http://precedings.nature.com/users/df93a01ccb99fb96a5197d0abe2fb43b/ Documents posted by Ulrike Wittig Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3322.1 The identification of a chemical compound solely based on its name requires comprehensive chemical knowledge and often extensive searches in chemical databases. However, it is crucial for the integration of biochemical data extracted from the literature, since many publications exclusively describe a compound by its name. We have developed an application which matches synonymic names of chemical compounds and thereby facilitates the bundling of corresponding data referring to the same compound.The tool that we have developed is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Matching of synonymous names is achieved by comparison of the normalized name forms. It is capable of normalizing a given name of a chemical compound and matching it against names in (bio-)chemical databases (e.g. SABIO-RK, ChEBI or PubChem), even when there is no exact name-to-name-match. The tool is also able to match a complete list of compound names against these databases which makes it useful for the automatic annotation of chemical data.This normalization and matching of various synonyms of a chemical compound constitutes a platform for the unambiguous identification of compounds described in the literature or in databases. http://dx.doi.org/10.1038/npre.2009.3322.1 Fri, 05 Jun 2009 20:06:57 UTC Normalization and Matching of Chemical Compound Names doi:10.1038/npre.2009.3322.1 2009-06-05 Martin Golebiewski Nature Precedings 2009-06-05T20:06:57Z Poster Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3085.1 SABIO-RK (http://sabio.villa-bosch.de/SABIORK/) is a curated, web-accessible database for modellers and wet-lab scientists to get comprehensive information about biochemical reactions and their kinetic properties. It integrates data from different origin in order to facilitate the access to reaction kinetics data and corresponding information. Since most of the kinetic data is exclusively found in the literature SABIO-RK offers data manually extracted from the literature and related information obtained from other publicly available biological databases. For instance, the kinetic data are related to reactions, organisms, tissues and cellular locations. The type of the kinetic mechanism and corresponding rate equations are presented together with their parameters and experimental conditions. Additionally, SABIO-RK also includes data about the detailed mechanism for some of the reactions based on literature information. This not only includes the graphical representation of the mechanism but also the single reaction steps with their corresponding kinetic data.The data in SABIO-RK are extracted manually from literature and the selection of articles is not restricted to any biological source (e.g. organisms or organism classifications). All the data are curated and annotated by biological experts using a web-based input interface. To support the curation process and data integration we have implemented different constraints in the input interface and offer several controlled vocabularies as lists of values, as well as additional semi-automatic consistency checks to avoid errors and inconsistencies in the database. Controlled vocabularies and annotations to external resources and ontologies were used to identify and relate the data to their biological context. All these efforts to unify and integrate the data augment the content and the semantics of the SABIO-RK database entries to enable a comprehensive understanding and comparison of the data for the user.SABIO-RK can be accessed via a web-based user interface or via web-services. The user interface allows the definition of complex queries by specifying reactions and reaction participants, kinetic parameters, environmental conditions or literature sources. Links to other databases based on the annotations of thedata enable the user to gather further information for example for compounds, reactions or proteins. Selected data about reactions and their kinetics, together with their annotations, can be exported in SBML (Systems Biology Mark-up Language), a widely used standard exchange format in systems biology. http://dx.doi.org/10.1038/npre.2009.3085.1 Mon, 20 Apr 2009 09:32:22 UTC SABIO-RK: Curated Kinetic Data of Biochemical Reactions doi:10.1038/npre.2009.3085.1 2009-04-21 Ulrike Wittig Nature Precedings 2009-04-20T09:32:22Z Presentation Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/