PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.
From 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997.
|Research center||United States National Library of Medicine (NLM)|
|Release date||January 1996|
In addition to MEDLINE, PubMed provides access to:
Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.
As of 6 December 2018, PubMed has more than 29.1 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. As of the same date, 13.1 million of PubMed's records are listed with their abstracts, and 14.2 million articles have links to full-text (of which 3.8 million articles are available, full-text for free for any user). Approximately 12% of the records in PubMed correspond to cancer-related entries, which have grown from 6% in the 1950s to 16% in 2016. Other significant proportion of records correspond to "chemistry" (8.69%), "therapy" (8.39%), and "infection" (5%).
In 2016, NLM changed the indexing system so that publishers will be able to directly correct typos and errors in PubMed indexed articles.
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 (Medical Subject Headings) 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])
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])
A new PubMed interface was launched in October 2009 and encouraged the use of such quick, Google-like search formulations; they have also been described as 'telegram' searches. By default the results are sorted by Most Recent, but this can be changed to Best Match, Publication Date, First Author, Last Author, Journal, or Title.
For optimal searches in PubMed, it is necessary to understand 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; reference librarians and search specialists offer search services.
When a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are: Article Type (MeSH terms, e.g., "Clinical Trial"), Secondary identifiers, (MeSH terms), Language, Country of the Journal or publication history (e-publication date, print journal publication date).
Since July 2005, the MEDLINE article indexing process extracts identifiers from the article abstract and puts those in a field called Secondary Identifier (SI). The secondary identifier field is to store accession numbers to various databases of molecular sequence data, gene expression or chemical compounds and clinical trial IDs. For clinical trials, PubMed extracts trial IDs for the two largest trial registries: ClinicalTrials.gov (NCT identifier) and the International Standard Randomized Controlled Trial Number Register (IRCTN identifier).
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 the authors of a paper suggested it can be used instead of a full search.
PubMed automatically links 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 feature is called Auto Term Mapping and is enacted, by default, in free text searching but not exact phrase searching (i.e. enclosing the search query with double quotes). This feature makes PubMed searches more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology.
The PubMed optional facility "My NCBI" (with free registration) provides tools for
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 (as of March 2010), from Aalborg University in Denmark to ZymoGenetics in Seattle. Users at these institutions see their institution's logo within the PubMed search result (if the journal is held at that institution) and can access the full-text.
In 2016, PubMed allows authors of articles to comment on articles indexed by PubMed. This feature was initially tested in a pilot mode (since 2013) and was made permanent in 2016. In February 2018, PubMed Commons was discontinued due to the fact that "usage has remained minimal".
PubMed/MEDLINE can be accessed via handheld devices, using for instance the "PICO" 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, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.
A PMID (PubMed identifier or PubMed unique identifier) is a unique integer value, starting at
1, assigned to each PubMed record. A PMID is not the same as a PMCID which is the identifier for all works published in the free-to-access PubMed Central.
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.
The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Embase, Ovid, Dialog, EBSCO, Knowledge Finder and many other commercial, non-commercial, and academic providers. As of October 2008, more than 500 licenses had been issued, more than 200 of them to providers outside the United States. As licenses 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:
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. Without the need to store about 90 GB of original PubMed Datasets, anybody can write PubMed applications using the eutils-application program interface as described in "The E-utilities In-Depth: Parameters, Syntax and More", by Eric Sayers, PhD. Various citation format generators, taking PMID numbers as input, are examples of web applications making use of the eutils-application program interface. Sample web pages include Citation Generator - Mick Schroeder, Pubmed Citation Generator - Ultrasound of the Week, PMID2cite, and Cite this for me.
Alternative methods to mine the data in PubMed use programming environments such as Matlab, Python or R. In these cases, queries of PubMed are written as lines of code and passed to PubMed and the response is then processed directly in the programming environment. Code can be automated to systematically queries with different keywords such as disease, year, organs, etc. A recent publication (2017) found that the proportion of cancer-related entries in PubMed has risen from 6% in the 1950s to 16% in 2016.
The data accessible by PubMed can be mirrored locally using an unofficial tool such as MEDOC.
ClinicalTrials.gov is a registry of clinical trials. It is run by the United States National Library of Medicine (NLM) at the National Institutes of Health, and is the largest clinical trials database, currently holding registrations from over 230,000 trials from 195 countries in the world.DNAH7
Dynein, axonemal, heavy chain 7 is a protein in humans that is encoded by the DNAH7 gene.
DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]. ##RefSeq-Attributes-START## Transcript_exon_combination_evidence :: AB023161.2, AF327442.1 [ECO:0000332] ##RefSeq-Attributes-END##Entrez
The Entrez (pronounced ɒnˈtreɪ) Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" (a greeting meaning "Come in!" in French) was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.
Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and protein sequences and chromosome maps. Some textbooks are also available online through the Entrez system.Europe PubMed Central
Europe PubMed Central (Europe PMC) is an on-line database that offers free access to a large and growing collection of biomedical research literature. It was known as UK PubMed Central until 1 November 2012. The Europe PMC project was originally launched in 2007 as the first 'mirror' site to PMC, which aims to provide international preservation of the open and free-access biomedical and life sciences literature. It forms part of a network of PMC International (PMCI) repositories that includes PubMed Central Canada. Europe PMC is not an exact "mirror" of the PMC database but has developed some different features. On February 15, 2013, CiteXplore was subsumed under Europe PubMed Central.The resource is managed and developed by the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), on behalf of an alliance of 27 biomedical and life sciences research funders, led by the Wellcome Trust. The Europe PMC funders group requires that articles describing the results of biomedical and life sciences research they have supported be made freely available in Europe PMC within 6 months of publication to maximise the impact of the work that they fund.Index Medicus
Index Medicus (IM) is a curated subset of MEDLINE, which is a bibliographic database of life science and biomedical science information, principally scientific journal articles. From 1879 to 2004, Index Medicus was a comprehensive bibliographic index of such articles in the form of a print index or (in later years) its onscreen equivalent. Medical history experts have said of Index Medicus that it is “America's greatest contribution to medical knowledge.”Inorganic Chemistry (journal)
Inorganic Chemistry is a biweekly peer-reviewed scientific journal published by the American Chemical Society since 1962. It covers research in all areas of inorganic chemistry.
Inorganic Chemistry is abstracted and indexed in Chemical Abstracts Service, Scopus, EBSCOhost, Thomson-Gale, ProQuest, PubMed, Web of Science, and SwetsWise.
The current editor-in-chief is William B. Tolman.Journal of Bacteriology
The Journal of Bacteriology is a peer-reviewed medical journal established in 1916. It is published by the American Society for Microbiology (ASM) and the editor in chief is Thomas J. Silhavy. The journal is delayed open access, content is available free at the journal's website and at PubMed Central after a six-month embargo. The journal is also hybrid open access allowing authors to pay $3,000 ($2,000 for ASM members) for their articles to be available free immediately.MEDLINE
MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) 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. MEDLINE also covers much of the literature in biology and biochemistry, as well as fields such as molecular evolution.
Compiled by the United States National Library of Medicine (NLM), MEDLINE is freely available on the Internet and searchable via PubMed and NLM's National Center for Biotechnology Information's Entrez system.Medical Subject Headings
Medical Subject Headings (MeSH) is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it serves as a thesaurus that facilitates searching. Created and updated by the United States National Library of Medicine (NLM), it is used by the MEDLINE/PubMed article database and by NLM's catalog of book holdings. MeSH is also used by ClinicalTrials.gov registry to classify which diseases are studied by trials registered in ClinicalTrials.
MeSH was introduced in the 1960s, with the NLM's own index catalogue and the subject headings of the Quarterly Cumulative Index Medicus (1940 edition) as precursors. The yearly printed version of MeSH was discontinued in 2007 and MeSH is now available online only. It can be browsed and downloaded free of charge through PubMed. Originally in English, MeSH has been translated into numerous other languages and allows retrieval of documents from different origins.Medical library
A health or medical library is designed to assist physicians, health professionals, students, patients, consumers, medical researchers, and information specialists in finding health and scientific information to improve, update, assess, or evaluate health care. Medical libraries are typically found in hospitals, medical schools, private industry, and in medical or health associations. A typical health or medical library has access to MEDLINE, a range of electronic resources, print and digital journal collections, and print reference books. The influence of open access (OA) and free searching via Google and PubMed has a major impact on the way medical libraries operate.
The United States National Library of Medicine (NLM) is the largest biomedical library in the world, and collects and provides access to some of the best health information in the world (due to its linkage to the National Institutes of Health). The NLM maintains numerous medical and genomic databases, searchable via its Entrez search system, including MEDLINE (PubMed) and OMIM (a genetic traits database).
The largest medical library in Europe is the German National Library of Medicine (ZB MED), which also has collections in the fields of nutrition, agriculture, and environmental science. ZB MED operates as the official European supplier of full texts in response to searches conducted in the NLM's bibliographic databases such as PubMed, and also operates its own search portals.MedlinePlus
MedlinePlus is an online information service produced by the United States National Library of Medicine. The service provides curated consumer health information in English and Spanish.
The site brings together information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), other U.S. government agencies, and health-related organizations. There is also a site optimized for display on mobile devices, in both English and Spanish. In 2015, about 400 million people from around the world used MedlinePlus. The service is funded by the NLM and is free to users.
MedlinePlus provides encyclopedic information on health and drug issues, and provides a directory of medical services. MedlinePlus Connect links patients or providers in electronic health record (EHR) systems to related MedlinePlus information on conditions or medications.
PubMed Health is another NLM site that offers consumer health information, in addition to information for health professionals.Mydriasis
Mydriasis is the dilation of the pupil, usually having a non-physiological cause, or sometimes a physiological pupillary response. Non-physiological causes of mydriasis include disease, trauma, or the use of drugs.
Normally, as part of the pupillary light reflex, the pupil dilates in the dark and constricts in the light to respectively improve vividity at night and to protect the retina from sunlight damage during the day. A mydriatic pupil will remain excessively large even in a bright environment. The excitation of the radial fibres of the iris which increases the pupillary aperture is referred to as a mydriasis. More generally, mydriasis also refers to the natural dilation of pupils, for instance in low light conditions or under sympathetic stimulation.
An informal term for mydriasis is blown pupil, and is used by medical providers. It is usually used to refer to a fixed, unilateral mydriasis, which could be a symptom of raised intracranial pressure.
The opposite, constriction of the pupil, is referred to as miosis. Both mydriasis and miosis can be physiological. Anisocoria is the condition of one pupil being more dilated than the other.NIH Public Access Policy
The NIH Public Access Policy is an open access mandate, drafted in 2004 and mandated in 2008, requiring that research papers describing research funded by the National Institutes of Health must be available to the public free through PubMed Central within 12 months of publication. PubMed Central is the self-archiving repository in which authors or their publishers deposit their publications. Copyright is retained by the usual holders, but authors may submit papers with one of the Creative Commons licenses.National Center for Biotechnology Information
The National Centre for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine.
NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. He also led an intramural research program, including groups led by Stephen Altschul (another BLAST co-author), David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka, and Zhiyong Lu. David Lipman stood down from his post in May 2017.Oncology
Oncology is a branch of medicine that deals with the prevention, diagnosis, and treatment of cancer. A medical professional who practices oncology is an oncologist. The name's etymological origin is the Greek word ὄγκος (ónkos), meaning "tumor", "volume" or "mass" and the word λόγος (logos), meaning "study".Cancer survival has improved due to three main components including improved prevention efforts to reduce exposure to risk factors (e.g., tobacco smoking and alcohol consumption), improved screening of several cancers (allowing for earlier diagnosis), and improvements in treatment.Cancers are often managed through discussion on multi-disciplinary cancer conferences where medical oncologists, surgical oncologists, radiation oncologists, pathologists, radiologists, and organ specific oncologists meet to find the best possible management for an individual patient considering the physical, social, psychological, emotional, and financial status of the patient. It is very important for oncologists to keep updated with respect to the latest advancements in oncology, as changes in management of cancer are quite common.PubMed Central
PubMed Central (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature. As one of the major research databases within the suite of resources that have been developed by the National Center for Biotechnology Information (NCBI), PubMed Central is much more than just a document repository. Submissions into PMC undergo an indexing and formatting procedure which results in enhanced metadata, medical ontology, and unique identifiers which all enrich the XML structured data for each article on deposit. Content within PMC can easily be interlinked to many other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to freely discover, read and build upon this portfolio of biomedical knowledge.PubMed Central is very distinct from PubMed. PubMed Central is a free digital archive of full articles, accessible to anyone from anywhere via a web browser (with varying provisions for reuse). Conversely, although PubMed is a searchable database of biomedical citations and abstracts, the full-text article physically resides elsewhere (in print or online, free or behind a subscriber paywall).
As of December 2018, the PMC archive contained over 5.2 million articles, with contributions coming directly from publishers or authors depositing their own manuscripts into the repository per the NIH Public Access Policy. Older data shows that from Jan 2013 to Jan 2014 author-initiated deposits exceeded 103,000 papers during this 12-month period. PMC also identifies about 4,000 journals which now participate in some capacity to automatically deposit their published content into the PMC repository. Some participating publishers will delay the release of their articles on PubMed Central for a set time after publication, this is often referred to as an "embargo period", and can range from a few months to a few years depending on the journal. (Embargoes of six to twelve months are the most common.) However, PubMed Central is a key example of "systematic external distribution by a third party" which is still prohibited by the contributor agreements of many publishers.Schadenfreude
Schadenfreude (; German: [ˈʃaːdn̩ˌfʁɔʏ̯də] (listen); lit. 'harm-joy') is the experience of pleasure, joy, or self-satisfaction that comes from learning of or witnessing the troubles, failures, or humiliation of another. It is one of four related emotions or concepts.
Schadenfreude is a complex emotion, where rather than feeling sympathy towards someone's misfortune, schadenfreude evokes joyful feelings that take pleasure from watching someone fail. This emotion is displayed more in children than adults, however adults also experience schadenfreude, they are just better at concealing their expressions.United States National Library of Medicine
The United States National Library of Medicine (NLM), operated by the United States federal government, is the world's largest medical library.Located in Bethesda, Maryland, the NLM is an institute within the National Institutes of Health. Its collections include more than seven million books, journals, technical reports, manuscripts, microfilms, photographs, and images on medicine and related sciences, including some of the world's oldest and rarest works.
The current director of the NLM is Patricia Flatley Brennan.Vancouver system
The Vancouver system, also known as Vancouver reference style or the author–number system, is a citation style that uses numbers within the text that refer to numbered entries in the reference list. It is popular in the physical sciences and is one of two referencing systems normally used in medicine, the other being the author–date, or "Harvard", system. Vancouver style is used by MEDLINE and PubMed.Hundreds of scientific journals use author-number systems. They all follow the same essential logic (that is, numbered citations pointing to numbered list entries), although the trivial details of the output mask, such as punctuation, casing of titles, and italic, vary widely among them. They have existed for over a century; the names "Vancouver system" or "Vancouver style" have existed since 1978. The latest version of the latter is Citing Medicine, per the References > Style and Format section of the ICMJE Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals. These recommendations, the Vancouver Convention and Vancouver guidelines, have a much broader scope than only the citation style: they provide ethical guidelines for writers and rules for co-authorship in scientific collaborations to avoid fraud. The Convention further entails compliance with the Helsinki Declaration, and research projects must be recommended by an independent ethics committee.In the broad sense, the Vancouver system refers to any author-number system regardless of the formatting details. A narrower definition of the Vancouver system refers to a specific author-number format specified by the ICMJE Recommendations (Uniform Requirements for Manuscripts, URM). For example, the AMA reference style is Vancouver style in the broad sense because it is an author-number system that conforms to the URM, but not in the narrow sense because its formatting differs in some minor details from the NLM/PubMed style (such as what is italicized and whether the citation numbers are bracketed).
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