Archive for the ‘PubMed’ Category
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 Offline with NLM “Sunrise Seminar” was held at the Annual Meeting of the Medical Library Association in Boston, MA, on May 6, 2013. The session was chaired by David Gillikin, Bibliographic Services Division. The meeting brought attendees up-to-date on some of the Library online systems as well as future plans.
Links to the following PowerPoint presentations are included in the NLM Technical Bulletin:
- PubMed Tips and Tricks – Margaret McGhee, MEDLARS Management Section, Bibliographic Services Division
- NLM Specialized Information Service Update – Janice Kelly, Division of Specialized Information Services
- NLM Digital Programs – Loren Frant, Public Services Division
- NLM’s Plan to Expand Collection Space – Martha Fishel, Public Services Division
Questions from the audience were taken at the end of the session. The questions and answers have been reprinted in the same article.
The NLM exhibit booth at the 2013 Annual Meeting of the Medical Library Association in Boston featured theater presentations to bring users up-to-date on several NLM products and services. The presentation recordings are captioned and accessible from the NLM Distance Education Program Resources page. The presentations include:
Note: To listen to the voice recordings and view the captions you may need the latest version of Flash® Player (download for free from the Adobe Web site). To zoom in to detailed screens, use the scroll button. For more information, go to the NLM Technical Bulletin page.
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.
PubMed now displays author keywords when supplied by publishers. NLM will not review author keywords for accuracy or add them to non-publisher supplied citations. Author keywords can be searched untagged or using the Other Term [OT] or Text Words [TW] tags. Author Keywords are available on the Abstract, MEDLINE, and XML displays. Author keywords are preceded by a KEYWORDS label and appear below the abstract text on the Abstract display:
Author keywords also appear in the OT field of the MEDLINE display, and users of the XML display will see author keywords in the Keyword element of KeywordList.
A “Download History” link will be added to the PubMed, MeSH and NLM Catalog Advanced page History feature. Using this link will generate History entries in the file “history.csv.” Since Microsoft Excel is typically unable to display or print more than a maximum of 1024 characters in a cell, users with long queries may want to open the CSV file with a text editor to display the complete searches.
The search bar will be updated to list up to the last four databases searched at the top of the pull-down database menu. The alphabetic list with all the databases will also include the recently searched databases. Further details about these changes are available in the 2013 January/February issue of the NLM Technical Bulletin.
In January 2013, NCBI released a new blog called NCBI Insights. The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology. Some NCBI resources include PubMed, GenBank, and BLAST. NCBI Insights was created to provide an insider’s perspective to help you better understand NCBI resources, explore issues of scientific interest that drive NCBI resource development, and demonstrate how you can use NCBI resources to help enhance your research.
The blog has four categories of posts:
- NCBI Explained – Provides an insider’s perspective on NCBI resources and policies to help you better understand NCBI, and avoid some common misconceptions and misunderstandings.
- What’s New – Introduces new and updated resources, including specific examples that demonstrate how you can use them to enhance your research.
- Quick Tips and Tricks – Explains how to perform specific tasks using the NCBI website. Selected topics will be chosen based on questions asked and suggestions provided by users.
- Science Features – Explores current topics in science and demonstrates how you can find relevant data or resources on the NCBI website for further exploration.
This blog is a complement to existing NCBI education and outreach efforts, such as News and Social Media publicity, Webinar and Workshop training programs, and Help Desk user support. Refer to the NCBI Educational Resources web page for more details on these programs. Be sure to check the NCBI Insights Blog regularly!
PubMed/MEDLINE citations, the MeSH database, and the NLM Catalog were updated to reflect 2013 MeSH on December 10, 2013. The MeSH translation tables were also updated. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2013 MeSH vocabulary. For details on the data changes, go to MEDLINE Data Changes — 2013. On December 11, NLM resumed daily (Tuesday-Saturday) MEDLINE updates to PubMed, including the backlog of citations indexed since November 14 with 2013 MeSH.
MeSH uploaded the disease portion of the Online Mendelian Inheritance in Man (OMIM) database available in the Unified Medical Language System. OMIM is a database that catalogues human diseases with genetic components. Although OMIM disease names are available for searches in PubMed, it is often difficult to index and search for the articles on rare diseases with genetic components due to multiple synonyms used by different scientists that often do not overlap. As was done with NIH Office of Rare Diseases and Research (ORDR) disease terms in 2010, OMIM terms were compared to the existing MeSH descriptors and SCR records. When matches were found, OMIM thesaurus tags were added to the matched MeSH record terms. Where there were no string matches, new disease SCRs were created and mapped to descriptor(s) using the Heading Mapped to (HM) field. MeSH created 3,774 new disease SCRs, and identified and tagged 1,498 existing ORDR SCRs as rare diseases with genetic components during the OMIM load. All OMIM disease names therefore will be available starting with MeSH 2013 for indexers and searchers. The use of the HM field in the disease SCRs will lead to more consistent indexing and retrieval for rare genetic diseases.
There were 2,165 terms in 772 descriptors (MeSH headings) matching OMIM terms and therefore, tagged with the Thesaursus ID (TH)=OMIM (2013). An additional 10,286 terms in 5,453 total SCRs (6,331 terms in 3,774 new SCRs and 3,955 terms in 1,498 existing SCRs) were identified during the load. All newly created SCRs were reviewed and mapped to at least one disease descriptor.
The NLM Technical Bulletin article, What’s New for 2013 MeSH, includes additional information on the OMIM tagging. The NLM Technical Bulletin article, What’s New for 2010 MeSH®, has additional information on the 2010 ORDR term merger into the MeSH vocabulary.
In order to keep pace with the continuing advances in web technology, PMC has launched PubReader, an alternative web presentation that offers another, more reader-friendly view of the articles in the PMC archive. Designed particularly for enhancing the readability of PMC journal articles on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers.
Like a printed paper, PubReader breaks an article into multiple columns and pages to improve readability and navigation. PubReader can expand a page to whatever fits on your screen — with multiple columns on a desktop monitor or a single column page on a small tablet. It will even switch to two columns if you rotate the tablet to a landscape view. When you adjust the font size or change the size of the browser window, page boundaries and columns are adjusted automatically.
PubReader can be activated by selecting the PubReader Format in the right-hand column of individual PMC articles. Additional information can be found in the NLM Technical Bulletin and the PubReader About webpage.