A further classification of the enzyme

Are connected to a reference. A further classification of the enzyme role, e.g. the pharmacological or diagnostic value of an enzyme or its malfunction, is described in this paper. The assignment of statements within a reference into the four categories causal interaction, ongoing research, therapeutic application and diagnostic usage allows to identify interesting biomedical aspects in the scientific literature of high information value. The categories were chosen so that it is quickly possible to get information on the role of enzymes in the context of diseases. The Fabry disease is an inherited disorder of glycosphingolipid metabolism due to a deficiency of the enzyme alpha-galactosidase (EC 4-tetrahydroquinoline 3.2.1.22), being an example for a causal interaction between an enzyme and a disease. The statement “…a disease-specific therapeutic option – enzyme replacement therapy using recombinant human alpha-galactosidase has been recently introduced…” [9] describes the therapeutic application in which the enzyme is the drug 2-Bromo-1,3-difluoro-4-nitrobenzene itself for the treatment of the disease. More frequently the enzyme is used as the drug target as, for example, in therapeutic strategies that focus on the inhibition of enzymes of pathogenic viruses andbacteria. The title “The HIV-1 protease as a therapeutic target for AIDS” [10] is easily assigned to the category therapeutic application. The title “Serum Alkaline Phosphatase Level as a Prognostic Tool in Colorectal Cancer…” [11] is an example for the assignment to the category diagnostic usage. The finding of abnormal activity of the isoenzymes (bone, liver) may indicate a broad range of pathological conditions like cirrhosis, hepatitis, liver tumours, drug intoxication, renal diseases, bone diseases and the presence of metastases. The category ongoing research comprises references that contain statements indicating a preliminary relation between enzyme and disease but more research effort is necessary, e.g. indicated in the reference title “N-acetylgalactosaminyl transferase-3 is a potential new marker for non-small cell PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/4155310 lung cancers.” [12]. This publication focuses on the development and content of DRENDA which provides information on diseases and enzymes and their categorised relations.MethodsWorkflow and auxiliary meansThe DRENDA work flow is based on the disease mining procedures already included in BRENDA [13] but strongly enhanced inter alia by the added classification feature. The work flow (Figure 1) is implemented in Python and uses MySQL as database back-end. The first step is the initial sentence splitting (Figure 1, Sentence splitting) and search for the co-occurrence PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/13867361 of enzyme and disease terms (Figure 1, Co-occurrence matching) within the title or an 1-(4-Bromo-2-pyridyl)piperazine abstract sentence of the references enlisted in PubMed. The BRENDA enzyme names andFigure 1 A schematic illustration of the DRENDA work flow. The BRENDA enzyme names and synonyms and the MeSH disease terms are used as dictionaries. The PubMed abstracts and titles are searched for co-occurring disease and enzyme entities. A test/train corpus was created for training an SVM and classifying the cooccurrence results according to the categories causal interaction, therapeutic application, diagnostic usage and ongoing research. The resulting entries are stored in the DRENDA database.S ngen et al. BMC Bioinformatics 2011, 12:329 http://www.biomedcentral.com/1471-2105/12/Page 3 ofsynonyms, derived from manual literature annotation, comprise currently around 100,000 terms. T.