PubMed
Overview
 
PubMed is a free database accessing primarily the MEDLINE
MEDLINE
MEDLINE is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care...

 database
Bibliographic database
A bibliographic database is a database of bibliographic records, an organized digital collection of references to published literature, including journal and newspaper articles, conference proceedings, reports, government and legal publications, patents, books, etc...

 of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine
United States National Library of Medicine
The United States National Library of Medicine , operated by the United States federal government, is the world's largest medical library. Located in Bethesda, Maryland, the NLM is a division of the National Institutes of Health...

 (NLM) at the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 maintains the database as part of the Entrez
Entrez
The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...

 information retrieval
Information retrieval
Information retrieval is the area of study concerned with searching for documents, for information within documents, and for metadata about documents, as well as that of searching structured storage, relational databases, and the World Wide Web...

 system. PubMed was first released in January 1996.
In addition to MEDLINE, PubMed provides access to:
  • older references from the print version of Index Medicus
    Index medicus
    Index Medicus is a comprehensive index of medical scientific journal articles, published since 1879. It was initiated by John Shaw Billings, head of the Library of the Surgeon General's Office, United States Army...

    back to 1951 and earlier;
  • references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science
    Science (journal)
    Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....

    , BMJ
    BMJ
    BMJ is a partially open-access peer-reviewed medical journal. Originally called the British Medical Journal, the title was officially shortened to BMJ in 1988. The journal is published by the BMJ Group, a wholly owned subsidiary of the British Medical Association...

    , and Annals of Surgery
    Annals of Surgery
    The Annals of Surgery is a monthly review journal of surgical science and practice. It was started in 1885.-External links:** @ PubMed Central...

    ;
  • very recent entries to records for an article before it is indexed with Medical Subject Headings
    Medical Subject Headings
    Medical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching...

     (MeSH) and added to MEDLINE; and
  • a collection of books available full-text and other subsets of NLM records.


Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central
PubMed Central
PubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine as an online archive of biomedical journal...

 and local mirrors such as UK PubMed Central
UK PubMed Central
' is an on-line database that offers free access to a vast and growing collection of biomedical and health research information.-Service:...

.

Information about the journals indexed in PubMed is found in the NLM Catalog.

, PubMed has over 21.2 million records going back to 1966, selectively to the year 1865, and very selectively to 1809; about 500,000 new records are added each year.
Encyclopedia
PubMed is a free database accessing primarily the MEDLINE
MEDLINE
MEDLINE is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care...

 database
Bibliographic database
A bibliographic database is a database of bibliographic records, an organized digital collection of references to published literature, including journal and newspaper articles, conference proceedings, reports, government and legal publications, patents, books, etc...

 of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine
United States National Library of Medicine
The United States National Library of Medicine , operated by the United States federal government, is the world's largest medical library. Located in Bethesda, Maryland, the NLM is a division of the National Institutes of Health...

 (NLM) at the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 maintains the database as part of the Entrez
Entrez
The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...

 information retrieval
Information retrieval
Information retrieval is the area of study concerned with searching for documents, for information within documents, and for metadata about documents, as well as that of searching structured storage, relational databases, and the World Wide Web...

 system. PubMed was first released in January 1996.

Content

In addition to MEDLINE, PubMed provides access to:
  • older references from the print version of Index Medicus
    Index medicus
    Index Medicus is a comprehensive index of medical scientific journal articles, published since 1879. It was initiated by John Shaw Billings, head of the Library of the Surgeon General's Office, United States Army...

    back to 1951 and earlier;
  • references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science
    Science (journal)
    Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....

    , BMJ
    BMJ
    BMJ is a partially open-access peer-reviewed medical journal. Originally called the British Medical Journal, the title was officially shortened to BMJ in 1988. The journal is published by the BMJ Group, a wholly owned subsidiary of the British Medical Association...

    , and Annals of Surgery
    Annals of Surgery
    The Annals of Surgery is a monthly review journal of surgical science and practice. It was started in 1885.-External links:** @ PubMed Central...

    ;
  • very recent entries to records for an article before it is indexed with Medical Subject Headings
    Medical Subject Headings
    Medical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching...

     (MeSH) and added to MEDLINE; and
  • a collection of books available full-text and other subsets of NLM records.


Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central
PubMed Central
PubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine as an online archive of biomedical journal...

 and local mirrors such as UK PubMed Central
UK PubMed Central
' is an on-line database that offers free access to a vast and growing collection of biomedical and health research information.-Service:...

.

Information about the journals indexed in PubMed is found in the NLM Catalog.

, PubMed has over 21.2 million records going back to 1966, selectively to the year 1865, and very selectively to 1809; about 500,000 new records are added each year. , 12.1 million articles are listed with their abstracts and 3.4 million articles are available full-text for free. To see the current size of the database type "1800:2100[dp]" or "all[sb]" into the PubMed search window.

Standard searches

Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMed's search window.

PubMed translates this initial search formulation and automatically adds field names, relevant MeSH terms, synonyms, Boolean operators, and ‘nests’ the resulting terms appropriately, enhancing the search formulation significantly, in particular by routinely combining (using the OR operator) textwords and MeSH terms.

The examples given in a PubMed tutorial demonstrate how this automatic process works:
Causes Sleep Walking is translated as ("etiology"[Subheading] OR "etiology"[All Fields] OR "causes"[All Fields] OR "causality"[MeSH Terms] OR "causality"[All Fields]) AND ("somnambulism"[MeSH Terms] OR "somnambulism"[All Fields] OR ("sleep"[All Fields] AND "walking"[All Fields]) OR "sleep walking"[All Fields])


Likewise,
Heart Attack Aspirin Prevention is translated as ("myocardial infarction"[MeSH Terms] OR ("myocardial"[All Fields] AND "infarction"[All Fields]) OR "myocardial infarction"[All Fields] OR ("heart"[All Fields] AND "attack"[All Fields]) OR "heart attack"[All Fields]) AND ("aspirin"[MeSH Terms] OR "aspirin"[All Fields]) AND ("prevention and control"[Subheading] OR ("prevention"[All Fields] AND "control"[All Fields]) OR "prevention and control"[All Fields] OR "prevention"[All Fields])


The new PubMed interface, launched in October 2009, encourages the use of such quick, Google-like search formulations; they have also been described as 'telegram' searches.

Comprehensive searches

For comprehensive, optimal searches 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. They may also require complex search strategies, use of field names (tags), proper use of limits and other features, and are best carried out by PubMed search specialists or librarians, who are able to select the right type of search and carefully adjust it for recall and precision. It has been suggested, though, that even complex literature reviews can be carried out using simple focused search formulations.

Clinical queries/systematic reviews

A special feature of PubMed is its "Clinical Queries" section, where "Clinical Categories", "Systematic Reviews", and "Medical Genetics" subjects can be searched, with study-type 'filters' automatically applied to identify substantial, robust studies. As these 'clinical queries' can generate small sets of robust studies with considerable precision, it has been suggested that this PubMed section can be used as a 'point-of-care' resource.

Related articles

A reference which is 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 (on PubMed or any of the other NCBI Entrez databases) using the 'Find related data' option. The related articles are then listed in order of "relatedness". To create these lists 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. The 'related articles' function has been judged to be so precise that some researchers suggest it can be used instead of a full search.

Mapping to MeSH headings and subheadings

A strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be: "bad breath" links to (and includes in the search) "halitosis", "heart attack" to "myocardial infarction", "breast cancer" to "breast neoplasms". Where appropriate, these MeSH terms are automatically "expanded", that is, include more specific terms. 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.

My NCBI

The PubMed optional facility "My NCBI" (with free registration) provides tools for
  • saving searches
  • filtering search results
  • setting up automatic updates sent by e-mail
  • saving sets of references retrieved as part of a PubMed search
  • configuring display formats or highlighting search terms

and a wide range of other options. The "My NCBI" area can be accessed from any computer with web-access.
An earlier version of "My NCBI" was called "PubMed Cubby".

LinkOut

LinkOut, a NLM facility to link (and make available full-text) local journal holdings. Some 3,200 sites (mainly academic institutions) participate in this NLM facility , from Aalborg University in Denmark to ZymoGenetics
ZymoGenetics
ZymoGenetics is a biotechnology/pharmaceutical company based in Seattle, Washington, involved in the development of therapeutic proteins.The company was founded in 1981 by Professors Earl W. Davie and Benjamin D. Hall of the University of Washington and 1993 Nobel Laureate in Chemistry Michael...

 in Seattle. Users at these institutions see their institutions logo within the PubMed search result (if the journal is held at that institution) and can access the full-text.

PubMed for handhelds / mobiles

PubMed / MEDLINE can be accessed via handheld devices, using for instance the 'PICO'
PICO process
The PICO process is a technique used in evidence based medicine to frame and answer a clinical question.The term is an acronym for patient problem or population , intervention , comparison and outcome ....

 option (for focused clinical questions) created by the NLM. A 'PubMed Mobile' option, providing access to a mobile friendly, simplified PubMed version, is also available.

askMEDLINE

askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.

PubMed identifier

A PMID (PubMed identifier or PubMed unique identifier) is a unique number
Unique identifier
With reference to a given set of objects, a unique identifier is any identifier which is guaranteed to be unique among all identifiers used for those objects and for a specific purpose...

 assigned to each PubMed record.

The assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed
Op-ed
An op-ed, abbreviated from opposite the editorial page , is a newspaper article that expresses the opinions of a named writer who is usually unaffiliated with the newspaper's editorial board...

 columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted
Retraction
A retraction is a public statement, by the author of an earlier statement, that withdraws, cancels, refutes, diametrically reverses the original statement or ceases and desists from publishing the original statement...

 for fraud, incompetence, or misconduct. The announcement about any corrections
Correction (newspaper)
A correction in a newspaper is usually the posting of the notice of a typographical error or mistake that appeared in a past issue of a newspaper. Usually, a correction notice appears in its own column....

 to original papers may be assigned a PMID.

Alternative interfaces

The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Ovid
Ovid Technologies
Ovid Technologies, Inc. , part of the Wolters Kluwer group of companies, provides access to online bibliographic databases, journals and other products, chiefly in the area of health sciences...

, Dialog
Dialog (online database)
Dialog is an online information service owned by ProQuest, who acquired it from Thomson Reuters in mid-2008.Dialog was one of the predecessors of the World Wide Web as a provider of information, though not in form. The earliest form of the Dialog system was completed in 1966 under the direction of...

, EBSCO
EBSCO Publishing
EBSCO Publishing, headquartered in Ipswich, Massachusetts, is an aggregator of premium full-text content. EBSCO Publishing's core business is providing online databases via EBSCOhost to libraries worldwide. EBSCOhost is used by libraries, schools, academic institutions, medical institutions, and...

, Knowledge Finder and many other commercial, non-commercial, and academic providers. , more than 500 licences had been issued, more than 200 of them to non-US providers. As licences to use MEDLINE data are available for free, the NLM in effect provides a free testing ground for a wide range of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option.

Lu identifies a sample of 28 current and free web based PubMed versions, requiring no installation or registration, which are grouped into four categories:
  • Ranking search results, for instance: eTBLAST
    ETBLAST
    eTBLAST is a free text similarity service search engine currently offering access to the MEDLINE database, the National Institutes of Health CRISP database, the Institute of Physics database, Wikipedia, arXiv, the NASA technical reports database, Virginia Tech class descriptions and a variety of...

    ; Hakia
    Hakia
    hakia is an Internet search engine. The company has invented QDEXing technology, an alternative new infrastructure to indexing that uses SemanticRank algorithm, a solution mix from the disciplines of ontological semantics, fuzzy logic, computational linguistics, and mathematics...

    ; MedlineRanker; MiSearch;
  • Clustering results by topics, authors, journals etc., for instance: Anne O'Tate
    Anne O'Tate
    Anne O'Tate is a free, web-based application that analyses sets of records identified on PubMed, the bibliographic database of articles from over 5,500 biomedical journals worldwide...

    ; ClusterMed;
  • Enhancing semantics and visualisation, for instance: CiteXplore; EBIMed; MedEvi;
  • Improved search interface and retrieval experience, for instance: askMEDLINE; BabelMeSH ;PubCrawler;


As most of these and other alternatives rely essentially on PubMed / MEDLINE data leased under license from the NLM / PubMed, the term "PubMed derivatives" has been suggested.

External links


The source of this article is wikipedia, the free encyclopedia.  The text of this article is licensed under the GFDL.
 
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