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.”
Archive for the ‘Search Tools’ Category
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.
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.
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.
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 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:
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.
Currently, the MeSH Browser allows for searches of MeSH terms, text-word searches of the Annotation and Scope Note, and searches of various fields for chemicals. These searches assume that users are familiar with MeSH terms and using the MeSH Browser. Wouldn’t it be great if you could find MeSH terms directly from your text such as an abstract or grant summary? MeSH on Demand has been developed in close collaboration among MeSH Section, NLM Index Section, and the Lister Hill National Center for Biomedical Communications to address this need.
Use MeSH on Demand to find MeSH terms relevant to your text up to 10,000 characters. One of the strengths of MeSH on Demand is its ease of use without any prior knowledge of the MeSH vocabulary and without any downloads. From the MeSH on Demand homepage, add your text, such as an abstract, into the box labeled “Text to be Processed.” Then, click the “Find MeSH Terms” button. Please read the Helpful Hints section of the homepage to improve your results.
For example, the abstract below contains the phrase “treatment-resistant depression.” The relevant MeSH Heading found for that concept is Depressive Disorder, Treatment-Resistant. MeSH on Demand finds MeSH Headings, Publication Types, and Supplementary Concepts, but not Qualifiers (Subheadings). Select the green question mark button next to the MeSH term or the MeSH term itself to open a new window with the MeSH Browser for that MeSH term.
Please note the Disclaimer that these MeSH terms are machine generated by MTI and do not reflect any human review. While the results will be different from human-generated indexing, MeSH on Demand does find relevant MeSH terms that can help jump-start finding MeSH terms in your search area. NLM welcomes your feedback on MeSH on Demand and MTI. Please send comments and questions to NLM Customer Service with “MeSH on Demand” in the subject box. NLM also looks forward to seeing your ideas for other helpful tools to utilize the MeSH vocabulary and NLM resources more easily. Please contact NLM at firstname.lastname@example.org.
In the summer of 1946, an Oklahoma newspaper editor sent a young reporter to complete a story on a state psychiatric hospital, where he found neglected, half-naked inmates, crowded together in filthy, dilapidated buildings, and fed on rotten food. He soon went back, taking along a photographer, and then he went to visit Oklahoma’s other state mental hospitals. His blistering series of newspaper articles about the institutions launched a grassroots reform movement: less than a year later, the state legislature voted huge budget increases for state hospitals, restructured the state hospital administration, and re-wrote the state’s commitment laws.
The young journalist was Mike Gorman (1913–1989). His work in Oklahoma earned him a Lasker Award in 1948, and changed the course of his career. Several decades later he would be called “the country’s greatest modern missionary for mental health.” Mike Gorman’s papers are now online at the National Library of Medicine’s Profiles in Science Web site, an NLM digital project that provides online access to the archival collections of more than 30 Nobel Laureates and other leading innovators in scientific and medical fields. The presentation features correspondence, photographs, speeches and addresses given by Gorman, speeches he wrote for members of Congress and several U.S. Presidents, along with published articles and reports from the Gorman collection. Visitors to the site can view his first series of articles for the Daily Oklahoman, drafts of speeches Gorman wrote for Presidents Truman and Kennedy, and the public service announcements issued by the Citizens for the Treatment of High Blood Pressure.
Gorman’s Oklahoma experience taught him that newspaper exposés alone would not produce substantive changes. Public attention to social problems faded quickly, and entrenched social and political practices did not change without constant agitating from outside. Gorman would spend the rest of his life providing that agitation: gathering the facts about mental illness and other diseases; speaking to governors, legislators, professional groups, and the public; testifying to Congressional appropriations committees; and writing books and articles.
Gorman came to Washington, D.C. in 1951 to be a member of President Truman’s Commission on the Health Needs of the Nation, and in 1953 became executive director of the National Committee Against Mental Illness, a lobbying and advocacy organization founded by philanthropist and health care activist Mary Lasker. In that post, he became perhaps America’s best known lobbyist and publicist in the crusade for psychiatric hospital reform and the community mental health center movement. Gorman played a key role in shaping many of the social programs of the Kennedy and Johnson administrations, including the Mental Retardation Facilities and Community Mental Health Centers Construction Act of 1963. During the 1970s and 1980s he also directed two other advocacy groups, Citizens for the Treatment of High Blood Pressure, which helped coordinate a highly successful national hypertension education and screening program, and the National Initiative for Glaucoma Control.
New on REMM, April, 2014:
- Key changes are noted below.
- Many more updates and changes appear throughout REMM.
- Managing Acute Radiation Syndrome (ARS): Interactive tool: completely redesigned, with clinical assessments, treatment suggestions, suggestion for referral venues
- Top 10 Items for Radiation Emergencies: new page
- How to Perform a Radiation Survey
- Target Levels for Decontamination of People
- Biodosimetry Bibliography: new page, improved navigation, many new references
- Radiation Units and Conversions: new interactive tools for unit conversions
- Understanding Radiation: new videos incorporated and new sections
- Radiological Dispersal Device: new guidance about safety and response perimeters
- Training and Education: new offerings from several US agencies
- Multimedia Library: new elements in many sections
- Emergency Contacts: updated for many US government agencies
- REMM bibliography: many new entries
New on Mobile REMM, April 2014, App Version 2.0.1:
- App has been completely redesigned for easier use and faster navigation
- Dose Estimator: faster data entry for vomiting and lymphocyte depletion kinetics tools
- New tools from REMM now available on Mobile REMM
- Scarce Resources for Interactive Triage Tool for Use after IND Detonation
- SALT triage system for radiation emergencies
- Updated emergency contact information
- Mobile platform compatibility updated
- iPhone and Androids compatibility remains up to date.
- Newer BlackBerry operating system, BlackBerry 10, is now supported; but older ones (BlackBerry 7 OS and earlier) are not.
The REMM Team strongly suggests updating any versions of REMM previously downloaded to computers, USB drives, or mobile devices.