D590 Nucleic Acids Research, 2009, Vol. 37, Database issue complete survey on enzyme data derived from the titles and abstracts of all articles from the literature database PubMed (7) and are the results of an automated text- mining procedure (3) that was revised and improved during the last months. FRENDA FRENDA provides links to all literature references indexed by PubMed that cover enzyme-speciﬁc informa- tion in combination with the name of the organism or one of its synonyms. Likewise, for each enzyme the EC number and its alternative names are considered which can constitute up to several hundreds for some enzymes. In order to create term dictionaries, enzyme names and their synonyms from BRENDA and organism names from the NCBI taxonomy (7) are used. The dictionaries are then employed for screening arti- cles of the PubMed database in a co-occurrence approach [see Figure 2 and ref. (3)]. Due to adaptations in the text-mining procedure FRENDA now also covers abbreviated scientiﬁc organ- ism names such as H. sapiens, E. coli or A. thaliana since these are frequently used throughout the literature. Furthermore, due to a signiﬁcant optimization of the text-mining computing time performance, the MeSH (Medical Subject Heading)-term-based preﬁltering step was removed (3) so that nearly 18 million PubMed abstracts were interpreted, thus minimizing the loss of enzyme-speciﬁc articles. Consequently, a manual evalua- tion with over 500 randomly chosen PubMed records yields a comparatively high recall of 84% whereas the corresponding precision of nearly 40% is still acceptable. Another enhancement of FRENDA is the consequent exclusion of ambiguous enzyme and organism names by manually compiled exclusion lists. In total more than 1.5 million distinct references (Table 2) are present in the current FRENDA release (June 2008) which means an increase by a factor of three Figure 2. Input data and their source databases used for the co-occur- ence based text-mining approach that generates the BRENDA supple- ments FRENDA and AMENDA. compared with the last described release of June 2006 (3). FRENDA now comprises more than 400 000 organism- speciﬁc enzyme hits (Table 2). AMENDA AMENDA is a subset of FRENDA comprising informa- tion on enzyme occurrence in organism, localization and source tissue. It includes the most reliable organism-spe- ciﬁc enzyme information from FRENDA (AMENDA Enzyme–Organism). In addition, it comprises data on the subcellular localization of enzymes (AMENDA Localization) and the source tissues in which the enzymes are active (AMENDA Source Tissue). Whereas the information in FRENDA is completely based on co-occurrence of enzyme names and organism names in title and abstract of a paper, for AMENDA a reﬁned and more rigorous text-mining procedure is used (3). The corresponding enzyme–organism combinations are stored in the new supplement AMENDA Enzyme– Organism (see Figure. 2) and rated according to four relia- bility ranks which reﬂect the degree of co-occurrence of the enzyme and organism name. The best rank is assigned when both, enzyme and organism name, occur in the title plus in the same sentence of the abstract and, additionally, the EC number is found in the abstract or among the MeSH terms. As of June 2008 AMENDA Enzyme–Organism com- prises more than 225 000 organism-speciﬁc enzyme hits. The tissues for AMENDA Source Tissue and the local- izations for AMENDA are obtained from the BRENDA Tissue Ontology (http://www.obofoundry.org/cgi-bin/ detail.cgi?id=brenda) and the Gene Ontology (8), respec- tively [see Figure. 2 and (3)]. From these two resources dictionaries are constructed which are used in addition to the enzyme and organism name dictionary that are employed for building up FRENDA and AMENDA Enzyme–Organism (see above). Thus, the underlying PubMed reference for each enzyme- and organism-speciﬁc hit in FRENDA is further analyzed for co-occurring localization and source tissue names or synonyms. Reliability ranks are assigned to AMENDA Source Tissue and to AMENDA Localization data according to the same principles as for AMENDA Enzyme–Organism. AMENDA Source Tissue contains more than 30 000 and AMENDA Localization more than 60 000 organism-speciﬁc hits, respectively (Table 2). The same manual evaluation as mentioned Table 2. Number of AMENDA and FRENDA entries obtained by the text-mining approach BRENDA supplement AMENDA Enzyme–Organism AMENDA Localization AMENDA Source Tissue FRENDA AMENDA: 1 036 066 distinct references. FRENDA: 1 577 622 distinct references. Number of entries 225 336 29 773 60 890 410 749