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PubChem - Wikipedia, the free encyclopedia PubChem can be accessed for free through a web user interface. The American Chemical Society have tried to get the U.S. Congress to restrict PubChem to its original intent, because they claim it competes with their Chemical Abstracts Service. PubChem has ignored a Congressional mandate to avoid competing with the private sector. en.wikipedia.org /wiki/PubChem   (296 words)

C&EN: Latest News - Database Debate The NIH database, known as PubChem, is a key piece of the Molecular Libraries and Imaging component of the agency's Roadmap for Medical Research. PubChem is designed to integrate chemical information on compounds produced by NIH's molecular libraries screening centers with other databases supported by the National Library of Medicine. PubChem is supposed to focus on connecting chemical information on small organic molecules that have potential use in drug development with biomedical research. pubs.acs.org /cen/news/83/i17/8317notw1.html   (548 words)

PubChem and the American Chemical Society PubChem is a freely accessible database created by NIH in 2004 to provide information about small organic molecules. PubChem is a critical part of the Molecular Libraries initiative of the NIH Roadmap for Medical Research. PubChem- The Committee is aware of the development of PubChem, the informatics component of the Molecular Libraries project of the NIH Roadmap for Medical Research. osc.universityofcalifornia.edu /news/acs_pubchem.html   (1553 words)

C&EN: GOVERNMENT & POLICY - NIH AND ACS SPAR OVER PUBCHEM While the idea of such a database fits nicely into the goals of the NIH Roadmap, the scope of compounds contained in PubChem has officials at the American Chemical Society deeply concerned and asking the agency to focus the database's contents on what the society understands to be the database's stated mission. PubChem, on the other hand, is a fledgling database that has been up and running for less than a year. ACS, however, contends that by populating PubChem with data not derived from or relevant to NIH Roadmap research, the agency is setting up at taxpayers' expense a general chemical structure database that replicates the CAS Registry. pubs.acs.org /cen/government/83/8324gov1.html   (2245 words)

[Marxism] Re: the academic-industrial complex   (Site not responding. Last check: 2007-10-09) PubChem was launched last fall by the National Institutes of Health (NIH) in Bethesda, Maryland, as a free storehouse of data on small organic molecules. PubChem's focus on biological information such as protein structures and toxicology is complementary, he says. NIH officials are worried that PubChem could suffer the same fate and hope to make their case this month to Senator Mike Dewine (R-OH). lists.econ.utah.edu /pipermail/marxism/2005-May/025072.html   (804 words)

The PubChem Project PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example "cancer cell line". PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. A PubChem FTP site and Deposition Gateway are also available. pubchem.ncbi.nlm.nih.gov   (255 words)

ALA | LAagency PubChem is a free, publicly available database created by NIH in 2004 to provide information about small molecules for use as research tools and as potential starting points that may lead to the development of new medications. PubChem is the latest member of the powerful family of integrated databases operated by the National Library of Medicine, including GenBank, PubMed, GEO, OMIM, and a host of other resources that are utilized millions of times a day by scientists all over the world. PubChem is the informatics backbone for virtually all of these components, and is intended to empower the scientific community to use small molecule chemical compounds in their research. www.ala.org /ala/washoff/WOissues/governmentinfo/laagency.htm   (2972 words)

| SPARC | SPARC E-News 04-05/2005 |   (Site not responding. Last check: 2007-10-09) PubChem is under assault by the American Chemical Society (ACS), who is calling on Congress to restrict the freely accessible database. PubChem connects chemical information with facts in numerous public databases and is a critical component of NIH's Molecular Libraries Initiative, which in turn is a key element of the NIH strategic “roadmap” to speed new medical treatments and improve healthcare. In our laboratories we are using PubChem for systematic research and are enhancing its value by publishing the results to the world….By sharing resources freely we detect and correct errors, and encourage innovation in the way we access information. www.arl.org /sparc/pubs/enews/apr05.html   (2467 words)

RFA-RM-04-017: MOLECULAR LIBRARIES SCREENING CENTERS NETWORK (MLSCN) Applicants should present a clear set of operational plans for ensuring that the informatics needs of the center are addressed, including the issue of integration to the extent that it contributes to the efficiency of the center’s operation. PubChem staff at NCBI will suggest specific formats for data deposition and will work with MLSCN centers as necessary to ensure accurate transmission. In such cases, a 60-day (calendar days) delay for the deposition of the select screening data to PubChem by the MLSCN may be acceptable to allow the MLSCN center applicant to file a patent on specific compounds. grants1.nih.gov /grants/guide/rfa-files/RFA-RM-04-017.html   (13436 words)

7th ICCS Session E The central purpose of PubChem is to act as a repository for chemical structure data and summary assay results from these experiments. PubChem links chemical structures to the results of bioassays, and augments this information with references to literature and auxiliary data describing these assays and other results. PubChem is tightly integrated into the cluster of biological and literature databases hosted at NCBI, such as PubMed and MMDB. www.int-conf-chem-structures.org /html/7th_iccs_session_e.html   (1099 words)

The PubChem Help In addition, PubChem deposit gateway help document also provides procedures and instructions for users to deposit their structure/assay data into PubChem system. PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features. Similarity links are pre-computed in PubChem using the Cactvs data system at the level of 90% similarity, where the percentage is the Tanimoto score calculated from Cactvs substructure-key (skeys) fingerprints. pubchem.ncbi.nlm.nih.gov /help.html   (5509 words)

NLM Technical Bulletin, January-February 2005, PubChem: An Entrez Database of Small Molecules The new databases compose the PubChem project at NCBI, a part of the NIH Roadmap Initiative. PubChem Compound also indexes these chemicals using 34 fields, many of which represent computed chemical properties such as the number of chiral centers, the number of hydrogen bond donors/acceptors, molecular formula and weight, total formal charge, and octanol-water partition coefficients (XlogP). In PubChem Substance, the query "gleevec" retrieves one record for Imatinib meslylate from ChemIDplus. www.nlm.nih.gov /pubs/techbull/jf05/jf05_pubchem.html   (741 words)

PubChem and ChEBI | nodalpoint.org   (Site not responding. Last check: 2007-10-09) I think PubChem is rather innovative and includes data that is not readily available elsewhere, such as all the small molecule ligands in the MMDB/PDB database. PubChem has over 825,000 structures, ~648,000 of which are unique. I imagine they'd be of use primarily for bioassays - another use might be in docking simulations, in which case some way of converting to the required file formats would be handy (and may exist, as I say I just glanced). www.nodalpoint.org /node/1553   (632 words)

Chemical publisher goes after NIH   (Site not responding. Last check: 2007-10-09) The American Chemical Society (ACS) is lobbying Congress to rein in a new National Institutes of Health database of biomedical research because, the society argues, the government-run database infringes on the private sector. NIH launched the database, PubChem, in 2004 as part of NIH's Roadmap Initiatives to speed new medical treatments and improved health care to Americans. Dougherty said ACS suggested a technical working group to set parameters for PubChem to focus on only the small molecules that relate to bioassay data, information collected about the strength or biological activity of a substance, such as a drug, by comparing its effects with those of a standard preparation on living cells. www.fcw.com /article88988-05-27-05-Web   (1019 words)

| SPARC | OAWG Evidence for UK House Committee |   (Site not responding. Last check: 2007-10-09) PubChem represents a vital next step for NIH in leveraging its investment in the human genome project, filling in the picture of small molecules. As you may know, PubChem is a critical component of NIH's Molecular Libraries initiative, which in turn is a lynchpin of the NIH strategic Roadmap to enhance health care and speed delivery of new medical treatments. It is a mistake to endanger the promise of the Roadmap by imposing restrictions on PubChem that fundamentally undermine its utility. www.arl.org /sparc/oa/PubChemlet.html   (524 words)

A Cauldron Bubbles: PubChem and the American Chemical Society   (Site not responding. Last check: 2007-10-09) PubChem is one of several databases developed by the National Center for Biotechnology Information (NCBI) as part of the Molecular Libraries Roadmap Initiative. Dennis explained, “PubChem is aggregating any small molecules they can get their hands on.” He also emphasized that the federal government should not be using taxpayer dollars to fund services available in the commercial sector. PubChem and CAS are tailored to the needs of different segments of the scientific community. www.infotoday.com /newsbreaks/nb050606-1.shtml   (1373 words)

Government-funded Free Information for Chemists 'Unfair' Competition for Private Monopolies | Digital Rights Network Rather worryingly it appears that PubChem are on the back foot, defending themselves by studiously avowing that their product will in no way compete with CAS' commercial product. CAS President Robert Massie said PubChem has the potential to cripple his company because PubChem is distributed free, while CAS charges subscription fees for access to its registry. PubChem, with 850,000 entries, is a critical piece because it will link molecular data to biomedical literature, said Jeremy Berg, director of the National Institute of General Medical Sciences. drn.okfn.org /node/56   (1181 words)

[No title]   (Site not responding. Last check: 2007-10-09) PubChem offers researchers public access to an array of structure and activity information for a diverse set of small molecules. PubChem contains the results of high-throughput biological screening experiments, and, when possible, PubChem's records are linked to other NCBI databases, such as the PubMed scientific literature database and NCBI's 3D protein structure database. Validation and standardization of chemical structure data is critical to PubChem, since it allows computation of properties, descriptors, and similarity relationships among entries in a uniform and accurate way. www.eyesopen.com /about/events/cup6/bolton   (196 words)

Publishers make appeal to lawmakers in NIH dispute American Chemical Society officials are asking lawmakers to rein in those responsible for a federal database of molecular structures because they say it will cut into the society's income from the sale of similar information. The National Institutes of Health created PubChem in 2004 as part of NIH's Roadmap for Medical Research initiative to speed the discovery of new medical treatments. PubChem has a list of names and structures of 850,000 chemicals. www.fcw.com /article89163-06-13-05-Print   (448 words)

Open Access News PubChem represents a vital next step for NIH in leveraging its investment in the Human Genome Project, integrating output from the Molecular Libraries Screening Center Netwowrk (MLSCN) and other publicly available data sources, such as NIH's protein structure resources and records of biomedical literature within PubMed and available full-text in the PubMed Central digital archive. PubChem is a powerful tool...that will...lead to medical breakthroughs for clinical treatment of diseases....We believe that [the ACS] concern is unfounded and that the American public is well served by continued development and maintenance of PubChem. He believes that there is about a 3 percent overlap between PubChem and CAS and that the taxpayer-funded activity makes sense because the database and its growth will come from publicly funded resources. www.earlham.edu /~peters/fos/2005_06_05_fosblogarchive.html   (9385 words)

Open Access News As an advisor to PubChem I am aware of what they are trying to do and it is in no way a threat to anything that ACS is doing. 'PubChem' is the database component of the molecular libraries initiative, integrating output from the small molecule screening centers with other publicly available data sources, such as NIH's protein structure resources and the biomedical citation literature in PubMed central. From home we were able to use PubChem to find out what the chemical formula of this material is and what its reported toxicity and biological properties are. www.earlham.edu /~peters/fos/2005_05_29_fosblogarchive.html#111736884965954932   (11812 words)

In support of PubChem: towards open chemical information In the article, Peter Murray-Rust, from the University of Cambridge, UK, and John Mitchell and Henry Rzepa from Imperial College London, UK argue using three case studies that conventional methods such as cutting-and-pasting chemical information are time-consuming and introduce errors. This comes as additional support for open chemical databases like the NIH's PubChem, which is currently at the centre of a legal battle between the NIH and the American Chemical Society (ACS). They can also be found using open semantically free identifiers such as those provided by PubChem or based on their common names using Open lexicons; or by systematic chemical name. www.eurekalert.org /pub_releases/2005-07/bc-iso071405.php   (693 words)

Yale University Science Libraries PubChem Contains the chemical structures of small organic molecules and information on their biological activities. PubChem Compound: Search for unique chemical structures using text terms such as names, synonyms, keywords, or depositor-supplied identifiers. PubChem BioAssay: Search for bioassay records using text terms from the bioassay description, such as the names of reagents used in the bioassay. www.library.yale.edu /science/help/chemname.html   (571 words)

[No title]   (Site not responding. Last check: 2007-10-09) The first database, PubChem (http://pubchem.ncbi.nlm.nih.gov/), is part of the US National Institutes of Health's 'Molecular Libraries' initiative, which already has 650,000 diverse small molecules in its collection and a further 100,000 to be included in 2005. PubChem will provide biomedical researchers with access to structural, chemical and physical information, which they can screen computationally or experimentally. Whereas PubChem will provide a diverse database of potential drug leads and molecular probes, ChEBI is essentially a dictionary with a controlled vocabulary for looking up information about a chemical entity of interest. www.nature.com /news/2004/041129/pf/nrd1596_pf.html   (613 words)

BW FAQ - Cheminformatics PubChem is a collection of databases provided by the NCBI, which contains the chemical structures of small organic molecules and information on their biological activities. PubChem also provides PubChem Structure Search, a fast chemical structure similarity search tool that links to the PubChem Compound and PubChem Substance databases. PubChem Substance contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in homepage.univie.ac.at /herbert.mayer/FaqsCHEM.html   (982 words)

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