- ChemSpider
-
Chemspider 
ChemspiderIndustry Internet, Information science Headquarters Raleigh, North Carolina February, 2007 Key people Antony J. Williams, VP of Strategic Development Parent Royal Society of Chemistry Website www.ChemSpider.com ChemsSpider is a free chemical database, owned by the Royal Society of Chemistry.
Contents
Database
The database contains more than 26 million unique molecules from over 400 data sources including those listed below.
- A-L: EPA DSSTox, U.S. Food and Drug Administration (FDA), Human Metabolome Database, Journal of Heterocyclic Chemistry, KEGG, KUMGM, LeadScope, LipidMAPS
- M-N: Marinlit, MDPI, MICAD, MLSMR, MMDB, MOLI, MTDP, Nanogen, Nature Chemical Biology, NCGC, NIAID, NIH/NLM, NINDS Approved Drug Screening Program, NIST, NIST Chemistry WebBook, NMMLSC, NMRShiftDB
- P-S: PANACHE, PCMD, PDSP, Peptides, Prous Science Drugs of the Future, QSAR, R&D Chemicals, San Diego Center for Chemical Genomics, SGCOxCompounds, SGCStoCompounds, SMID, Specs, Structural Genomics Consortium, SureChem, Synthon-Lab
- T-Z: Thomson Pharma, Total TOSLab Building-Blocks, UM-BBD, UPCMLD, UsefulChem, Web of Science, xPharm, ZINC
Crowdsourcing
The ChemSpider database can be updated with user contributions including chemical structure deposition, spectra deposition and user curation. This is a crowdsourcing approach to develop an online chemistry database. Crowdsourced based curation of the data has produced a dictionary of chemical names associated with chemical structures that has been used in text-mining applications of the biomedical and chemical literature [1].
Searching
A number of available search modules are provided:
- The standard search allows querying for systematic names, trade names and synonyms and registry numbers
- The advanced search allows interactive searching by chemical structure, chemical substructure, using also molecular formula and molecular weight range, CAS numbers, suppliers, etc. The search can be used to widen or restrict already found results.
Chemistry document mark-up
The ChemSpider database has been used in combination with text mining as the basis of chemistry document markup. ChemMantis[2], the Chemistry Markup And Nomenclature Transformation Integrated System uses algorithms to identify and extract chemical names from documents and web pages and converts the chemical names to chemical structures using name-to-structure conversion algorithms and dictionary look-ups in the ChemSpider database. The result is an integrated system between chemistry documents and information look-up via ChemSpider into over 150 data sources.
History
ChemSpider was acquired by the Royal Society of Chemistry in May, 2009.[3] Prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a beta release form and transitioned to release in March 2008. ChemSpider has expanded the generic support of a chemistry database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation.
Services
A number of services are made available online. These include the conversion of chemical names to chemical structures, the generation of SMILES and InChI strings as well as the prediction of many physicochemical parameters and integration to a web service allowing NMR prediction. The organization is working with RSC to develop a hash table resolver for InChIKeys, shorter hashed forms of InChIs.
Open PHACTS
ChemSpider is serving as the chemical compound repository as part of the Open PHACTS project, an Innovative Medicines Initiative. Open PHACTS will deploy a highly innovative open standards, open access, semantic web approach to address key bottlenecks in small molecule drug discovery - disparate information sources, lack of standards and information overload.
See also
- eMolecules
- NIST
- PubChem
- DrugBank
- ChEBI
- ChEMBL
- Software for molecular modeling
References
- ^ Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining, Kristina M Hettne, Antony J Williams, Erik M van Mulligen, Jos Kleinjans, Valery Tkachenko and Jan A Kors, Journal of Cheminformatics, Volume 2, Number 1, 3 DOI
- ^ Welcome ChemMantis to ChemZoo and a Call for Contributions from the Community,2008-10-23, A. Williams,blog post
- ^ "RSC acquires ChemSpider". Royal Society of Chemistry. 11 May 2009. http://www.rsc.org/AboutUs/News/PressReleases/2009/ChemSpider.asp. Retrieved 2009-05-11.
Further reading
- Chemical & Engineering News 85 (24). June 11, 2007.
- Antony Williams (Jan-Feb 2008). "ChemSpider and Its Expanding Web: Building a Structure-Centric Community for Chemists". Chemistry International 30 (1). http://www.iupac.org/publications/ci/2008/3001/ic_chemspider.html.
- Antony Williams (Apr - May 2008). "Public Chemical Compound Databases". Current Opinion in Drug Discovery & Development 11 (3).
- Sean Ekins, Manisha Iyer, Matthew D. Krasowski and Evan D. Kharasch (2008). "Molecular Characterization of CYP2B6 Substrates". Current Drug Metabolism 9 (5): 363–73. PMC 2426921. PMID 18537573. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2426921.
- Geoff Brumfiel (2008-05-07). "Chemists Spin a Web of Data". Nature 453 (7192): 139. doi:10.1038/453139a. PMID 18464701.
- E. Curry, A. Freitas, and S. O’Riáin, “The Role of Community-Driven Data Curation for Enterprises,” in Linking Enterprise Data, D. Wood, Ed. Boston, MA: Springer US, 2010, pp. 25-47.
External links
Categories:- Chemical databases
- Websites which use Wikipedia
- Internet properties established in 2007
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