MIARE/PubChem Workshop, DPM
Dr Steve Bryant and Dr Yanli Wang, NCBI, NLM, NIH.
DPM, in collaboration with NCBI, is hosting a workshop with the objective of incorporating MIARE, the RNAi minimum information standard, into PubChem, the NCBI database of small bio-active molecules, so that meaningful chemical and chemical biology comparisons of cross-screen/assays of pathways from disparate datasets can be made.
The establishment and implementation of minimum information standards (www.mibbi.org) to facilitate sharing of screening data within the wider RNAi community is one of the founding goals of RNAi Global (www.rnaiglobal.org) and is a core initiative overseen by its Informatics Working Group (IWG). As a founding member of the IWG, the Division of Pathway Medicine has a central role coordinating the MIARE (Minimum Information About an RNAi Experiment, www.miare.org) reporting guidelines.
PubChem (http://pubchem.ncbi.nlm.nih.gov) is a repository of small biologically active molecules, including their chemical structures, with links to assays that screen the biological activity of these substances. PubChem records link to many of NCBI's primary resources, such as PubMed, and can be queried from within Entrez search. A number of tools are available for data analysis, including structure clustering.
Stephen Bryant Seminar
4pm Lecture Theatre 2 (G.26), Rutherford Building, Kings Buildings
'PubChem: An Open Repository for Chemical Structure and Biological Activity Information'
PubChem is an online public information resource from the National Center for Biotechnology Information (NCBI). The system provides information on the biological activities of chemical substances, linking together results from multiple sources on the basis of chemical structure and/or bioactivity-profile similarity. Following the deposition model introduced by the GenBank genomic sequence database, PubChem's content is derived from user depositions of chemical structure and bioactivity results, including high-throughput biological screening results from the NIH Molecular Libraries program. PubChem’s information retrieval tools support basic searches by chemical names and structures, as well as searches by target names or other terms used in descriptions of bioactivity experiments. Additional tools provide structure-activity analysis within and between multiple sets of bioactivity results. PubChem provides further information on biological activities via links to other NCBI information resources, such as the PubMed biomedical literature database and NCBI's protein 3D structure database, as well as via links to depositor web sites.
This article was published on Jun 9, 2010