PubChem


PubChem

. [http://osc.universityofcalifornia.edu/news/acs_pubchem.html] . More than 80 database vendors contribute to the growing PubChem database. [http://pubchem.ncbi.nlm.nih.gov/sources/sources.cgi]

Databases

PubChem consists of three dynamically growing primary databases. As of July 2008:

* Compounds, 19 million entries, contains pure and characterized chemical compounds. [ [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=all%5Bfilt%5D all [filt - PubChem Compound Results ] ]
* Substances, 41 million entries, contains also mixtures, extracts, complexes and uncharacterized substances. [ [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=all%5Bfilt%5D all [filt - PubChem Substance Results ] ]
* BioAssay, bioactivity results from 1156 high-throughput screening programs with several million values. [ [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcassay&term=all%5Bfilt%5D all [filt - PubChem BioAssay Results ] ]

Searching

Searching the databases is possible for a broad range of properties including chemical structure, name fragments, chemical formula, molecular weight, XLogP, and hydrogen bond donor and acceptor count.

PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments.

Each hit provides information about synonyms, chemical properties, chemical structure including SMILES and InChI strings, bioactivity, and links to structurally related compounds and other NCBI databases like PubMed.

In the text search form the database fields can be searched by adding the field name in square brackets to the search term. A numeric range is represented by two numbers separated by a colon. The search terms and field names are case-insensitive. Parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used.

Example (Lipinski's Rule of Five):

0:500 [mw] 0:5 [hbdc] 0:10 [hbac] -5:5 [logp]

ACS's concerns

The American Chemical Society has raised serious concerns about the publicly supported PubChem database, since it appears to directly compete with their existing Chemical Abstracts Service. [cite journal | doi = 10.1126/science.308.5723.774a | year = 2005 | month = May | author = Kaiser, J | title = Science resources. Chemists want NIH to curtail database | volume = 308 | issue = 5723 | pages = 774 | pmid = 15879180 | journal = Science] They have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the society's revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress. They are reported to have paid the lobbying firm Hicks Partners LLC at least $100,000 in 2005 to try to persuade congressional members, the NIH, and the Office of Management and Budget (OMB) against establishing a publicly funded database. They also were reported to have spent $180,000 to hire Wexler & Walker Public Policy Associates to promote the 'use of [a] commercial database.'

Database fields

See also

* Chemical database
** Comparative Toxicogenomics Database
** Chemexper
** ChemSpider
** eMolecules
** DrugBank
** Moltable
* National Center for Biotechnology Information (NCBI)
* Entrez
* PubMed
* GenBank
* Chemistry resources

References

External links

* [http://pubchem.ncbi.nlm.nih.gov PubChem homepage]
* [http://pubchem.ncbi.nlm.nih.gov/search/ PubChem searchpage]
* [http://pubchem.ncbi.nlm.nih.gov/help.html#faq PubChem FAQ]
* [http://pubchem.ncbi.nlm.nih.gov/help.html PubChem Help]
* [http://cheminfo.informatics.indiana.edu/PubChemSR/ PubChemSR Search Aid]
* [http://depth-first.com/articles/2007/09/26/pubchem-for-newbies/ PubChem for Newbies]


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