Because these complexes were derived from the experi- mental literature, they could be a valuable training set for programs that predict protein–protein interactions. When chemically modiﬁed forms of a protein exist, they are represented within EcoCyc as separate DB objects to allow their activities to be accurately encoded. EcoCyc collects extensive sets of synonyms for E. coli genes and gene products. The DB contains 16 799 gene names and synonyms (an average of 3.8 names per gene), and it contains 21 330 names and synonyms for gene products (an average of 4.8 names per gene product). Gene product summaries EcoCyc contains an extensive collection of mini-reviews that describe the functions of individual gene products, and of the multimeric complexes formed by E. coli gene products. These summaries were written by the EcoCyc curators, and are found in the display pages for gene products (proteins and RNAs). They are not found in gene pages, although they are only one click away from gene pages (click on the name of the gene product). Summaries are written after reviewing the literature for a gene, protein or protein complex, and cover information such as gene product function, interactions with other gene products, mutant phenotypes, multimeric structure, crystal structure and regulation. Summaries are of particular importance in the genomics era, when research- ers frequently work in areas outside their area of specialization, such as during the annotation of newly sequenced microbial genomes. In the summer of 2006, EcoCyc reached an important milestone: as of that time, EcoCyc curators had performed literature searches for every known E. coli K-12 gene and had authored summaries for every gene for which experimental literature was found. A total of 3332 (75%) E. coli genes are ‘covered by a summary’, meaning that a summary is found in the gene-product DB object, or in the DB object for a multimeric complex in which the gene product is a subunit. The remaining 1133 EcoCyc genes contain a brief, standardized summary stating that no information about the gene has been found by the EcoCyc curators in the biomedical literature, and the date on which a literature search was last performed. We recently introduced a DB ﬁeld that records the date on which an EcoCyc gene was last curated, indicating when a curator last performed a systematic literature search for information about that gene. See the ﬁeld ‘Last Curated’ within the gene product pages for that date of last curation. Summaries cite the literature from which their informa- tion was derived. Because the number of articles per E. coli gene varies greatly, from zero to hundreds, summary lengths also vary, from one line of text to thousands of words. Table 2 presents the length in words of the summaries found in EcoCyc gene product and protein- complex objects. The information in EcoCyc has been derived from the 14 950 publications that EcoCyc cites. This number is a small fraction of the 239 344 publications returned by a PubMed search on ‘Escherichia coli’, because whereas Nucleic Acids Research, 2007, Vol. 35, No. 22 7579 EcoCyc is principally concerned with the molecular biology and biochemistry of E. coli K-12, the latter set of articles covers medical aspects of E. coli, other E. coli strains and uses of E. coli as a cloning vector. Over time, more references will be added as EcoCyc curators review and update older EcoCyc entries, and as we curate additional types of regulation information into EcoCyc. It would be particularly helpful to our eﬀorts in adding older omitted references to EcoCyc if E. coli scientists would review EcoCyc gene product pages for genes within their expertise and alert us to missing references and to incomplete or incorrect information using the button ‘Report Errors or Provide Feedback’ that is found at the bottom of most EcoCyc pages. Gene functions How close is the scientiﬁc community to knowing the function of every E. coli gene? Biochemical functions have been assigned to 3384 (76%) of them; the remaining 1077 (24%) E. coli genes have no functional assignment, or only a partial assignment. By ‘partial functions’, we mean approximate descriptions of function, usually resulting from sequence similarity, such as ‘oxidoreduc- tase’ or ‘ABC transporter of unknown substrate’. Although some of the 3384 E. coli genes with known functions had their functions assigned by sequence analysis of the E. coli genome, most genes in EcoCyc had their functions elucidated experimentally, and reported in the literature. EcoCyc makes use of a controlled set of evidence codes (7) that allows the DB to capture what type of evidence supports the functions of E. coli genes, and to capture what types of evidence support the presence of operons and pathways. Of the EcoCyc genes with assigned functions, 2941 had their functions elucidated experimentally (87% of genes with assigned functions, and 66% of all E. coli genes). This value of 66% with experimentally deﬁned functions is extremely high given that it is common in microbial genome projects to be unable to assign any gene function, even computationally, to half the genes in the genome. The ﬁrst gene ontology ever developed—MultiFun— was developed for E. coli (8,9), and the EcoCyc project has been assigning E. coli genes to MultiFun categories since 1993. In 2006, we also began curating GO term assign- ments for E. coli. We obtained an initial set of GO term assignments by running all MultiFun assignments within EcoCyc through a MultiFun-to-GO mapping (see http:// geneontology.org/GO.indices.shtml). This mapping could not assign evidence codes to the GO terms in EcoCyc. Table 2. Number of EcoCyc gene products for which the written gene product summary is of a given length in words Words in gene-product summaries Number of gene products 0–20 21–50 51–100 101–200 201–2000 306 671 694 776 812