PubMed

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PubMed is a free search engine for accessing the MEDLINE database of citations and abstracts of biomedical research articles. The core subject is medicine, and PubMed covers fields related to medicine, such as nursing and other allied health disciplines. It also provides very full coverage of the related biomedical sciences, such as biochemistry and cell biology. It is offered by the United States National Library of Medicine at the National Institutes of Health as part of the Entrez information retrieval system. As with other indexes, the inclusion of an article in PubMed does not endorse that article's contents. 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 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 PubMed Central 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.[2]

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 access to research and is an evolution from the 2005 policy, in which the NIH asked researchers to voluntarily add the their research to PubMed Central.[1]

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.[2]

Searching PubMed

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.

Telegram-Style Search

However, simple telegram-style search formulations can also be used; they produce very acceptable results[3]. 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[4] 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[5]


  • 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.[6]


Searching with Tags and Booleans

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)
  • [ti] -- title words -- e.g., endothelial [ti] (all articles with "endothelial" in the title)
  • [vol] -- volume -- e.g., 101 [vol] (for volume number 101)

Booleans

The Boolean operators are AND (intersection), OR (union), or NOT (exclusion). NOT should be used with care as it may generate 'false-negative' results.

When no operator is used in a search formulation AND is assumed.

For example:

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]

whereas

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.

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 Science do 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 script, but it relies on the incomplete data in Google Scholar. A built-in functionality is not yet available.

Alternative interfaces

  • GoPubMed - Explore PubMed/MEDLINE with Gene Ontology
  • 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 MEDLINE and other text databases.
  • PubMed slicer - an alternative interface to the PubMed, with clear interface
  • 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.
  • BIOWIZARD - a Digg-style site for PubMed/MEDLINE with search functionality through Medical Subject Headings (MeSH)
  • 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.
  • Authoratory - contact info, interests, social connections and funding of thousands of leading scientists from PubMed/MEDLINE
  • CiteMD - Explore PubMed/MEDLINE, create a free account and organize your references into projects, export to spreadsheet and word processor and email medical citations.
  • PubMed Reader - A free web-based alternative interface for PubMed search
  • Unbound MEDLINE - Clinician-friendly access to PubMed searcing via PDA, wireless devices and the Web

See also

  • PMID — an acronym for PubMed Identifier, on searching within PubMed
  • HubMed — an alternative to PubMed

References

  1. Public access to NIH research made law, science codex, Posted On: December 26, 2007 - 9:50pm
  2. Literature Databases, PubMed (accessed 2007-05-03).
  3. Clarke J, Wentz R. Pragmatic approach is effective in evidence based health care. BMJ. 2000 Sep 2;321(7260):566-7
  4. 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
  5. Glasziou P. Do all fractures need full immobilisation? BMJ. 2007;335(7620):612-3
  6. 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.

External links


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