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PubMed is provided by the United States National Library of Medicine.

PubMed is a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health (NIH) maintains PubMed as part of the Entrez information retrieval system. Listing an article or journal in PubMed is not endorsement. In addition to MEDLINE, PubMed also offers access to

  • OLDMEDLINE for pre-1966 citations. This has recently been 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 MeSH and 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 the PubMed Central digital library and 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.[1]

Many PubMed citations contain links to full text articles which are freely available, often in PubMed Central. In late 2007, President George W. Bush signed the Consolidated Appropriations Act of 2007 (H.R. 2764) into law; this law 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 access to research and is an evolution from the 2005 policy, in which the NIH asked researchers to voluntarily add their research to PubMed Central.[1] With an effective date of 7 April 2008, the Department of Health and Human Services gave notice: "The Director of the National Institutes of Health shall 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 copyright law".[2]

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.

As of 28 January 2010 (2010 -01-28), PubMed has approximately 19.5 million citations going back to the year 1865.[3] To see the current size of the database simply type "1800:2100[dp]" into the search bar and click "search".

Contents

Searching PubMed

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Comprehensive search

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.

The new PubMed interface, launched in October 2009, encourages the use of quick, Google-like search formulations:

Quick search

Quick, simple telegram-style search formulations can also be used, and they generally produce acceptable results.[4] 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 simple 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[5] 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[6]

  • 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: 8 records found, several relevant, e.g. Madea/Rödig (2006)[7]

Clinical Queries / Systematic Reviews

A special feature of PubMed is the 'Clinical Queries' and 'Systematic Reviews' option which can be used to identify more relevant (robust) studies by automatically applying ‘quality filters’ to be applied to each search.

Related articles

After a quick search, references which are judged particularly relevant can be marked and 'related articles' can be identified. If relevant, several studies can be selected and 'related articles' to all of them can be generated. The 'related articles' are then listed on order or 'relatedness' (not chronological order). To create the list of 'related articles' PubMed compares words from the Title and Abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm.[8]

Mapping to MeSH (headings) and Subheadings

A strong feature of PubMed is its ability to automatically link to Medical Subject Headings (MeSH) and Subheadings. Examples would be: 'bad breath' links to (and includes in the search) 'Halitosis', 'Writers cramp' to 'focal dystonia', 'breast cancer' to 'breast neoplasms'. Where appropriate, these MeSH terms are automatically 'expanded'. Terms like 'nursing' are automatically linked to 'Nursing [Mesh]' or 'Nursing [Subheading]'. This important feature makes PubMed searches automatically more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology.

Searching with tags and Boolean operators

Tags

(For a complete list of tags, see 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 case sensitive)
  • [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)

It should be noted that using field qualifiers automatically disables PubMed's 'mapping' function.

- Note also with the [dp] tag that this searches for publications by both online publication date and print date. Therefore one paper can be associated with two publication years. For example "Schizophrenia 2007[dp]" will return some of the same papers as "Schizophrenia 2008[dp]".

Boolean operators

There are three Boolean operators: AND (intersection); OR (union); NOT (exclusion). NOT should be used with care as it may generate 'false-negative' results.

For example:

pnas drexler ke 1981

will yield a single reference, and is the equivalent of

pnas AND drexler ke AND 1981

whereas

pnas OR drexler ke OR 1981

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 concepts in parentheses. The terms inside the parentheses are processed first as a unit and then incorporated into the overall strategy.

For example:

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.

Alternative interfaces

The new PubMed interface, launched in October 2009, with its simple search window, encourages focused search formulations (instead of complex search strategies) when appropriate. It may disourage use of some of the alternative interfaces listed below which offered this simple search option at their opening search page.

  • iPubmed - Fast Interactive Type-ahead, fuzzy search on Pubmed/MEDLINE articles developed at University of California-Irvine.
  • MEDSUM - a PubMed/MEDLINE summary tool. Takes standard PubMed queries and returns information in the form of graphs and tables. Used for 'profiling' authors and journals, or exploring life-science research trends.
  • eTBLAST - a natural language text similarity engine for MEDLINE and other text databases.
  • GoPubMed - Explore PubMed/MEDLINE with Gene Ontology (GO) and Medical Subject Headings (MeSH)
  • HighWire Press - a medical search engine created by an online journal publishing house that searches within its collection of journals.
  • HubMed - An alternative interface to the PubMed medical literature database.
  • NextBio - based on MEDLINE. Provides tag clouds for filtering, searches full article text when available and offers rank by relevance.
  • Novoseek - A free biomedical search engine developed with bioalma's text mining technology. novoseek indexes Medline, US awarded grants and PubMed Central articles.
  • XTractor - Knowledgebase of manually annotated relationships from PUBMED publications with regular Free alerts for favorite entities
  • Pubget - Based on PubMed/MEDLINE but gets to the PDF right away.
  • Q-Sensei - A free search engine which indexes the PubMed/MEDLINE database and provides context-sensitive search suggestions for every search.

See also

  • DOI — A permanent identifier given to electronic documents, such as journal articles
  • Entrez
  • JournalReview.org
  • PMID — an acronym for PubMed Identifier, on searching within PubMed
  • Pubget— a search engine for PubMed and other content that delivers the PDF right away

References

  1. ^ "Public access to NIH research made law". Science Codex. 2007-12-26. http://www.sciencecodex.com/public_access_mandate_made_law. 
  2. ^ "Revised Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research". National Institutes of Health. 2008-01-11. http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html. 
  3. ^ "Yearly Citation Totals from 2008 MEDLINE/PubMed Baseline". NIH. 2007-12-17. http://www.nlm.nih.gov/bsd/licensee/2008_stats/2008_Totals.html. Retrieved 2008-10-20. 
  4. ^ Clarke, J.; Wentz, R. (2000). "Pragmatic approach is effective in evidence based health care". BMJ 321 (7260): 566–567. doi:10.1136/bmj.321.7260.566/a (inactive 2009-03-25). 
  5. ^ Liow, R. Y.; et al. (2002). "Early mobilisation for minimally displaced radial head fractures is desirable. A prospective randomised study of two protocols". Injury 33 (9): 801–806. doi:10.1016/S0020-1383(02)00164-X. 
  6. ^ Glasziou, P. (2007). "Do all fractures need full immobilisation?". BMJ 335 (7620): 612–613. doi:10.1136/bmj.39272.565810.80. PMID 17884906. 
  7. ^ Madea, B.; Rödig, A. (2006). "Time of death dependent criteria in vitreous humor: accuracy of estimating the time since death". Forensic Science International 164 (2–3): 87–92. doi:10.1016/j.forsciint.2005.12.002. 
  8. ^ "Computation of Related Articles explained". NCBI. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Appendices#pubmedhelp.Computation_of_Relat. 

External links

  • MEDLINE/PubMed
  • PubMed Online Tutorials
  • PubMed Help
  • Advanced PubMed search tutorial — from OpenWetWare.org
  • PubFocus — performs semantic analysis and ranking of PubMed search with journal ranking and ontology databases
  • PubMeddy — Pubmed articles published based on most searched keywords
  • GoPubMed — allows to explore PubMed results with Mesh and the GeneOntology
  • NextBio — search engine with tag clouds and alternate heuristics for ranking
  • Novoseek — search engine based on semantic web displaying related concepts to a search
  • XTractor - Knowledgebase of manually annotated relationships from PUBMED publications with regular Free alerts for favorite entities
  • PubCrawler — an alert service which runs scheduled custom queries
  • PubMed Reader — a free web-based research program for displaying customized PubMed search results
  • Other PubMed Search Engines Resource Guide
  • Pubget — Based on PubMed/MEDLINE but gets to the PDF right away
  • PubAnatomy — based on Medline but combines rich background information with interactive visualization
  • PubRad — PubMed search specific for Radiology

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