ChemSpider

ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.[3][4][5][6][7]

ChemSpider
ChemSpider Logo
Content
DescriptionA chemical structure database providing fast access to over 63 million structures, properties and associated information.
Contact
Research centerRaleigh, North Carolina, United States
Laboratory
Access
Websitewww.chemspider.com
Tools
Standalonehttps://itunes.apple.com/us/app/chemspider/id458878661
Miscellaneous
LicenseCreative Commons Attribution Share-alike[2]

Database

The database contains information on more than 63 million molecules from over 280 data sources including:[8]

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.[10]

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:[11] 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)[12] and for the Android (operating system).[13]

Chemistry document mark-up

The ChemSpider database has been used in combination with text mining as the basis of chemistry document markup. ChemMantis,[14] 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.[15] 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.

SyntheticPages

SyntheticPages is a free interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry.[16] 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 announced[17] 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.[18]

See also

References

  1. ^ Van Noorden, R. (2012). "Chemistry's web of data expands". Nature. 483 (7391): 524. Bibcode:2012Natur.483..524V. doi:10.1038/483524a. PMID 22460877.
  2. ^ "ChemSpider Blog » Blog Archive » ChemSpider Adopts Creative Commons Licenses". www.chemspider.com. Archived from the original on 2015-04-02. Retrieved 2014-03-21.
  3. ^ Antony John Williams (Jan–Feb 2008). "ChemSpider and Its Expanding Web: Building a Structure-Centric Community for Chemists". Chemistry International. 30 (1).
  4. ^ Williams, A. J. (2008). "Public chemical compound databases". Current Opinion in Drug Discovery & Development. 11 (3): 393–404. PMID 18428094.
  5. ^ Brumfiel, G. (2008). "Chemists spin a web of data". Nature. 453 (7192): 139. Bibcode:2008Natur.453..139B. doi:10.1038/453139a. PMID 18464701.
  6. ^ Williams, A. J. (2011). "Chemspider: A Platform for Crowdsourced Collaboration to Curate Data Derived from Public Compound Databases". Collaborative Computational Technologies for Biomedical Research. pp. 363–386. doi:10.1002/9781118026038.ch22. ISBN 9781118026038.
  7. ^ Pence, H. E.; Williams, A. (2010). "ChemSpider: An Online Chemical Information Resource". Journal of Chemical Education. 87 (11): 1123. Bibcode:2010JChEd..87.1123P. doi:10.1021/ed100697w.
  8. ^ "Data Sources". Chemspider. Retrieved May 16, 2019.
  9. ^ "ChemSpider Blog » Blog Archive » The US EPA DSSTox Browser Connects to ChemSpider". ChemSpider. August 23, 2008. Retrieved 7 November 2017.
  10. ^ 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.
  11. ^ "ChemSpider Blog » Blog Archive » Who Would Like to Have the Entire ChemSpider Database?". www.chemspider.com. Archived from the original on 2015-09-24. Retrieved 2014-04-18.
  12. ^ "ChemSpider on the App Store". App Store.
  13. ^ "ChemSpider Mobile - Android Apps on Google Play". play.google.com.
  14. ^ Welcome ChemMantis to ChemZoo and a Call for Contributions from the Community,2008-10-23, A. Williams,blog post Archived 2015-09-24 at the Wayback Machine
  15. ^ "RSC acquires ChemSpider". Royal Society of Chemistry. 11 May 2009. Retrieved 2009-05-11.
  16. ^ "ChemSpider SyntheticPages". ChemSpider SyntheticPages. Royal Society of Chemistry. Retrieved 26 June 2012.
  17. ^ "ChemSpider and SyntheticPages support synthetic chemistry". RSC Publishing. Royal Society of Chemistry. 2010-02-05. Archived from the original on 26 July 2012. Retrieved 2012-06-26.
  18. ^ 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.
4-Bromomethcathinone

4-Bromomethcathinone (4-BMC, Brephedrone) is a psychoactive drug and research chemical of the phenethylamine, amphetamine, and cathinone chemical classes. It acts as a serotonin and norepinephrine reuptake inhibitor, but acts more like an antidepressant than a stimulant. It is currently unclear whether the 4-halogenated cathinones share the selective serotonergic neurotoxicity of their corresponding amphetamines.

Enterodiol

Enterodiol is a lignan formed by the action of intestinal bacteria on lignan precursors found in plants.

Epanolol

Epanolol is a beta blocker.

Ethyldienolone

Ethyldienolone, also known as 17α-methyl-19-nor-δ9-testosterone, as well as 17α-methylestra-4,9-dien-17β-ol-3-one, is synthetic, orally active anabolic-androgenic steroid (AAS) and a 17α-alkylated derivative of 19-nortestosterone. It is slightly more active than methyltestosterone when given orally. Ethyldienolone is closely related to dienolone and methyldienolone.

Fazadinium bromide

Fazadinium bromide is a muscle relaxant which acts as a nicotinic acetylcholine receptor antagonist through neuromuscular blockade.

Fenamic acid

Fenamic acid is an organic compound, which, especially in its ester form, is called fenamate. serves as a parent structure for several nonsteroidal anti-inflammatory drugs (NSAIDs), including mefenamic acid, tolfenamic acid, flufenamic acid, and meclofenamic acid. These drugs are commonly referred to as "anthranilic acid derivatives" or "fenamates" because fenamic acid is a derivative of anthranilic acid.

Galanolactone

Galanolactone is a diterpenoid lactone first isolated from ginger. It is known to be present in acetone extracts of ginger, and appears to be an antagonist at 5-HT3 receptors.

Glycitein

Glycitein is an O-methylated isoflavone which accounts for 5-10% of the total isoflavones in soy food products. Glycitein is a phytoestrogen with weak estrogenic activity, comparable to that of the other soy isoflavones.Glycitin (glycitein 7-O-glucoside) can be transformed to glycetein by human intestinal flora.

Hetacillin

Hetacillin is a beta-lactam antibiotic that is part of the aminopenicillin family. It is a prodrug and it has no antibacterial activity itself, but quickly splits of acetone in the human body to form ampicillin, which is active against a variety of bacteria.

Isoliquiritigenin

Isoliquiritigenin is a phenolic chemical compound found in licorice.

Leukotriene B4

Leukotriene B4 (LTB4) is a leukotriene involved in inflammation. It has been shown to promote insulin resistance in obese mice.

Naftopidil

Naftopidil (INN, marketed under the brand name Flivas) is a drug used in benign prostatic hypertrophy which acts as a selective α1-adrenergic receptor antagonist or alpha blocker.

Nuciferine

Nuciferine is an alkaloid found within the plants Nymphaea caerulea and Nelumbo nucifera. It has a profile of action associated with dopamine receptor blockade. It induces sedation, hypothermia, ptosis, and (in higher doses) catalepsy; it inhibits spontaneous motor activity, conditioned avoidance response, amphetamine toxicity and stereotypy. Nuciferine may also potentiate morphine analgesia. The median lethal dose in mice is 289 mg/kg. It is structurally related to apomorphine.

Phloretin

Phloretin is a dihydrochalcone, a type of natural phenol. It can be found in apple tree leaves and the Manchurian apricot.

Setoperone

Setoperone is a compound that is a ligand to the 5-HT2A receptor.

It can be radiolabeled with the radioisotope fluorine-18 and used as a radioligand with positron emission tomography (PET).

Several research studies have used the radiolabeled setoperone in neuroimaging for the studying neuropsychiatric disorders, such as depression

or schizophrenia.

Sunifiram

Sunifiram (developmental code name DM-235) is an experimental drug which has antiamnesic effects in animal studies and with significantly higher potency than piracetam. Sunifiram is a molecular simplification of unifiram (DM-232). Another analogue is sapunifiram (MN-19). As of 2016, sunifiram had not been subjected to toxicology testing, nor to any human clinical trials, and is not approved for use anywhere in the world.

Talinolol

Talinolol is a beta blocker.

Thymine

Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves' thymus glands, hence its name.

Tolonidine

Tolonidine is an antihypertensive.

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