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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.WWW-module.html">Package WWW</a> ::
Module NCBI
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module NCBI</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html">source code</a></span></p>
<p>Provides code to access NCBI over the WWW.</p>
<p>The main Entrez web page is available at:
http://www.ncbi.nlm.nih.gov/Entrez/</p>
<p>A list of the Entrez utilities is available at:
http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html</p>
<p>Documentation for the e-utilies are available at:
http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html</p>
<p>The main Blast web page is available at:
http://www.ncbi.nlm.nih.gov/BLAST/</p>
<p>Functions: query Query Entrez; retrieve results in HTML format.
pmfetch Retrieve results using a unique identifier. pmqty
Search PubMed. pmneighbor Return a list of related articles for a
PubMed entry.</p>
<p>efetch Access the efetch script. _open</p>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Functions</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Functions"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">handle</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#query" class="summary-sig-name">query</a>(<span class="summary-sig-arg">cmd</span>,
<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.ncbi.nlm.nih.gov/sites/entrez'</span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Query Entrez and return a handle to the results, consisting of a web
page in HTML format.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#query">source code</a></span>
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#pmfetch" class="summary-sig-name">pmfetch</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">report</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">mode</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">"http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi"</span>)</span><br />
Query PmFetch and return a handle to the results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmfetch">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">handle</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#pmqty" class="summary-sig-name">pmqty</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">term</span>,
<span class="summary-sig-arg">dopt</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi'</span>)</span><br />
Query PmQty and return a handle to the results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmqty">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">handle</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#pmneighbor" class="summary-sig-name">pmneighbor</a>(<span class="summary-sig-arg">pmid</span>,
<span class="summary-sig-arg">display</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi'</span>)</span><br />
Query PMNeighbor and return a handle to the results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmneighbor">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">handle</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#epost" class="summary-sig-name">epost</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default">...</span>)</span><br />
Query Entrez and return a handle to the results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#epost">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#efetch" class="summary-sig-name">efetch</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
efetch(db[, cgi][...]) -> handle</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#efetch">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#esearch" class="summary-sig-name">esearch</a>(<span class="summary-sig-arg">db</span>,
<span class="summary-sig-arg">term</span>,
<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
esearch(db, term[, cgi][...]) -> handle</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#esearch">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#elink" class="summary-sig-name">elink</a>(<span class="summary-sig-arg">cgi</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
elink([, cgi][...]) -> handle</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#elink">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">UndoHandle</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.WWW.NCBI-module.html#_open" class="summary-sig-name" onclick="show_private();">_open</a>(<span class="summary-sig-arg">cgi</span>,
<span class="summary-sig-arg">params</span>=<span class="summary-sig-default">{}</span>,
<span class="summary-sig-arg">get</span>=<span class="summary-sig-default">1</span>)</span><br />
Open a handle to Entrez.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#_open">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.WWW.NCBI-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.WWW.NCBI is deprecated. The functions in Bio.WWW.NCBI are now a\
vailable from Bio.Entrez; except for the pm* functions which the NCBI \
have retired.',
<type 'exceptions.DeprecationWarning'>,
33): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.WWW.NCBI is deprecated. The funct</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="query"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">query</span>(<span class="sig-arg">cmd</span>,
<span class="sig-arg">db</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.ncbi.nlm.nih.gov/sites/entrez'</span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#query">source code</a></span>
</td>
</tr></table>
<p>Query Entrez and return a handle to the results, consisting of a web
page in HTML format. See the online documentation for an explanation of
the parameters:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
<dt>Returns: handle</dt>
</dl>
</td></tr></table>
</div>
<a name="pmfetch"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">pmfetch</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">id</span>,
<span class="sig-arg">report</span>=<span class="sig-default">None</span>,
<span class="sig-arg">mode</span>=<span class="sig-default">None</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">"http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi"</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmfetch">source code</a></span>
</td>
</tr></table>
<p>Query PmFetch and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="pmqty"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">pmqty</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">term</span>,
<span class="sig-arg">dopt</span>=<span class="sig-default">None</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi'</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmqty">source code</a></span>
</td>
</tr></table>
<p>Query PmQty and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
<dt>Returns: handle</dt>
</dl>
</td></tr></table>
</div>
<a name="pmneighbor"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">pmneighbor</span>(<span class="sig-arg">pmid</span>,
<span class="sig-arg">display</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">'http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi'</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#pmneighbor">source code</a></span>
</td>
</tr></table>
<p>Query PMNeighbor and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
<dt>Returns: handle</dt>
</dl>
</td></tr></table>
</div>
<a name="epost"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">epost</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">id</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default">...</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#epost">source code</a></span>
</td>
</tr></table>
<p>Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
<dt>Returns: handle</dt>
</dl>
</td></tr></table>
</div>
<a name="efetch"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">efetch</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#efetch">source code</a></span>
</td>
</tr></table>
<p>efetch(db[, cgi][...]) -> handle</p>
<p>Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="esearch"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">esearch</span>(<span class="sig-arg">db</span>,
<span class="sig-arg">term</span>,
<span class="sig-arg">cgi</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#esearch">source code</a></span>
</td>
</tr></table>
<p>esearch(db, term[, cgi][...]) -> handle</p>
<p>Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="elink"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">elink</span>(<span class="sig-arg">cgi</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**keywds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#elink">source code</a></span>
</td>
</tr></table>
<p>elink([, cgi][...]) -> handle</p>
<p>Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html</p>
<p>Raises an IOError exception if there's a network error.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_open"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_open</span>(<span class="sig-arg">cgi</span>,
<span class="sig-arg">params</span>=<span class="sig-default">{}</span>,
<span class="sig-arg">get</span>=<span class="sig-default">1</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.WWW.NCBI-pysrc.html#_open">source code</a></span>
</td>
</tr></table>
<p>Open a handle to Entrez. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used. Does some simple error
checking, and will raise an IOError if it encounters one.</p>
<dl class="fields">
<dt>Returns: UndoHandle</dt>
</dl>
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<h3 class="epydoc">__warningregistry__</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.WWW.NCBI is deprecated. The functions in Bio.WWW.NCBI are now a</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">vailable from Bio.Entrez; except for the pm* functions which the NCBI </code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">have retired.</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
33<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
</pre></td></tr></table>
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