The MetaCyc Literature-Based Curation Process

Curation is the process of manually refining and updating a bioinformatics database. The MetaCyc project uses a literature-based [def] curation approach in which database contents are extracted in a step-wise manner from evidence in the experimental literature collected from more than 1,600 organisms, as depicted below.

The literature curation manual used by MetaCyc curators can be found here.

Information Types Captured During the MetaCyc Curation Process

Pathways

A summary that includes:

• What the pathway does
• Its start point
• Its end product
• Relationship with other pathways
• Significance of the pathway
• Organism within which the pathway exists
• Experimental evidence for the pathway
• Contradictory evidence
• Citations

Other data:

• Synonyms
• Taxonomic range
• Key reactions

Reactions

• EC number of enzyme activities, if applicable
• Free energy of activation (delta G)
• Comments, such as:
  • Whether this is a novel reaction
  • Whether this is a hypothetical reaction
  • Whether the reaction is spontaneous, in vitro or in vivo
  • Whether the reaction can be balanced

Enzymes & Enzyme Complexes

A summary that includes:

• Experimental evidence
• Isoforms
• Substrate specificity of each isoform
• Tissue type
• Subcellular localization
• Developmental stage
• Citations

Other data:

• Common name of the enzyme and synonym(s)
• Subcellular location
• Native molecular weight (KDa)
• Name of the enzymatic activity (for each reaction associated with the enzyme)
• Name(s) of cofactor(s), activator(s) and inhibitor(s)
• Km
• pI
• Optimum pH
• Optimum temperature

Genes

• Common name of the gene and synonym(s)
• Citations
• A link to an external database that contains sequence information, such as Entrez Nucleotide or Gene.

Compounds

• Synonym(s) of the compound name
• Compound structure
• In some case, a summary describing the compound and its importance in Biology