Archive for the ‘Search Tools’ Category
The NIH Big Data to Knowledge (BD2K) initiative has released a Funding Opportunity Announcement (FOA) to support a U24 resource award for Development of an NIH BD2K Data Discovery Index Coordination Consortium. The purpose of this FOA is to create a consortium to begin development of an NIH Data Discovery Index (DDI) to allow discovery, access, and citation of biomedical data. Letters of intent to apply are due by February 6, 2014, and completed applications are due by March 6, 2014. Budgets are limited to $2,000,000 in direct costs per year but must reflect the actual needs of the proposed project. The maximum project period is three years.
As part of the NIH Big Data to Knowledge (BD2K) initiative, the DDI seeks to fulfill the recommendation from the Data and Informatics Working Group (DIWG) Report to the Advisory Council to the Director to “Promote Data Sharing Through Central and Federated Catalogues.” The awardee in response to this FOA will constitute a DDI Coordination Consortium (DDICC, U24) to conduct outreach, fund small pilot projects, manage communication with stakeholders, constitute and coordinate Task Forces to study relevant questions related to access, discoverability, citation for all biomedical data and assure community engagement in the development, testing, and validation of an NIH DDI. Part of this effort will be to assemble a user interface (website) through which the results of development and testing of models for an NIH DDI may be communicated.
The National Library of Medicine Library has announced the enhancement of In His Own Words: Martin Cummings and the NLM, a digital edition of selected speeches and articles by the man who served as its director from 1964 to 1983. During his tenure, Dr. Cummings guided NLM into the computer age and significantly broadened its mission. Originally launched in February 2012, In His Own Words now includes Dr. Cummings’ annual Congressional appropriations testimonies, along with commentary provided by Dr. Cummings through interviews with Dr. Cheryl Dee of San Jose State University School of Library and Information Science and Florida State University School of Library and Information Services. These enhancements document Dr. Cummings’s opinion that the testimonies and commentaries together offer the most valuable window into NLM’s program development from the 1960s to the 1980s. Reflecting on his testimonies, and the subsequent question and answer sessions defending them, Dr. Cummings’s commentary provides contextual insight on significant turning points in the Library’s history and the political personalities that influenced them.
Martin Marc Cummings, MD (1920–2011), was a medical educator, physician, scientific administrator and medical librarian. Highly respected in all of these disciplines, he made significant contributions to medical informatics and librarianship. As a whole, In His Own Words represents the NLM’s ongoing commitment to collecting materials related to its institutional history and programmatic impact—as part of the NLM Archives—as well as to digitizing these collections and making them widely available for the benefit of researchers, educators, and students.
What do air travel, dandruff, patient harm, and social determinants of health have in common? They are all new 2014 MeSH descriptors!
The Introduction to MeSH 2014 is now available, including information on its use and structure, as well as recent updates and availability of data. MeSH vocabulary changes for 2014 lists include:
Additionally, the entire MeSH vocabulary is available to download in XML and ASCII format.
F. W. “Wilf” Lancaster, professor emeritus at the University of Illinois Graduate School of Library and Information Science and former NLM employee, passed away on Sunday, August 25, 2013, in Urbana, IL. Wilf’s contributions to the NLM in the early days of automated information retrieval have had a lasting impact on our information systems and services. His work as a professor and mentor also benefited the Library, as he led many fine graduate students to pursue careers at the NLM. With his passing, NLM remembers a colleague and friend.
Wilf earned a reputation for greatness in the evaluation of information storage and retrieval systems, based in part on his early experience with a comprehensive evaluation of NLM’s MEDLARS (MEDical Literature Analysis and Retrieval System). The evaluation of the MEDLARS Demand Search Service in 1966 and 1967 was one of the earliest evaluations of a computer-based retrieval system and the first application of recall and precision measures in a large, operational database setting. The use of computers for bibliographic retrieval systems was in its infancy, and many of the extant systems were small or experimental. Planning for the evaluation began in December 1965, when Wilf joined the NLM staff as Information Systems Evaluator. Following completion of the MEDLARS evaluation, he developed NLM training programs in his roles as Deputy Chief of the Bibliographic Services Division and Special Assistant to the Associate Director for Library Operations.
In 1970-1971, Wilf conducted an evaluation of the MEDLARS AIM-TWX system, an innovative experimental service that was the precursor of MEDLINE/PubMed. This was an important study of early online systems and their direct use by end users. Written more than 40 years ago, his report reflects his signature forward-thinking attitude toward system design, as relevant today as then: “We should always look for ways of improving retrieval systems and making them more attractive to potential users. The philosophy that ‘the system is used, therefore it is good’ is a very shallow one. We must not assume that a system having appeal today will always retain this appeal….novelty wears off and system designers cannot afford to rest too long on their laurels. In the past, users have been required to adapt to the information system. In the future systems must be designed that adapt to the users.”
For further information on Wilf’s extraordinary accomplishments and influence, see the Festschrift published in his honor by Library Trends in 2008, “Essays Honoring the Legacy of F. W. Lancaster,” (Volume 56, Issue 4). One of the articles, entitled “Excellence in Evaluation: Early Landmarks at the National Library of Medicine,” focuses on his work at NLM and was used as the source for the above summary of contributions to NLM. His obituary is also available online.
Thelma Golden Charen, former indexer, trainer in the Index Section, and senior technical advisor in the MeSH (Medical Subject Headings) Section of the National Library of Medicine, died July 14, 2013, in Bethesda, MD, one day shy of her 97th birthday. Mrs. Charen first joined the Army Medical Library (precursor of the Armed Forces Medical Library and ultimately, the National Library of Medicine) in 1944 as a pre-cataloger in the Acquisitions Section. She had degrees in Greek and Latin; her natural facility with these languages led to her mastery of medical terminology and to positions as Indexer, training specialist for indexers and searchers, manual developer, and vocabulary specialist. She retired in 1997, ending a renowned 53-year career at NLM.
Mrs. Charen was notably awarded the Marcia C. Noyes Award, highest professional distinction offered by the Medical Library Association in 1985, as an acknowledgement of a career that resulted in lasting, outstanding contributions to health sciences librarianship. At the awards ceremony, Lois Ann Colaianni, then NLM Associate Director for Library Operations, commented, “Her wit and spontaneity in the classroom are as legendary as her logic. She has trained an entire generation of medical indexers working at NLM and around the world. It is not an exaggeration to say that the success of Index Medicus and the MEDLARS system is in great measure the result of Mrs. Charen’s high standards for the quality indexing of the biomedical literature.” At the same ceremony, current NLM Deputy Director Betsy Humphreys recalls that when Mrs. Colaianni asked all those present who had been taught online searching by Mrs. Charen to raise their hands, the vast majority of those in the room did so, including all members of the MLA Board. Mrs. Charen also received two awards given to staff: the NLM Director’s Award in 1983 and the Regents’ Award for Scholarship or Technical Achievement in 1972 “for conceiving, developing and implementing the MEDLARS indexing manual and training program.” In addition to her considerable professional skills, she was known for a seemingly endless supply of dramatic eyeglass frames!
Amongst her other achievements, Mrs. Charen also:
- Authored or co-authored numerous publications on indexing, training for indexers, and manuals used by librarians all over the world, including Structure and Use of Medical Subject Headings: Annotations and Medical Subject Headings; Tree Annotations. Mrs. Charen wrote every MeSH annotation for indexers and online searchers for over 20 years; and
- Served on the three-person task force, along with James L. Wood of the Chemical Abstracts Service, and Harold Oatfield of Pfizer Medical Research Laboratories to revise the ANSI Z39.5 standard for journal title abbreviations, resulting in the 1969 publication of the American National Standard for the Abbreviation of Titles of Periodicals.
It is a mark of Mrs. Charen’s great love of NLM and its staff that during her lifetime she and her husband, Sol Charen, anonymously endowed NLM’s Frank Bradway Rogers Award. The award, given annually, is presented to an individual who has made a significant contribution to the Library’s fundamental operational programs and services. Mrs. Charen’s career covered the time from when the Library began indexing articles for the print publication, Index Medicus, and through development of accessibility of journal citations in the online database MEDLINE/PubMed. Today, over 750,000 citations are indexed annually for MEDLINE/PubMed from over 5,600 biomedical journals. MEDLINE contains over 20,000,000 citations to the biomedical literature. Where indexing the literature was once a process entirely handled manually, today 93% of citations are submitted electronically in XML format by publishers, enabling NLM to concentrate on quality control and indexing rather than original creation of the bibliographic citation, and 74% of MEDLINE journals are indexed from the online version, which accounts for 88% of all new citations being processed. The Index Section now also uses in production the Medical Text Indexer (MTI), a software indexing assistant tool that is optimized to suggest precise MeSH headings from analyzing the article title and abstract for the indexer to consider.
The National Library of Medicine has announced that Extensible Markup Language (XML) data from the IndexCat™ database is now available for free download. Released with a Document Type Definition (DTD) that allows researchers to validate the data, this new XML release includes the digitized content of more than 3.7 million bibliographic items from the printed, 61-volume Index-Catalogue of the Library of the Surgeon-General’s Office, originally published from 1880 to 1961. The XML describes items spanning five centuries, including millions of journal and newspaper articles, obituaries, and letters; hundreds of thousands of monographs and dissertations; and thousands of portraits. Together, these items cover a wide range of subjects such as the basic sciences, scientific research, civilian and military medicine, public health, and hospital administration.
The NLM release of the Index-Catalogue in XML format opens this key resource in the history of medicine and science to new uses and users. It is one of the monuments of the Library’s longstanding, systematic indexing of the medical literature, an effort which William Henry Welch (1850-1934), the great pathologist and bibliophile, considered to be “America’s greatest contribution to medical knowledge.” This indexing, begun by John Shaw Billings in the nineteenth century at the Library of the Surgeon-General’s Office, United States Army (known today as the NLM), eventually created two distinct products: the Index-Catalogue of the Library of the Surgeon-General’s Office, United States Army, and the Index Medicus, forerunner of MEDLINE®, and now the largest component of PubMed.®
Released alongside the IndexCatalogue XML are an integrated XML file and associated DTD for two collections developed from the electronic database of A Catalogue of Incipits of Mediaeval Scientific Writings in Latin (rev.), by Lynn Thorndike and Pearl Kibre (eTK), and the updated and expanded version of Scientific and Medical Writings in Old and Middle English: An Electronic Reference (eVK2), edited by Linda Ehrsam Voigts and Patricia Deery Kurtz. Also available via the online IndexCat, these resources encompass over 42,000 records of incipits, or the beginning words of a medieval manuscript or early printed book, covering various medical and scientific writings on topics as diverse as astronomy, astrology, geometry, agriculture, household skills, book production, occult science, natural science, and mathematics, as these disciplines and others were largely intermingled in the medieval period of European history. The NLM release of these resources in XML format joins many other freely downloadable resources, including the XML for MEDLINE®/PubMed® data, which includes over 22 million references to biomedical and life sciences journal articles back to 1946, and, for some journals, much earlier.
The release also coincides with the NLM’s participation in “Shared Horizons: Data, Biomedicine, and the Digital Humanities,” an interdisciplinary symposium exploring the intersection of digital humanities and biomedicine, being held April 10-12, 2013, in partnership with the National Endowment for the Humanities’ Office of Digital Humanities, Maryland Institute for Technology in the Humanities at the University of Maryland, and Research Councils UK. Shared Horizons will create opportunities for disciplinary cross-fertilization through a mix of formal and informal presentations, combined with breakout sessions designed to promote a rich exchange of ideas about how large-scale quantitative methods can lead to new understandings of human culture. Bringing together researchers from the digital humanities and bioinformatics communities, the symposium will explore ways in which these two communities might fruitfully collaborate on projects that bridge the humanities and medicine around the topics of sequence alignment and network analysis, two modes of analysis that intersect with “big data.” All Shared Horizons sessions will be live-streamed with a monitored back channel for the public to post/tweet comments. Recordings of all talks will also be posted to the Shared Horizons website, with the ability to comment pre- and post-event.
For the first time, the Census Bureau’s American Community Survey is providing access to detailed demographic data on congressional districts for the 113th Congress. These statistics include age, education, occupation, income and veteran status. They are accessible via Easy Stats, the Census Bureau’s new online tool offering quick and easy access to American Community Survey data. These statistics are drawn from the most recent one-year American Community Survey sample, tabulated for redistricted congressional districts of the 113th Congress. Easy Stats provides statistics on a wide range of topics, such as income, occupation, housing and education, down to the local level, including states, counties, cities and towns, and now, congressional districts.
I tried Easy Stats and obtained useful demographic data for sample counties that I was able to export into an Excel spreadsheet! Consider using this tool when you are applying for funding for your communities!
The official press release is from the US Census Bureau.
Following are some tips for faster, more focused search results using Google:
- Exclude terms. If you are looking for information on the term “myocardial,” but not “myocardial infarction,” place a minus sign in front of the word you wish to exclude, e.g., myocardial -infarction.
- Site search. Limit your search to a single website or a specific group of sites, by using site: followed by a Web address or ending. For example, entering “stroke site:gov” as the search will provide information about strokes from government agencies, including MedlinePlus!
- Wildcard search. Use the asterisk to substitute for any word in a phrase. This can be especially useful for identifying a particular fact or even finding a missing word in a song lyric! Put phrases in quotes; for example, “Las Vegas is in * county.”
- Math and conversions. Enter a math problem into Google Search, and it will give you the answer (use * for multiplication and / for division). It will also convert currencies and temperatures. For example, enter “$100 in euros.”
- Definitions. Place the word “define” before any word, for example “define popliteal,” and Google provides a definition at the top of the results list. You can also enter “movies” or “weather” before a ZIP Code or city name to see a list of films playing nearby or a weather forecast for that area.
NLM has decided to end its support for ToxSeek. For ten years the National Library of Medicine has supported ToxSeek, a research project involving natural language processing and semantic technology. This federated-search engine helped users to search across diverse biomedical and environmental health resources and provided a method for locating information resources on topics related to toxicology and environmental health. Since there are now several comparable alternatives for users needing a federated search, such as Science.gov, NLM will realign the resources to support other mission-critical programs.
ToxSeek will not be available after March 23rd, 2012. Please direct any questions to email@example.com.
Google Realtime Search allows you to keep up with developments as they happen from Twitter, Facebook, and blogs around the web. Go to http://www.google.com/realtime and conduct a search on a topic of interest. The results will appear on a constantly refreshing screen so you can see new updates as they happen. You can also access Realtime by clicking “More” from the regular Google menu.