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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%.

NCBI RefSeq Release 67 Available on FTP

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.

National Library of Medicine Resource Update: Environmental Health Student Portal

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.

Household Products Database Update

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.

September 2014 Issue of NIH News in Health is Now Available!

Illustration of a man declining a beer that’s being offered by his friend at a picnic.Check out the September issue of NIH News in Health, the monthly newsletter bringing you practical health news and tips based on the latest NIH research. In this issue:

  • Drinking to Excess: Recognize and Treat Alcohol Problems
    Some people enjoy an occasional glass of wine with dinner. Others might grab a beer while watching a football game. Most people drink alcohol moderately, within their limits. Others overdo it occasionally. But some people find they can’t control their drinking. How do you know when drinking is becoming a problem? And what can you do if it is?
  • Focusing on ADHD: Attention Deficit Hyperactivity Disorder
    Most children get restless, rowdy, or distracted at times. That’s all part of being a kid. But some kids have such trouble paying attention, staying focused, and finishing tasks that it interferes with their schoolwork, home life, and friendships. These difficulties might be signs of a developmental disorder called attention deficit hyperactivity disorder, or ADHD.
  • Genetic Sites Tied to Schizophrenia
    Researchers linked more than 100 genetic regions to schizophrenia, including 83 that were previously unrecognized. The findings may lead to new strategies for treating this serious brain disorder.
  • Featured Website: Gut Check
    This site offers easy-to-read information about screening for colorectal cancer, the 2nd leading cause of cancer-related deaths nationwide. Screening may detect growths called polyps that can be removed before they develop into cancer. It can also detect cancer early, when treatment may be most effective. Videos and other resources help you decide which screening test is right for you.

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. Visit the NIH News in Health Facebook page to suggest topics you’d like to see covered, or share what you find helpful about the newsletter!

American Evaluation Association’s Potent Presentation Information

The American Evaluation Association (AEA) sponsors a Potent Presentations Initiative (p2i) that has a stated purpose of helping evaluators improve their presentation skills, both within a conference setting and as part of individual practice. P2i challenges evaluators to hone in on three concepts: Their message, their design, and their delivery.

There are a wealth of handouts available as PDF files, Word documents, and Powerpoint presentations available from the p2i tools website that sometimes include AEA conference specifications in addition to many great messaging, designing and delivery principles. For an example of each principle be sure to check out the Presentation Preparation Checklist, How to Design a Research Poster, and the Delivery Glue Handout.

NLM Announces New VSAC Tutorial

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.

Haz-Map Update

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.

University of Maryland, Baltimore, Health Sciences and Human Services Library, Announces Release of Student Health Advocates Redefining Empowerment Curriculum

The Health Sciences and Human Services Library, University of Maryland, Baltimore, has announced the release of the Student Health Advocates Redefining Empowerment (SHARE) Curriculum, developed as the result of a three-year Health Information Resource Grant to Reduce Health Disparities (G08LM0011079) from the National Library of Medicine. The grant aimed to empower high school students as community health advocates, improve health in Baltimore neighborhoods, and develop a replicable student health advocacy program. The entire curriculum consists of six modules. Each module can be used independently as well. The modules are:

  1. Overview of Health Disparities
  2. Quality Health Information
  3. Taking Charge of Your Health
  4. Smart Food Choices
  5. Crafting and Delivering the Message
  6. Promoting Health and Wellness in Your Community

These modules were developed after working with two cohorts of students from Vivien T. Thomas Medical Arts Academy in Baltimore. In addition to detailed lesson plans, each class has assignments and handouts and is aligned with national standards. Supplemental activities are also provided. In order to build a community around the curriculum, a blog is available to share ideas and suggestions and discuss the curriculum. For more information, please contact Project SHARE.