Eric Sayers, PubChem: An Entrez Database of Small Molecules, NLM Technical Bulletin, January-February 2005 (reprinted from NCBI News, Summer-Fall 2004). Excerpt: 'The NCBI has released three new Entrez databases that link small organic molecules to bioactivity assays, PubMed abstracts, and protein sequences and structures. The new databases compose the PubChem project at NCBI, a part of the NIH Roadmap Initiative. They are PubChem Substance, PubChem Compound, and PubChem Bioassay. PubChem Substance contains over 800,000 chemical samples imported from 14 public sources including ChemIDplus, the Developmental Therapeutics Program at the National Cancer Institute (NCI), KEGG, NCBI Molecular Modeling Database (MMDB), and the NIST Chemistry WebBook. Chemical entities in PubChem Substance records that have known structures are validated, converted to a standardized form, and imported into PubChem Compound. This standardizing allows NCBI to compute chemical parameters and similarity relationships between compounds....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). These groups are provided as Entrez links that allow similar compounds to be retrieved quickly....PubChem Bioassay allows one to search for bioactivity. For instance, the query "leukemia AND lc50[tid description]" in PubChem Bioassay retrieves eight growth inhibition assays with measured LC50 values in various leukemia cell lines. Links are then provided to PubChem Substance and PubChem Compound for these chemicals so that they may be further explored.'
Posted by
Peter Suber at 1/04/2005 11:32:00 AM.
The open access movement:
Putting peer-reviewed scientific and scholarly literature
on the internet. Making it available free of charge and
free of most copyright and licensing restrictions.
Removing the barriers to serious research.
I recommend the OA tracking project (OATP) as the best way to stay on top of new OA developments. You can read the OATP feed on a blog-like web page or subscribe to it by RSS, email, or Twitter. You can also help build the feed by tagging new developments you encounter.
