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Archive for 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

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.

NLM Releases New After School Science Club Curriculum for Middle School Students!

The National Library of Medicine has released Discovering the Connection: Your Environment, Your Health, an after school science club curriculum for middle school students. The curriculum combines research on the Tox Town web site with hands-on experiments and communication, including social action activities. The objective is to introduce middle school students to environmental health issues in their everyday life, emphasizing the relevance of science to informed citizenship. The curriculum lessons can also be used to support the existing middle school science curriculum, as well as to reinforce the science/society connection in the social science or language arts classroom.

The curriculum was developed as a collaboration between the NLM, the University of Maryland College of Education, and an inter-disciplinary group of middle school teachers. It is based on National Science Education Standards, and is grounded in a problem-based learning approach that promotes in-depth understanding and critical thinking. The curriculum contains six units; each of which introduces one environmental health topic, and includes three to four 50-60 minute lessons. The units include: 1) Water Quality; 2) Air Quality; 3) Chemicals in Your Home; 4) Food Safety; 5) Runoff, Impervious Surfaces, and Smart Development; and 6) The Great Debate: Bottled Water vs. Tap Water in Our School.

New NLM Resources Announced for Toxicology and Laboratory Safety!

The National Library of Medicine (NLM) Specialized Information Services (SIS) has released Especially for Toxicologists, a guide to NLM resources on environmental health, toxicology, and chemical information for toxicologists. Also announced is a new Enviro-Health Links page, Laboratory Safety, which offers links to information for clinical, academic and school laboratories, including resources for handling chemical, biological and nanotechnology safely. Also included are links to regulations and policy, hazard analysis, MSDS, waste management, and pre-formulated TOXNET and PubMed searches.

Other Enviro-Health Links available include Developing and Using Medicines for Children; Education, Careers, and Outreach in Toxicology and Environmental Health; Lead and Human Health; Mercury and Human Health; and Water Pollution.

New Course Announced for Spring 2013 at the National Library of Medicine: A Librarian’s Guide to NCBI!

A Librarian’s Guide to NCBI comprises a pre-course, “Fundamentals in Bioinformatics and Searching,” offered online (asynchronous), during March 2013, and a five-day, in-person course offered at the National Library of Medicine, April 15-19, 2013. The course provides basic knowledge and skills for librarians interested in helping their clientele use online molecular databases and tools from the NLM’s National Center for Biotechnology Information (NCBI). Topics include using the BLAST sequence similarity search and Entrez text search systems to find relevant data. The course describes the various kinds of molecular data available, and explains how these are generated and used in modern biomedical research. Instructors will be NCBI staff and Diane Rein, Ph.D., from the University at Buffalo. The course will be limited to 18 students. More information and an online application will be available in December, 2012.

DOCLINE Tip of the Month: Do Not Route To List

Tugger the DOCLINE Mascot

The “Do Not Route To” list may be used to prevent requests from routing to individual libraries in Library Groups in a Routing Table, Resource Libraries, or “All Other Libraries;” or to temporarily prevent requests from routing to lenders listed individually in Routing Table cells.

Borrowers can prevent their requests from routing to a specific member of a Library Group in their Routing Table by adding the LIBID to the Do Not Route To list. This can be done for an individual request during the Borrow process, or with a default list of Do Not Route To LIBIDs in the Borrowing Preferences, Serial Routing section of the Institution record.

Note: No more than 20 LIBIDs are allowed on this list. Users wanting to permanently prevent requests from routing to libraries listed individually in their Routing Instructions should remove the LIBIDs from their Routing Table or M/A/N Map rather than using the Do Not Route To feature.

To learn more about how DOCLINE routing works, go to the FAQ DOCLINE page. If you have any questions or need assistance, please don’t hesitate to call us at 1-800-338-7657 or e-mail us at!

New Resource: “Walk Softly And Listen Carefully, Building Research Relationships With Tribal Communities”

The National Congress of American Indians Policy Research Center and Montana State University’s Center for Native Health Partnerships have published a new resource, Walk Softly and Listen Carefully: Building Research Relationships with Tribal Communities. A PDF version of the document is available for downloading. This new resource was developed with insights from those involved with tribal research in Montana and elsewhere.

Increasingly, tribal leaders acknowledge that research is a key tool of tribal sovereignty in providing data and information to guide community planning, cross-community coordination, and program and policy development. Efforts to address longstanding issues, such as health disparities for American Indians and Alaska Natives (AI/AN), have increasingly used partnership research approaches. This document seeks to strengthen these partnerships by providing insight about how culture, sovereignty, and experience matter in research with Native communities.