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Archive for the ‘NLM Resources’ Category

NCBI HIV-1 Website Updated

The HIV-1, human interaction database has been updated and is now on an improved page. The improved interface includes help documentation and supports structured queries against Gene, as well as browsing, filtering and downloading the protein and replication interaction data sets. The most recent data release (June 2014) includes 12,785 HIV-1, human protein-protein interactions for 3,142 human genes and 1,316 replication interactions for 1,250 human genes. The HIV-1, human interactions project, collates published reports of two types of interactions – HIV-1, human protein interactions, and human gene knock-downs that affect virus replication which are reported as “replication interactions.”

National Library of Medicine Joins The Commons on Flickr!

Nurse wearing a uniform

The National Library of Medicine has announced that it is now a participating institution of the Commons on Flickr. The Commons on Flickr was launched in 2008 as a pilot project in partnership with the Library of Congress in order to increase access to publicly-held photography collections and to invite the general public to provide information about the collections. The National Library of Medicine now joins a distinguished, international group of nearly one hundred cultural institutions in providing greater access to its collection and inviting public use of and engagement with these images held in the public trust through The Commons on Flickr.

Images from the historical collections of the History of Medicine Division, including public health posters, book illustrations, photographs, fine art work, and ephemera, have always been available through the Images from the History of Medicine database, which includes over 70,000 images illustrating the social and historical aspects of medicine dated from the 15th to the 21st century. Now, they can also be accessed through the Commons on Flickr via a photostream, where visitors can contribute information about the images by adding comments and tags. By adding a new way to see its collections through Flickr NLM hopes to learn more details about its collections, create dialog about its holdings, and share knowledge with the public. The collection of images on Flickr will continue to grow so visitors can check back regularly for new content!

Apply Now to Participate in the “A Librarian’s Guide to NCBI” 2015 Bioinformatics Course!

Health science librarians in the United States are invited to participate in the next offering of the bioinformatics training course, A Librarian’s Guide to NCBI, sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC). The course provides knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Prior knowledge of molecular biology and genetics is not required. Participating in the Librarian’s Guide course will improve your ability to initiate or extend bioinformatics services at your institution. Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo. There is no charge for the classes. Travel and lodging costs for the in-person class are at the expense of the participant.

There are two parts to A Librarian’s Guide to NCBI, listed below. Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2). Part 1: Fundamentals in Bioinformatics and Searching is an online (asynchronous) course, January 12-February 13, 2015, and Part 2 is a 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, MD, March 9-13, 2015. Students successfully completing the Fundamentals course (Part 1) will earn 18 MLA CE credits. Those successfully completing the 5-day in-person class (Part 2) will earn 36 additional MLA CE credits.

Applications are open to health science librarians in the United States. Applicants will be accepted both from libraries currently providing bioinformatics services as well as from those desiring to implement services. Enrollment is limited to 25 participants. The application deadline is November 17, 2014, and acceptance notification will be on or about December 15, 2014. Visit the A Librarian’s Guide to NCBI course page for additional information.

NLM’s DailyMed Web Site Redesigned With New Features and Improved Usability!

DailyMed web site

On September 18 the National Library of Medicine launched a newly redesigned DailyMed web site. DailyMed provides trustworthy information about marketed drugs in the United States, and is the official provider of Food and Drug Administration (FDA) label information. The web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling found in medication package inserts. Since 2005, when DailyMed was first launched, its usage has increased significantly.

Based on the needs and feedback received from the public, NLM began redesigning the DailyMed web site in 2013. The new site is a responsive design which is now easily accessible on all types of devices, adjusting and optimizing automatically for smart phones to large screen desktop displays. Based on the size of the screen, content will relocate, images will resize, the layout will change, and even the navigation will adjust, to deliver an exceptional user experience no matter what device is being used to view the site.

In addition to responsive design, the following new features are available:

  • Enhanced Search Results to include displaying of NDC Codes, Pill Images, and Package Label Images on the search result page. The information will help users easily identify the drug label. The thumbnail images of drugs, magnification feature, accordions, etc. provide a more user friendly experience.
  • Improved user interface by displaying an accordion-style data presentation, so users don’t have to scroll through the entire label.
  • Simplified page navigation and added definitions & tooltips for industry-specific phrases.
  • A dedicated News page and Article & Presentation Page for users to easily access DailyMed and NLM/FDA drug-related news.

TOXMAP and Native American Populations

Although the National Library of Medicine’s TOXMAP resource is not specifically designed for any one particular group, the TRI and Superfund Programs can be of interest to specific populations such as Native Americans, by helping to find sources of chemical releases and contamination in locations of interest to them.

In the beta version of TOXMAP, click on the “Zoom to Location” icon, enter “reservation” or “rancheria” into the “Address or Place” search box, and then click “Zoom to.” In TOXMAP classic, click on “Zoom to a Place,” enter “reservation” or “rancheria” into the “other place name” search box, and then click “Submit.” You can also overlay US Census data by race: “American Indian and Alaskan Native” (1990) or “One Race: American Indian and Alaska Native” and “Two or More Races Including American Indian and Alaska Native” (2000). For more information, visit the TOXMAP and Native American Populations webpage.

MeSH Browser Now Updated More Frequently

Beginning on September 4, 2014, the MeSH Browser is being updated each business day. The MeSH XML and ASCII format files for Supplementary Concept Records (SCRs) will be available on this same Monday through Friday schedule starting the week of September 15, 2014. Prior to this change, the MeSH Browser and MeSH XML and ASCII files for SCRs were updated and made available once per week.

This new update schedule releases new and edited SCRs, mostly for chemicals and drugs, in a more timely way for use by both indexers and searchers. Descriptors and qualifiers are changed only on an annual basis.

2015 Medical Subject Headings (MeSH) Now Available!

MeSH Vocabulary Changes for 2015 is now available! Lists of new descriptors, changed descriptors, deleted descriptors, and new descriptors by tree subcategory are available on the NLM website. For more information about MeSH use and structure, as well as recent updates and availability of data, visit the updated Introduction to MeSH – 2015 webpage.

Note: The default year in the MeSH Browser remains 2014 MeSH for now, but the alternate link provides access to 2015 MeSH. The MeSH Section will continue to provide access via the MeSH Browser for two years of the vocabulary; the current year and an alternate year. Sometime in November or December, the default year will change to 2015 MeSH and the alternate link will provide access to the 2014 MeSH.

Population Health Added to Special Queries

The NLM PubMed Special Queries page includes a link to a new MEDLINE/PubMed Population Health search. A definition for population health is “the health outcomes of a group of individuals, including the distribution of such outcomes within the group. The field of population health includes health outcomes, patterns of health determinants, and policies and interventions that link these to differences between groups of people.” 1

The Population Health Special Query is a PubMed search of relevant MeSH headings and text words combined strategically to retrieve PubMed citations. MeSH headings were selected with the assistance of members of the Institute of Medicine Board on Population Health and Public Health.

1 Kindig D, Stoddart G. What is population health? Am J Public Health. 2003 Mar;93(3):380-3. PubMed PMID: 12604476.

PubChem Turns Ten!

PubChem logoSeptember 16, 2004 is a special day in the history of PubChem. It marks the beginning of PubChem as an on-line resource! Now fast forward ten years. PubChem provides information daily to many tens of thousands of users. Despite the passage of time, PubChem’s primary mission remains the same: providing comprehensive information on the biological activities of chemical substances.

Providing chemical information to researchers in the biomedical science community is a key part of PubChem’s purpose. Over the years, PubChem introduced and incrementally developed several interfaces, each with its own distinct purpose and set of use cases. Primary to these is the Entrez search interface, where PubChem is organized as three distinct databases: Substance, Compound, and BioAssay. Substance provides substance descriptions (accession number: SID), Compound provides the unique small-molecule chemical content of Substance (accession number: CID), and BioAssay provides biological experiment results for substances (accession number: AID). Each of these databases has an advanced search interface and contain numerous indexes and filters, which can be combined to construct elaborate queries. Additional interfaces exist to search and analyze information in PubChem, including the ability to analyze bioactivity information, download chemical and assay data, search by chemical structure or protein sequence, navigate using integrated classifications, visualize chemical 3-D information, and more.

PubChem continues to evolve the way it provides on-line content. External search engines (like Google, Bing, and others) are now a key way in which researchers locate data. In addition, programmatic interfaces now account for a significant portion of PubChem’s overall usage (+50%). Key programmatic interfaces to PubChem include Entrez Utilities and PUG/REST.

NLM Medical Text Indexer Plays Role in International Challenge

For the second year in a row, the National Library of Medicine (NLM) Medical Text Indexer was used as one of the baselines for the international BioASQ Challenge. The Medical Text Indexer (MTI) combines the expertise of indexers working at NLM with natural language processing technology to curate the biomedical literature with Medical Subject Headings (MeSH®) more efficiently and consistently. BioASQ is a series of challenges on biomedical semantic indexing and question answering with the aim of advancing the state of the art accessibility for researchers and clinicians to biomedical text. The MTI indexing results are providing one of the baselines used in the “large-scale online biomedical semantic indexing” part of the challenge, which is designed to parallel the human indexing currently being done at NLM. The NLM Medical Text Indexer is a product of the close collaboration between the NLM Index Section and the Lister Hill National Center for Biomedical Communications, an Intramural Research Division of the National Library of Medicine.

The BioASQ Challenge evaluation of approaches to biomedical semantic indexing provided a continuous assessment of the indexing suggestions that are automatically generated by the MTI system used in support of the MEDLINE® indexing process at the NLM. The benefits of participating in this community-wide evaluation for MTI were two-fold: firstly, MTI was rigorously compared to systems developed by a world-wide community of researchers and industrial teams all performing the same task; and secondly, the free exchange of the methods and ideas allowed the MTI team to incorporate the best practices explored by the participating teams. Incorporating some of these approaches into the MTI workflow in 2013-2014 improved the accuracy of MTI indexing suggestions by 4.5%.