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<h1 id="psi-mi-feature-tab-format">PSI-MI Feature TAB Format</h1>
<h2 id="introduction">Introduction</h2>
<p>PSI-MI FeatureTab is a new format, it takes inspiration from the existing PSI-MI XML and tab-delimited formats (1, 2, 3), which is actively supported by the MI worktrack. Most users will continue to use PSI-MI MITAB or PSI-MI XML2.5/3.0 to exchange experimental-based interaction data, the PSI-MI FeatureTab will be required only for specialist use cases.</p>
<p>(1) <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC5896046/" target="_blank">https://pmc.ncbi.nlm.nih.gov/articles/PMC5896046/</a></p>
<p>(2) <a href="https://europepmc.org/article/MED/30602777" target="_blank">https://europepmc.org/article/MED/30602777</a></p>
<p>(3) <a href="https://europepmc.org/article/MED/30793173" target="_blank">https://europepmc.org/article/MED/30793173</a></p>
<h2 id="column-definitions">Column definitions</h2>
<p>The column contents should be as follows:</p>
<ol>
<li><strong>Feature AC</strong>, is designed to report the accession number for a feature such as mutations, binding sites, PTMs, etc. (ex. EBI-489661; EBI-1000504; EBI-1234567).</li>
<li><strong>Feature short label</strong>, contains human-readable short label summarizing the amino acid changes and their positions, compliant with the Human Genome Variation Society recommendations (see <a href="http://varnomen.hgvs.org/recommendations/protein/" target="_blank">http://varnomen.hgvs.org/recommendations/protein/</a>), in case of mutation features or the binding range involved in an interactions, the exact aa range.</li>
<li><strong>Feature range(s)</strong>, contains position(s) in the protein sequence involved in that specific feature (Ex: mutation, binding sites, PTMs, etc).</li>
<li><strong>Original sequence</strong>, contains the wild type amino acid residue(s) affected, in one letter code.</li>
<li><strong>Resulting sequence</strong>, contains the replacement sequence (or deletion) in one letter code.</li>
<li><strong>Feature type</strong>, contains the feature type, following the PSI-MI controlled vocabularies (EX: mutation (MI:0118); mutation decreasing (MI:0119); mutation disrupting strength(MI:1128); Necessary binding region (MI:0429), etc.)</li>
<li><strong>Feature annotation</strong>, contains specific comments, on free text, about the annotated feature that can be of interest.</li>
<li><strong>Affected protein AC</strong>, contains affected protein identifier (preferably UniProtKB accession, if available, Ex: uniprotkb:P12346). It is represented as databaseName:identifier, where databaseName is the name of the corresponding database as defined in the <a href="https://www.ebi.ac.uk/ols4/ontologies/mi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMI_0444" target="_blank">PSI-MI controlled vocabulary</a>, and identifier is the unique primary identifier of the molecule in the database.</li>
<li><strong>Affected protein symbol</strong>, contains the protein symbol of the protein affected by a specific feature, as given by UniProtKB (EX. Gene name, DLG4).</li>
<li><strong>Affected protein full name</strong>, contains the protein full name of the protein affected by a specific feature, as given by UniProtKB (EX. DLG4, Postsynaptic density protein 95 Synapse-associated protein 90 ).</li>
<li><strong>Affected protein organism</strong>, contains the TaxID and species name as given by UniProtKB. It is represented as taxid:identifier(organism name) where the identifier is the taxon id of the organism and organism name can either be the common name or scientific name (EX. 9606 - Homo sapiens).</li>
<li><strong>Interaction participants</strong>, contains information about the identifiers for all participants in the affected interaction, along with their species and molecule type between brackets. Ex.: (uniprotkb:P15153(protein(MI:0326), 9606 - Homo sapiens)|ensembl:ENSP00000356505.4(protein(MI:0326), 9606 - Homo sapiens)).</li>
<li><strong>PubMedID</strong>, contains the reference to the publication where the interaction evidence was reported. It is recommended to give one pubmed id per MITAB line and IMEx ids can be added. Ex: pubmed:16980971|imex:IM-1</li>
<li><strong>Figure legend</strong>, contains the reference to the specific figures in the paper where the interaction evidence was reported.</li>
<li><strong>Interaction AC</strong>, describes the interaction accession within our databases. This can be used to obtain further information about the interaction (EX.: EBI-489644; EBI-8285478).</li>
<li><strong>Xref ID</strong>, contains whenever is available the Xref Identifier associated to a feature.It is represented as databaseName:ac(text), where databaseName is the name of the corresponding database as defined in the <a href="https://www.ebi.ac.uk/ols4/ontologies/mi/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMI_0444" target="_blank">PSI-MI controlled vocabulary</a>, and ac is the primary accession in the database. For example, the InterPro cross references associated to a binding domain. Multiple cross references separated by "|".</li>
</ol>
<p>Empty columns should be represented with '-' to keep track of the columns.</p>
<h2 id="syntax">Syntax</h2>
<p>Columns are normally formed by fields delimited by "|", with a structure like this one:</p>
<pre><code><XREF>:<VALUE>(<DESCRIPTION>)
</code></pre><p>Due to the unsafe use of reserved characters in the values, we have recently added the possibility to surround <code><XREF></code>, <code><VALUE></code> or <code><DESCRIPTION></code> with quotes if they contain a special symbol.</p>
<p>In MI-TAB, the reserved characters are:</p>
<pre><code>|
(
)
:
\t (tabulation)
</code></pre><p>Whenever this happen in your data, surround the value with double quotes:</p>
<pre><code>"<XREF_WITH_RESERVED_CHARS>":"<VALUE_WITH_RESERVED_CHARS>"("<DESCRIPTION>")
</code></pre><p>Note that the quotes are before and after each part. The escaped data should look like in the following examples:</p>
<pre><code>psi-mi:"MI:0000"(a cv term)
psi-mi:"MI:0000"("I can now use braces ()()() or pipes ||| here and ::colons::")
</code></pre><p>If you want to use a quote within a quote, escape it:</p>
<pre><code>uniprotkb:P12345("a \"nice\" protein")
</code></pre>
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