Abstract
AbstractChEBI (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.
Highlights
ChEBI (Chemical Entities of Biological Interest) [1] is a manually curated database of molecular entities which provides a chemical ontology
In order to harness efficiently the data submitted by users we have introduced the ChEBI submission tool
As a chemoinformatics resource it is essential to provide a facility for chemical structure searching
Summary
ChEBI: an Open-access Chemistry Resource for the Life Sciences: Facilities for On-line Submission and Curation. ChEBI (Chemical Entities of Biological Interest) [1] is a manually curated database of molecular entities which provides a chemical ontology. ChEBI contains approximately 22,000 manually curated entities and approximately 620,000 entities in total. It provides a wide range of information including nomenclature, structures and related calculated values, and interrelationships between entities in the chemical ontology. Owing to the high demand for good quality curated chemical entities, ChEBI operates completely on a user-request basis. This means that all our curators work full-time on annotation of requests made by users. The ChEBI submission tool is available at: http://www.ebi.ac.uk/chebi/submissions/
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