D514 Nucleic Acids Research, 2006, Vol. 34, Database issue Table 3. The size of MetaCyc as a function of time from its first release in 1999 to the latest release in 2005 (version 9.5) Database objects Metabolic pathways Metabolic pathways with comments Enzymatic reactions Enzymes Enzymes with comments Genes Compounds Literature citations 1999 296 39 3779 82 75 0 1949 184 2000 366 83 4002 344 234 0 2180 604 2001 445 160 4218 1115 1054 0 2335 2381 2002 460 180 4294 1267 1123 600 2404 2718 2003 491 232 4817 1543 1389 1554 2951 3070 2004 528 280 4955 1940 1716 1821 3551 5050 2005 621 412 5428 2698 2376 2662 4620 7368 Each row depicts the number of different database objects in MetaCyc during the final release for that year. object¼Pathways). Selection criteria for the curation of these plant pathways include generality of occurrence across taxa, investigation in a model species like Arabidopsis and agro- nomic or medicinal importance. Arabidopsis pathways are 5 exported to AraCyc, the Arabidopsis metabolism database (5) that was computationally predicted using MetaCyc as the reference database. In mammalian metabolism we added multiple new path- ways, including those describing human neurotransmitter 10 biosynthesis (in collaboration with experimentalists in this ﬁeld), drug metabolism, cholesterol biosynthesis, arsenate detoxiﬁcation and glutathione metabolism. These pathways were either curated within MetaCyc, or propagated from the HumanCyc database (3). In addition, several existing 15 pathways of intermediary metabolism were curated with rat enzymes and genes. In parallel with curating new pathways, we extensively edited previously existing pathways. Approximately 60 micro- bial and 7 plant pathways have been updated and enhanced 20 since 2003. One of our highest priorities is the curation of existing pathways that are in need of updating with enzymes, EC numbers, genes and comments with literature citations. While adding new pathways or revising existing pathways, we are also expanding coverage of pathway variants found 25 in different organisms. In addition to curation within MetaCyc, we continue to import pathways from other databases. At each quarterly release we propagate newly curated pathways from EcoCyc (6) and HumanCyc (3) into MetaCyc. We encourage outside 30 curators of our BioCyc family of PGDBs to submit curated pathways to us for possible inclusion in MetaCyc. For example, we incorporated several new yeast pathways in col- laboration with curators from the Saccharomyces Genome Database (SGD) (4). We minimize redundancy by associating 35 several representative species with a pathway that is shared among them. We are in the process of reﬁning the database by deleting pathways that are deemed redundant, dividing large pathways that contain overlapping sections into separate, smaller pathways, and assembling small, related pathways 40 into superpathways, to give an overview of metabolic interrelationships. A new pathway evidence code, EV-EXP-TAS (evidence- experimental-traceable author statement) was created to allow curators to cite review articles containing direct references to 45 the primary literature in support of the pathways. We found this type of reference to be the most useful for large, complex pathways. We are increasingly enhancing the quality of enzyme information in MetaCyc by adding more kinetic data, includ- ing Km values and optima5l0 pH and temperature, and listing enzyme regulators, including activators, inhibitors, cofactors and alternative substrates. We have revised and extended the categories for enzyme regulators based on their kinetics. Activators are now classiﬁed as allosteric, nonallosteric or of unknown mechanism, 55 and inhibitors are classiﬁed as competitive, noncompetitive, uncompetitive, allosteric, irre- versible, none of the preceding or of unknown mechanism. Deﬁnitions of these types of regulators are provided in Appendix I of (7). It should be noted that while kinetic data are present for most60 enzymes curated within the last 2 years, there are still many enzymes in the database which lack kinetic data, either because they were curated earlier and have not yet been updated, or because no such data are available in the literature. We introduced hyperlink6s5 within pathway and enzyme com- ments, which can link commentary text to any data in the database. This dynamic linking greatly improves the ability of users to navigate between related database objects. Our chemical library has grown signiﬁcantly in the past 2 years, from 2951 to 462070 compounds. Currently, over 93% of our compounds have structures. In addition, last year we began adding stereochemistry representations to the structures. Taxonomies We signiﬁcantly enhanced the cellular component ontology to annotate the subcellular lo7c5ations of enzymes and to encode the cellular compartments involved in transport reactions. The ontology, which has been described recently (8), currently comprises 160 terms. More about the enhanced cell com- ponent ontology can be found at http://bioinformatics.ai.sri. com/CCO/. 80 MetaCyc is routinely updated with the latest data from the Nomenclature Committee of the International Union of Bio- chemistry and Molecular Biology (NC-IUBMB), which includes new and modiﬁed EC numbers. The last supplement to have been incorporated i s85 supplement 10 (http://www.chem. qmul.ac.uk/iubmb/enzyme/supplements/sup2004/). Links to other databases While MetaCyc (unlike organism-speciﬁc PGDBs) does not contain sequence information, we use extensive linking to external amino acid and90 nucleotide sequence databases. Whenever possible, enzyme and gene entries include links