http://precedings.nature.com/tags/chemistry Recently posted documents tagged with 'chemistry' 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.2009.3714.1 We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective typing of resources, the identification of ambiguity and supports chemical text mining. http://dx.doi.org/10.1038/npre.2009.3714.1 Thu, 03 Sep 2009 13:08:10 UTC ChemAxiom – An Ontological Framework for Chemistry in Science doi:10.1038/npre.2009.3714.1 2009-09-03 Nico Adams Nature Precedings 2009-09-03T13:08:10Z Manuscript Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/ 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://precedings.nature.com/documents/1482/version/1 All known life requires phosphorus (P) in the form of inorganic phosphate (PO4- or Pi) and phosphate-containing organic molecules. Pi serves as the backbone of the nucleic acids that constitute genetic material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic precisely because As and P are similar enough that organisms attempt this substitution. We hypothesize that ancient biochemical systems, analogous to but distinct from those known today, could have utilized arsenate in the equivalent biological role of phosphate. Organisms utilizing such “weird life” biochemical pathways may have supported a “shadow biosphere” at the time of the origin and early evolution of life on Earth or on other planets. Such organisms may even persist on Earth today, undetected, in unusual niches. http://precedings.nature.com/documents/1482/version/1 Wed, 02 Jan 2008 22:43:38 UTC Did nature also choose arsenic? hdl:10101/npre.2008.1482.1 2008-01-02 Felisa Wolfe-Simon Nature Precedings 2008-01-02T22:43:38Z Manuscript Chemistry Evolutionary Biology http://creativecommons.org/licenses/by/3.0/