ChemSpider

From Wikipedia, the free encyclopedia
Jump to: navigation, search
ChemSpider
ChemSpider Logo.png
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 www.chemspider.com
Tools
Standalone https://itunes.apple.com/us/app/chemspider/id458878661
Miscellaneous
License Creative Commons Attribution Share-alike2

ChemSpider is a chemical database owned by the Royal Society of Chemistry.345678910111213

Database

The database contains 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 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 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.

SyntheticPages

SyntheticPages is a free interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry.20 Users submit synthetic procedures which they have conducted themselves for publication on the site. These procedures may be original works, but they are more often based on literature reactions. Citations to the original published procedure are made where appropriate. They are checked by a scientific editor before posting. The pages do not undergo formal peer-review like a scientific journal article but comments can be made by logged-in users. The comments are also moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab. While experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Informality is encouraged. Comments by submitters are included as well. Other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses. The SyntheticPages site was originally set up by Professors Kevin Booker-Milburn (University of Bristol), Stephen Caddick (University College London), Peter Scott (University of Warwick) and Dr Max Hammond. In February 2010 a merger was announced21 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 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.22

References

  1. ^ Van Noorden, R. (2012). "Chemistry's web of data expands". Nature 483 (7391): 524. doi:10.1038/483524a. PMID 22460877. 
  2. ^ http://www.chemspider.com/blog/chemspider-adopts-creative-commons-licenses.html
  3. ^ Chemical & Engineering News 85 (24). June 11, 2007. 
  4. ^ Antony John Williams (Jan–Feb 2008). "ChemSpider and Its Expanding Web: Building a Structure-Centric Community for Chemists". Chemistry International 30 (1). 
  5. ^ Williams, A. J. (2008). "Public chemical compound databases". Current opinion in drug discovery & development 11 (3): 393–404. PMID 18428094. 
  6. ^ Ekins, S; Iyer, M; Krasowski, M. D.; Kharasch, E. D. (2008). "Molecular characterization of CYP2B6 substrates". Current drug metabolism 9 (5): 363–73. PMC 2426921. PMID 18537573. 
  7. ^ Brumfiel, G. (2008). "Chemists spin a web of data". Nature 453 (7192): 139. doi:10.1038/453139a. PMID 18464701. 
  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). "Chemspider: A Platform for Crowdsourced Collaboration to Curate Data Derived from Public Compound Databases". Collaborative Computational Technologies for Biomedical Research. p. 363. doi:10.1002/9781118026038.ch22. ISBN 9781118026038. 
  12. ^ Pence, H. E.; Williams, A. (2010). "ChemSpider: An Online Chemical Information Resource". Journal of Chemical Education 87 (11): 1123. doi:10.1021/ed100697w. 
  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. doi:10.1007/s13361-011-0265-y. PMID 22069037. 
  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. doi:10.1186/1758-2946-2-3. PMC 2848622. PMID 20331846. 
  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. ^ Williams, A. J.; Harland, L.; Groth, P.; Pettifer, S.; Chichester, C.; Willighagen, E. L.; Evelo, C. T.; Blomberg, N.; Ecker, G.; Goble, C.; Mons, B. (2012). "Open PHACTS: Semantic interoperability for drug discovery". Drug Discovery Today 17 (21–22): 1188–1198. doi:10.1016/j.drudis.2012.05.016. PMID 22683805. 

See also








Creative Commons License