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<a href="Bio-module.html">Package Bio</a> ::
Module PubMed
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module PubMed</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PubMed-pysrc.html">source code</a></span></p>
<p>This module provides code to work with PubMed from the NCBI.
http://www.ncbi.nlm.nih.gov/PubMed/</p>
<p>Online documentation for linking to PubMed is available at:
http://www.ncbi.nlm.nih.gov/PubMed/linking.html</p>
<p>Classes: Dictionary Access PubMed articles using a dictionary
interface.</p>
<p>Functions: search_for Search PubMed. find_related Find related
articles in PubMed. download_many Download many articles from PubMed in
batch mode.</p>
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<span class="summary-type"> </span>
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<a href="Bio.PubMed.Dictionary-class.html" class="summary-name">Dictionary</a><br />
Access PubMed using a read-only dictionary interface.
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<td><span class="summary-sig"><a href="Bio.PubMed-module.html#search_for" class="summary-sig-name">search_for</a>(<span class="summary-sig-arg">search</span>,
<span class="summary-sig-arg">reldate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">mindate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">maxdate</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">batchsize</span>=<span class="summary-sig-default">100</span>,
<span class="summary-sig-arg">callback_fn</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">start_id</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">max_ids</span>=<span class="summary-sig-default">None</span>)</span><br />
search_for(search[, reldate][, mindate][, maxdate] [, batchsize][,
callback_fn][, start_id][, max_ids]) -> ids</td>
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<span class="codelink"><a href="Bio.PubMed-pysrc.html#search_for">source code</a></span>
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<span class="summary-type">ids</span>
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<td><span class="summary-sig"><a href="Bio.PubMed-module.html#find_related" class="summary-sig-name">find_related</a>(<span class="summary-sig-arg">pmid</span>)</span><br />
Search PubMed for a list of citations related to pmid.</td>
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<span class="codelink"><a href="Bio.PubMed-pysrc.html#find_related">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PubMed-module.html#download_many" class="summary-sig-name">download_many</a>(<span class="summary-sig-arg">ids</span>,
<span class="summary-sig-arg">callback_fn</span>,
<span class="summary-sig-arg">broken_fn</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">batchsize</span>=<span class="summary-sig-default">500</span>,
<span class="summary-sig-arg">parser</span>=<span class="summary-sig-default">None</span>)</span><br />
download_many(ids, callback_fn[, broken_fn][, batchsize])</td>
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<span class="codelink"><a href="Bio.PubMed-pysrc.html#download_many">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">search_for</span>(<span class="sig-arg">search</span>,
<span class="sig-arg">reldate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">mindate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">maxdate</span>=<span class="sig-default">None</span>,
<span class="sig-arg">batchsize</span>=<span class="sig-default">100</span>,
<span class="sig-arg">callback_fn</span>=<span class="sig-default">None</span>,
<span class="sig-arg">start_id</span>=<span class="sig-default">0</span>,
<span class="sig-arg">max_ids</span>=<span class="sig-default">None</span>)</span>
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<p>search_for(search[, reldate][, mindate][, maxdate] [, batchsize][,
callback_fn][, start_id][, max_ids]) -> ids</p>
<p>Search PubMed and return a list of the PMID's that match the criteria.
search is the search string used to search the database. reldate is the
number of dates prior to the current date to restrict the search.
mindate and maxdate are the dates to restrict the search, e.g.
2002/01/01. batchsize specifies the number of ids to return at one time.
By default, it is set to 10000, the maximum. callback_fn is an optional
callback function that will be called as passed a PMID as results are
retrieved. start_id specifies the index of the first id to retrieve and
max_ids specifies the maximum number of id's to retrieve.</p>
<p>XXX The date parameters don't seem to be working with NCBI's script.
Please let me know if you can get it to work.</p>
<dl class="fields">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">find_related</span>(<span class="sig-arg">pmid</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PubMed-pysrc.html#find_related">source code</a></span>
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<p>Search PubMed for a list of citations related to pmid. pmid can be a
PubMed ID, a MEDLINE UID, or a list of those.</p>
<dl class="fields">
<dt>Returns: ids</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">download_many</span>(<span class="sig-arg">ids</span>,
<span class="sig-arg">callback_fn</span>,
<span class="sig-arg">broken_fn</span>=<span class="sig-default">None</span>,
<span class="sig-arg">batchsize</span>=<span class="sig-default">500</span>,
<span class="sig-arg">parser</span>=<span class="sig-default">None</span>)</span>
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><span class="codelink"><a href="Bio.PubMed-pysrc.html#download_many">source code</a></span>
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<p>download_many(ids, callback_fn[, broken_fn][, batchsize])</p>
<p>Download many records from PubMed. ids is a list of either the
Medline Unique ID or the PubMed ID's of the articles. Each time a record
is downloaded, callback_fn is called with the text of the record.
broken_fn is an optional function that is called with the id of records
that were not able to be downloaded. batchsize is the number of records
to request each time.</p>
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