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Advanced Search — ena-browser-docs latest documentation

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  <div class="section" id="advanced-search">
<h1>Advanced Search<a class="headerlink" href="#advanced-search" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>Customise your own search query and retrieve a set of ENA records tailored to your
search criteria.</p>
<p>All searches are performed against a subset of the archive specified by
the <em>Data type</em> you choose to search against. You can then build your search
query to specify what data you are looking for and select what fields you want to
retrieve from your search. There are additional options to include/exclude specific
datasets as well as filter the number of results you wish to return.</p>
<p>If you intend to repeat the same search at a later date, you can save this
as a Rule using <a class="reference external" href="https://www.ebi.ac.uk/ena/browser/rulespace">Rulespace</a>. If you
want to access the same data programmatically, you can copy the produced curl request and run
this yourself against the <a class="reference external" href="https://www.ebi.ac.uk/ena/portal/api/">ENA Portal API</a>.</p>
</div>
<div class="section" id="data-types">
<h2>Data Types<a class="headerlink" href="#data-types" title="Permalink to this headline">¶</a></h2>
<p>Each data type is a subset of the data and metadata held within the ENA.</p>
<p>You must specify which datatype you wish to search across before you can
narrow down your search results with any additional criteria.</p>
<div class="section" id="what-is-in-each-data-type">
<h3>What is in each data type?<a class="headerlink" href="#what-is-in-each-data-type" title="Permalink to this headline">¶</a></h3>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="54%" />
<col width="25%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><strong>Data Type</strong></td>
<td><strong>Description</strong></td>
<td><strong>API Result type</strong></td>
</tr>
<tr class="row-even"><td>Studies</td>
<td><div class="first last line-block">
<div class="line">All studies in ENA. Studies can be</div>
<div class="line">searched by the study metadata, e.g.</div>
<div class="line">title or by related taxonomy of data.</div>
</div>
</td>
<td><em>study</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Studies used</div>
<div class="line">for raw reads</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All studies that hold raw read datasets.</div>
<div class="line">Searching across this data type can give</div>
<div class="line">you information on these studies and can</div>
<div class="line">be filtered down by sample metadata</div>
<div class="line">(information about the collected samples</div>
<div class="line">in the study).</div>
</div>
</td>
<td><em>read_study</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Studies used</div>
<div class="line">for nucleotide</div>
<div class="line">sequence</div>
<div class="line">analyses from</div>
<div class="line">reads</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All studies that hold any nucleotide</div>
<div class="line">analyses. Searching across this data type</div>
<div class="line">can give you information on these studies</div>
<div class="line">and can be filtered down by sample</div>
<div class="line">metadata (information about the collected</div>
<div class="line">samples in the study).</div>
</div>
</td>
<td><em>analysis_study</em></td>
</tr>
<tr class="row-odd"><td>Samples</td>
<td><div class="first last line-block">
<div class="line">All samples in ENA. Samples can be</div>
<div class="line">searched by sample metadata.</div>
</div>
</td>
<td><em>sample</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Environmental</div>
<div class="line">samples</div>
<div class="line"><br /></div>
<div class="line"><br /></div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All samples in ENA that the submitter has</div>
<div class="line">flagged as ‘evironmental’ during sample</div>
<div class="line">registration. Please note, this does not</div>
<div class="line">include all environmental samples.</div>
</div>
</td>
<td><em>environmental</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Experiments</div>
<div class="line">used for raw</div>
<div class="line">reads</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All metadata associated with sequencing</div>
<div class="line">event used to generate raw reads</div>
<div class="line">submitted to ENA.</div>
</div>
</td>
<td><em>read_experiment</em></td>
</tr>
<tr class="row-even"><td>Raw reads</td>
<td><div class="first last line-block">
<div class="line">All raw read datasets in ENA. This</div>
<div class="line">datatype can be filtered by sample</div>
<div class="line">metadata (information about the collected</div>
<div class="line">sample) as well as return directly</div>
<div class="line">downloadable files.</div>
</div>
</td>
<td><em>read_run</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Nucleotide</div>
<div class="line">sequence</div>
<div class="line">analyses from</div>
<div class="line">reads</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All nucleotide analyses held in ENA.</div>
<div class="line">This datatype can be filtered by sample</div>
<div class="line">metadata (information about the collected</div>
<div class="line">sample) as well as return directly</div>
<div class="line">downloadable files.</div>
</div>
</td>
<td><em>analysis</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Genome</div>
<div class="line">assemblies</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All genome assembly records (excluding</div>
<div class="line">primary or binned metagenomes which are</div>
<div class="line">considered <em>analyses</em>). This datatype can</div>
<div class="line">only be filtered by assembly metadata</div>
<div class="line">e.g. project accession or taxonomy.</div>
</div>
</td>
<td><em>assembly</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Genome</div>
<div class="line">assembly</div>
<div class="line">contig sets</div>
<div class="line">(WGS)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All genome assembly contig sets in ENA.</div>
<div class="line">This datatype can be filtered by sample</div>
<div class="line">metadata (information about the collected</div>
<div class="line">sample).</div>
</div>
</td>
<td><em>wgs_set</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Transcriptome</div>
<div class="line">assembly</div>
<div class="line">contig sets</div>
<div class="line">(TSA)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All transcriptome assembly contig sets in</div>
<div class="line">ENA. This datatype can be filtered by</div>
<div class="line">sample metadata (information about the</div>
<div class="line">collected sample).</div>
</div>
</td>
<td><em>tsa_set</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Nucleotide</div>
<div class="line">sequences</div>
<div class="line">(Release)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">The most recent snapshot of all assembled</div>
<div class="line">and annotated sequences publicly</div>
<div class="line">available in ENA on the last quarterly</div>
<div class="line">release date (including high level</div>
<div class="line">sequences from assembly submissions e.g.</div>
<div class="line">fully assembled chromosomes).</div>
</div>
</td>
<td><em>sequence_release</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Nucleotide</div>
<div class="line">sequences</div>
<div class="line">(Update)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">Any changes to public assembled and</div>
<div class="line">annotated sequences held in ENA since the</div>
<div class="line">last quarterly release.</div>
</div>
</td>
<td><em>sequence_update</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Protein coding</div>
<div class="line">sequences</div>
<div class="line">(Release)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">The most recent snapshot of all protein</div>
<div class="line">coding sequences publicly available in</div>
<div class="line">ENA on the last quarterly release date.</div>
</div>
</td>
<td><em>coding_release</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Protein coding</div>
<div class="line">sequences</div>
<div class="line">(Update)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">Any changes to protein coding sequences</div>
<div class="line">held in ENA since the last quarterly</div>
<div class="line">release.</div>
</div>
</td>
<td><em>coding_update</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Non-coding</div>
<div class="line">sequences</div>
<div class="line">(Release)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">The most recent snapshot of all non</div>
<div class="line">coding sequences publicly available in</div>
<div class="line">ENA on the last quarterly release date.</div>
</div>
</td>
<td><em>noncoding_release</em></td>
</tr>
<tr class="row-even"><td><div class="first last line-block">
<div class="line">Non-coding</div>
<div class="line">sequences</div>
<div class="line">(Update)</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">Any changes to non coding sequences</div>
<div class="line">held in ENA since the last quarterly</div>
<div class="line">release.</div>
</div>
</td>
<td><em>noncoding_update</em></td>
</tr>
<tr class="row-odd"><td><div class="first last line-block">
<div class="line">Taxonomic</div>
<div class="line">classification</div>
</div>
</td>
<td><div class="first last line-block">
<div class="line">All taxa and their tax IDs. Search for a</div>
<div class="line">specific taxa or look for all taxa below</div>
<div class="line">a tax node.</div>
</div>
</td>
<td><em>taxon</em></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section" id="search-query">
<h2>Search Query<a class="headerlink" href="#search-query" title="Permalink to this headline">¶</a></h2>
<p>To build a query you need to create a list of rules that the resulting
data sets should be restricted to.</p>
<p>This is done by clicking any relevant metadata types you would like to
restrict (listed as buttons on the left) then selecting the relevant filters
and specifying the desired restrictions for those:</p>
<img alt="../../_images/example-tax-filter.png" src="../../_images/example-tax-filter.png" />
<p>When specifying taxonomy in your search, you can include all subordinate taxa
within that tax tree and when searching by geographical range you can
interactively drag the box or circle over the desired region to automatically fill out
the location range.</p>
<p>These rules can be grouped and nested within AND or OR logical statements.
For example, a query for <em>all metagenomic analyses where the sample was
collected after 01 Jan 2019 AND the environmental material is either dental OR
saliva</em> would look as follows:</p>
<img alt="../../_images/example-query.png" src="../../_images/example-query.png" />
</div>
<div class="section" id="inclusion-exclusion-of-datasets">
<h2>Inclusion/Exclusion of datasets<a class="headerlink" href="#inclusion-exclusion-of-datasets" title="Permalink to this headline">¶</a></h2>
<p>If there are any known public datasets that do or do not fit the criteria
you have specified that you wish to include or exclude from the results,
you can list the accessions in a comma separated list here (with no spaces).</p>
</div>
<div class="section" id="return-fields">
<h2>Return Fields<a class="headerlink" href="#return-fields" title="Permalink to this headline">¶</a></h2>
<p>By default, you will receive the accession and description/title
of the main datatype you are searching against. If you wish to customise the
metadata which your search will return, you can manually select your search
return fields from a list of all indexed fields for the specified datatype.</p>
<div class="section" id="select-and-order-fields">
<h3>Select and order fields<a class="headerlink" href="#select-and-order-fields" title="Permalink to this headline">¶</a></h3>
<p>To select fields you would like returned from your search, drag across any
desired fields from the <strong>Available Fields</strong> list to the <strong>Selected Fields</strong>
list. Alternatively, use the arrow buttons in the middle to move fields across
from one list to the other.</p>
<p>The order of the <strong>Selected Fields</strong> list will define the order that you
receive those metadata from your search. To specify the return order of these
fields, you can drag and drop these into the desired order.</p>
</div>
<div class="section" id="field-sets">
<h3>Field sets<a class="headerlink" href="#field-sets" title="Permalink to this headline">¶</a></h3>
<p>Field sets are a pre-defined set of fields that can be returned together and
are available for some data types. For example, for the analysis datatype,
you can toggle the ‘Submitted Files’ field set which can be used to return
all relavent fields relating to the original set of submitted files (e.g.
this set includes the aspera, ftp and galaxy links for the submitted files,
the size of the files (in bytes) and the files’ md5 checksums).</p>
</div>
</div>
<div class="section" id="data-filters">
<h2>Data Filters<a class="headerlink" href="#data-filters" title="Permalink to this headline">¶</a></h2>
<div class="section" id="offset">
<h3>Offset<a class="headerlink" href="#offset" title="Permalink to this headline">¶</a></h3>
<p>You can specify an offset for the number of records you would like to skip
from the beginning of your search. This can be used to view results
beyond the maximum number of records that can be viewed in the
results table (100 000) or to break up queries that result in a large
number of records into smaller batches.</p>
<p>If you do not wish to skip any records, you can leave this field blank or
enter an offset of ‘0’.</p>
</div>
<div class="section" id="limit">
<h3>Limit<a class="headerlink" href="#limit" title="Permalink to this headline">¶</a></h3>
<p>You can specify a data limit for the maximum number of records you would like
to retrieve from your search.</p>
<p>If you wish to fetch the full result set, leave this field blank or enter ‘0’.
The browser table display will only show up to 100 000 results but for large
datasets, you can see all the results if you download the report or copy and run
the curl request.</p>
</div>
</div>
<div class="section" id="download-ena-records">
<h2>Download ENA records<a class="headerlink" href="#download-ena-records" title="Permalink to this headline">¶</a></h2>
<p>Here you can download the ENA records resulting from your search.</p>
<p>This will download the whole ENA record stored for each of the results. If you
wish to only download the fields returned that were specified in your search,
use one of the <strong>Download report</strong> options (JSON or TSV).</p>
<div class="section" id="xml-records">
<h3>XML records<a class="headerlink" href="#xml-records" title="Permalink to this headline">¶</a></h3>
<p>XML records are available for all standard metadata objects held within ENA (all
results with the exception of sequence records).</p>
<p>XML records hold <strong>all</strong> the metadata for each object concatonated into a single
bulk XML file. These XML metadata records are formatted in the standard ENA XML
format (the same XML format that is used for data submission and for data to be
displayed in the browser).</p>
</div>
<div class="section" id="fasta-records">
<h3>FASTA records<a class="headerlink" href="#fasta-records" title="Permalink to this headline">¶</a></h3>
<p>FASTA records hold all sequences resulting from your search concatonated into one
FASTA file. FASTA records are only available when searching against sequence
datatypes.</p>
</div>
<div class="section" id="text-records">
<h3>TEXT records<a class="headerlink" href="#text-records" title="Permalink to this headline">¶</a></h3>
<p>TEXT records hold all sequences resulting from your search and their annotation (if
available) concatonated into a single EMBL flat file. TEXT records are only available
when searching against sequence datatypes.</p>
</div>
</div>
<div class="section" id="download-results-report">
<h2>Download results report<a class="headerlink" href="#download-results-report" title="Permalink to this headline">¶</a></h2>
<p>This feature allows you to download all the results from your search in the
format of a JSON or TSV file. Any data filters set by you will apply here.</p>
</div>
<div class="section" id="download-associated-data-files">
<h2>Download associated data files<a class="headerlink" href="#download-associated-data-files" title="Permalink to this headline">¶</a></h2>
<div class="section" id="pre-conditions">
<h3>Pre-Conditions<a class="headerlink" href="#pre-conditions" title="Permalink to this headline">¶</a></h3>
<p>To see file download columns in your results, you have to search against either
the analysis or read_run data types and select the relevant fields that end with ‘_ftp’.</p>
<p>For example:</p>
<p><strong>Data Type</strong> = analysis and <strong>fields</strong> = submitted_ftp</p>
<p><strong>Data Type</strong> = read_run and <strong>fields</strong> = fastq_ftp / sra_ftp / submitted_ftp</p>
</div>
<div class="section" id="download-data-files">
<h3>Download data files<a class="headerlink" href="#download-data-files" title="Permalink to this headline">¶</a></h3>
<p>You can download the data files resulting from your search in one of three ways:</p>
<ol class="arabic simple">
<li>You can download a single file by clicking on its link in the FASTQ FTP, SRA FTP, or SUBMITTED FTP column.</li>
<li>You can select one or more files using the check boxes, and either download these as a bundled ZIP file
or as individual files using the “Bundled ZIP” or “Individually” links above the table.</li>
<li>You can download ALL files resulting from your search as a bundled ZIP file by clicking the download icon in the column header.</li>
</ol>
<img alt="../../_images/download-all.png" src="../../_images/download-all.png" />
<div class="section" id="tips">
<h4>Tips:<a class="headerlink" href="#tips" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li>If you wish to exclude any records from your search results before you download all the resulting files,
you can go back and list these in the “Exclude Accessions” field and then repeat the search.</li>
<li>If you selected multiple files and clicked the “Individually” link but only the first file is downloading, this could
be because your browser is restricting multiple download pop-ups. Look for a browser warning or confirmation dialog
to allow this.</li>
<li>If selesting many files and using the download “Individually” option, you may wish to change
the default download location of your browser. Look in your browser settings for this.</li>
<li>You can also download files using a terminal from ENA using <a class="reference external" href="https://github.com/enasequence/enaBrowserTools">enaBrowserTools</a>.</li>
</ul>
</div>
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