PubMed is a free search engine for accessing the
MEDLINEdatabase of citations and abstracts of biomedical research articles. The core subject is medicine, and PubMed covers fields related to medicine, such as nursingand other allied healthdisciplines. It also provides very full coverage of the related biomedical sciences, such as biochemistryand cell biology. It is offered by the United States National Library of Medicineat the National Institutes of Healthas part of the Entrez information retrievalsystem. As with other indexes, the inclusion of an article or journal in PubMed is not endorsement. In 2007 MEDLINE contained over 17,000,000 records from more than 5,000 journals published in the United States and more than 80 other countries primarily from 1950 onwards. In addition to MEDLINE, PubMed also offers access to
*OLDMEDLINE for pre-1966 citations. This has recently been [http://www.nlm.nih.gov/pubs/techbull/so06/so06_oldmedline_status.html enhanced] , and records for 1951+, even those parts in the printed indexes, are now included within the main portion.
*Citations to all articles, even those that are out-of-scope (e.g., covering plate tectonics or astrophysics) from certain MEDLINE journals, primarily the most important general science and chemistry journals, from which the life sciences articles are indexed for MEDLINE.
*In-process citations which provide a record for an article before it is indexed with
MeSHand added to MEDLINE or converted to out-of-scope status.
*Citations that precede the date that a journal was selected for MEDLINE indexing (when supplied electronically by the publisher).
*Some life science journals that submit full text to
PubMed Centraland may not have been recommended for inclusion in MEDLINE although they have undergone a review by NLM, and some physics journals that were part of a prototype PubMed in the early to mid-1990s. [http://www.nlm.nih.gov/pubs/factsheets/pubmed.html]
Many PubMed citations contain links to full text articles which are freely available, often in the
PubMed Central digital library. In late 2007, the Consolidated Appropriations Act of 2007(H.R. 2764) was signed into law and included a provision requiring the NIH to modify its policies and require inclusion into PubMed Central complete electronic copies of their peer-reviewed research and findings from its funded research. This is the first time the US government has required an Agency to provide open accessto research and is an evolution from the 2005 policy, in which the NIH asked researchers to voluntarily add their research to PubMed Central. [http://www.sciencecodex.com/public_access_mandate_made_law Public access to NIH research made law] , science codex, Posted On: December 26, 2007 - 9:50pm] With an effective date of April 7, 2008, the Department of Health and Human Serviceshas given [http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html notice] : "The Director of the National Institutes of Healthshall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyrightlaw."
PubMed is one of a number of search engines through which it is possible to search the MEDLINE database; the National Library of Medicine also leases the MEDLINE information to a number of private vendors such as Ovid and
SilverPlatter--as well as many other vendors. PubMed has been available free on the Internet since the mid-1990s.
Information about the journals indexed in PubMed is found in its Journals Database, searchable by subject or journal title, Title Abbreviation, the NLM ID (NLM's unique journal identifier), the ISO abbreviation, and both the print and electronic
International Standard Serial Numbers (pISSN and eISSN). The database includes all journals in all Entrez databases. PubMed has over 14 million citations. [http://www.ncbi.nlm.nih.gov/About/tools/restable_lit.html Literature Databases] , PubMed (accessed 2007-05-03).]
For comprehensive, optimal searching in PubMed, it is necessary to have a thorough understanding of its core component, MEDLINE, and especially of the MeSH (Medical Subject Headings) controlled vocabulary used to index MEDLINE articles.
However, simple telegram-style search formulations can also be used; they produce very acceptable results [Clarke J, Wentz R. Pragmatic approach is effective in evidence based health care. BMJ. 2000 Sep 2;321(7260):566-7] . PubMed automatically links textwords to relevant MeSH terms. Aspects of the question can then be added successively, in a Google-like fashion, until a number of ‘hits’ judged manageable is achieved. No knowledge of actual MeSH terms, Boolean operators, English or American spelling, ‘nesting’, or record-fields is required. PubMed’s intelligent search algorithm does (or implies) this in the background. Examples of such telegram-style questions and results they produce on PubMed:
*Question 1: Optimal management of radial head fractures? Randomized controlled trials?
"Telegram-style question in PubMed search window:"radial head fractures randomized
"Result:" 9 records found, one [Liow RY et al. Early mobilisation for minimally displaced radial head fractures is desirable. A prospective randomised study of two protocols. Injury. 2002 Nov;33(9):801-6] judged highly relevant
*Question 2: Paper by Glasziou on radial fractures in the BMJ in 2007?
"Telegram-style question in PubMed search window:" glasziou fractures bmj 2007
"Result:" 1 record (the target) found [Glasziou P. Do all fractures need full immobilisation? BMJ. 2007;335(7620):612-3]
*Question 3: State of vitreous body (of the eye) and time of death? A review, perhaps?
"Telegram-style question in PubMed search window:"vitreous body time death review
"Result:"7 records found, several relevant, e.g. [Madea B, Rödig A. Time of death dependent criteria in vitreous humor: accuracy of estimating the time since death. Forensic Sci Int. 2006;164(2-3):87-92. ]
earching with Tags and Booleans
(For a complete list of tags, see [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip Search Field Descriptions and Tags] )
Search-field tags can be used for searching PubMed, some of the most common being:
* [au] -- author -- e.g., Miller RA [au] or miller ra [au] (not
* [dp] -- date published -- e.g., 1998 [dp] or 1998/11/06 (YYYY/MM/DD, where MM/DD are optional)
* [ip] -- issue, part or supplement -- e.g., 4 [ip] (for issue four of a volume)
* [la] -- language -- e.g., eng [la] (to only find articles in English)
* [pg] -- first page number of the article -- e.g., 673 [pg] (for an article starting on page 673)
* [pmid] -- PubMed ID -- e.g., 15094092 [pmid] (to find the PubMed article with ID 15094092)
* [pt] -- publication type -- e.g., review [pt] (to only see review articles)
* [ta] -- journal title -- e.g., rejuvenation res [ta] (all articles in the journal Rejuvenation Research)
* [ti] -- title words -- e.g., endothelial [ti] (all articles with "endothelial" in the title)
* [vi] -- volume -- e.g., 101 [vol] (for volume number 101)
When no operator is used in a search formulation AND is assumed.
:pnas [ta] drexler ke [au] 1981 [dp]
will yield a single reference, and is the equivalent of
:pnas [ta] AND drexler ke [au] AND 1981 [dp]
:pnas [ta] OR drexler ke [au] OR 1981 [dp]
will yield hundreds of thousands of articles, including all article published in 1981, all articles in PNAS (Proceedings of the National Academy of Sciences) and all articles by K.E. Drexler.
All Boolean operators are processed in a left-to-right sequence. The order in which PubMed processes a search statement can be changed by enclosing individual concepts in parentheses. The terms inside the parentheses are processed first as a unit and then incorporated into the overall strategy.
:g1p3 AND (response element OR promoter)
is processed by ORing the search (response element OR promoter) first and then ANDing the resulting set of documents with g1p3.
Citation Indexing in PubMed
Although PubMed is very popular and ostensibly has access to the largest literature database in its field, PubMed searches do not include citation data for the journal articles. Commercial search engines such as
Scopus, and Web of Sciencedo provide this service, but they are not free. Citation data is provided by the free service Google Scholar, but it has limited search capabilities and incomplete coverage, both with respect to publishers and to years. So, some effort has been made to supplement PubMed with citation index data via a Greasemonkey[http://userscripts.org/scripts/show/13704 script] , but it relies on the incomplete data in Google Scholar.
* [http://www.bioforge.be/intermedi/ InterMedi] - Collaborative Intelligence for Biomed. InterMedi is a Social-Networking-Oriented Pubmed Mashup. Make search on authors, collaborators, etc. Allows searching for pathways between researchers.
GoPubMed- Explore PubMed/MEDLINE with Gene Ontology
* [http://webtools.mf.uni-lj.si/public/medsum.html MEDSUM] - a PubMed/MEDLINE summary tool. Returns number of papers associated with authors, journals or subjects; broken down by years, MeSH terms, ages, journals, authors etc. Used for exploring authors or journals. Alternatively, useful for generating data on a field of research for review paper purposes.
MeshPubMed- Explore PubMed/MEDLINE with Medical Subject Headings(MeSH)
HubMed- An alternative interface to the PubMed medical literature database.
eTBLAST- a natural language text similarity engine for MEDLINEand other text databases.
* [http://datacalmers.hoito.org/pubmedslicer/loadabstracts.php PubMed slicer] - an alternative interface to the PubMed, with clear interface
* [http://fable.chop.edu FABLE] - a gene-centric text-mining search engine for MEDLINE
HighWire Press- a medical search engine similar to PubMed in function and purpose but with some notable differences.
* [http://biowizard.com BIOWIZARD] - a
Digg-style site for PubMed/MEDLINE with search functionality through Medical Subject Headings(MeSH)
* [http://www.esrnexus.com ESRNexus] - free searchable database of medical and societal references including human-extracted summary data. The ESRNexus is maintained by the research community. References from a broad spectrum of sources including gray literature, independent databases and PubMed/Medline.
* [http://www.authoratory.com Authoratory] - contact info, interests, social connections and funding of thousands of leading scientists from PubMed/MEDLINE
* [http://www.citemd.com CiteMD] - Explore PubMed/MEDLINE, create a free account and organize your references into projects, export to spreadsheet and word processor and email medical citations.
* [http://www.pubmedreader.com/ PubMed Reader] - A free web-based alternative interface for PubMed search
* [http://www.unboundmedicine.com/medline/ebm/clinical Unbound MEDLINE] - Clinician-friendly access to PubMed searcing via PDA, wireless devices and the Web.
* [http://www.shrubmed.com ShrubMed] - A PubMed index focusing on herbal and alternative medicine.
* [http://www.pubget.com/ Pubget.com] - Allows you to get the PDFs right away.
*DOI — A permanent identifier given to electronic documents, such as journal articles
PMID— an acronym for PubMed Identifier, on searching within PubMed
* [http://pubmed.gov/ MEDLINE/PubMed]
* [http://www.nlm.nih.gov/bsd/disted/pubmed.html PubMed Online Tutorials]
* [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.chapter.pubmedhelp PubMed Help]
* [http://openwetware.org/wiki/Hardcore_PubMeding_%28advanced_PubMed_searching%29 Advanced PubMed search tutorial in OpenWetWare wiki]
* [http://www.gopubmed.org GoPubMed] allows to explore PubMed results with Mesh and the GeneOntology
* [http://pubcrawler.gen.tcd.ie/ PubCrawler, an alert service which runs scheduled custom queries]
* [http://www.pubmedreader.com/ PubMed Reader] - A free web-based research program for displaying customized PubMed search results
* [http://lindenb.googlecode.com/svn/trunk/src/xsl/pubmed2wiki.xsl pubmed2wiki.xsl] an
XSLTstylesheet transforming the XML output of pubmed to wikipedia
* [http://www.library.vcu.edu/tml/bibs/altpubmed.html Other PubMed Search Engines Resource Guide]
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