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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>Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. </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/helpeutils/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpeutils-lrg.png" alt="Cover of Entrez Programming Utilities Help" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>Entrez Programming Utilities Help [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK25499_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK25499_dtls__"><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>; 2010-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpeutils/">Contents</a></li></ul></div><div class="bk_noprnt"><form method="get" action="/books/n/helpeutils/" id="bk_srch"><div class="bk_search"><label for="bk_term" class="offscreen_noflow">Search term</label><input type="text" title="Search this book" id="bk_term" name="term" value="" data-jig="ncbiclearbutton" /> <input type="submit" class="jig-ncbibutton" value="Search this book" submit="false" style="padding: 0.1em 0.4em;" /></div></form></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpeutils/chapter3/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpeutils/chapter5/" 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="_NBK25499_"><span class="title" itemprop="name">The E-utilities In-Depth: Parameters, Syntax and More</span></h1><p class="contrib-group"><span itemprop="author">Eric Sayers</span>, PhD.</p><a data-jig="ncbitoggler" href="#__NBK25499_ai__" style="border:0;text-decoration:none">Author Information and Affiliations</a><div style="display:none" class="ui-widget" id="__NBK25499_ai__"><p class="contrib-group"><h4>Authors</h4><span itemprop="author">Eric Sayers</span>, PhD<sup><img src="/corehtml/pmc/pmcgifs/corrauth.gif" alt="corresponding author" /></sup><sup>1</sup>.</p><h4>Affiliations</h4><div class="affiliation"><sup>1</sup> NCBI<div><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@sreyas" class="oemail">vog.hin.mln.ibcn@sreyas</a></div></div><div><sup><img src="/corehtml/pmc/pmcgifs/corrauth.gif" alt="corresponding author" /></sup>Corresponding author.</div></div><p class="small">Created: <span itemprop="datePublished">May 29, 2009</span>; Last Update: <span itemprop="dateModified">November 30, 2022</span>.</p><p><em>Estimated reading time: 20 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="chapter4.Introduction"><h2 id="_chapter4_Introduction_">Introduction</h2><p>This chapter serves as a reference for all supported parameters for the E-utilities, along with accepted values and usage guidelines. This information is provided for each E-utility in sections below, and parameters and/or values specific to particular databases are discussed within each section. Most E-utilities have a set of parameters that are required for any call, in addition to several additional optional parameters that extend the tool's functionality. These two sets of parameters are discussed separately in each section.</p></div><div id="chapter4.General_Usage_Guidelines"><h2 id="_chapter4_General_Usage_Guidelines_">General Usage Guidelines</h2><p>Please see <a href="/books/n/helpeutils/chapter2/">Chapter 2</a> for a detailed discussion of E-utility usage policy. The following two parameters should be included in all E-utility requests.</p><div id="chapter4.tool"><h3>tool</h3><p>Name of application making the E-utility call. Value must be a string with no internal spaces.</p></div><div id="chapter4.email"><h3>email</h3><p>E-mail address of the E-utility user. Value must be a string with no internal spaces, and should be a valid e-mail address.</p><p>If you expect to post more than 3 E-utility requests per second from a single IP address, consider including the following parameter:</p></div><div id="chapter4.api_key"><h3>
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<b>api_key</b>
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</h3><p>Value of the API key for sites that post more than 3 requests per second. Please see <a href="/books/n/helpeutils/chapter2/">Chapter 2</a> for a full discussion of this policy.</p></div></div><div id="chapter4.Eutilities_DTDs"><h2 id="_chapter4_Eutilities_DTDs_">E-utilities DTDs</h2><p>With the exception of EFetch, the E-utilities each generate a single XML output format that conforms to a DTD specific for that utility. Links to these DTDs are provided in the XML headers of the E-utility returns.</p><p>ESummary version 2.0 produces unique XML DocSums for each Entrez database, and as such each Entrez database has a unique DTD for version 2.0 DocSums. Links to these DTDs are provided in the version 2.0 XML.</p><p>EFetch produces output in a variety of formats, some of which are XML. Most of these XML formats also conform to DTDs or schema specific to the relevant Entrez database. Please follow the appropriate link below for the PubMed DTD:</p><ul><li class="half_rhythm"><div>
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|
<a href="http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180601.dtd" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed DTD June 2018 – current PubMed DTD</a>
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</div></li><li class="half_rhythm"><div>
|
|
<a href="http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed DTD January 2019 – forthcoming DTD</a>
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|
</div></li></ul></div><div id="chapter4.EInfo"><h2 id="_chapter4_EInfo_">EInfo</h2><div id="chapter4.Base_URL"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi</p></div><div id="chapter4.Functions"><h3>Functions</h3><ul><li class="half_rhythm"><div>Provides a list of the names of all valid Entrez databases</div></li><li class="half_rhythm"><div>Provides statistics for a single database, including lists of indexing fields and available link names</div></li></ul></div><div id="chapter4.Required_Parameters"><h3>Required Parameters</h3><p>None. If no <b>db</b> parameter is provided, einfo will return a list of the names of all valid Entrez databases.</p></div><div id="chapter4.Optional_Parameters"><h3>Optional Parameters</h3><div id="chapter4.db"><h4>db</h4><p>Target database about which to gather statistics. Value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a>.</p></div><div id="chapter4.version"><h4>version</h4><p>Used to specify version 2.0 EInfo XML. The only supported value is ‘2.0’. When present, EInfo will return XML that includes two new fields: <IsTruncatable> and <IsRangeable>. Fields that are truncatable allow the wildcard character ‘*’ in terms. The wildcard character will expand to match any set of characters up to a limit of 600 unique expansions. Fields that are rangeable allow the range operator ‘:’ to be placed between a lower and upper limit for the desired range (e.g. 2008:2010[pdat]).</p></div><div id="chapter4.retmode"><h4>retmode</h4><p>Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for EInfo XML, but ‘json’ is also supported to return output in JSON format.</p></div></div><div id="chapter4.Examples"><h3>Examples</h3><p>Return a list of all Entrez database names:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi</a>
|
|
</span>
|
|
</p><p>Return version 2.0 statistics for Entrez Protein:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=protein&version=2.0" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=protein&version=2.0</a>
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</span>
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</p></div></div><div id="chapter4.ESearch"><h2 id="_chapter4_ESearch_">ESearch</h2><div id="chapter4.Base_URL_1"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi</p></div><div id="chapter4.Functions_1"><h3>Functions</h3><ul><li class="half_rhythm"><div>Provides a list of UIDs matching a text query</div></li><li class="half_rhythm"><div>Posts the results of a search on the History server</div></li><li class="half_rhythm"><div>Downloads all UIDs from a dataset stored on the History server</div></li><li class="half_rhythm"><div>Combines or limits UID datasets stored on the History server</div></li><li class="half_rhythm"><div>Sorts sets of UIDs</div></li></ul><p>API users should be aware that some NCBI products contain search tools that generate content from searches on the web interface that are not available to ESearch. For example, the PubMed web interface (pubmed.ncbi.nlm.nih.gov) contains citation matching and spelling correction tools that are only available through that interface. Please see ECitMatch and ESpell below for API equivalents.</p></div><div id="chapter4.Required_Parameters_1"><h3>Required Parameters</h3><div id="chapter4.db_1"><h4>db</h4><p>Database to search. Value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed).</p></div><div id="chapter4.term"><h4>term</h4><p>Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the <a href="https://pubmed.ncbi.nlm.nih.gov/help/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PubMed</a> or <a href="/books/n/helpentrez/EntrezHelp/">Entrez</a> help for information about search field descriptions and tags. Search fields and tags are database specific.</p><pre>esearch.fcgi?db=pubmed&term=asthma</pre><p>PubMed also offers “<a href="https://pubmed.ncbi.nlm.nih.gov/help/#proximity-searching" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">proximity searching</a>” for multiple terms appearing in any order within a specified number of words from one another in the [Title] or [Title/Abstract] fields.</p><pre>esearch.fcgi?db=pubmed&term=”asthma treatment”[Title:~3]</pre></div></div><div id="chapter4.Optional_Parameters__History_Se"><h3>Optional Parameters – History Server</h3><div id="chapter4.usehistory"><h4>usehistory</h4><p>When <b>usehistory</b> is set to 'y', ESearch will post the UIDs resulting from the search operation onto the History server so that they can be used directly in a subsequent E-utility call. Also, <b>usehistory</b> must be set to 'y' for ESearch to interpret query key values included in <b>term</b> or to accept a <b>WebEnv</b> as input.</p></div><div id="chapter4.WebEnv"><h4>WebEnv</h4><p>Web environment string returned from a previous ESearch, EPost or ELink call. When provided, ESearch will post the results of the search operation to this pre-existing WebEnv, thereby appending the results to the existing environment. In addition, providing <b>WebEnv</b> allows query keys to be used in <b>term</b> so that previous search sets can be combined or limited. As described above, if <b>WebEnv</b> is used, <b>usehistory</b> must be set to 'y'.</p><pre>esearch.fcgi?db=pubmed&term=asthma&WebEnv=<webenv string>&usehistory=y</pre></div><div id="chapter4.query_key"><h4>query_key</h4><p>Integer query key returned by a previous ESearch, EPost or ELink call. When provided, ESearch will find the intersection of the set specified by <b>query_key</b> and the set retrieved by the query in <b>term</b> (i.e. joins the two with AND). For <b>query_key</b> to function, <b>WebEnv</b> must be assigned an existing WebEnv string and <b>usehistory</b> must be set to 'y'.</p><p>Values for query keys may also be provided in <b>term</b> if they are preceeded by a '#' (%23 in the URL). While only one <b>query_key</b> parameter can be provided to ESearch, any number of query keys can be combined in <b>term</b>. Also, if query keys are provided in <b>term</b>, they can be combined with OR or NOT in addition to AND.</p><pre>The following two URLs are functionally equivalent:<br /><br />esearch.fcgi?db=pubmed&term=asthma&query_key=1&WebEnv=<br /><webenv string>&usehistory=y<br /><br />esearch.fcgi?db=pubmed&term=%231+AND+asthma&WebEnv=<br /><webenv string>&usehistory=y</pre></div></div><div id="chapter4.Optional_Parameters__Retrieval"><h3>Optional Parameters – Retrieval</h3><div id="chapter4.retstart"><h4>retstart</h4><p>Sequential index of the first UID in the retrieved set to be shown in the XML output (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with <b>retmax</b> to download an arbitrary subset of UIDs retrieved from a search.</p></div><div id="chapter4.retmax"><h4>retmax</h4><p>Total number of UIDs from the retrieved set to be shown in the XML output (default=20). By default, ESearch only includes the first 20 UIDs retrieved in the XML output. If <b>usehistory</b> is set to 'y', the remainder of the retrieved set will be stored on the History server; otherwise these UIDs are lost. Increasing <b>retmax</b> allows more of the retrieved UIDs to be included in the XML output, up to a maximum of 10,000 records.</p><p>To retrieve more than 10,000 UIDs from databases other than PubMed, submit multiple esearch requests while incrementing the value of <b>retstart</b> (see Application 3). For PubMed, ESearch can only retrieve the first 10,000 records matching the query. To obtain more than 10,000 PubMed records, consider using <EDirect> that contains additional logic to batch PubMed search results automatically so that an arbitrary number can be retrieved.</p></div><div id="chapter4.rettype"><h4>rettype</h4><p>Retrieval type. There are two allowed values for ESearch: 'uilist' (default), which displays the standard XML output, and 'count', which displays only the <Count> tag.</p></div><div id="chapter4.retmode_1"><h4>retmode</h4><p>Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for ESearch XML, but ‘json’ is also supported to return output in JSON format.</p></div><div id="chapter4.sort"><h4>sort</h4><p>Specifies the method used to sort UIDs in the ESearch output. The available values vary by database (<b>db</b>) and may be found in the Display Settings menu on an Entrez search results page. If <b>usehistory</b> is set to ‘y’, the UIDs are loaded onto the History Server in the specified sort order and will be retrieved in that order by ESummary or EFetch. Example values are ‘relevance’ and ‘name’ for Gene. Users should be aware that the default value of <b>sort</b> varies from one database to another, and that the default value used by ESearch for a given database may differ from that used on NCBI web search pages.</p><p>Values of <b>sort</b> for PubMed are as follows:</p><ul><li class="half_rhythm"><div><i>pub_date</i> – descending sort by publication date</div></li><li class="half_rhythm"><div><i>Author</i> – ascending sort by first author</div></li><li class="half_rhythm"><div><i>JournalName</i> – ascending sort by journal name</div></li><li class="half_rhythm"><div><i>relevance</i> – default sort order, (“Best Match”) on web PubMed</div></li></ul></div><div id="chapter4.field"><h4>field</h4><p>Search field. If used, the entire search term will be limited to the specified Entrez field. The following two URLs are equivalent:</p><pre>esearch.fcgi?db=pubmed&term=asthma&field=title<br /><br />esearch.fcgi?db=pubmed&term=asthma[title]</pre></div><div id="chapter4.idtype"><h4>idtype</h4><p>Specifies the type of identifier to return for sequence databases (nuccore, popset, protein). By default, ESearch returns GI numbers in its output. If <b>idtype</b> is set to ‘acc’, ESearch will return accession.version identifiers rather than GI numbers.</p></div></div><div id="chapter4.Optional_Parameters__Dates"><h3>Optional Parameters – Dates</h3><div id="chapter4.datetype"><h4>datetype</h4><p>Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for <b>datetype</b>.</p></div><div id="chapter4.reldate"><h4>reldate</h4><p>When <b>reldate</b> is set to an integer <i>n</i>, the search returns only those items that have a date specified by <b>datetype</b> within the last <i>n</i> days.</p></div><div id="chapter4.mindate_maxdate"><h4>mindate, maxdate</h4><p>Date range used to limit a search result by the date specified by <b>datetype</b>. These two parameters (<b>mindate, maxdate</b>) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.</p></div></div><div id="chapter4.Examples_1"><h3>Examples</h3><p>Search in PubMed with the term <i>cancer</i> for abstracts that have an Entrez date within the last 60 days; retrieve the first 100 PMIDs and translations; post the results on the History server and return a <b>WebEnv</b> and <b>query_key</b>:</p><p>
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<span class="bk_pgobj">
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<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=y" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=y</a>
|
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</span>
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</p><p>Search in PubMed for the journal PNAS, Volume 97, and retrieve six PMIDs starting with the seventh PMID in the list:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PNAS%5Bta%5D+AND+97%5Bvi%5D&retstart=6&retmax=6&tool=biomed3" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PNAS[ta]+AND+97[vi]&retstart=6&retmax=6&tool=biomed3</a>
|
|
</span>
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</p><p>Search in the NLM Catalog for journals matching the term <i>obstetrics</i>:</p><p>
|
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<span class="bk_pgobj">
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|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=obstetrics+AND+ncbijournals%5bfilter%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nlmcatalog&term=obstetrics+AND+ncbijournals[filter]</a>
|
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</span>
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</p><p>Search PubMed Central for free full text articles containing the query <i>stem cells</i>:</p><p>
|
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<span class="bk_pgobj">
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|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pmc&term=stem+cells+AND+free+fulltext%5bfilter%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pmc&term=stem+cells+AND+free+fulltext[filter]</a>
|
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</span>
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</p><p>Search in Nucleotide for all tRNAs:</p><p>
|
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<span class="bk_pgobj">
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<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=biomol+trna%5bprop%5d%20" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=biomol+trna[prop]</a>
|
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</span>
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</p><p>Search in Protein for a molecular weight range:</p><p>
|
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<span class="bk_pgobj">
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|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=70000:90000%5bmolecular+weight%5d" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=70000:90000[molecular+weight]</a>
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</span>
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</p></div></div><div id="chapter4.EPost"><h2 id="_chapter4_EPost_">EPost</h2><div id="chapter4.Base_URL_2"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi</p></div><div id="chapter4.Functions_2"><h3>Functions</h3><ul><li class="half_rhythm"><div>Uploads a list of UIDs to the Entrez History server</div></li><li class="half_rhythm"><div>Appends a list of UIDs to an existing set of UID lists attached to a Web Environment</div></li></ul></div><div id="chapter4.Required_Parameters_2"><h3>Required Parameters</h3><div id="chapter4.db_2"><h4>db</h4><p>Database containing the UIDs in the input list. The value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed).</p></div><div id="chapter4.id"><h4>id</h4><p>UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by <b>db</b>. For PubMed, no more than 10,000 UIDs can be included in a single URL request. For other databases there is no set maximum for the number of UIDs that can be passed to epost, but if more than about 200 UIDs are to be posted, the request should be made using the HTTP POST method.</p><p>For sequence databases (nuccore, popset, protein), the UID list may be a mixed list of GI numbers and accession.version identifiers. <b>Note:</b> When using accession.version identifiers, there is a conversion step that takes place that causes large lists of identifiers to time out, even when using POST. Therefore, we recommend batching these types of requests in sizes of about 500 UIDs or less, to avoid retrieving only a partial amount of records from your original POST input list.</p><pre>epost.fcgi?db=pubmed&id=19393038,30242208,29453458<br />epost.fcgi?db=protein&id=15718680,<a href="/protein/157427902/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">NP_001098858.1</a>,119703751</pre></div></div><div id="chapter4.Optional_Parameter"><h3>Optional Parameter</h3><div id="chapter4.WebEnv_1"><h4>WebEnv</h4><p>Web Environment. If provided, this parameter specifies the Web Environment that will receive the UID list sent by post. EPost will create a new query key associated with that Web Environment. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. If no <b>WebEnv</b> parameter is provided, EPost will create a new Web Environment and post the UID list to <b>query_key</b> 1.</p><pre>epost.fcgi?db=protein&id=15718680,157427902,119703751&WebEnv=<br /><webenv string></pre></div></div><div id="chapter4.Example"><h3>Example</h3><p>Post records to PubMed:</p><p>
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<span class="bk_pgobj">
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<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi?db=pubmed&id=11237011,12466850" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi?db=pubmed&id=11237011,12466850</a>
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</span>
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</p></div></div><div id="chapter4.ESummary"><h2 id="_chapter4_ESummary_">ESummary</h2><div id="chapter4.Base_URL_3"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi</p></div><div id="chapter4.Functions_3"><h3>Functions</h3><ul><li class="half_rhythm"><div>Returns document summaries (DocSums) for a list of input UIDs</div></li><li class="half_rhythm"><div>Returns DocSums for a set of UIDs stored on the Entrez History server</div></li></ul></div><div id="chapter4.Required_Parameter"><h3>Required Parameter</h3><div id="chapter4.db_3"><h4>db</h4><p>Database from which to retrieve DocSums. The value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed).</p></div></div><div id="chapter4.Required_Parameter__Used_only_w"><h3>Required Parameter – Used only when input is from a UID list</h3><div id="chapter4.id_1"><h4>id</h4><p>UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by <b>db</b>. There is no set maximum for the number of UIDs that can be passed to ESummary, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.</p><p>For sequence databases (nuccore, popset, protein), the UID list may be a mixed list of GI numbers and accession.version identifiers.</p><pre>esummary.fcgi?db=pubmed&id=19393038,30242208,29453458<br />esummary.fcgi?db=protein&id=15718680,<a href="/protein/157427902/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">NP_001098858.1</a>,119703751</pre></div></div><div id="chapter4.Required_Parameters__Used_only"><h3>Required Parameters – Used only when input is from the Entrez History server</h3><div id="chapter4.query_key_1"><h4>query_key</h4><p>Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ESummary. Query keys are obtained from the output of previous ESearch, EPost or ELink calls. The <b>query_key</b> parameter must be used in conjunction with <b>WebEnv</b>.</p></div><div id="chapter4.WebEnv_2"><h4>WebEnv</h4><p>Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to ESummary. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. The <b>WebEnv</b> parameter must be used in conjunction with <b>query_key</b>.</p><pre>esummary.fcgi?db=protein&query_key=<key>&WebEnv=<webenv string></pre></div></div><div id="chapter4.Optional_Parameters__Retrieval_1"><h3>Optional Parameters – Retrieval</h3><div id="chapter4.retstart_1"><h4>retstart</h4><p>Sequential index of the first DocSum to be retrieved (default=1, corresponding to the first record of the entire set). This parameter can be used in conjunction with <b>retmax</b> to download an arbitrary subset of DocSums from the input set.</p></div><div id="chapter4.retmax_1"><h4>retmax</h4><p>Total number of DocSums from the input set to be retrieved, up to a maximum of 10,000. If the total set is larger than this maximum, the value of <b>retstart</b> can be iterated while holding <b>retmax</b> constant, thereby downloading the entire set in batches of size <b>retmax</b>.</p></div><div id="chapter4.retmode_2"><h4>retmode</h4><p>Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for ESummary XML, but ‘json’ is also supported to return output in JSON format.</p></div><div id="chapter4.version_1"><h4>version</h4><p>Used to specify version 2.0 ESummary XML. The only supported value is ‘2.0’. When present, ESummary will return version 2.0 DocSum XML that is unique to each Entrez database and that often contains more data than the default DocSum XML.</p></div></div><div id="chapter4.Examples_2"><h3>Examples</h3><p>PubMed:</p><p>
|
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<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=11850928,11482001" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=11850928,11482001</a>
|
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</span>
|
|
</p><p>PubMed, version 2.0 XML:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=11850928,11482001&version=2.0" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=11850928,11482001&version=2.0</a>
|
|
</span>
|
|
</p><p>Protein:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&id=28800982,28628843" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&id=28800982,28628843</a>
|
|
</span>
|
|
</p><p>Nucleotide:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nucleotide&id=28864546,28800981" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nucleotide&id=28864546,28800981</a>
|
|
</span>
|
|
</p><p>Structure:</p><p>
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<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=structure&id=19923,12120" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=structure&id=19923,12120</a>
|
|
</span>
|
|
</p><p>Taxonomy:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&id=9913,30521" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&id=9913,30521</a>
|
|
</span>
|
|
</p><p>UniSTS:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=unists&id=254085,254086" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=unists&id=254085,254086</a>
|
|
</span>
|
|
</p></div></div><div id="chapter4.EFetch"><h2 id="_chapter4_EFetch_">EFetch</h2><div id="chapter4.Base_URL_4"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi</p></div><div id="chapter4.Functions_4"><h3>Functions</h3><ul><li class="half_rhythm"><div>Returns formatted data records for a list of input UIDs</div></li><li class="half_rhythm"><div>Returns formatted data records for a set of UIDs stored on the Entrez History server</div></li></ul></div><div id="chapter4.Required_Parameters_3"><h3>Required Parameters</h3><div id="chapter4.db_4"><h4>db</h4><p>Database from which to retrieve records. The value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed). Currently EFetch does not support all Entrez databases. Please see <a href="/books/n/helpeutils/chapter2/#chapter2.T._entrez_unique_identifiers_ui">Table 1</a> in Chapter 2 for a list of available databases.</p></div></div><div id="chapter4.Required_Parameter__Used_only_w_1"><h3>Required Parameter – Used only when input is from a UID list</h3><div id="chapter4.id_2"><h4>id</h4><p>UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by <b>db</b>. There is no set maximum for the number of UIDs that can be passed to EFetch, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.</p><p>For sequence databases (nuccore, popset, protein), the UID list may be a mixed list of GI numbers and accession.version identifiers.</p><pre>efetch.fcgi?db=pubmed&id=19393038,30242208,29453458<br />efetch.fcgi?db=protein&id=15718680,<a href="/protein/157427902/?report=GenPept" class="bk_tag" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=genpept">NP_001098858.1</a>,119703751</pre><p>
|
|
<i>Special note for sequence databases.</i>
|
|
</p><p>NCBI is no longer assigning GI numbers to a growing number of new sequence records. As such, these records are not indexed in Entrez, and so cannot be retrieved using ESearch or ESummary, and have no Entrez links accessible by ELink. EFetch <i>can</i> retrieve these records by including their accession.version identifier in the <b>id</b> parameter.</p></div></div><div id="chapter4.Required_Parameters__Used_only_1"><h3>Required Parameters – Used only when input is from the Entrez History server</h3><div id="chapter4.query_key_2"><h4>query_key</h4><p>Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to EFetch. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The <b>query_key</b> parameter must be used in conjunction with <b>WebEnv</b>.</p></div><div id="chapter4.WebEnv_3"><h4>WebEnv</h4><p>Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to EFetch. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. The <b>WebEnv</b> parameter must be used in conjunction with <b>query_key</b>.</p><pre>efetch.fcgi?db=protein&query_key=<key>&WebEnv=<webenv string></pre></div></div><div id="chapter4.Optional_Parameters__Retrieval_2"><h3>Optional Parameters – Retrieval</h3><div id="chapter4.retmode_3"><h4>retmode</h4><p>Retrieval mode. This parameter specifies the data format of the records returned, such as plain text, HMTL or XML. See <a href="/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly" target="object" rid-ob="figobchapter4Tvalidvaluesofretmodeand">Table 1</a> for a full list of allowed values for each database.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figchapter4Tvalidvaluesofretmodeand"><a href="/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly" target="object" title="Table 1 " class="img_link icnblk_img" rid-ob="figobchapter4Tvalidvaluesofretmodeand"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="chapter4.T._valid_values_of__retmode_and"><a href="/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly" target="object" rid-ob="figobchapter4Tvalidvaluesofretmodeand">Table 1 </a></h4><p class="float-caption no_bottom_margin">– Valid values of &retmode and &rettype for EFetch (null = empty string) </p></div></div></div><div id="chapter4.rettype_1"><h4>rettype</h4><p>Retrieval type. This parameter specifies the record view returned, such as Abstract or MEDLINE from PubMed, or GenPept or FASTA from protein. Please see <a href="/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly" target="object" rid-ob="figobchapter4Tvalidvaluesofretmodeand">Table 1</a> for a full list of allowed values for each database.</p></div><div id="chapter4.retstart_2"><h4>retstart</h4><p>Sequential index of the first record to be retrieved (default=0, corresponding to the first record of the entire set). This parameter can be used in conjunction with <b>retmax</b> to download an arbitrary subset of records from the input set.</p></div><div id="chapter4.retmax_2"><h4>retmax</h4><p>Total number of records from the input set to be retrieved, up to a maximum of 10,000. Optionally, for a large set the value of <b>retstart</b> can be iterated while holding <b>retmax</b> constant, thereby downloading the entire set in batches of size <b>retmax</b>.</p></div></div><div id="chapter4.Optional_Parameters__Sequence_D"><h3>Optional Parameters – Sequence Databases</h3><div id="chapter4.strand"><h4>strand</h4><p>Strand of DNA to retrieve. Available values are "1" for the plus strand and "2" for the minus strand.</p></div><div id="chapter4.seq_start"><h4>seq_start</h4><p>First sequence base to retrieve. The value should be the integer coordinate of the first desired base, with "1" representing the first base of the seqence.</p></div><div id="chapter4.seq_stop"><h4>seq_stop</h4><p>Last sequence base to retrieve. The value should be the integer coordinate of the last desired base, with "1" representing the first base of the seqence.</p></div><div id="chapter4.complexity"><h4>complexity</h4><p>Data content to return. Many sequence records are part of a larger data structure or "blob", and the <b>complexity</b> parameter determines how much of that blob to return. For example, an mRNA may be stored together with its protein product. The available values are as follows:</p><div id="chapter4.Tc" class="table"><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK25499/table/chapter4.Tc/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__chapter4.Tc_lrgtbl__"><table><thead><tr><th id="hd_h_chapter4.Tc_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Value of complexity</th><th id="hd_h_chapter4.Tc_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Data returned for each requested GI</th></tr></thead><tbody><tr><td headers="hd_h_chapter4.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>0</p>
|
|
</td><td headers="hd_h_chapter4.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>entire blob</p>
|
|
</td></tr><tr><td headers="hd_h_chapter4.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>1</p>
|
|
</td><td headers="hd_h_chapter4.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>bioseq</p>
|
|
</td></tr><tr><td headers="hd_h_chapter4.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>2</p>
|
|
</td><td headers="hd_h_chapter4.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>minimal bioseq-set</p>
|
|
</td></tr><tr><td headers="hd_h_chapter4.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>3</p>
|
|
</td><td headers="hd_h_chapter4.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>minimal nuc-prot</p>
|
|
</td></tr><tr><td headers="hd_h_chapter4.Tc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>4</p>
|
|
</td><td headers="hd_h_chapter4.Tc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
|
|
<p>minimal pub-set</p>
|
|
</td></tr></tbody></table></div></div></div></div><div id="chapter4.Examples_3"><h3>Examples</h3><p>
|
|
<b>PubMed</b>
|
|
</p><p>Fetch PMIDs 17284678 and 9997 as text abstracts:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=17284678,9997&retmode=text&rettype=abstract" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=17284678,9997&retmode=text&rettype=abstract</a>
|
|
</span>
|
|
</p><p>Fetch PMIDs in XML:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11748933,11700088&retmode=xml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11748933,11700088&retmode=xml</a>
|
|
</span>
|
|
</p><p>
|
|
<b>PubMed Central</b>
|
|
</p><p>Fetch XML for PubMed Central ID 212403:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=212403" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=212403</a>
|
|
</span>
|
|
</p><p>
|
|
<b>Nucleotide/Nuccore</b>
|
|
</p><p>Fetch the first 100 bases of the plus strand of GI 21614549 in FASTA format:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=1&seq_start=1&seq_stop=100&rettype=fasta&retmode=text" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=1&seq_start=1&seq_stop=100&rettype=fasta&retmode=text</a>
|
|
</span>
|
|
</p><p>Fetch the first 100 bases of the minus strand of GI 21614549 in FASTA format:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=2&seq_start=1&seq_stop=100&rettype=fasta&retmode=text" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=2&seq_start=1&seq_stop=100&rettype=fasta&retmode=text</a>
|
|
</span>
|
|
</p><p>Fetch the nuc-prot object for GI 21614549:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&complexity=3" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&complexity=3</a>
|
|
</span>
|
|
</p><p>Fetch the full ASN.1 record for GI 5:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5</a>
|
|
</span>
|
|
</p><p>Fetch FASTA for GI 5:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta</a>
|
|
</span>
|
|
</p><p>Fetch the GenBank flat file for GI 5:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb</a>
|
|
</span>
|
|
</p><p>Fetch GBSeqXML for GI 5:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb&retmode=xml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=gb&retmode=xml</a>
|
|
</span>
|
|
</p><p>Fetch TinySeqXML for GI 5:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta&retmode=xml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=5&rettype=fasta&retmode=xml</a>
|
|
</span>
|
|
</p><p>
|
|
<b>Popset</b>
|
|
</p><p>Fetch the GenPept flat file for Popset ID 12829836:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=popset&id=12829836&rettype=gp" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=popset&id=12829836&rettype=gp</a>
|
|
</span>
|
|
</p><p>
|
|
<b>Protein</b>
|
|
</p><p>Fetch the GenPept flat file for GI 8:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp</a>
|
|
</span>
|
|
</p><p>Fetch GBSeqXML for GI 8:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp&retmode=xml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=8&rettype=gp&retmode=xml</a>
|
|
</span>
|
|
</p><p>
|
|
<b>Sequences</b>
|
|
</p><p>Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sequences&id=312836839,34577063&rettype=fasta&retmode=text" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sequences&id=312836839,34577063&rettype=fasta&retmode=text</a>
|
|
</span>
|
|
</p><p>
|
|
<b>Gene</b>
|
|
</p><p>Fetch full XML record for Gene ID 2:</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2&retmode=xml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2&retmode=xml</a>
|
|
</span>
|
|
</p></div></div><div id="chapter4.ELink"><h2 id="_chapter4_ELink_">ELink</h2><div id="chapter4.Base_URL_5"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi</p></div><div id="chapter4.Functions_5"><h3>Functions</h3><ul><li class="half_rhythm"><div>Returns UIDs linked to an input set of UIDs in either the same or a different Entrez database</div></li><li class="half_rhythm"><div>Returns UIDs linked to other UIDs in the same Entrez database that match an Entrez query</div></li><li class="half_rhythm"><div>Checks for the existence of Entrez links for a set of UIDs within the same database</div></li><li class="half_rhythm"><div>Lists the available links for a UID</div></li><li class="half_rhythm"><div>Lists LinkOut URLs and attributes for a set of UIDs</div></li><li class="half_rhythm"><div>Lists hyperlinks to primary LinkOut providers for a set of UIDs</div></li><li class="half_rhythm"><div>Creates hyperlinks to the primary LinkOut provider for a single UID</div></li></ul></div><div id="chapter4.Required_Parameters_4"><h3>Required Parameters</h3><div id="chapter4.db_5"><h4>db</h4><p>Database from which to retrieve UIDs. The value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed). This is the destination database for the link operation.</p></div><div id="chapter4.dbfrom"><h4>dbfrom</h4><p>Database containing the input UIDs. The value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed). This is the origin database of the link operation. If <b>db</b> and <b>dbfrom</b> are set to the same database value, then ELink will return computational neighbors within that database. Please see the <a href="https://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">full list of Entrez links</a> for available computational neighbors. Computational neighbors have linknames that begin with <i>dbname_dbname</i> (examples: protein_protein, pcassay_pcassay_activityneighbor).</p></div><div id="chapter4.cmd"><h4>cmd</h4><p>ELink command mode. The command mode specified which function ELink will perform. Some optional parameters only function for certain values of &cmd (see below).</p><p>
|
|
<b>cmd=neighbor (default)</b>
|
|
</p><p>ELink returns a set of UIDs in <b>db</b> linked to the input UIDs in <b>dbfrom.</b></p><p>
|
|
<i>Example: Link from protein to gene</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=neighbor_score</b>
|
|
</p><p>ELink returns a set of UIDs within the same database as the input UIDs along with computed similarity scores<b>.</b></p><p>
|
|
<i>Example: Find related articles to PMID 20210808</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=20210808&cmd=neighbor_score" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=20210808&cmd=neighbor_score</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=neighbor_history</b>
|
|
</p><p>ELink posts the output UIDs to the Entrez History server and returns a <b>query_key</b> and <b>WebEnv</b> corresponding to the location of the output set.</p><p>
|
|
<i>Example: Link from protein to gene and post the results on the Entrez History</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902&cmd=neighbor_history" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902&cmd=neighbor_history</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=acheck</b>
|
|
</p><p>ELink lists all links available for a set of UIDs.</p><p>
|
|
<i>Example: List all possible links from two protein GIs</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&id=15718680,157427902&cmd=acheck" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&id=15718680,157427902&cmd=acheck</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Example: List all possible links from two protein GIs to PubMed</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=pubmed&id=15718680,157427902&cmd=acheck" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=pubmed&id=15718680,157427902&cmd=acheck</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=ncheck</b>
|
|
</p><p>ELink checks for the existence of links <i>within the same database</i> for a set of UIDs. These links are equivalent to setting <b>db</b> and <b>dbfrom</b> to the same value.</p><p>
|
|
<i>Example: Check whether two nuccore sequences have "related sequences" links.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&id=21614549,219152114&cmd=ncheck" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&id=21614549,219152114&cmd=ncheck</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=lcheck</b>
|
|
</p><p>Elink checks for the existence of external links (LinkOuts) for a set of UIDs.</p><p>
|
|
<i>Example: Check whether two protein sequences have any LinkOut providers.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&id=15718680,157427902&cmd=lcheck" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&id=15718680,157427902&cmd=lcheck</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=llinks</b>
|
|
</p><p>For each input UID, ELink lists the URLs and attributes for the LinkOut providers that are not libraries.</p><p>
|
|
<i>Example: List the LinkOut URLs for non-library providers for two pubmed abstracts.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=llinks" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=llinks</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=llinkslib</b>
|
|
</p><p>For each input UID, ELink lists the URLs and attributes for <i>all</i> LinkOut providers including libraries.</p><p>
|
|
<i>Example: List all LinkOut URLs for two PubMed abstracts.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=llinkslib" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=llinkslib</a>
|
|
</span>
|
|
</p><p>
|
|
<b>cmd=prlinks</b>
|
|
</p><p>ELink lists the primary LinkOut provider for each input UID, or links directly to the LinkOut provider's web site for a single UID if <b>retmode</b> is set to <i>ref</i>.</p><p>
|
|
<i>Example: Find links to full text providers for two PubMed abstracts.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=prlinks" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848,19822630&cmd=prlinks</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Example: Link directly to the full text for a PubMed abstract at the provider's web site.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848&cmd=prlinks&retmode=ref" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=19880848&cmd=prlinks&retmode=ref</a>
|
|
</span>
|
|
</p></div></div><div id="chapter4.Required_Parameter__Used_only_w_2"><h3>Required Parameter – Used only when input is from a UID list</h3><div id="chapter4.id_3"><h4>id</h4><p>UID list. Either a single UID or a comma-delimited list of UIDs may be provided. All of the UIDs must be from the database specified by <b>dbfrom</b>. There is no set maximum for the number of UIDs that can be passed to ELink, but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method.</p><p>
|
|
<i>Link from protein to gene.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902,119703751" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680,157427902,119703751</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Find related sequences (link from nuccore to nuccore).</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=nuccore&id=34577062" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=nuccore&id=34577062</a>
|
|
</span>
|
|
</p><p>If more than one <b>id</b> parameter is provided, ELink will perform a separate link operation for the set of UIDs specified by each <b>id</b> parameter. This effectively accomplishes "one-to-one" links and preserves the connection between the input and output UIDs.</p><p>
|
|
<i>Find one-to-one links from protein to gene.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680&id=157427902&id=119703751" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680&id=157427902&id=119703751</a>
|
|
</span>
|
|
</p><p>For sequence databases (nuccore, popset, protein), the UID list may be a mixed list of GI numbers and accession.version identifiers.</p><p>
|
|
<i>Find one-to-one links from protein to gene.</i>
|
|
</p><p>
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680&id=NP_001098858.1&id=119703751" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=gene&id=15718680&id=NP_001098858.1&id=119703751</a>
|
|
</p></div></div><div id="chapter4.Required_Parameters__Used_only_2"><h3>Required Parameters – Used only when input is from the Entrez History server</h3><div id="chapter4.query_key_3"><h4>query_key</h4><p>Query key. This integer specifies which of the UID lists attached to the given Web Environment will be used as input to ELink. Query keys are obtained from the output of previous ESearch, EPost or ELInk calls. The <b>query_key</b> parameter must be used in conjunction with <b>WebEnv</b>.</p></div><div id="chapter4.WebEnv_4"><h4>WebEnv</h4><p>Web Environment. This parameter specifies the Web Environment that contains the UID list to be provided as input to ELink. Usually this WebEnv value is obtained from the output of a previous ESearch, EPost or ELink call. The <b>WebEnv</b> parameter must be used in conjunction with <b>query_key</b>.</p><pre>Link from protein to gene:<br />elink.fcgi?dbfrom=protein&db=gene&query_key=<key>&WebEnv=<webenv string><br /><br />Find related sequences (link from protein to protein):<br />elink.fcgi?dbfrom=protein&db=protein&query_key=<key>&WebEnv=<br /><webenv string></pre></div></div><div id="chapter4.Optional_Parameter__Retrieval"><h3>Optional Parameter – Retrieval</h3><div id="chapter4.retmode_4"><h4>retmode</h4><p>Retrieval type. Determines the format of the returned output. The default value is ‘xml’ for ELink XML, but ‘json’ is also supported to return output in JSON format.</p></div><div id="chapter4.idtype_1"><h4>idtype</h4><p>Specifies the type of identifier to return for sequence databases (nuccore, popset, protein). By default, ELink returns GI numbers in its output. If <b>idtype</b> is set to ‘acc’, ELink will return accession.version identifiers rather than GI numbers.</p></div></div><div id="chapter4.Optional_Parameters__Limiting_t"><h3>Optional Parameters – Limiting the Output Set of Links</h3><div id="chapter4.linkname"><h4>linkname</h4><p>Name of the Entrez link to retrieve. Every link in Entrez is given a name of the form</p><p><i>dbfrom_db_subset</i>.</p><p>The values of <i>subset</i> vary depending on the values of <i>dbfrom</i> and <i>db</i>. Many <i>dbfrom/db</i> combinations have no <i>subset</i> values. See <a href="https://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">the list of Entrez links</a> for a listing of all available linknames. When <b>linkname</b> is used, only the links with that name will be retrieved.</p><p>The <b>linkname</b> parameter only functions when <b>cmd</b> is set to <i>neighbor</i> or <i>neighbor_history</i>.</p><p>
|
|
<i>Find all links from gene to snp.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=93986" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=93986</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Find snps with genotype data linked to genes.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=93986&linkname=gene_snp_genegenotype" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=93986&linkname=gene_snp_genegenotype</a>
|
|
</span>
|
|
</p></div><div id="chapter4.term_1"><h4>term</h4><p>Entrez query used to limit the output set of linked UIDs. The query in the <b>term</b> parameter will be applied after the link operation, and only those UIDs matching the query will be returned by ELink. The <b>term</b> parameter only functions when <b>db</b> and <b>dbfrom</b> are set to the same database value.</p><p>
|
|
<i>Find all related articles for a PMID.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=19879512" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=19879512</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Find all related review articles published in 2008 for a PMID.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=19879512&term=review%5Bfilter%5D+AND+2008%5Bpdat%5D" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=19879512&term=review%5Bfilter%5D+AND+2008%5Bpdat%5Dh</a>
|
|
</span>
|
|
</p></div><div id="chapter4.holding"><h4>holding</h4><p>Name of LinkOut provider. Only URLs for the LinkOut provider specified by <b>holding</b> will be returned. The value provided to <b>holding</b> should be the abbreviation of the LinkOut provider's name found in the <NameAbbr> tag of the ELink XML output when <b>cmd</b> is set to <i>llinks</i> or <i>llinkslib</i>. The <b>holding</b> parameter only functions when <b>cmd</b> is set to <i>llinks</i> or <i>llinkslib</i>.</p><p>
|
|
<i>Find information for all LinkOut providers for a PMID.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=llinkslib&id=16210666" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=llinkslib&id=16210666</a>
|
|
</span>
|
|
</p><p>
|
|
<i>Find information from clinicaltrials.gov for a PMID.</i>
|
|
</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=llinkslib&id=16210666&holding=CTgov" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&cmd=llinkslib&id=16210666&holding=CTgov</a>
|
|
</span>
|
|
</p></div></div><div id="chapter4.Optional_Parameters__Dates_1"><h3>Optional Parameters – Dates</h3><p>These parameters only function when <b>cmd</b> is set to <i>neighbor</i> or <i>neighbor_history</i> and <b>dbfrom</b> is <i>pubmed</i>.</p><div id="chapter4.datetype_1"><h4>datetype</h4><p>Type of date used to limit a link operation. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for <b>datetype</b>.</p></div><div id="chapter4.reldate_1"><h4>reldate</h4><p>When <b>reldate</b> is set to an integer <i>n</i>, ELink returns only those items that have a date specified by <b>datetype</b> within the last <i>n</i> days.</p></div><div id="chapter4.mindate_maxdate_1"><h4>mindate, maxdate</h4><p>Date range used to limit a link operation by the date specified by <b>datetype</b>. These two parameters (<b>mindate, maxdate</b>) must be used together to specify an arbitrary date range. The general date format is YYYY/MM/DD, and these variants are also allowed: YYYY, YYYY/MM.</p></div></div></div><div id="chapter4.EGQuery"><h2 id="_chapter4_EGQuery_">EGQuery</h2><div id="chapter4.Base_URL_6"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi</p></div><div id="chapter4.Function"><h3>Function</h3><p>Provides the number of records retrieved in all Entrez databases by a single text query.</p></div><div id="chapter4.Required_Parameter_1"><h3>Required Parameter</h3><div id="chapter4.term_2"><h4>term</h4><p>Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the <a href="/books/n/helppubmed/pubmedhelp/#pubmedhelp.Search_Field_Descrip">PubMed</a> or <a href="/books/n/helpentrez/EntrezHelp/">Entrez</a> help for information about search field descriptions and tags. Search fields and tags are database specific.</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=asthma" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=asthma</a>
|
|
</span>
|
|
</p></div></div></div><div id="chapter4.ESpell"><h2 id="_chapter4_ESpell_">ESpell</h2><div id="chapter4.Base_URL_7"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi</p></div><div id="chapter4.Function_1"><h3>Function</h3><p>Provides spelling suggestions for terms within a single text query in a given database.</p></div><div id="chapter4.Required_Parameters_5"><h3>Required Parameters</h3><div id="chapter4.db_6"><h4>db</h4><p>Database to search. Value must be a valid <a href="/books/n/helpeutils/chapter2/#chapter2.chapter2_table1">Entrez database name</a> (default = pubmed).</p></div><div id="chapter4.term_3"><h4>term</h4><p>Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. For very long queries (more than several hundred characters long), consider using an HTTP POST call. See the <a href="/books/n/helppubmed/pubmedhelp/#pubmedhelp.Search_Field_Descrip">PubMed</a> or <a href="/books/n/helpentrez/EntrezHelp/">Entrez</a> help for information about search field descriptions and tags. Search fields and tags are database specific.</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?db=pubmed&term=asthmaa+OR+alergies" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?db=pubmed&term=asthmaa+OR+alergies</a>
|
|
</span>
|
|
</p></div></div></div><div id="chapter4.ECitMatch"><h2 id="_chapter4_ECitMatch_">ECitMatch</h2><div id="chapter4.Base_URL_8"><h3>Base URL</h3><p>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi</p></div><div id="chapter4.Function_2"><h3>Function</h3><p>Retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings.</p></div><div id="chapter4.Required_Parameters_6"><h3>Required Parameters</h3><div id="chapter4.db_7"><h4>db</h4><p>Database to search. The only supported value is ‘pubmed’.</p></div><div id="chapter4.rettype_2"><h4>rettype</h4><p>Retrieval type. The only supported value is ‘xml’.</p></div><div id="chapter4.bdata"><h4>bdata</h4><p>Citation strings. Each input citation must be represented by a citation string in the following format:</p><p>journal_title|year|volume|first_page|author_name|your_key|</p><p>Multiple citation strings may be provided by separating the strings with a carriage return character (%0D). The <i>your_key</i> value is an arbitrary label provided by the user that may serve as a local identifier for the citation, and it will be included in the output. Be aware that all spaces must be replaced by ‘+’ symbols and that citation strings should end with a final vertical bar ‘|’.</p><p>
|
|
<span class="bk_pgobj">
|
|
<a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=proc+natl+acad+sci+u+s+a|1991|88|3248|mann+bj|Art1|%0Dscience|1987|235|182|palmenberg+ac|Art2|" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=proc+natl+acad+sci+u+s+a|1991|88|3248|mann+bj|Art1|%0Dscience|1987|235|182|palmenberg+ac|Art2|</a>
|
|
</span>
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</p></div></div></div><div id="chapter4.Release_Notes"><h2 id="_chapter4_Release_Notes_">Release Notes</h2><div id="chapter4.EFetch_ELink_JSON_ouput_June_24"><h3>EFetch; ELink JSON ouput: June 24, 2015</h3><ul><li class="half_rhythm"><div>EFetch now supports ClinVar and GTR</div></li><li class="half_rhythm"><div>ELink now provides output in JSON format</div></li></ul></div><div id="chapter4.ESearch__sort_JSON_output_forma"><h3>ESearch &sort; JSON output format: February 14, 2014</h3><ul><li class="half_rhythm"><div>ESearch now provides a supported <b>sort</b> parameter</div></li><li class="half_rhythm"><div>EInfo, ESearch and ESummary now provide output data in JSON format</div></li></ul></div><div id="chapter4.ECitMatch_EInfo_Version_2_0_EFe"><h3>ECitMatch, EInfo Version 2.0, EFetch: August 9, 2013</h3><ul><li class="half_rhythm"><div>ECitMatch is a new E-utility that serves as an API to the PubMed <a href="https://www.ncbi.nlm.nih.gov/pubmed/batchcitmatch" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">batch citation matcher</a></div></li><li class="half_rhythm"><div>EInfo has an updated XML output that includes two new fields: <IsTruncatable> and <IsRangeable></div></li><li class="half_rhythm"><div>EFetch now supports the BioProject database.</div></li></ul></div><div id="chapter4.EFetch_Version_2_0_Target_relea"><h3>EFetch Version 2.0. Target release date: February 15, 2012</h3><ul><li class="half_rhythm"><div>EFetch now supports the following databases: biosample, biosystems and sra</div></li><li class="half_rhythm"><div>EFetch now has defined default values for &retmode and &rettype for all supported databases (please see <a href="/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly" target="object" rid-ob="figobchapter4Tvalidvaluesofretmodeand">Table 1</a> for all supported values of these parameters)</div></li><li class="half_rhythm"><div>EFetch no longer supports &retmode=html; requests containing &retmode=html will return data using the default &retmode value for the specified database (&db)</div></li><li class="half_rhythm"><div>EFetch requests including &rettype=docsum return XML data equivalent to ESummary output</div></li></ul></div><div id="chapter4.Release_of_new_Genome_database"><h3>Release of new Genome database: November 9, 2011</h3><ul><li class="half_rhythm"><div>Entrez Genome has been completely redesigned, and database records now correspond to a species rather than an individual chromosome sequence. Please see full details of the change at <a href="https://www.ncbi.nlm.nih.gov/About/news/17Nov2011.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/About/news/17Nov2011.html</a></div></li><li class="half_rhythm"><div>Old Genome IDs are no longer valid. A file is available on the NCBI FTP site that maps old Genome IDs to Nucleotide GIs: <a href="ftp://ftp.ncbi.nih.gov/genomes/old_genomeID2nucGI" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp.ncbi.nih.gov/genomes/old_genomeID2nucGI</a></div></li><li class="half_rhythm"><div>EFetch no longer supports retrievals from Genome (db=genome).</div></li><li class="half_rhythm"><div>The ESummary XML for Genome has been recast to reflect the new data model.</div></li><li class="half_rhythm"><div>To view the new search fields and links supported for the new Genome database, please see <a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=genome" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=genome</a></div></li></ul></div><div id="chapter4.ESummary_Version_2_0_November_4"><h3>ESummary Version 2.0. November 4, 2011</h3><ul><li class="half_rhythm"><div>ESummary now supports a new, alternative XML presentation for Entrez document summaries (DocSums). The new XML is unique to each Entrez database and generally contains more extensive data about the record than the original DocSum XML.</div></li><li class="half_rhythm"><div>There are no plans at present to discontinue the original DocSum XML, so developers can continue to use this presentation, which will remain the default.</div></li><li class="half_rhythm"><div>Version 2.0 XML is returned when &version=2.0 is included in the ESummary URL.</div></li></ul></div></div><div id="chapter4.Demonstration_Programs"><h2 id="_chapter4_Demonstration_Programs_">Demonstration Programs</h2><p>Please see <a href="/books/n/helpeutils/chapter1/#chapter1.Demonstration_Programs">Chapter 1</a> for sample Perl scripts.</p></div><div id="chapter4.For_More_Information"><h2 id="_chapter4_For_More_Information_">For More Information</h2><p>Please see <a href="/books/n/helpeutils/chapter1/#chapter1.For_More_Information_8">Chapter 1</a> for getting additional information about the E-utilities.</p></div><div id="bk_toc_contnr"></div></div></div>
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