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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. </p></div><div class="bk_msg_box bk_bttm_mrgn clearfix bk_noprnt"><div class="iconblock clearfix"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook2e/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook2e-lrg.png" alt="Cover" height="100px" width="80px" /></a><div class="icnblk_cntnt"><ul class="messages"><li class="info icon"><span class="icon"><a href="/books/n/handbook2e/">See "The NCBI Handbook, 2nd Edition"</a></span></li></ul></div></div></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" alt="Cover of The NCBI Handbook" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>The NCBI Handbook [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK21094_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK21094_dtls__"><div>McEntyre J, Ostell J, editors.</div><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2002-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/handbook/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch1/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch3/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK21094_"><span class="label">Chapter 2</span><span class="title" itemprop="name">PubMed: The Bibliographic Database</span></h1><p class="contrib-group"><span itemprop="author">Kathi Canese</span>, <span itemprop="author">Jennifer Jentsch</span>, and <span itemprop="author">Carol Myers</span>.</p><p class="small">Created: <span itemprop="datePublished">October 9, 2002</span>; Last Update: <span itemprop="dateModified">August 13, 2003</span>.</p><p><em>Estimated reading time: 14 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><h2 id="__abs_rndgid__">Summary</h2><p><a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> is a database developed by the National Center for Biotechnology Information (<a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>) at the National Library of Medicine (<a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>), one of the institutes of the National Institutes of Health (<a class="def" href="/books/n/handbook/A1237/def-item/app120/">NIH</a>). The database was designed to provide access to citations (with abstracts) from biomedical journals. Subsequently, a linking feature was added to provide access to full-text journal articles at Web sites of participating publishers, as well as to other related Web resources. PubMed is the bibliographic component of the NCBI's <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> retrieval system.</p></div><div id="A43"><h2 id="_A43_">Data Sources</h2><div id="A44"><h3>MEDLINE<sup>®</sup></h3><p>
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<a href="/books/n/handbook/A1237/#app150">PubMed</a>'s primary data resource is <a href="/books/n/handbook/A1237/#app102">MEDLINE</a>, the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>'s premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences, such as molecular biology. <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> contains bibliographic citations and author abstracts from about 4,600 biomedical journals published in the United States and 70 other countries. The database contains about 12 million citations dating back to the mid-1960s. Coverage is worldwide, but most records are from English-language sources or have English abstracts.</p></div><div id="A45"><h3>Non-MEDLINE</h3><p>In addition to <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> citations, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a><sup>®</sup> provides access to non-MEDLINE resources, such as out-of-scope citations, citations that precede MEDLINE selection, and PubMed Central (<a class="def" href="/books/n/handbook/A1237/def-item/app138/">PMC</a>; see <a href="/books/n/handbook/ch9/">Chapter 9</a>) citations. Together, these are often referred to as “PubMed-only citations.” Out-of-scope citations are primarily from general science and chemistry journals that contain life sciences articles indexed for MEDLINE, e.g., the plate tectonics or astrophysics articles from <i>Science</i> magazine. Publishers can also submit citations with publication dates that precede the journal's selection for MEDLINE indexing, usually because they want to create links to older content. PMC citations are taken from life sciences journals (MEDLINE or non-MEDLINE) that submit full-text articles to PMC. In addition to the incorporation of PubMed-only citations, PubMed has been enhanced recently by the incorporation of citations from the following unique databases: HealthSTAR, AIDSLINE, HISTLINE, SPACELINE, BIOETHICSLINE, and POPLINE.</p><p>In response to new approaches to electronic publishing, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> can now also accommodate articles published electronically in advance of being collected into an issue. We refer to these citations as "ahead of print" or "epub" citations.</p></div><div id="A46"><h3>Journal Selection Criteria</h3><p>All content in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> ultimately comes from publishers of biomedical journals, and journals that are to be included in <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> are subject to a selection process. The <a href="http://www.nlm.nih.gov/pubs/factsheets/jsel.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Fact Sheet</a> on <i>Journal Selection for Index Medicus<sup>®</sup>/MEDLINE<sup>®</sup></i> describes the journal selection policy, criteria, and procedures for data submission.</p></div></div><div id="A47"><h2 id="_A47_">Electronic Data Submission</h2><p>Electronic data submission benefits everyone: publishers, the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>, and users. For the NLM, it eliminates the tremendous costs associated with entering data by hand. For publishers and users, it means that newly published data appear rapidly and accurately in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>. Some publishers are now making pre-publication material available before it is formally published (“ahead of print” or “epub” citations); others are publishing electronic-only journals. By close collaboration with the publisher, the citations for these publications can appear in PubMed on the same day as the article is published.</p><p>Furthermore, electronic data submission allows publishers to create links from abstracts in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> to the full text of the appropriate articles available on their own Web site. This can be achieved using <a class="def" href="/books/n/handbook/A1237/def-item/app94/">LinkOut</a> (<a href="/books/n/handbook/ch17/">Chapter 17</a>). Both subscribers to the journals and other PubMed users can access the full text according to criteria that are determined by the publishers, increasing traffic to their sites.</p><p>Although the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a> works with many publishers directly, some publishers contract with commercial data aggregators, companies that prepare and submit the publisher's data to the NLM. Many aggregators also host publisher data on their Web sites.</p><div id="A48"><h3>Electronic Data Submission Process</h3><p>All electronic data are supplied via <a href="/books/n/handbook/A1237/#app58">FTP</a> to <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> in <a class="def" href="/books/n/handbook/A1237/def-item/app198/">XML</a> format, in accordance with the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>'s specifications (document type definition, or <a href="/books/n/handbook/A1237/#app40">DTD</a>). These specifications can be found in <a href="/entrez/query/static/spec.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NLM Standard Publisher Data Format</a> document. The document includes information on XML tag descriptions, how to handle special characters (e.g., α or β), examples of tagged records, the <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> <a class="def" href="/books/n/handbook/A1237/def-item/app40/">DTD</a>, and a FAQ section for participating or potential data providers. Publishers or other data providers who want to submit electronic data should write to: <a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@rehsilbup" class="oemail">vog.hin.mln.ibcn@rehsilbup</a>.</p><p><a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> staff will guide new data providers through the approval process for file submission. New providers are asked to submit test files, which are then checked for <a class="def" href="/books/n/handbook/A1237/def-item/app198/">XML</a> formatting and syntax and for bibliographic accuracy and completeness. The files are revised and resubmitted as many times as necessary until all criteria are met. Once approved, a private account is set up on our <a class="def" href="/books/n/handbook/A1237/def-item/app58/">FTP</a> site to receive new journal issues, or in the case of online publications, individual articles as they are added to the publisher's Web site. We run a file-loading script that automatically processes the files daily, Monday through Friday at approximately 9:00 a.m. (Eastern Time). The new citations are assigned a <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> ID number (<a class="def" href="/books/n/handbook/A1237/def-item/app139/">PMID</a>), a confirmation report is sent to the provider, and the new citations usually become available in PubMed sometime after 11:00 a.m. the next day, Tuesday through Saturday.</p><p>After posting in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, the citations are forwarded to <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>'s Indexing Section for bibliographic data verification and for the addition of subject indexing terms from Medical Subject Headings [<a href="/books/n/handbook/A1237/#app104">MeSH</a>]. This process can take several weeks, after which time completed citations flow back into PubMed, replacing the originally submitted data.</p></div></div><div id="A49"><h2 id="_A49_">Database Management and Hardware</h2><p><a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> is one of the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> databases within the relational database management system, <a href="/books/n/handbook/A1237/#app45">Entrez</a> (see <a href="/books/n/handbook/ch15/">Chapter 15</a>). <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> is a text-based search and retrieval system based on in-house software that uses an indexing system for rapid retrieval of information.</p><p>Requests for <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> services, including <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, are first proxied through three load-balanced Dell PowerEdge 1650 servers, each with two central processing units. The proxy servers, in turn, load-balance requests forwarded on to the Web servers for PubMed and other NCBI services.</p><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> Web servers comprise eight Dell PowerEdge 8450 servers. The Dell servers have eight central processing units, 8 <a class="def" href="/books/n/handbook/A1237/def-item/app60/">GB</a> of memory, and about 300 GB of disk space and run the Linux operating system.</p><p>The Web servers retrieve <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> records from two <a class="def" href="/books/n/handbook/A1237/def-item/app176/">Sybase</a> SQL database servers, which run on Sun Enterprise 450s. To accommodate the data volume output by PubMed and other Web-based services, the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a> has a high-speed connection (OC-3, up to 155 Mbits/sec) to the Internet, as well as a 622 Mbits/sec connection (OC-12) to Internet2, the noncommercial network used by many leading research universities.</p></div><div id="A50"><h2 id="_A50_">Indexing</h2><div id="A51"><h3>PubMed Citation Status and Assignment of MeSH Terms</h3><p>Citations in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> are assigned one of three citation status tags that display next to the PubMed ID (<a class="def" href="/books/n/handbook/A1237/def-item/app139/">PMID</a>) numbers on all PubMed citations. The citation status tags indicate the citation's stage in the <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> indexing process. The three tags are:</p><p>
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<b>[<a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> - as supplied by publisher]</b>: This tag is displayed on citations added recently to PubMed via electronic submission from a publisher (which may or may not move on for <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> indexing).</p><p>
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<b>[<a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> - in process]</b>: This tag is displayed on citations that have had the first stage of quality review to verify that the journal, date, volume, and/or issue are correct. They will be reviewed for other accurate bibliographic data at the article level (e.g., pagination, authors, article title, and abstract) and indexed, i.e., the articles will be reviewed and <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> vocabulary will be assigned (if the subject of the article is within the scope of <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a>).</p><p>
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<b>[<a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> - indexed for <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a>]</b>: This tag is displayed on citations that have been indexed with <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a>, Publication Types, Registry Numbers, etc., and have been completely reviewed for accurate bibliographic data. This is an intellectual process of assigning controlled vocabulary terms to describe the contents of the journal article and verifying other aspects of the citation data.</p><p>Most citations that are received electronically from publishers progress through “in process” status to <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> status. Those citations not indexed for MEDLINE remain tagged [<a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> - as supplied by publisher]. Citations with “in process” status proceed to MEDLINE status after <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> terms, publication types, sequence Accession numbers, and other indexing data are added.</p><p>All records are added to <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> Monday through Friday and become available for viewing Tuesday through Saturday. For additional information, please see the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a> <a href="http://www.nlm.nih.gov/pubs/factsheets/dif_med_pub.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Fact Sheet</a>: <i>What's the Difference Between <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a><sup>®</sup> and PubMed<sup>®</sup>?</i>
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</p></div><div id="A52"><h3>The Automatic Computer Indexing Process</h3><p>The aim of the computer indexing process is to automatically create multiple machine-readable access points that refer to the different components of the journal citations for use when searching <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>. The citations are loaded into PubMed from both the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a> Data Creation and Maintenance System (<a class="def" href="/books/n/handbook/A1237/def-item/app34/">DCMS</a>) and directly from journal publishers (<a class="figpopup" href="/books/NBK21094/figure/A53/?report=objectonly" target="object" rid-figpopup="figA53" rid-ob="figobA53">Figure 1</a>). Both sources are in <a class="def" href="/books/n/handbook/A1237/def-item/app198/">XML</a>.
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</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA53" co-legend-rid="figlgndA53"><a href="/books/NBK21094/figure/A53/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figA53" rid-ob="figobA53"><img class="small-thumb" src="/books/NBK21094/bin/ch2f1.gif" src-large="/books/NBK21094/bin/ch2f1.jpg" alt="Figure 1. A schematic representation of PubMed data flow." /></a><div class="icnblk_cntnt" id="figlgndA53"><h4 id="A53"><a href="/books/NBK21094/figure/A53/?report=objectonly" target="object" rid-ob="figobA53">Figure 1</a></h4><p class="float-caption no_bottom_margin">A schematic representation of PubMed data flow. </p></div></div><p>During the computer indexing process, the citation information is broken down into index fields such as Journal Name, Author Name, and Title/Abstract. The words in each of the fields are checked against the corresponding index (i.e., title words in a new citation are looked up in the Title/Abstract Index). If the word already exists, the <a class="def" href="/books/n/handbook/A1237/def-item/app139/">PMID</a> of the citation is listed with that index term. If the word is a new one for the Index, it is added as a new Index term, and the PMID is listed alongside it. (In the first instance that the term already exists, the new term will have only this one citation associated with it; this is how the <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> indexes grow.)</p><p>Each <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> citation is, therefore, associated with several indexes, and in cases similar to the Title/Abstract Index, many different index terms can refer back to a single citation. Likewise, commonly used terms will refer to thousands of citations (the term “cell”, for example, is found in the Title/Abstract of 1,092,124 citations at the time of this writing). The Field Indexes can be browsed by using PubMed's <a href="/entrez/query.fcgi?CMD=IndexView&DB=PubMed" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Preview/Index</a> function.</p></div></div><div id="A54"><h2 id="_A54_">How PubMed Queries Are Processed</h2><div id="A55"><h3>Automatic Term Mapping</h3><p><a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> uses <a href="/entrez/query/static/help/pmhelp.html#AutomaticTermMapping" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Automatic Term Mapping</a> to process words entered in the query box by someone searching PubMed. Terms entered without a qualifier, i.e., a simple text phrase that does not specify a search field, are looked up against the following translation tables and indexes in a distinct order:</p><p>1. <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Translation Table</p><p>2. Journals Translation Table</p><p>3. Author Index</p><div id="A56"><h4>1. MeSH Translation Table</h4><p>The <a href="/entrez/query/static/help/pmhelp.html#MeSHTranslationTable" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">MeSH Translation Table</a> contains:</p>
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<ul><li id="A57" class="half_rhythm"><div><a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Terms</div></li><li id="A58" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#subheadingslist" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Subheadings</a>
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</div></li><li id="A59" class="half_rhythm"><div>See-Reference mappings (also known as entry terms) for <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> terms</div></li><li id="A60" class="half_rhythm"><div>Mappings derived from the Unified Medical Language System (<a href="/books/n/handbook/A1237/#app185">UMLS</a>) that have equivalent synonyms or lexical variants in English</div></li><li id="A61" class="half_rhythm"><div>Names of Substances and synonyms to the Names of Substances (now known as Supplementary Concept Substance Names)</div></li></ul>
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<p>If the search term is found in this translation table, the term will be mapped to the appropriate <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> term, and the Indexes will be searched as both the text word entered by the user and the MeSH term:</p><div id="box1" class="box"><h3><span class="title">Search term: gallstones</span></h3><p>“Gallstones” is an entry term for the <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> term “cholelithiasis” in the MeSH translation table.</p><p>Search translated to: “cholelithiasis” [<a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Terms] OR gallstones [Text Word]</p></div><p>When a term is searched as a <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> term, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> automatically searches that term plus the more specific terms underneath in the <a href="/entrez/meshbrowser.cgi?retrievestring=&mbdetail=n&term=breast+cancer" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">MeSH hierarchy</a>:</p><div id="box2" class="box"><h3><span class="title">Search term: breast cancer</span></h3><p>“Breast cancer” is an entry term for the <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> term “breast neoplasms” in the MeSH translation table.</p><p>“Breast neoplasms” has the specific headings “breast neoplasms, male”, “mammary neoplasms”, “mammary neoplasms, experimental”, and “phyllodes tumor”, all of which are also searched.</p></div></div><div id="A62"><h4>2. Journals Translation Table</h4><p>If the search term(s) is not found in the <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Translation Table, the <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> search algorithm then looks up the term in the <a href="/entrez/query/static/help/pmhelp.html#JournalsTranslationTable" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Journals Translation Table</a>, which contains the full journal title, <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> abbreviation, and International Standard Serial Number (<a href="/books/n/handbook/A1237/#app90">ISSN</a>):</p><div id="box3" class="box"><h3><span class="title">Search term: New England Journal of Medicine</span></h3><p>“New England Journal of Medicine” maps to N Engl J Med.</p><p>Search translated to: “N Engl J Med” [Journal Name]</p></div><p>If a journal name is also a <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> term, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> will search the term as both a MeSH term and as a Text Word, but not as a <a href="/entrez/query/static/help/pmhelp.html#JournalTitles" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">journal name</a>, for a search that does not specify the “journal” field:</p><div id="box4" class="box"><h3><span class="title">Search term: Cell</span></h3><p>Search translated as: “cells” [<a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Terms] OR cell [Text Word]</p></div><div id="box5" class="box"><h3><span class="title">Search term: Cell [Journal]</span></h3><p>Search translated as: “Cell” [Journal]</p></div></div><div id="A64"><h4>3. Author Index</h4><p>If the phrase is not found in <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> or the Journals Translation Table and is a word with one or two letters after it, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> then checks the <a href="/entrez/query/static/help/pmhelp.html#AuthorIndex" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Author Index</a>. The author's name should be entered in the form: Last Name (space) Initials, e.g., o'malley f, smith jp, or gomez-sanchez m.</p><p>If only one initial is used, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> finds all names with that first initial, and if only an author's last name is entered, PubMed will search that name in All Fields. It will not default to the Author Index because an initial does not follow the last name:</p><div id="box6" class="box"><h3><span class="title">Search term: o'malley f</span></h3><p>Search translated as: o'malley fa, o'malley fb, o'malley fc, o'malley fd, o'malley f jr, etc.</p></div><div id="box7" class="box"><h3><span class="title">Search term: o'malley</span></h3><p>Search translated as: “o'malley” [All Fields]</p></div><p>A history of the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>'s author indexing policy regarding the number of authors to include in a citation is outlined in <a class="figpopup" href="/books/NBK21094/table/A65/?report=objectonly" target="object" rid-figpopup="figA65" rid-ob="figobA65">Table 1</a>.
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</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figA65"><a href="/books/NBK21094/table/A65/?report=objectonly" target="object" title="Table 1" class="img_link icnblk_img figpopup" rid-figpopup="figA65" rid-ob="figobA65"><img class="small-thumb" src="/books/NBK21094/table/A65/?report=thumb" src-large="/books/NBK21094/table/A65/?report=previmg" alt="Table 1. History of NLM author-indexing policy." /></a><div class="icnblk_cntnt"><h4 id="A65"><a href="/books/NBK21094/table/A65/?report=objectonly" target="object" rid-ob="figobA65">Table 1</a></h4><p class="float-caption no_bottom_margin">History of NLM author-indexing policy. </p></div></div></div></div><div id="A66"><h3>Search Rules and Field Abbreviations</h3><p>It is possible to override <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>'s Automatic Term Mapping by using search rules, syntax, and qualifying terms with search field abbreviations.</p><p>The <a href="/books/n/handbook/A1237/#app16">Boolean</a> operators AND, OR, and NOT must be entered in uppercase letters and are processed left to right. Nesting of search terms is possible by enclosing concepts in parentheses. The terms inside the set of parentheses will be processed as a unit and then incorporated into the overall strategy. Terms may be qualified using <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>'s <a href="/entrez/query/static/help/pmhelp.html#SearchFieldDescriptionsandTags" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Search Field Descriptions and Tags</a>. Each search term should be followed by the appropriate search field tag, which indicates which field will be searched:</p><p>Search term: o'malley [au] will search only the author field. Specifying the field precludes the Automatic Term Mapping, which would result in the search o'malley[All Fields] if the field were not specified. Similarly, using the search term Cell [Journal] avoids using the <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Translation Table, which would interpret Cell as only a text word and MeSH term.</p></div></div><div id="A67"><h2 id="_A67_">Using PubMed</h2><div id="A68"><h3>Searching</h3><div id="A69"><h4>Simple Searching</h4><p>A simple search can be conducted from the <a href="http://www.ncbi.nih.gov/entrez/query.fcgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed</a> homepage by entering terms in the query box and pressing Enter from the keyboard or clicking on the <b>Go</b> button on the screen.</p><p>If more than one term is entered in the query box, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> will go through the Automatic Term Mapping protocol described in the previous section, first looking for all the terms, as typed, to find an exact match. If the exact phrase is not found, PubMed clips a term off the end and repeats Automatic Term Mapping, again looking for an exact match, but this time to the abbreviated query. This continues until none of the words are found in any one of the translation tables. In this case, PubMed combines terms (with the AND <a class="def" href="/books/n/handbook/A1237/def-item/app16/">Boolean</a> operator) and applies the Automatic Term Mapping process to each individual word. PubMed ignores <a href="/entrez/query/static/help/pmhelp.html#Stopwords" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Stopwords</a>, such as “about”, “of”, or “what”. People can also apply their own Boolean operators (AND, OR, NOT) to multiple search terms; the Boolean operators must be in uppercase.</p><div id="box8" class="box"><h3><span class="title">Search term: vitamin c common cold</span></h3><p>Translated as: ((“ascorbic acid” [<a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Terms] OR vitamin c [Text Word]) AND (“common cold” [MeSH Terms] OR common cold [Text Word]))</p></div><div id="box9" class="box"><h3><span class="title">Search term: single cell separation brain</span></h3><p>Translated as: (((“single person” [<a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> Terms] OR single [Text Word]) AND (“cell separation” [MeSH Terms] OR cell separation [Text Word])) AND (“brain” [MeSH Terms] OR brain [Text Word]))</p></div><p>If a phrase of more than two terms is not found in any translation table, then the last word of the phrase is dropped, and the remainder of the phrase is sent through the entire process again. This continues, removing one word at a time, until a match is found.</p><p>If there is no match found during the Automatic Term Mapping process, the individual terms will be combined with AND and searched in All Fields.</p><p>One can see how <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> interpreted a search by selecting <b>Details</b> from the Features Bar on the PubMed search pages after completing a search. For more information, see <a href="/entrez/query/static/help/pmhelp.html#Details" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Details</a>.</p></div><div id="A70"><h4>Complex Searching</h4><p>There are a variety of ways that <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> can be searched in a more sophisticated manner than simply typing search terms into the search box and selecting <b>Go</b>. It is possible to construct complex search strategies using <a class="def" href="/books/n/handbook/A1237/def-item/app16/">Boolean</a> operators and the various functions listed below, provided in the <a href="/entrez/query/static/help/pmhelp.html#FeaturesBar" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Features Bar</a>:</p>
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<ul><li id="A71" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#Limits" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Limits</a> restricts search terms to a specific search field.</div></li><li id="A72" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#Index" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Preview/Index</a> allows users to view and select terms from search field indexes and to preview the number of search results before displaying citations.</div></li><li id="A73" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#History" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">History</a> holds previous search strategies and results. The results can be combined to make new searches.</div></li><li id="A74" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#Clipboard" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Clipboard</a> allows users to save or view selected citations from one search or several searches.</div></li><li id="A75" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#Details" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Details</a> displays the search strategy as it was translated by <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, including error messages.</div></li></ul>
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</div></div></div><div id="A76"><h2 id="_A76_">Additional PubMed Features</h2><p>The following resources are available to facilitate effective searches:</p>
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<ul><li id="A77" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#MeSHBrowser" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">MeSH Database</a> allows searching of MeSH, <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a>'s controlled vocabulary. Users can find MeSH terms appropriate to a search strategy, obtain information about each term, and view the terms within their hierarchical structure.</div></li><li id="A78" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#ClinicalQueries" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Clinical Queries</a> is a set of search filters developed for clinicians to retrieve clinical studies of the etiology, prognosis, diagnosis, prevention, or treatment of disorders. The Systematic Reviews feature retrieves systematic reviews and meta-analysis studies by topic.</div></li><li id="A79" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#JournalBrowser" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Journal Database</a> allows searches of journal names, <a class="def" href="/books/n/handbook/A1237/def-item/app102/">MEDLINE</a> abbreviations, or <a class="def" href="/books/n/handbook/A1237/def-item/app90/">ISSN</a> numbers for journals that are included in the <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> system. A list of journals with links to full text is also included.</div></li><li id="A80" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#SingleCitationMatcher" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Single Citation Matcher</a> is a “fill-in-the-blank” form that allows a user to find the <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> ID (<a class="def" href="/books/n/handbook/A1237/def-item/app139/">PMID</a>) number for a single article or all citations in a given journal issue by entering partial journal citation information.</div></li><li id="A81" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#BatchCitationMatcher" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Batch Citation Matcher</a> allows users to find <a class="def" href="/books/n/handbook/A1237/def-item/app139/">PMID</a> numbers that correspond to their own list of citations. Publishers or other database providers who want to link directly from bibliographic references on their Web sites to entries in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> use this service frequently.</div></li><li id="A82" class="half_rhythm"><div><a href="/entrez/query/static/help/pmhelp.html#Cubby" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cubby</a> is a place for users to store search strategies, <a class="def" href="/books/n/handbook/A1237/def-item/app94/">LinkOut</a> preferences, and changes to the default <a href="/entrez/query/static/help/pmhelp.html#DocumentDeliveryServices" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Document Delivery Services</a>.</div></li></ul>
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</div><div id="A83"><h2 id="_A83_">Results</h2><p><a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> retrieves and displays search results in the Summary format in the order the record was initially added to PubMed, with the most recent first. (Note that this date can differ widely from the publication date.) Citations can be viewed in several other <a href="/entrez/query/static/help/pmhelp.html#DisplayingFormats" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">formats</a> and can be <a href="/entrez/query/static/help/pmhelp.html#Sort" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">sorted</a>, <a href="/entrez/query/static/help/pmhelp.html#Saving" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">saved</a>, and <a href="/entrez/query/static/help/pmhelp.html#Printing" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">printed</a>, or the full text can be <a href="/entrez/query/static/help/pmhelp.html#Ordering" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ordered</a>.</p></div><div id="A84"><h2 id="_A84_">Links from PubMed</h2><p>A variety of links can be found on <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> citations including:</p><p>
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<a href="/entrez/query/static/help/pmhelp.html#RelatedPubMedArticlesLink" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Related Articles</a>, which retrieves a precalculated set of <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> citations that are closely related to the selected article. PubMed creates this set by comparing words from the title, abstract, and <a class="def" href="/books/n/handbook/A1237/def-item/app104/">MeSH</a> terms using a word-weighted <a href="/entrez/query/static/computation.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">algorithm</a>.</p><p>
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<a href="/entrez/linkout/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">LinkOut</a>, which provides links to publishers, aggregators, libraries, biological databases, sequencing centers, and other Web sites. These link to the provider's site to obtain the full text of articles or related resources, e.g., consumer health information or molecular biology database records. There may be a charge to access the text or information, depending on the policy of the provider.</p><p>
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<a href="http://web.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Books</a>, which provides links to textbooks so that users can explore unfamiliar concepts found in search results. In collaboration with book publishers, <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> is adapting textbooks for the Web and linking them to <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>. The Books link displays a facsimile of the abstract, in which some words or phrases show up as hypertext links to the corresponding terms in the books available at NCBI. Selecting a hyperlinked word or phrase takes you to a list of book entries in which the phrase is found.</p><p><a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> databases, as well as other resources, may be available from the <b>Links</b> pull-down menu to the right of each citation and from the <b>Display</b> pull-down menu. <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> will return only the first 500 items when using the <b>Display</b> pull-down menu, from which the following links are available:</p>
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<ul><li id="A85" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Protein" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Protein</a> – amino acid (protein) sequences from <a href="/books/n/handbook/A1237/#app175">SWISS-PROT</a>, <a href="/books/n/handbook/A1237/#app137">PIR</a>, <a href="/books/n/handbook/A1237/#app143">PRF</a>, and <a href="/books/n/handbook/A1237/#app130">PDB</a> and translated protein sequences from the <a class="def" href="/books/n/handbook/A1237/def-item/app37/">DNA</a> sequences databases.</div></li><li id="A86" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Nucleotide" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Nucleotide</a> – <a class="def" href="/books/n/handbook/A1237/def-item/app37/">DNA</a> sequences from <a href="/books/n/handbook/A1237/#app62">GenBank</a>, <a href="/books/n/handbook/A1237/#app44">EMBL</a>, and <a href="/books/n/handbook/A1237/#app35">DDBJ</a>.</div></li><li id="A87" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Popset" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PopSet</a> – aligned sequences submitted as a set from a population, phylogenetic, or <a class="def" href="/books/n/handbook/A1237/def-item/app115/">mutation</a> study describing such events as evolution and population variation.</div></li><li id="A88" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Structure" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Structure</a> – three-dimensional structures from the Molecular Modeling Database (<a href="/books/n/handbook/A1237/#app112">MMDB</a>) that were determined by X-ray crystallography and <a href="/books/n/handbook/A1237/#app122">NMR</a> spectroscopy.</div></li><li id="A89" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Genome" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Genome</a> – records and graphic displays of entire genomes and chromosomes for megabase-scale sequences.</div></li><li id="A90" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=geo" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ProbeSet</a> – gene expression data repository and online resource for the retrieval of gene expression data from any organism or artificial source.</div></li><li id="A91" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=OMIM" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">OMIM</a> – directory of human genes and genetic disorders.</div></li><li id="A1633" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=SNP" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">SNP</a> – dbSNP is a database of single nucleotide polymorphisms.</div></li><li id="A1634" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=cdd" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Domains</a> – The Domains database is used to identify the conserved domains present in a protein sequence.</div></li><li id="A1758" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=Domains" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">3D Domains</a> – the domains from <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Structure.</div></li><li id="A1759" class="half_rhythm"><div><a href="/entrez/query.fcgi?db=pmc" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PMC</a> – <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> Central.</div></li></ul>
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</div><div id="A92"><h2 id="_A92_">How to Create Hyperlinks to PubMed</h2><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> system provides three distinct ways to create Web <a href="/books/n/handbook/A1237/#app190">URL</a> links that search and retrieve items from <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> and the molecular biology databases: (1) by using the <a href="/entrez/query/static/eutils_help.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez Programming Utilities</a>; (2) via the <a href="/entrez/query/static/help/pmhelp.html#SavingaSearchStrategy" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">URL button</a> on the <b>Details</b> screen; and (3) by constructing URLs <a href="/entrez/query/static/linking.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">by hand</a>.</p><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Programming Utilities can be used to create <a class="def" href="/books/n/handbook/A1237/def-item/app190/">URL</a> links directly to all Entrez data, including <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> citations and their link information, without using the front-end Entrez query engine. These Utilities provide a fast, efficient way to search and download citation data.</p></div><div id="A93"><h2 id="_A93_">Customer Support</h2><p>If you need more assistance, please contact our <a href="/entrez/query/static/help/pmhelp.html#ForMoreAssistance" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Customer Support</a> services by selecting the <b>Support Center</b> link displayed on all <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> pages or by sending an email to <a href="mailto:dev@null" data-email="vog.hin.mln@vrestsuc" class="oemail">vog.hin.mln@vrestsuc</a>. You may also contact the <a class="def" href="/books/n/handbook/A1237/def-item/app121/">NLM</a> Customer Service Desk at 1-888-346-3656 [(1-888)-FINDNLM]. Hours of operation are Monday through Friday from 8:30 a.m. to 8:45 p.m. and Saturday from 9:00 a.m. to 5:00 p.m. (Eastern Time).</p><p>Additional information is also available in the <a href="http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed Tutorial</a>, <a href="http://www.nlm.nih.gov/pubs/web_based.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed Training Manuals</a>, and <a href="http://www.nlm.nih.gov/pubs/techbull/tb.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NLM Technical Bulletin</a>.</p><p>
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<a href="/entrez/query/static/faq.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">FAQs</a> are available on all <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> pages.</p></div><div id="bk_toc_contnr"></div></div></div>
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