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Archive for December, 2012

Submit Your Application to Participate in a New Bioinformatics Training Course: “A Librarian’s Guide to NCBI!”

In sponsored partnership, the National Center for Biotechnology Information (NCBI) and the National Library of Medicine Training Center (NTC) are pleased to invite participation of health sciences librarians in a new bioinformatics training course: “A Librarian’s Guide to NCBI.” Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo.

The course provides basic knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Attending this course will improve your ability to initiate bioinformatics services at your institution and/or extend current initiatives. Prior knowledge of molecular biology and genetics is not required. Participants who complete the class will be eligible for MLA Continuing Education credits. The course is free but travel costs are at the expense of the participant.

There are two parts to the course and applicants must take both parts:

Part 1: “Fundamentals in Bioinformatics and Searching,” a three-week, online, (asynchronous) self-paced pre-course, March 4-18, 2013. The aim is to provide, from a librarian’s professional perspective, the fundamental knowledge and background information necessary for the subsequent, more intensive, hands-on second portion of the course onsite at NCBI. Bioinformatics will be introduced both as a discipline and as a research practice. Select NCBI databases, tools (including search tools) and bioinformatics records will be previewed. A beginning working knowledge of the necessary molecular biology vocabulary necessary to enable successful NCBI searches will be developed.

Part 2: A 5-day, in-person course offered onsite at the National Library of Medicine in Bethesda, MD, April 15th-19th, 2013. Topics will include using the BLAST sequence similarity search and Entrez text search systems to find relevant data. This portion of A Librarian’s Guide to NCBI describes the various kinds of molecular data available, and explains how these are generated and used in modern biomedical research.

Applications are open to health science librarians in the United States. Applications will be accepted from librarians currently providing bioinformatics services, as well as from those desiring to implement services. The application deadline is January 25, 2013. Applicants will need to fill out the application form, submit a supervisor letter of support form, and provide a curriculum vitae (CV). Applicants will be notified of acceptance on or about February 15, 2013.

Please view the application form and the course page for additional information. Please direct any questions to ncbi_course@lists.utah.edu.

Newly Maintained MEDLINE for 2013 MeSH Now Available in PubMed

PubMed/MEDLINE citations, the MeSH database, and the NLM Catalog were updated to reflect 2013 MeSH on December 10, 2013. The MeSH translation tables were also updated. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2013 MeSH vocabulary. For details on the data changes, go to MEDLINE Data Changes — 2013. On December 11, NLM resumed daily (Tuesday-Saturday) MEDLINE updates to PubMed, including the backlog of citations indexed since November 14 with 2013 MeSH.

What’s New for 2013 MeSH for Rare Diseases

MeSH uploaded the disease portion of the Online Mendelian Inheritance in Man (OMIM) database available in the Unified Medical Language System. OMIM is a database that catalogues human diseases with genetic components. Although OMIM disease names are available for searches in PubMed, it is often difficult to index and search for the articles on rare diseases with genetic components due to multiple synonyms used by different scientists that often do not overlap. As was done with NIH Office of Rare Diseases and Research (ORDR) disease terms in 2010, OMIM terms were compared to the existing MeSH descriptors and SCR records. When matches were found, OMIM thesaurus tags were added to the matched MeSH record terms. Where there were no string matches, new disease SCRs were created and mapped to descriptor(s) using the Heading Mapped to (HM) field. MeSH created 3,774 new disease SCRs, and identified and tagged 1,498 existing ORDR SCRs as rare diseases with genetic components during the OMIM load. All OMIM disease names therefore will be available starting with MeSH 2013 for indexers and searchers. The use of the HM field in the disease SCRs will lead to more consistent indexing and retrieval for rare genetic diseases.

There were 2,165 terms in 772 descriptors (MeSH headings) matching OMIM terms and therefore, tagged with the Thesaursus ID (TH)=OMIM (2013). An additional 10,286 terms in 5,453 total SCRs (6,331 terms in 3,774 new SCRs and 3,955 terms in 1,498 existing SCRs) were identified during the load. All newly created SCRs were reviewed and mapped to at least one disease descriptor.

The NLM Technical Bulletin article, What’s New for 2013 MeSH, includes additional information on the OMIM tagging. The NLM Technical Bulletin article, What’s New for 2010 MeSH®, has additional information on the 2010 ORDR term merger into the MeSH vocabulary.

NIH News in Health, December 2012 Issue Now Available!

Illustration of a woman wearing a pedometer and walking along a trail.The December 2012 issue of NIH News in Health is now available online! NIH News in Health is a monthly newsletter from the National Institutes of Health, part of the U.S. Department of Health and Human Services. The National Institutes of Health (NIH) plays a major role in finding better ways to diagnose, treat, cure or prevent diseases. The practical health information in NIH News in Health is reviewed by NIH’s medical experts and based on research conducted either by NIH’s own scientists or by our grantees at universities and medical schools around the country. This issue features:

  • Don’t Just Sit There! Move for Your Health
  • Counting Carbs? Understanding Glycemic Index and Glycemic Load
  • Technique May Improve COPD Detection
  • Videos Highlight Behavior and Health
  • NIH Director’s Blog

NIH News in Health is available online in both HTML and PDF formats. Print copies are available free of charge for offices, clinics, community centers and libraries within the U.S.

The PubReader View: A New Way to Read Articles in PMC

Full PubReader screen showing first page of an article with the journal banner.In order to keep pace with the continuing advances in web technology, PMC has launched PubReader, an alternative web presentation that offers another, more reader-friendly view of the articles in the PMC archive. Designed particularly for enhancing the readability of PMC journal articles on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers.

Like a printed paper, PubReader breaks an article into multiple columns and pages to improve readability and navigation. PubReader can expand a page to whatever fits on your screen — with multiple columns on a desktop monitor or a single column page on a small tablet. It will even switch to two columns if you rotate the tablet to a landscape view. When you adjust the font size or change the size of the browser window, page boundaries and columns are adjusted automatically.

PubReader can be activated by selecting the PubReader Format in the right-hand column of individual PMC articles. Additional information can be found in the NLM Technical Bulletin and the PubReader About webpage.