Archive for the ‘NLM Resources’ Category
September 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.
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%.
The full RefSeq release 67 is now available on the NCBI FTP site with over 61 million records describing 45,166,402 proteins; 8,163,775 RNAs; and sequences from 41,913 different NCBI TaxIDs. More details about the RefSeq release 67 are included in the release statistics and release notes. In addition, reports indicating the accessions included in the release and the files installed are available.
To subscribe to the ncbi-announce mailing list, visit http://www.ncbi.nlm.nih.gov/mailman/listinfo/ncbi-announce.
The National Library of Medicine Environmental Health Student Portal has added Mercury and Your Health, an animation about the uses of mercury and how exposure can impact human health. The 16-minute video introduces children to mercury and its basic properties, discusses mercury exposure routes, outlines health impacts of mercury, describes mercury containing products, discusses mercury contamination in the environment, outlines the proper disposal of mercury containing products, discusses bioaccumulation and mercury contamination of fish, and describes additional sources that children could use to find credible health information on mercury.
The Environmental Health Student Portal connects middle school students and science teachers with free, reliable, and engaging environmental health education resources. The Student Portal offers a diverse array of engaging educational materials such as videos, games and activities, lesson plans, experiments and projects, fun challenges, as well as additional resources for further reading. Mercury is one of the chemicals covered in this resource.
The National Library of Medicine (NLM) Household Products Database (HPD) now contains over 14,000 products. The latest update includes a new product category “commercial/institutional.” Product manufacturers of the more than 300 products in this category use various descriptions, including professional grade, professional use, hospital grade, and more. Users can locate products using the new “commercial/institutional” link under “Browse by Category” on the HPD homepage or by entering the category/description terms (e.g. commercial, institutional, professional, hospital) as a Quick Search.
The Household Products Database links over 14,000 consumer brands to health effects from Material Safety Data Sheets (MSDS) provided by manufacturers, and allows scientists and consumers to research products based on chemical ingredients. The database is designed to help answer the following typical questions:
- What are the chemical ingredients and their percentage in specific brands?
- Which products contain specific chemical ingredients?
- Who manufactures a specific brand? How do I contact this manufacturer?
- What are the acute and chronic effects of chemical ingredients in a specific brand?
- What other information is available about chemicals in the toxicology-related databases of the National Library of Medicine?
Information in the Household Products Database comes from a variety of publicly available sources, including brand-specific labels and Material Safety Data Sheets when available from manufacturers and manufacturers’ web sites.
The National Library of Medicine has announced a new Value Set Authority Center (VSAC) tutorial, Updating Value Sets. The nine-minute tutorial is available as a link from the UMLS Video Learning Resources page, the NLM Distance Education Resources page, and is posted at the NLM YouTube site. Additional tutorials designed to assist users with VSAC and VSAC authoring tools are in development. NLM encourages comments about the tutorial and suggestions for further topics, which may be sent to NLM Customer Service.
The NLM Value Set Authority Center is developed by NLM in collaboration with Office of the National Coordinator for Health IT (ONC) and the Centers for Medicare & Medicaid Services (CMS) to provide searchable access to value sets that are used to define concepts used in clinical quality measures, and to support effective health information exchange and many other biomedical informatics applications and programs. Since October 2013, VSAC also offers the Authoring Tool that allows users to author value sets.
The National Library of Medicine (NLM) has updated Haz-Map with 497 new agents. It now covers 10,133 biological and chemical agents. Haz-Map is an occupational health database designed for health and safety professionals and for consumers seeking information about the health effects of exposure to chemicals and biologicals at work. Haz-Map links jobs and hazardous tasks with occupational diseases and their symptoms. More information is available from the Haz-Map Fact Sheet.
The National Library of Medicine (NLM) and the Association of Health Care Journalists (AHCJ) are pleased to announce the 2014 AHCJ-NLM Fellows. This year’s class features eight reporters and editors representing diverse media backgrounds and interests. The program, now in its sixth year, brings journalists selected by AHCJ to NLM for four days of training in use of NLM’s health information resources, such as PubMed, PubMed Health, Genetics Home Reference, TOXMAP, ClinicalTrials.gov, and MedlinePlus. The Fellows also receive briefings about health care issues, such as the adoption of electronic health records by patients and health care providers, as well as consumer health resources provided by the National Cancer Institute. New in 2014, the Patient-Centered Outcomes Research Institute (PCORI) will update the AHCJ-NLM Fellows about innovative health care issues, such as comparative effectiveness research.
The 2014 AHCJ-NLM Fellows are:
- Karen Bouffard, health care writer, The Detroit News. Bouffard was a 2013 National Health Journalism Fellow with the University of Southern California’s Annenberg School of Journalism.
- Matthew Glasser, health and medical producer, NBC Southern California. Glasser is an Emmy Award-winning journalist and was the co-creator and executive producer of NurseTV and Healthcare Heroes.
- Sarah Karlin, senior writer, The Pink Sheet and The Pink Sheet DAILY. Karlin formerly was the FDANews’ congressional and generic drugs editor.
- Kimberly Leonard, health reporter and producer, U.S. News & World Report. Leonard was a health reporter with the Center for Public Integrity prior to joining U.S. News & World Report.
- Cheryl Platzman Weinstock, freelance health/science writer, who specializes in women’s health issues. Weinstock’s work frequently appears in the New York Times, Women’s Day, and the Oprah Magazine. She contributed to the New York Times’ Pulitzer Prize-winning coverage of 9/11.
- Marie Powers, staff writer, BioWorld Today. Powers was part of the BioWorld Today team, which received the Best Daily Publication award in 2013 and 2014 from the Specialized Information Publishers Association.
- Cindy Sharp, health and medical reporter, Associated Press Television and Online Video. Sharp previously worked for MSNBC and Tribune Broadcasting.
- J.K. Wall, health care reporter, Indianapolis Business Journal, and The Dose, a blog on health care finance. Wall worked as a business reporter at The Indianapolis Star before joining the Indianapolis Business Journal.
Due to recent software updates on nnlm.gov, Internet Explorer 8 is no longer supported. Some read-only sections of nnlm.gov will continue to be available via IE8. However, anyone using IE8 will probably not be able to submit assignments in online courses utilizing the NN/LM Moodle framework, and may not even be able to access and log into Moodle courses. Other nnlm.gov services that require data to be posted to the server are also likely to fail. In addition, DOCLINE will not support IE8 after the end of 2014. Please visit the NN/LM System Requirements page to see a complete list of supported browsers. For best usability, NLM recommends that libraries should begin talking to their local IT departments about upgrading their browsers to at least Internet Explorer 10.
Starting January 12, 2016, Microsoft will drop support, including security updates, for older Internet Explorer browser versions. Only the most recent version of IE for a supported operating system will receive technical support and security updates. Microsoft’s Stay up-to-date with Internet Explorer blog page provides a good explanation of why IE users should upgrade to the most current version.
The National Library of Medicine Disaster Information Management Research Center (DIMRC) has announced a new resource directed at the needs of children in disasters and emergencies, which present unique planning challenges for health officials, responders, and providers. Multiple U.S. Department of Health and Human Services agencies and funded organizations collaborated to develop this comprehensive online guide to serve as a central source for pediatric-related disaster and emergency health information, which brings into one place professional-level materials, documents, Web sites, and articles distinctly about children from authoritative sources; including government, private, non-profit and international organizations and agencies.
To learn about this robust new resource, the collaboration behind it, and how it can make information searching more efficient, attend the next Disaster Information Specialist Webinar on Thursday, September 11, at 1:00 – 2:00 PM PDT. Four featured presenters will address the topic Not Just Small Adults: Health Resources on Children in Disasters and Emergencies.