domain families, taxonomic identifiers, genes
ULS linear subpathway

  • A unique identifier (ulsid)

  • A label, automatically computed from its terminal compounds [product(s) from substrates]

  • A (ordered) list of UERs
UPA pathway

  • A unique identifier (upaid)

  • A label (from a controlled vocabulary of pathway names)

  • One or more parent pathways (UPA)

  • A set of subpathways (ULS) and their connecting compounds

  • Cross-references to pathway resources: KEGG, MetaCyc, Gene Ontology

  • Bibliographic references (PubMed)