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NCBI News, April 2010

, Ph.D. and , M.S.

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Created: ; Last Update: May 5, 2010.

New Databases and Tools

NIH Roadmap Epigenomics Project

The NIH Roadmap Epigenomics Mapping Consortium has the goal of producing a public resource of human epigenomic data to catalyze basic biological and disease-oriented research. Data from the project are now being deposited in the Gene Expression Omnibus (GEO) database at NCBI. The Epigenomics data listings page provided by GEO also allows for simple data downloading as well as data visualization in NCBI's Sequence Viewer. To view the project data listings page along with information on data access policies please see: www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/

Microbial Genomes

Twenty-five finished microbial genomes were released during April 2010. The original sequence data files submitted to GenBank/EMBL/DDBJ are available on the FTP site: ftp.ncbi.nih.gov/genbank/genomes/Bacteria/. The RefSeq provisional versions of these genomes are also available: ftp.ncbi.nih.gov/genomes/Bacteria/.

GenBank News

GenBank release 177.0 is available on the NCBI web and FTP sites. The current release includes information available as of April 14, 2010. The FTP site also provides the GenBank release notes describing the current release an upcoming changes: ftp.ncbi.nih.gov/genbank/gbrel.txt

Updates and Enhancements

OMIM’s New Look

The record display for the Online Mendelian Inheritance in Man (OMIM) database was recently updated. These changes are an aspect of the migration of OMIM to the updated display and retrieval system in Entrez. The text on the OMIM records has been re-styled to make it consistent with the rest of the Entrez system. The blue sidebar has been eliminated, and the Table of Contents, with embedded links for each section of the record, has been moved to the right-hand column. The Links menu is now displayed in a fully expanded format in this column with links to related information in other databases such as PubMed and Entrez Gene, as well as tools such as Map Viewer. OMIM also now works with the simplified URL format available in many other Entrez databases that allows direct access to a record using the appropriate identifier, in this case the MIM number. For example, the OMIM records for Breast Cancer 1 Gene, BRCA1 (MIM: 113705) can be accessed through the URL: www.ncbi.nlm.nih.gov/omim/113705.

Entrez Gene

Entrez Gene has added new links to the links menu on the right-hand side of records that provide easy access to gene-specific RefSeq sequences. The RefSeq Proteins link retrieves the RefSeq protein records specific to the gene being displayed. Another new link, RefSeq RNAs, retrieves the corresponding RefSeq transcript records. For a subset of human genes, the RefSeqGene link is available that retrieves the curated RefSeqGene record spanning the annotated genomic region containing the gene.

PubMed

PubMed now includes citations from specific online books and book chapters on the NCBI Bookshelf. Citations from GeneReviews and Essentials of Glycobiology are currently included with more books coming. The new book citations are provided by a link to the bookshelf labeled Books and Documents. In order to accommodate the book citations, the PubMed Related Articles link has been renamed Related Citations. The March-April 2010 issue of the NLM Technical Bulletin presents more information on the new book citations: www.nlm.nih.gov/pubs/techbull/ma10/ma10_pm_books.html.

Announce Lists and RSS Feeds

Eighteen topic-specific mailing lists are available which provide email announcements about changes and updates to NCBI resources including dbGaP, BLAST, GenBank, and Sequin. The various lists are described on the Announcement List summary page: www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html. To receive updates on the NCBI News, please see: www.ncbi.nlm.nih.gov/About/news/announce_submit.html.

Twelve RSS feeds are now available from NCBI including news on PubMed, PubMed Central, NCBI Bookshelf, LinkOut, HomoloGene, UniGene, and NCBI Announce. Please see: www.ncbi.nlm.nih.gov/feed/.

The NCBI Facebook (http://www.facebook.com/ncbi.nlm) and Twitter (http://twitter.com/NCBI) accounts provide another source for NCBI news, updates, and events.

Send comments and questions about NCBI resources to: vog.hin.mln.ibcn@ofni, or by calling 301-496-2475 between the hours of 8:30 a.m. and 5:30 p.m. EST, Monday through Friday.

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