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Archive for the ‘Search Tools’ Category

New NLM Subject Guide for Genetic/Genomics Information!

The National Library of Medicine has released a new Genetics/Genomics Information subject guide as the latest update in its subject guide series. These guides, based on most frequently asked questions, are starting points for health professionals, researchers, librarians, students, and others. The guide is designed to help you find introductory materials relating to Genetics and Genomics, such as basic features of the human genome and its organization into chromosomes. It is not comprehensive in scope or coverage, particularly for specific genetic conditions or new and improved technologies. The guide provides links to bioinformatics gateways for more genetic information, and points primarily to free electronic items, or records for materials that may be available via your library. The guide has a section of links for professional education, and a section suggesting how to use PubMed to search for citations to published research journal literature for more information about a particular disease or condition. Other published guides in the NLM series include:

NLM will develop more subject guides as needed. NLM welcomes comments, questions, and suggestions about all of the guides.

NLM Resource Update: ChemIDplus Drawing Feature

The National Library of Medicine’s (NLM) ChemIDplus resource is a dictionary of over 400,000 chemicals (names, synonyms, and structures). It includes links to NLM and to other databases and resources, including ones to federal, state and international agencies. You can draw a chemical structure and search for similar substances using the ChemIDplus Advanced search interface. This feature also performs similarity and substructure searches. A four-minute tutorial is available for using the drawing feature of ChemIDplus. The ChemIDplus Lite interface is designed for simple searching on name or registry number.

National Library of Medicine Resource Update: Drug Information Portal

The National Library of Medicine (NLM) Drug Information Portal is a free web resource that provides an informative, user–friendly gateway to current drug information for over 53,000 substances. The Portal links to sources from the NLM, the National Institutes of Health (NIH), and other government agencies such as the U.S. FDA. Current information regarding consumer health, clinical trials, AIDS–related drug information, MeSH pharmacological actions, PubMed biomedical literature, and physical properties and structure is easily retrieved by searching a drug name. A varied selection of focused topics in medicine and drug–related information is also available from displayed subject headings.

The Drug Portal retrieves by the generic or trade name of a drug or its category of usage. Records provide a description of how the drug is used, its chemical structure and nomenclature, and include up to 20 Resource Locators which link to more information in other selected resources. Recent additions to these Locators include clinical experience with drugs in PubMed Health, substances reviewed in NLM’s LiverTox, information from the Dietary Supplement Label Database, and drug images in the Pillbox database. Data in the Drug Information Portal is updated daily, and is also available on mobile devices. More information is available from the Drug Information Portal Fact Sheet.

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.”

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.

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%.

Upcoming NCBI Discovery Workshops at UC Davis and UC Berkeley!

NCBI Discovery Workshops, consisting of four 2.5-hour hands-on training sessions emphasizing NCBI resources such as BLAST and Nucleotide, will be presented by NCBI staff at the University of California, Davis, on September 15-16, and at the University of California, Berkeley, on September 17-18:

  • Session 1: Navigating NCBI Molecular Data Through the Integrated Entrez System. 9 am – 11:30 am, 9/15 (UC Davis) & 9/17 (UC Berkeley)
  • Session 2: NCBI Genomes, Assemblies and Annotation Products: Microbes to Human. 1 pm – 3:30 pm, 9/15 (UC Davis) & 9/17 (UC Berkeley)
  • Session 3: Advanced NCBI BLAST. 9 am – 11:30 am, 9/16 (UC Davis) & 9/18 (UC Berkeley)
  • Session 4: Gene Expression Resources at NCBI. 1 pm – 3:30 pm, 9/16 (UC Davis) & 9/18 (UC Berkeley)

​For more information or to register:

For Questions:

NLM Mourns William G. Harless, PhD, Creator of the First Natural Language Computer Patient Simulation Model

William G. Harless, President and CEO of Interactive Drama Inc. and former National Library of Medicine employee and contractor, passed away this past May. Dr. Harless’ contributions to the NLM were many, including the creation of the first voice-activated interactive video patient simulation model in the mid-1980s. As Director of NLM’s Technological Innovations in Medical Education (TIME) Project, he received the 1986 NLM Regents Award for Scholarship or Technical Achievement and an award in the category of Best Educational Achievement at the University of Nebraska, both for the development of his model which combined voice recognition, interactive video, and computer technologies.

Bill Harless held a PhD degree in psychology and learning theory. He also had held faculty positions at five major universities and the Union for Experimenting Colleges and Universities, where accredited doctorate degrees are awarded from a multidisciplinary, experientially based curriculum. He developed the first natural language computer patient simulation model at the University of Illinois School of Medicine in Chicago in the early 1960s. Dr. Harless published over 50 articles on natural language interactive simulation as a learning strategy and was a recognized expert in the field. In 1991, he was awarded a patent for his voice-controlled video simulation model. He was awarded a second patent in 1996 for his dynamic prompting system. In 2005, a third patent was awarded on a method of distributing his model over a computer network, and in 2010 he was awarded a patent for his method for analyzing natural language text to yield a meaningful response to a free-speech inquiry.