medic/README.html at master · henn/medic · GitHub

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<div class="document" id="medic">
<h1 class="title">medic</h1>
<h2 class="subtitle" id="a-command-line-tool-to-manage-a-mirror-of-medline">a command-line tool to manage a mirror of MEDLINE</h2>

<p>The Swiss Army knife to parse <a class="reference external" href="http://www.nlm.nih.gov/bsd/mms/medlineelements.html">MEDLINE</a> XML files or
download eUtils' <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed">PubMed</a> XML records,
bootstrapping a local MEDLINE/PubMed database,
updating and/or deleting the records, and
writing the contents of selected PMIDs into flat-files.</p>
<div class="section" id="synopsis">
<h1>Synopsis</h1>
<pre class="literal-block">
medic [options] CMD FILE|PMID...

man medic
medic --help
medic --output /tmp parse baseline/medline*.xml.gz
medic --update parse update/medline*.xml.gz
medic --info delete delete.txt
medic --url sqlite:///tmp.db insert pubmed.xml
medic --pmid-lists update pmids_to_fetch_online.txt
medic --all update medline13n1000.xml
medic --format html write 1028734 1298474 &gt; out.html
medic --logfile log.txt write pmid_list.txt
</pre>
</div>
<div class="section" id="setup">
<h1>Setup</h1>
<p>If you are <strong>not</strong> using <tt class="docutils literal">pip install medic</tt>, install all
dependencies/requirements:</p>
<pre class="literal-block">
pip install sqlalchemy
# only if using python3 &lt; 3.2:
pip install argparse
</pre>
<p>Install the <strong>DB driver</strong> you prefer to use (supported are PostgreSQL
and SQLite, with the latter part of the Python StdLib):</p>
<pre class="literal-block">
pip install psycopg2
</pre>
<p>Create the PostgreSQL database:</p>
<pre class="literal-block">
createdb medline
</pre>
<p>If you are fine working with SQLite, you only need to use the path to the
SQLite DB file in the URL option (that will implicitly &quot;create&quot; the DB):</p>
<pre class="literal-block">
medic insert --url sqlite:///tmp.db 123456
</pre>
<p>To create the tables in the DB, you can &quot;try&quot; to fetch a record: As the DB
is empty, this will not write anything, but SQL Alchemy will create the tables
for you in the DB:</p>
<pre class="literal-block">
medic write 123 # for PostgreSQL
medic --url sqlite:///tmp.db write 123 # for SQLite
</pre>
</div>
<div class="section" id="description">
<h1>Description</h1>
<p><tt class="docutils literal">medic [options] COMMAND <span class="pre">PMID|FILE...</span></tt></p>
<p>The <tt class="docutils literal"><span class="pre">--url</span> URL</tt> option represents the DSN of the database and might
be needed (default: <tt class="docutils literal"><span class="pre">postgresql://localhost/medline</span></tt>); For example:</p>
<dl class="docutils">
<dt>PostgreSQL</dt>
<dd><tt class="docutils literal"><span class="pre">postgresql://host//dbname</span></tt></dd>
<dt>SQLite DB</dt>
<dd><tt class="docutils literal"><span class="pre">sqlite:////absolute/path/to/foo.db</span></tt> or
<tt class="docutils literal"><span class="pre">sqlite:///relative/path/to/foo.db</span></tt></dd>
</dl>
<p>The five <strong>COMMAND</strong> arguments:</p>
<dl class="docutils">
<dt><tt class="docutils literal">insert</tt></dt>
<dd>Create records in the DB by parsing MEDLINE XML files or
by downloading PubMed XML from NCBI eUtils for a list of PMIDs.
The insert fails if the record already exists in the DB.</dd>
<dt><tt class="docutils literal">write</tt> *</dt>
<dd>Write records as <a class="reference external" href="http://www.nlm.nih.gov/bsd/mms/medlineelements.html">MEDLINE</a> files to a directory, each file named as
&quot;&lt;pmid&gt;.txt&quot;. Alternatively, just the TIAB (title and abstract) plain-text
can be output, and finally, a single file in TSV or HTML format can be
generated (see option <tt class="docutils literal"><span class="pre">--format</span></tt>).
If the requested PMID does not exist in the DB, the command does not fail,
but the relevant file, row, or element will not have been written.</dd>
<dt><tt class="docutils literal">update</tt></dt>
<dd>Insert or update records in the DB (instead of creating them); note that
if a record exists, but is added with <tt class="docutils literal">create</tt>, this would throw an
<cite>IntegrityError</cite>. If you are not sure if the records are in the DB or
not, use <tt class="docutils literal">update</tt> (N.B. that <tt class="docutils literal">update</tt> is slower).</dd>
<dt><tt class="docutils literal">delete</tt> *</dt>
<dd>Delete records from the DB for a list of PMIDs (using <tt class="docutils literal"><span class="pre">--pmid-lists</span></tt>)</dd>
<dt><tt class="docutils literal">parse</tt></dt>
<dd>Does not interact with the DB, but rather creates &quot;.tab&quot; files for each
table that later can be used to load a database, particularly useful when
bootstrapping a large collection.</dd>
</dl>
<p>* Note that <tt class="docutils literal">write</tt> and <tt class="docutils literal">delete</tt> can only use PMID lists (option
<tt class="docutils literal"><span class="pre">--pmid-lists</span></tt>), so for these two commands, that option is always active
(implicitly).</p>
<p>For example, to download two PubMed records by PMID and update them in
the DB:</p>
<pre class="literal-block">
medic update 100000 123456
</pre>
<p>Add a single MEDLINE or PubMed XML file to the database:</p>
<pre class="literal-block">
medic insert pudmed.xml
</pre>
<p>Export a few records from the database as HTML (to STDOUT):</p>
<pre class="literal-block">
medic write --format html 292837491 128374 213487
</pre>
<p>Note that if the suffix &quot;.gz&quot; is present, the parser automatically
decompresses the XML file(s) first. This feature <em>only</em> works with
GNU-zipped files and the &quot;.gz&quot; suffix must be present.</p>
<p>Therefore, command line arguments are treated as follows:</p>
<dl class="docutils">
<dt>integer values</dt>
<dd>are always treated as PMIDs to download PubMed XML data</dd>
<dt>all other values</dt>
<dd>are always treated as MEDLINE XML files to parse
<strong>unless</strong> you use the option <tt class="docutils literal"><span class="pre">--pmid-lists</span></tt></dd>
<dt>files ending in &quot;.gz&quot;</dt>
<dd>are treated as gzipped MEDLINE XML files</dd>
</dl>
</div>
<div class="section" id="requirements">
<h1>Requirements</h1>
<ul class="simple">
<li>Python 3.2+</li>
<li>SQL Alchemy 0.8+</li>
<li>PostgreSQL 8.4+ or SQLite 3.7+</li>
</ul>
<p><em>Note</em> that while any DB supported by SQL Alchemy should work, all other DBs
are <strong>untested</strong>.</p>
</div>
<div class="section" id="loading-medline">
<h1>Loading MEDLINE</h1>
<p>Please be aware that the MEDLINE distribution <strong>is not unique</strong>, meaning that
it contains a few records multiple times (see the section about
<strong>Version IDs</strong>).</p>
<p>Parsing and loading the baseline into a PostgreSQL DB on the same machine:</p>
<pre class="literal-block">
medic parse baseline/medline14n*.xml.gz

for table in citations abstracts authors chemicals databases \
descriptors identifiers keywords publication_types qualifiers sections;
  do psql medline -c &quot;COPY $table FROM '`pwd`/${table}.tab';&quot;;
done
</pre>
<p>For the update files, you need to go <em>one-by-one</em>, adding each one <em>in order</em>,
and using the flag <tt class="docutils literal"><span class="pre">--update</span></tt> when parsing the XML. After parsing an XML file
and <em>before</em> loading the dump, run <tt class="docutils literal">medic delete delete.txt</tt> to get rid of
all entities that will be updated or should be removed (PMIDs listed as
<tt class="docutils literal">DeleteCitation</tt>s):</p>
<pre class="literal-block">
# parse a MEDLINE update file:
medic --update parse medline14n1234.xml.gz

# delete its updated and DeleteCitation records:
medic delete delete.txt

# load (COPY) all tables for that MEDLINE file:
for table in citations abstracts authors chemicals databases \
descriptors identifiers keywords publication_types qualifiers sections;
  do psql medline -c &quot;COPY $table FROM '`pwd`/${table}.tab';&quot;;
done
</pre>
<p>Alternatively - simpler but slower - you can just <tt class="docutils literal">update</tt> from the XML
directly:</p>
<pre class="literal-block">
medic update medline14n1234.xml.gz
</pre>
</div>
<div class="section" id="version-ids">
<h1>Version IDs</h1>
<p>MEDLINE has began to use versions to allow publishers to add multiple citations
for the same PMID. This only occurs with 71 articles from one journal,
&quot;PLOS Curr&quot;, in the 2013 baseline, creating a total of 149 non-unique records.</p>
<p>As this is the only journal and as there may only be one record per PMID in the
database, alternative versions are currently being ignored. In other words, if
a MedlineCitation has a VersionID value other than &quot;1&quot;, those records can be
skipped to avoid DB errors from non-unique records.</p>
<p>For example, in the 2013 baseline, PMID 20029614 is present ten times in the
baseline, each version at a different stage of revision. Because it is the
first entry (in the order they appear in the baseline files) without a
<tt class="docutils literal">VersionID</tt> or a version of &quot;1&quot; that is the relevant record, <tt class="docutils literal">medic</tt> by
default filters citations with other versions than &quot;1&quot;. If you do want to
process other versions of a citation, use the option <tt class="docutils literal"><span class="pre">--all</span></tt>.</p>
<p>To summarize, <em>medic</em> by default <strong>removes</strong> alternate citations.</p>
</div>
<div class="section" id="database-tables">
<h1>Database Tables</h1>
<dl class="docutils">
<dt>Citation (citations)</dt>
<dd><strong>pmid</strong>:BIGINT, <em>status</em>:ENUM(state), <em>title</em>:TEXT, <em>journal</em>:VARCHAR(256),
<em>pub_date</em>:VARCHAR(256), issue:VARCHAR(256), pagination:VARCHAR(256),
<em>created</em>:DATE, completed:DATE, revised:DATE, modified:DATE</dd>
<dt>Abstract (abstracts)</dt>
<dd><strong>pmid</strong>:FK(Citation), <strong>source</strong>:ENUM(type), copyright:TEXT</dd>
<dt>Section (sections)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>source</strong>:ENUM(type), <strong>seq</strong>:SMALLINT,
<em>name</em>:ENUM(section), label:VARCHAR(256), <em>content</em>:TEXT</dd>
<dt>Author (authors)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>pos</strong>:SMALLINT, <em>name</em>:TEXT,
initials:VARCHAR(128), forename:VARCHAR(128), suffix:VARCHAR(128),</dd>
<dt>PublicationType (publication_types)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>value</strong>:VARCHAR(256)</dd>
<dt>Descriptor (descriptors)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>num</strong>:SMALLINT, major:BOOL, <em>name</em>:TEXT</dd>
<dt>Qualifier (qualifiers)</dt>
<dd><strong>pmid</strong>:FK(Descriptor), <strong>num</strong>:FK(Descriptor), <strong>sub</strong>:SMALLINT, major:BOOL, <em>name</em>:TEXT</dd>
<dt>Identifier (identifiers)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>namespace</strong>:VARCHAR(32), <em>value</em>:VARCHAR(256)</dd>
<dt>Database (databases)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>name</strong>:VARCHAR(32), <strong>accession</strong>:VARCHAR(256)</dd>
<dt>Chemical (chemicals)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>idx</strong>:VARCHAR(32), uid:VARCHAR(256), <em>name</em>:VARCHAR(256)</dd>
<dt>Keyword (keywords)</dt>
<dd><strong>pmid</strong>:FK(Medline), <strong>owner</strong>:ENUM(owner), <strong>cnt</strong>:SMALLINT, major:BOOL, <em>value</em>:TEXT</dd>
</dl>
<ul class="simple">
<li><strong>bold</strong> (Composite) Primary Key</li>
<li><em>italic</em> NOT NULL (Strings that may not be NULL are also never empty.)</li>
</ul>
</div>
<div class="section" id="supported-xml-elements">
<h1>Supported XML Elements</h1>
<div class="section" id="entities">
<h2>Entities</h2>
<ul class="simple">
<li>MedlineCitation and ArticleTitle (<tt class="docutils literal">Medline</tt> and <tt class="docutils literal">Identifier</tt>)</li>
<li>Abstract and OtherAbstract (<tt class="docutils literal">Abstract</tt> and <tt class="docutils literal">Section</tt>)</li>
<li>Author (<tt class="docutils literal">Author</tt>)</li>
<li>Chemical (<tt class="docutils literal">Chemical</tt>)</li>
<li>DataBank (<tt class="docutils literal">Database</tt>)</li>
<li>Keyword (<tt class="docutils literal">Keyword</tt>)</li>
<li>MeshHeading (<tt class="docutils literal">Descriptor</tt> and <tt class="docutils literal">Qualifier</tt>)</li>
<li>PublicationType (<tt class="docutils literal">PublicationType</tt>)</li>
<li>DeleteCitation (for deleting records when parsing updates)</li>
</ul>
</div>
<div class="section" id="fields-values">
<h2>Fields/Values</h2>
<ul class="simple">
<li>Abstract (with &quot;NLM&quot; as <tt class="docutils literal">Abstract.source</tt>)</li>
<li>AbstractText (<tt class="docutils literal">Section.name</tt> &quot;Abstract&quot; or the <em>NlmCategory</em>, <tt class="docutils literal">Section.content</tt> with <em>Label</em> as <tt class="docutils literal">Section.label</tt>)</li>
<li>AccessionNumber (<tt class="docutils literal">Database.accession</tt>)</li>
<li>ArticleId (<tt class="docutils literal">Identifier.value</tt> with <em>IdType</em> as <tt class="docutils literal">Identifier.namesapce</tt>; only available in online PubMed XML)</li>
<li>ArticleTitle (<tt class="docutils literal">Citation.title</tt>)</li>
<li>CollectiveName (<tt class="docutils literal">Author.name</tt>)</li>
<li>CopyrightInformation (<tt class="docutils literal">Abstract.copyright</tt>)</li>
<li>DataBankName (<tt class="docutils literal">Database.name</tt>)</li>
<li>DateCompleted (<tt class="docutils literal">Medline.completed</tt>)</li>
<li>DateCreated (<tt class="docutils literal">Medline.created</tt>)</li>
<li>DateRevised (<tt class="docutils literal">Medline.revised</tt>)</li>
<li>DescriptorName (<tt class="docutils literal">Descriptor.name</tt> with <em>MajorTopicYN</em> as <tt class="docutils literal">Descriptor.major</tt>)</li>
<li>ELocationID (<tt class="docutils literal">Identifier.value</tt> with <em>EIdType</em> as <tt class="docutils literal">Identifier.namespace</tt>)</li>
<li>ForeName (<tt class="docutils literal">Author.forename</tt>)</li>
<li>Initials (<tt class="docutils literal">Author.initials</tt>)</li>
<li>Issue (<tt class="docutils literal">Medline.issue</tt>)</li>
<li>Keyword (<tt class="docutils literal">Keyword.value</tt> with <em>Owner</em> as <tt class="docutils literal">Keyword.owner</tt> and <em>MajorTopicYN</em> as <tt class="docutils literal">Keyword.major</tt>)</li>
<li>LastName (<tt class="docutils literal">Author.name</tt>)</li>
<li>MedlineCitation (with <em>Status</em> as <tt class="docutils literal">Medline.status</tt>)</li>
<li>MedlineTA (<tt class="docutils literal">Medline.journal</tt>)</li>
<li>NameOfSubstance (<tt class="docutils literal">Chemical.name</tt>)</li>
<li>MedlinePgn (<tt class="docutils literal">Medline.pagination</tt>)</li>
<li>OtherAbstract (with <em>Type</em> as <tt class="docutils literal">Abstract.source</tt>)</li>
<li>OtherID (<tt class="docutils literal">Identifier.value</tt> iff <em>Source</em> is &quot;PMC&quot; with <tt class="docutils literal">Identifier.namespace</tt> as &quot;pmc&quot;)</li>
<li>PMID (<tt class="docutils literal">Medline.pmid</tt>)</li>
<li>PubDate (<tt class="docutils literal">Medline.pub_date</tt>)</li>
<li>PublicationType (<tt class="docutils literal">PublicationType.value</tt>)</li>
<li>QualifierName (<tt class="docutils literal">Qualifier.name</tt> with <em>MajorTopicYN</em> as <tt class="docutils literal">Qualifier.major</tt>)</li>
<li>RegistryNumber (<tt class="docutils literal">Chemical.uid</tt>)</li>
<li>Suffix (<tt class="docutils literal">Author.suffix</tt>)</li>
<li>VernacularTitle (<tt class="docutils literal">Section.name</tt> &quot;Vernacular&quot;, <tt class="docutils literal">Section.content</tt>)</li>
<li>Volume (<tt class="docutils literal">Medline.issue</tt>)</li>
</ul>
</div>
</div>
<div class="section" id="version-history">
<h1>Version History</h1>
<dl class="docutils">
<dt>2.1.2</dt>
<dd><ul class="first last simple">
<li>fixed a bug where SQLite did not find the implicit FK-&gt;PK reference
(thanks to Jason Hennessey for reporting the issue)</li>
</ul>
</dd>
<dt>2.1.1</dt>
<dd><ul class="first last simple">
<li>added SQLite temporary DB example URL to help output</li>
<li>refactored HTML output code</li>
</ul>
</dd>
<dt>2.1.0</dt>
<dd><ul class="first last simple">
<li>DB schema change from: <tt class="docutils literal">records() <span class="pre">-&gt;</span> sections(content)</tt>
to: <tt class="docutils literal">citations(title) <span class="pre">-&gt;</span> abstracts(copyright) <span class="pre">-&gt;</span> sections(content)</tt></li>
<li>name change: the entity/table Medline/records is now called Citation/citations</li>
<li>title and copyright text is no longer stored in Section/sections</li>
<li>added a new Abstract/abstracts entity/table with a <tt class="docutils literal">copyright</tt> attribute
(formerly stored in <tt class="docutils literal">sections.content</tt> with <tt class="docutils literal">name</tt> = 'Copyright')</li>
<li>added a new <tt class="docutils literal">citations.title</tt> attribute
(formerly stored in <tt class="docutils literal">sections.content</tt> with <tt class="docutils literal">name</tt> = 'Title')</li>
<li>added a new <tt class="docutils literal">source</tt> primary-key attribute to Section and Abstract
(set to either 'NLM' for regular Abstract elements or to
the value of the OtherAbstract Type attribute for other abstracts)</li>
<li>skipping &quot;Abstract available from the publisher.&quot;-only abstracts</li>
</ul>
</dd>
<dt>2.0.2</dt>
<dd><ul class="first last simple">
<li>made the use of <tt class="docutils literal"><span class="pre">--pmid-lists</span></tt> for <tt class="docutils literal">delete</tt> and <tt class="docutils literal">write</tt> implicit</li>
<li>added instructions to bootstrap the tables in a PostgreSQL DB</li>
<li>minor improvements to this manual</li>
<li>fixed a bug when inserting/updating from MEDLINE XML files</li>
</ul>
</dd>
<dt>2.0.1</dt>
<dd><ul class="first last simple">
<li>fixed a bug that lead to skipping of abstracts
(thanks to Chris Roeder for detecting the issue)</li>
</ul>
</dd>
<dt>2.0.0</dt>
<dd><ul class="first last simple">
<li>added Keywords and PublicationTypes</li>
<li>added MEDLINE publication date, volume, issue, and pagination support</li>
<li>added MEDLINE output format and made it the default</li>
<li>DB structure change: descriptors.major and qualifiers.major columns swapped</li>
<li>DB structure change: section.name is now an untyped varchar (OtherAbstract separation)</li>
<li>cleaned up the ORM test cases</li>
</ul>
</dd>
<dt>1.1.1</dt>
<dd><ul class="first last simple">
<li>code cleanup (PEP8, PyFlake)</li>
<li>fixed an issue where the parser would not leave the skipping state</li>
</ul>
</dd>
<dt>1.1.0</dt>
<dd><ul class="first last simple">
<li><tt class="docutils literal"><span class="pre">--update</span> parse</tt> now writes a file to use with <tt class="docutils literal"><span class="pre">--pmid-lists</span> delete</tt></li>
<li>fixed a bug with CRUD manager</li>
<li>added a man page</li>
</ul>
</dd>
<dt>1.0.2</dt>
<dd><ul class="first last simple">
<li>fixes to make the PyPi version and <tt class="docutils literal">pip install medic</tt> work</li>
</ul>
</dd>
<dt>1.0.1</dt>
<dd><ul class="first last simple">
<li>updates to the setup.py and README.rst files</li>
</ul>
</dd>
<dt>1.0.0</dt>
<dd><ul class="first last simple">
<li>initial release</li>
</ul>
</dd>
</dl>
</div>
<div class="section" id="copyright-and-license">
<h1>Copyright and License</h1>
<p>License: <a class="reference external" href="http://www.gnu.org/licenses/gpl-3.0.html">GNU GPL v3</a>.
Copyright 2012, 2013 Florian Leitner. All rights reserved.</p>
</div>
</div>
</body>
</html>