User:Thorwald/PubMed

PubMed is a free database accessing primarily the MEDLINE database of citations and abstracts 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. PubMed was first released in January 1996.

Content
In addition to MEDLINE, PubMed also provides access to:


 * OLDMEDLINE for pre-1966 citations. This was enhanced in 2006, 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 records which provide a record for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE or converted to out-of-scope status (PREMEDLINE).
 * Records 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.

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. 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".

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 was first released in January 1996.

Information about the journals indexed in PubMed is found in the NLM Catalog Database, searchable by subject or journal title, the NLM ID (NLM's unique journal identifier), the ISO abbreviation of the title, and both the print and electronic International Standard Serial Numbers (pISSN and eISSN). The database includes all journals in all NCBI databases.

, PubMed has over 20 million citations going back to 1966, and selectively to the year 1865, and very selectively to 1809 and about 1 million new numbers are added each year. Some 11.5 million articles are listed with their abstract and 3.1 million articles are available full-text for free, either from the publisher or as part of NCBI's PubMed Central collection.

PMID
A PMID (PubMed identifier or PubMed unique identifier ) is a unique number assigned to each PubMed citation of life sciences and biomedical scientific journal articles. The related Pubmed Central archive may additionally assign a separate number, a PMCID (PubMed Central identifier), normally written with a PMC prefix.

, there are roughly between 15 and 16 million PMID numbers in use, starting from 1, and about 1 million new numbers are added each year. 'Unique identifier' (UID) is the search field tag used in the PubMed search query.

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 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 for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.

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 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. 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:

Telegram-style question in PubMed search window: radial head fractures randomized
 * Question 1: Optimal management of radial head fractures? Randomized controlled trials?

Result: 9 records found, one 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


 * 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)

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 study-type 'filters’ to a 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 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.

Mapping to MeSH headings and subheadings
A strong feature of PubMed is its ability to automatically link to MeSH headings 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.

Tags
Field names / tags are not normally required in a search formulation. For example:
 * pnas drexler ke 1981

will yield a single reference, and is the equivalent (in this example) of
 * pnas [ta] AND drexler ke[au] AND 1981[dp]

For strings of characters which may appear in different fields the field tag has to be added, for example:
 * 1981[pg] pnas

correctly identifies a few article starting on page 1981 in PNAS.
 * green[ti] green[au]

will identify a few papers by an author named Green with the word 'green' in the title

Some of the most common Tags / Field Names are:
 * [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)
 * [page] -- 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)
 * [vol] -- volume—e.g., 101 [vol] (for volume number 101)

(For a complete list of tags, see Search Field Descriptions and Tags) It should be noted that using field qualifiers automatically disables PubMed's 'mapping' function.

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. The AND operator is assumed by default. All Boolean operators are processed in a left-to-right sequence. The order in which PubMed processes a search statement can be specified 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:
 * dogs OR cats AND spleen

will correctly identify some 4,300 papers.
 * Spleen AND cats OR dogs

will incorrectly find some 120,000 articles.
 * Spleen AND (cats OR dogs) is correct.

If in doubt brackets should be used when 'mixing' Boolean operators.

Alternative interfaces

 * eTBLAST - a natural language text similarity engine for MEDLINE and other text databases.
 * GoPubMed - searching PubMed/MEDLINE with Gene Ontology and MeSH
 * HighWire Press - a medical search engine created by apublishing house that searches within its collection of journals
 * HubMed - an alternative interface to the PubMed medical literature database
 * Pubget - based on PubMed/MEDLINE but gets to the PDF right away, provided the journal is available for free or the subscription is being paid for
 * Quertle - a free, semantic-based search engine for PubMed, full-text articles, NIH Grants, TOXLINE, and news