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- 8 June 2018
- alternate interfaces, bibliometrics, data-mining, GoPubMed, text-mining, PubReMiner, socio-semantic
See also Expert searching | GoPubMed | Open search | PubMed - MEDLINE | PubReMiner | Semantic search | Web 2.0
Alternative PubMed interfaces refers to a range of alternate search tools and interfaces that can search PubMed - MEDLINE in such a way that newer information patterns or insights into the medical literature can be ascertained. Via a combination of data mining, linguistic analysis, statistical methodologies and semantic algorithms, a range of alternative PubMed interfaces provide librarians and researchers with new ways to examine the biomedical literature from unique perspectives. Interestingly, many of the sites listed below are frequently down, or inaccessible, so caution is advised. The National Library of Medicine (U.S.) encourages software developers to create innovative tools to search Medline. Commercial services such as Dialog and EBSCO - as well as academic libraries, bioinformatics organizations, pharmaceutical companies and software startups - lease copies of the PubMed database (see leasing data) and build alternate interfaces to search it. For a different view of searching the biomedical literature, try some of the tools below. In 2016, the AHRQ (Agency for Healthcare Research and Quality) sketched out the use of text-mining tools as an emerging methodology within a number of systematic review processes; they sought to provide information addressing pressing questions individuals and organizations face when considering utilizing text-mining tools.
Criteria for inclusion
An alternative PubMed interface is one that:
- searches a current (live or recent) version of the PubMed - MEDLINE database
- is in active development or maintenance
- has an interface or features that distinguish it from PubMed - MEDLINE
For a comprehensive evaluation of alternative PubMed interfaces, see 28 systems surveyed in Lu, Database 2011.
Alternative PubMed search tools
- Selected text mining tools are also listed in the Systematic Reviews Toolbox (http://systematicreviewtools.com/)
- BabelMeSH - http://babelmesh.nlm.nih.gov/
- "Search MEDLINE/PubMed using medical terms or phrases in Arabic, Chinese, English, French, German, Italian, Japanese, Korean, Portuguese, Russian, and Spanish. Citations and abstracts retrieved will be in English only."
- DataMed - https://datamed.org/
- DataMed prototype(v3.0) is being developed for the NIH BD2K Data Discovery Index (DDI) by the bioCADDIE project team. DataMed, once completed, will be of use to the scientific community to allow users to search for and find data across different repositories in one space.
- EBI Search
- somewhat slow in retrieving results; allows a very low number (20) of query terms
- FABLE - http://fable.chop.edu/ retired 2018
- Article Finder: find articles mentioning a gene of interest.
- Gene Lister: find genes associated with one or more keywords.
- an information extraction tool, FACTA+ was a winner in the National Library of Medicine’s software development challenge. The algorithms extract relationships from your query, searching in PubMed, PubMedCentral, TOXLINE, Biomed Central, NIH, FDA, and other agency grant proposals, as well as biomedical news sources
- GoPubMed - http://www.gopubmed.com retired 2018
- The search bar auto-completes queries similar to the functionality provided by Google's Autocomplete feature.
- Faceted browsing by term frequency, MeSH headings, author, location and date of publication.
- Statistics for query results, including top years, countries, cities, journals, terms, and authors.
- Visualization of publications over time, location, and network of authors.
- Good graphics as well as usability improvements.
- Mapping MEDLINE, a new tool to visualize MEDLINE results
- Most citations in PubMed are from MEDLINE, and MEDLINE records are indexed with (typically around 10 to 12) Medical Subject Headings. These MeSH headings include not only topic areas but geographic regions — around 15% of all indexed records are tagged with the name of a continent, country or city. Mapping MEDLINE searches your results against these goegraphical headings. Of course some articles might mention a country name in a title or abstract without a corresponding index term, so Mapping MEDLINE searches those fields by country name as well
- MeSH On Demand
- identifies MeSH Terms in your text using NLM's Medical Text Indexer (MTI) tool; a list of MeSH Terms relevant to your text will be shown
- PubFocus - http://www.pubfocus.com/ Note: does not seem to be updated as of 2013
- Provides statistics based on publication trends, publishing journals (Journal Rank and H-index) and first and last author.
- Whatizit European Bioinformatics Institute
- text-processing system that allows you to do textmining tasks on text, including MEDLINE abstracts
- Yale MeSH Analyzer. MeSH Analysis Grid Generator - http://mesh.med.yale.edu/
- From the website: "...When conducting a comprehensive search, it is critical to design a strategy that retrieves all potentially relevant articles. Experienced searchers know the power of using controlled vocabularies but also the frustration of not being able to pinpoint articles known to be relevant but missing from the initial retrieval set. Librarians have long analyzed Medical Subject Headings to design and refine searches. A MeSH analysis grid can help identify the problems in your search strategy by presenting the ways articles are indexed in the MEDLINE database in an easy-to-scan tabular format. Typically, each column in the grid represents an article, with identifying information of the article at the top of the column, such as the PMID, the author, and the year of publication. The MeSH terms are sorted and grouped alphabetically for ease of scanning. Librarians can then easily scan the grid and identify appropriate MesH terms, term variants, indexing consistency, and the reasons why some articles are retrieved and others are not. This inevitably leads to fresh iterations of the search strategy to include missing important terms. In addition to MeSH terms, author-assigned keywords, article titles, and abstracts can be included in the analysis grid..."
'Best of breed' alternative PubMed interfaces?
- Biblimed - http://www.biblimed.fr/
- smart, Gallic, streamlined
- new(ish) alternative interface to PubMed; made improvements to its search interface
- easy to navigate & intuitive, system suggests keywords from MeSH and awaits validation before running search
- GoPubMed - http://www.gopubmed.com
- social, semantic, multifaceted classifier
- auto-completes queries similar to Google's Autocomplete
- faceted browsing by term frequency, MeSH headings, author, location and date of publication
- statistics for query results, top years, countries, cities, journals, terms and authors
- visualization of publications over time, location, and network of authors
- good graphics as well as usability improvements; use with caution some numbers are inaccurate
- #GoPubmed - http://twitter.com/#!/search?q=%23GoPubmed
- Quetzal - https://www.quetzal-search.info/
- Quetzal(R) (a product of Quertle) is a linguistic-based search engine for biomedical information
- Other search engines try to find anything might be relevant, forcing you to spend hours (or more) weeding through long lists of results. The patent-pending technology recognizes key points authors make in each document so you can Find What Matters™ right away.
- built from the ground up to address the unique needs of this technical literature
- PubFocus - http://www.pubfocus.com/ Note: does not seem to be updated as of 2013
- bibliometric, rank-enabled, analytical
- statistics provided based on publication trends, journal rank & H-index, first and last authors
- discerns research activity in any given biomedical area; search outputs generated by MEDLINE/PubMed are not well classified requiring lengthy analysis
- automates analysis of search by enriching it with two bibliometric indicators of publication quality: journal impact factor and volume of forward references
- provides basic volumetric statistics; prioritizes citations and evaluates author impact on field; analyses occurrences of key terms within citations by utilizing controlled vocabularies
- AHRQ. EPC Methods: an exploration of the use of text-mining software in systematic reviews. AHRQ Publication No. 16-EHC023-EF. Rockville, MD: Agency for Healthcare Research and Quality; April 2016.
- Bassett H. How many Medline platforms on the web? Slideshare http://www.slideshare.net/hbasset/how-many-medline-platforms-on-the-web
- Bradley S, Giustini D. GoPubMed versus PubReMiner for analyzing PubMed search results: a head to head comparison of two free web ‘data mining’ tools. CHLA/ABSC Conference, 2011.
- Coccia P. New web tools to improve PubMed searches for the biomedical community. Drug Inform J. 2009;43:2:115-122.
- Connor E. PubMed® search interface alternatives: a descriptive comparison. J Electron Resour Med Libr. 2010;7(2):126-134.
- Featherstone R. PubMed & beyond. 23 March 2011. http://www.slideshare.net/featherr/pubmed-beyond
- Gasparyan AY, Ayvazyan L, Kitas GD. Multidisciplinary bibliographic databases. J Korean Med Sci. 2013 Sep;28(9):1270-1275.
- Glynn RW, Kerin MJ, Sweeney KJ. Authorship trends in the surgical literature. Br J Surg. 2010 Aug;97(8):1304-8.
- Hausner E, Waffenschmidt S, Kaiser T, Simon M. Routine development of objectively derived search strategies. Systematic reviews. 2012 Feb 29;1(1):1.
- Lewis J, Ossowski S, Hicks J, Errami M, Garner HR. Text similarity: an alternative way to search MEDLINE. Bioinformatics. 2006;22(18):2298-304.
- Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford). 2011 Jan 18;2011:baq036.
- National Network of Libraries of Medicine, Pacific Northwest Region. Third-Party PubMed Tools. Slideshare.net
- NCBI: Entrez Programming utilities http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
- NLM: PubMed programming utilities user requirements http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements
- NLM: Leasing data from the National Library of Medicine http://www.nlm.nih.gov/databases/leased.html
- O’Mara-Eves A, Thomas J, McNaught J, Miwa M, Ananiadou S. Using text mining for study identification in systematic reviews: a systematic review of current approaches. Systematic reviews. 2015 Jan 14;4(1):1.
- Ripple AS. Expert Googling: best practices and advanced strategies for using Google in health sciences libraries. Med Ref Serv Q. 2006;25:97-107.
- Slater L. Review: PubMed PubReMiner. JCHLA / JABSC. 2012;33(02):106-107.
- Text Mining and Finding Connections. Virginia Commonwealth University. VCU Libraries.
- Tusruoka Y, Miwa M, Mamamota k, Tsujii, J, Ananiadou A. Discovering and visualizing indirect associations between biomedical concepts. Bioiniformatics. 2008;27(13):i111-i119.
- Von Isenburg M. HubMed. J Med Libr Assoc. 2007;95(1):95-97.
- Wildgaard LE, Wildgaard LE, Lund H, Lund H. Advancing PubMed? A comparison of third-party PubMed/Medline tools. Library Hi Tech. 2016 Nov 21;34(4):669-84.