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Journal of Cheminformatics 05/2012; 3:1-1. · 3.42 Impact Factor
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ABSTRACT: Chemical proteomics is concerned with the identification of protein targets interacting with small molecules. Hence, the availability of a high quality and free resource storing small molecules is essential for the future development of the field. The Chemical Entities of Biological Interest (ChEBI) database is one such database. The scope of ChEBI includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. These entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. In addition, ChEBI contains a chemical ontology which relates the small molecules with each other thereby making it easier for users to discover data. The ontology also describes the biological roles that the small molecules are active in. The ChEBI database also provides a central reference point in which to access a variety of bioinformatics data points such as pathways and their biochemical reactions; expression data; protein sequence and structures.
Methods in molecular biology (Clifton, N.J.) 01/2012; 803:273-96.
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ABSTRACT: Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).
PLoS ONE 01/2011; 6(10):e25513. · 4.09 Impact Factor
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Nico Adams,
Paula de Matos,
Adriano Dekker,
Marcus Ennis,
Janna Hastings,
Kenneth Haug,
Duncan Hull,
Zara Josephs,
Pablo Moreno,
Steve Turner,
Christoph Steinbeck
Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, Amsterdam, The Netherlands, November 20, 2009; 01/2009
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Marcus Ennis, Nico Adams,
Adriano Dekker,
Paula de Matos,
Janna Hastings,
Kenneth Haug,
Duncan Hull,
Zara Josephs,
Gareth Owen,
Steve Turner,
Christoph Steinbeck
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ABSTRACT: ChEBI (Chemical Entities of Biological Interest) is a database of ‘small’ molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures. To invite the community to participate more directly in the future growth and development of ChEBI, we have developed a web-based software utility to enable direct user submissions. Users are encouraged to carry out as much of their own manual curation as possible, e.g. by adding multiple synonyms and database cross-references, and by creating multiple relationships within the ontology. The submissions are automatically validated for uniqueness (both of name and chemical structure) and correctness (such as checking that no non-allowed cycles have inadvertently been created in the ontology graph structure, and that the ontology relationships which have been specified are allowed between entities of the relevant types). Once a submission has passed the required validations, it is submitted to the ChEBI database, at which time it receives its unique ChEBI identifier. It will then become visible to the public (as a preliminary entry) as part of the monthly ChEBI release. To date, ChEBI has received over 750 such external submissions.
Nature Precedings.
