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ChemSpider

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ChemSpider

ChemSpider
Content
Description A chemical structure database providing fast access to over 30 million structures, properties and associated information.
Contact
Research center Raleigh, North Carolina, United States
Laboratory
Access
Website .com.chemspiderwww
Tools
Standalone https://itunes.apple.com/us/app/chemspider/id458878661
Miscellaneous
License Creative Commons Attribution Share-alike[2]

ChemSpider is a database of chemicals which is owned by the Royal Society of Chemistry.[3][4][5][6][7][8][9][10][11][12][13]

Database

The database contains information on more than 30 million unique molecules from over 450 data sources including:

Each chemical is given a unique identifier, which forms part of a corresponding URL. For example, acetone is 175, and thus has the URL http://www.chemspider.com/Chemical-Structure.175.html

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.[14]

However, database rights are not waived and a data dump is not available; in fact, the FAQ even states that only limited downloads are allowed:[15] therefore the right to fork is not guaranteed and the project can't be considered free/open.

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.
  • Structure searching on mobile devices can be done using free apps for iOS (iPhone/iPod/iPad)[16] and for the Android (operating system).[17]

Chemistry document mark-up

The ChemSpider database has been used in combination with text mining as the basis of chemistry document markup. ChemMantis,[18] 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 (RSC) in May, 2009.[19] 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 WorldHeritage chemical structure collection via their WiChempedia implementation.

Services

A number of services are made available online. These include the conversion of chemical names to hash table resolver for InChIKeys, shorter hashed forms of InChIs.

SyntheticPages

SyntheticPages is a free interactive database of University of Bristol), Stephen Caddick (University College London), Peter Scott (University of Warwick) and Dr Max Hammond. In February 2010 a merger was announced[21] with the Royal Society of Chemistry's chemical structure search engine ChemSpider and the formation of ChemSpider|SyntheticPages (CS|SP).

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 an open standards, open access, semantic web approach to address bottlenecks in small molecule drug discovery - disparate information sources, lack of standards and information overload.[22]

References

  1. ^ Van Noorden, R. (2012). "Chemistry's web of data expands". Nature 483 (7391): 524.  
  2. ^ http://www.chemspider.com/blog/chemspider-adopts-creative-commons-licenses.html
  3. ^ Chemical & Engineering News 85 (24). June 11, 2007. 
  4. ^  
  5. ^  
  6. ^ Ekins, S; Iyer, M; Krasowski, M. D.; Kharasch, E. D. (2008). "Molecular characterization of CYP2B6 substrates". Current drug metabolism 9 (5): 363–73.  
  7. ^ Brumfiel, G. (2008). "Chemists spin a web of data". Nature 453 (7192): 139.  
  8. ^ 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.
  9. ^ Links to Multiple Presentations about ChemSpider
  10. ^ Identification of Nontargeted Species Using Accurate Mass/Mass Spectrometry Data and ChemSpider
  11. ^ Williams, A. J. (2011). "Collaborative Computational Technologies for Biomedical Research". p. 363.  
  12. ^ Pence, H. E.; Williams, A. (2010). "ChemSpider: An Online Chemical Information Resource". Journal of Chemical Education 87 (11): 1123.  
  13. ^ Little, J. L.; Williams, A. J.; Pshenichnov, A.; Tkachenko, V. (2011). "Identification of "Known Unknowns" Utilizing Accurate Mass Data and Chem Spider". Journal of the American Society for Mass Spectrometry 23 (1): 179–85.  
  14. ^ Hettne, K. M.; Williams, A. J.; Van Mulligen, E. M.; Kleinjans, J.; Tkachenko, V.; Kors, J. A. (2010). "Automatic vs. Manual curation of a multi-source chemical dictionary: The impact on text mining". Journal of Cheminformatics 2 (1): 3.  
  15. ^ http://www.chemspider.com/blog/who-would-like-to-have-the-entire-chemspider-database.html
  16. ^ http://itunes.apple.com/us/app/chemspider/id458878661
  17. ^ https://play.google.com/store/apps/details?id=com.mmi.android.chemspider
  18. ^ Welcome ChemMantis to ChemZoo and a Call for Contributions from the Community,2008-10-23, A. Williams,blog post
  19. ^ "RSC acquires ChemSpider". Royal Society of Chemistry. 11 May 2009. Retrieved 2009-05-11. 
  20. ^ "ChemSpider SyntheticPages". ChemSpider SyntheticPages. Royal Society of Chemistry. Retrieved 26 June 2012. 
  21. ^ "ChemSpider and SyntheticPages support synthetic chemistry". RSC Publishing. Royal Society of Chemistry. 2010-02-05. Retrieved 2012-06-26. 
  22. ^  

See also

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