Archive for the ‘Events’ 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 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.
With eye-catching models, interactive displays and engaging elements, the Genome: Unlocking Life’s Code exhibition is going on tour after having completed a 14-month engagement at the Smithsonian’s National Museum of Natural History in Washington, D.C. On Sept. 1, 2014, the contemporary, high-impact exhibition, a collaboration between the museum and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, starts engagements at museums and science centers throughout North America.
The exhibit opened a decade after the completion of the Human Genome Project and 60 years after the discovery of the double-helical structure of DNA by Drs. James Watson and Francis Crick. Dr. Watson toured the exhibition in July, one of its estimated 3 million visitors since the opening. Museum designers and education programming experts took almost two years to conceptualize and build the 4,400 square-foot exhibition. By illustrating and explaining genomics, the exhibition offers visitors a new perspective from which to view oneself, as an individual, a member of a family, a representative of a species, and part of the diversity of life on Earth.
The initial stops for the traveling exhibition are
- Reuben H. Fleet Science Center, San Diego, Sept. 24, 2014 – Jan. 4, 2015
- The Tech Museum of Innovation, San Jose, California, Jan. 22 – April 27, 2015
- St. Louis Science Center, May 15 – Sept. 10, 2015
- Oregon Museum of Science and Industry, Portland, Oct. 2, 2015 – Jan. 3, 2016
- Discovery World, Milwaukee, Winter 2016
- Exploration Place, Wichita, Kansas, Sept. 30, 2016 – Jan. 1, 2017
- Peoria (Illinois) Riverfront Museum, Jan. 28 – May 29, 2017
- Science North, Sudbury, Ontario, Sept. 30, 2017 – Jan. 1, 2018
The exhibition is accompanied by a website with educational resources that can be used to teach students about DNA, and educational videos for learners of all ages. Videos of many of the public educational programs, including lectures, symposia, discussion panels and informal gatherings, held in conjunction with the exhibition, are also available.
The National Library of Medicine is sponsoring a free public meeting, SPL/DailyMed Jamboree 2014 Workshop – Practical use of DailyMed and RxNorm Drug Data. Speakers from the Federal government (NLM and IHS), industry (Bayer, Wolters-Kluwer), academia, and non-profit sectors will speak on their experience with Structured Product Label (SPL) drug data as well as RxNorm. The emphasis is on practical and novel ways to use this free data, which is produced cooperatively by NLM and FDA. Topics include SPLs and clinical decision support, extracting indication and drug interaction data from SPLs using natural language processing, e-prescribing experience within the Indian Health Service, Linked Data and SPLs, the use of RxNorm by the United States Pharmacopeia (USP), and more. The proceedings will be webcast and archived.
When: September 18, 9:30 AM to 4:15 PM (ET)
Where: Lister Hill Auditorium, National Library of Medicine, 8600 Rockville Pike, NIH Building 38A, 1st Floor, Bethesda, Maryland 20894
Visit the SPL/DailyMed Jamboree 2014 Workshop webpage to register for the in-person meeting and to view the agenda and speakers. The link to the webcast will be added when available.
The National Center for Advancing Translational Sciences (NCATS) has announced the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition.
The goal of the challenge is to crowdsource data analysis by independent researchers in order to develop computational models that can better predict chemical toxicity. It is designed to improve current toxicity assessment methods, which are often slow and costly. The model submission deadline is November 14, 2014. NCATS will showcase the winning models in January 2015. Registration for the challenge and more information is available on the web site.
Tox21 scientists are currently testing a library of more than 10,000 chemical compounds in NCATS’s high-throughput robotic screening system. To date, the team has produced nearly 50 million data points from screening the chemical library against cell-based assays. Data generated from twelve of these assays form the basis of the 2014 challenge. For more information on the Tox21 Modeling Challenge and Tox21 Program, contact Anna Rossoshek.
Disaster Research Response Workshop: Enabling Public Health Research During Disasters will be held June 12-13, 2014, at the National Institutes of Health (NIH) campus in Bethesda, MD. There is no registration cost. This workshop will examine strategies and partnerships for methodologically and ethically sound public health and medical research during future emergencies. Discussions will include issues with obtaining informed consent, obtaining approval from Institutional Review Boards, coordinating research efforts with emergency response, and ensuring timely collection of data. The workshop is a collaboration of the NIH Disaster Research Response Project, the IOM Forum on Medical and Public Health Preparedness for Catastrophic Events, the HHS Office of the Assistant Secretary for Preparedness and Response, and the Centers for Disease Control and Prevention.
The NIH Disaster Research Response Project is a pilot project led by the National Institute of Environmental Health Sciences (NIEHS) and supported by the National Library of Medicine (NLM), aimed at developing ready-to-go research data collection tools and a network of trained research responders. The project’s goal is to make it as easy as possible for researchers to begin collecting health and other data following a major disaster. The focus is on data collection tools and protocols, the creation of networks of health experts also trained as research responders, and integration of the effort into federal response plans for future disasters. Although initially focused on environmental health issues, the hope is this project will be a model for timely collection of data supporting a range of medical and public health research.
As part of this project, NIEHS recently held a tabletop exercise in Long Beach, CA, to test how a “research response” might work and what would be expected of researchers choosing to be trained research responders, i.e. first on the scene to begin collecting data once it is safe and reasonable to do so. The article “Tsunami exercise helps prepare research community for disaster response” describes the exercise and there is also a video. The “Disaster Lit” section of the Resource Guide for Disaster Medicine and Public Health (from NLM) now includes records for research tools, such as online surveys and interview scripts, to aid researchers in quickly selecting appropriate measures.
The National Library of Medicine has announced that Georgia Regents University (GRU) will serve as the host organization for the NLM-sponsored biomedical informatics course. The NLM Biomedical Informatics Course, now entering its 22nd year, offers participants a week-long immersive experience in biomedical informatics taught by experts in the field. The course was previously held at the Marine Biological Laboratory (MBL) in Woods Hole, MA, with Cathy Norton, MLS, as the MBL principal investigator. NLM plans to take the skills shaped over the past two decades at MBL to its new colleagues at GRU. The first course organized at Georgia Regents University will be held September 14-20, 2014, followed by an additional session April 12-18, 2015. The course will be held at a conference center at the Brasstown Resort in Young Harris, GA, at no cost to participants.
Application to the course is open to anyone, but space is limited. Preference will be given to American applicants who demonstrate, through a brief application letter, that they have the significant need for an understanding of the informatics solutions that are available to address their biomedical research, practice and education challenges and that, through their official position, they are significant “change agents” who can influence the adoption of best practices in their own environment and expand the influence of the course to others through teaching or by example. The application deadline is July 7.
The course, co-directed by James J. Cimino, MD, Chief, Laboratory for Informatics Development at the National Library of Medicine and the NIH Clinical Center, and NLM Director Donald Lindberg, MD, will guide participants through topics including biomedical informatics methods, clinical informatics, big data and imaging, genomics, consumer health informatics, mathematical modeling, and telemedicine and telehealth. The co-principal investigators from GRU are Brenda L. Seago, MLS, MA, PhD, Professor and Director of Libraries, and Kathy J. Davies, MLS, Chair, Research and Education Services, Robert B. Greenblatt, MD Library.
Terrence Sejnowski, PhD, will give the 2014 Joseph Leiter NLM/Medical Library Association (MLA) Lecture, “The BRAIN Initiative: Connecting the Dots,” on Thursday, June 12, 2014, at 10:00 am PDT at the National Library of Medicine. The lecture will be recorded and broadcast live on the Web. Dr. Sejnowski is a pioneer in computational neuroscience and his goal is to understand the principles that link brain to behavior. His laboratory uses both experimental and modeling techniques to study the biophysical properties of synapses and neurons and the population dynamics of large networks of neurons. New computational models and new analytical tools have been developed to understand how the brain represents the world and how new representations are formed through learning algorithms for changing the synaptic strengths of connections between neurons. By studying how the resulting computer simulations can perform operations that resemble the activities of the hippocampus, Dr. Sejnowski hopes to gain new knowledge of how the human brain is capable of learning and storing memories. This knowledge ultimately may provide medical specialists with critical clues to combating Alzheimer’s disease and other disorders that rob people of the critical ability to remember faces, names, places and events.
Dr. Sejnowski is an Investigator with the Howard Hughes Medical Institute and holds the Francis Crick Chair at The Salk Institute for Biological Studies. He is also a Professor of Biology at the University of California, San Diego, where he is co-director of the Institute for Neural Computation and co-director of the Temporal Dynamics of Learning Center. He has published over 400 scientific papers and 12 books, including The Computational Brain, with Patricia Churchland. He is a member of the Institute of Medicine, National Academy of Sciences, and the National Academy of Engineering, one of only 13 living persons to be a member of all 3 national academies. Dr. Sejnowski was instrumental in shaping the BRAIN Initiative that was announced from the White House on April 2, 2013, and serves on the Advisory Committee to the Director of NIH for the BRAIN Initiative.
On May 14, 2014, the Board of Regents of the National Library of Medicine (NLM), the Friends of the NLM, and the Medical Library Association are co-sponsoring a symposium The National Library of Medicine, 1984-2014: Voyaging to the Future, to be held at the Natcher Center on the NIH campus in Bethesda, MD. The purpose of the symposium is to review the influence of NLM’s long range planning over the past 30 years; to reflect on key factors that contributed to successes and setbacks; and to consider opportunities for the future, all as background for the next NLM long range planning effort, to commence in 2015. The symposium is free, but registration is required. A preliminary program is also available. The symposium will be available for remote simultaneous viewing and also archived for future viewing.
In conjunction with this event, NLM is collecting written recollections and images reflecting the Library’s impacts over the last 30 years, as well as ideas for future opportunities and directions. Anyone who has advised and worked with/for NLM and/or benefited from its programs and services is encouraged to submit contributions to a moderated blog. Comments will be accepted throughout the year.