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<h2 id="purpose">Purpose</h2>
<p>This document focuses on several aspects of the <a href="MITAB27Format.html">MITAB27 data representation</a> in the context of data distribution via PSICQUIC services. As MITAB 2.7 is backward compatible with MITAB 2.5 and MITAB 2.6, the best practices also apply to these formats except for the new columns. The implementation of these best practices in the data served by a PSICQUIC services should improve users searches, data consistency and visualization as well as clustering of this data with other PSICQUIC services.</p>
<h2 id="best-practices">Best Practices</h2>
<h3 id="a-describing-an-interacting-molecule">A. Describing an Interacting Molecule</h3>
<p>Typically, an interacting molecule is described using up to 12 columns of the <a href="MITAB27Format.html">MITAB format</a>:</p>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column name</strong></th>
<th style="text-align:left"><strong>Columns for Interactor A</strong></th>
<th style="text-align:left"><strong>Columns for Interactor B</strong></th>
<th style="text-align:left"><strong>Definition</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">Unique identifier</td>
<td style="text-align:left">1</td>
<td style="text-align:left">2</td>
<td style="text-align:left">represented as <strong>databaseName:ac</strong>, where databaseName is the name of the corresponding database as defined in the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI:0444&termName=database%20citation" target="_blank">PSI-MI controlled vocabulary</a>, and ac is the unique primary identifier of the molecule in the database. Even though the MITAB format can accept several identifiers from multiple databases (separated by "|") in the 'unique identifier' columns, it is recommended to give only one identifier. It is also recommended that proteins are identified by stable identifiers such as their UniProtKB, RefSeq, Ensembl, ddbj/genbank/embl or Chebi accession number.</td>
</tr>
<tr>
<td style="text-align:left">Alternative Identifier</td>
<td style="text-align:left">3</td>
<td style="text-align:left">4</td>
<td style="text-align:left">represented as <strong>databaseName:ac</strong>, where databaseName is the name of the corresponding database as defined in the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI:0444&termName=database%20citation" target="_blank">PSI-MI controlled vocabulary</a>, and ac is the primary identifier of the molecule in the database. Multiple identifiers separated by "|". It is recommended that only database identifiers for the interactors are given in these columns. Other cross references for these interactors such as GO xrefs should be moved to columns 23 and 24 and interactor names such as gene names should be moved to columns 5 and 6.</td>
</tr>
<tr>
<td style="text-align:left">Aliases</td>
<td style="text-align:left">5</td>
<td style="text-align:left">6</td>
<td style="text-align:left">represented as databaseName:name, where databaseName is the name of the corresponding database as defined in the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI:0444&termName=database%20citation" target="_blank">PSI-MI controlled vocabulary</a>, and name is the name of the molecule in the database (Ex gene names, protein recommended name, ORF, locus name, drug name, Chebi recommended name, etc.). Multiple names separated by "|".</td>
</tr>
<tr>
<td style="text-align:left">Xrefs</td>
<td style="text-align:left">23</td>
<td style="text-align:left">24</td>
<td style="text-align:left">represented as <strong>databaseName:ac</strong>, where databaseName is the name of the corresponding database as defined in the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI:0444&termName=database%20citation" target="_blank">PSI-MI controlled vocabulary</a>, and ac is the primary accession in the database. Multiple accessions separated by "|". This columns can contain for instance GO xrefs.</td>
</tr>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier</td>
<td style="text-align:left">10</td>
<td style="text-align:left">11</td>
<td style="text-align:left">Database name for NCBI taxid taken from the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI:0444&termName=database%20citation" target="_blank">PSI-MI controlled vocabulary</a>, represented as <strong>taxid:identifier(organism common name)</strong>. Even though the MITAB format can accept several taxon ids per column (Multiple identifiers separated by "|"), it is strongly recommended to have only one organism per protein per MITAB line. Currently no taxonomy identifiers other than NCBI taxid are anticipated, apart from the use of -2 to indicate "chemical synthesis" and -3 indicates "unknown".</td>
</tr>
<tr>
<td style="text-align:left">checksum</td>
<td style="text-align:left">33</td>
<td style="text-align:left">34</td>
<td style="text-align:left">represented as <strong>methodName:value</strong>, where methodName is the name of the corresponding checksum method, and value is the checksum for this interactor. Multiple checksums separated by "|". This columns can contain for instance rogid, or standard inchi key</td>
</tr>
</tbody>
</table>
<p><br></p>
<p>It is recommended that the unique identifier and alternative identifier column should be used as follow:</p>
<ul>
<li>unique identifier column: Ideally indicate a single reference to a chosen primary sequence database (e.g. one of UniProt or RefSeq). The unique identifier should not be ambiguous. If the interactor can match several RefSeq identifiers are used but only one master UniProt ac, it is recommended to give the master UniProt ac as 'unique identifier' and the RefSeq identifiers as 'alternative identifiers'.</li>
<li>alternative identifier column: any other database identifier referring to your interacting molecule. Here are two examples:<ul>
<li>if you are UniProt centric, you could add mapping to RefSeq,</li>
<li>if you are a gene centric, you could add mapping to UniProt and/or RefSeq.</li>
</ul>
</li>
</ul>
<p>The first two columns 'unique identifier' should never be both empty columns. If a unique identifier to a sequence database cannot be found, it is important to give at least one identifier from the interaction database that created the interactor entry (Ex : IntAct accession, MINT accessions, etc.). One empty column is allowed in case of intra-molecular interactions (a single molecule interacts with itself). If one 'unique identifier' column is empty, it is expected to have empty columns for the matching 'alternative identifier', 'alias', 'taxid', 'interactor xref', 'checksum', 'biological role', 'experimental role', 'interactor type', 'feature', 'participant identification method'.</p>
<p>It is recommended to give gene names, ORF, locus names, gene synonyms, Chebi recommended name, drug name and/or protein recommended names in the alias columns.</p>
<p>Other cross references which can describe the interactors but ARE NOT identifiers such as GO xrefs could be added in columns 23 and 24.</p>
<p>In a single MITAB line, the interactors should only be associated with a single taxon id.</p>
<p>When it is available, a checksum of the interactor can be used in column 33 and 34 such as rogid, crogid and standard inchi key. These checksums could then be used for clustering interactors and taking into account their sequence.</p>
<p>Here is a recommendation for various molecule types:</p>
<h4 id="1-complexes">1. Complexes</h4>
<p>In case of complexes (several protein chains for instance), no reference database can be recommended. The UniprotKB database does not generate unique identifiers for complexes. For now, only identifiers generated by the interaction databases can be used. For clustering purposes, if one interaction database such as IntAct did create an entry for describing a specific complex, the accession of the interaction generated by the database (IntAct) could be used across several different interaction databases to point to the same complex.</p>
<h4 id="2-proteins">2. Proteins</h4>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data required</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">Unique identifier</td>
<td style="text-align:left">Use preferentially a single cross references to uniprotkb or RefSeq</td>
<td style="text-align:left"><code>uniprotkb:P51587</code><br> <code>uniprotkb:P51123-3</code><br> <code>refseq:NP_000059</code></td>
</tr>
<tr>
<td style="text-align:left">Alternative identifier</td>
<td style="text-align:left">Use <strong>secondary cross references</strong> in primary database, <br> Use model organism databases.</td>
<td style="text-align:left"><code>uniprotkb:O00183</code></td>
</tr>
<tr>
<td style="text-align:left">Interactor Xrefs</td>
<td style="text-align:left">Use cross references to databases that can give more information about the protein but cannot be used as identifier. This columns can also contain secondary identifiers that are ambiguous (can be shared by two different proteins for instance, uniprot demerge) and that cannot be used to identify a single protein.</td>
<td style="text-align:left"><code>go:"GO:0003824"</code></td>
</tr>
<tr>
<td style="text-align:left">Alias</td>
<td style="text-align:left">use the gene name found in your reference database. 'orf name', 'gene name synonym', 'locus names' and 'protein recommended name' can also be added</td>
<td style="text-align:left"><code>uniprotkb:BRCA2(gene name)</code> <br><code>uniprotkb:FACD(gene name synonym)</code></td>
</tr>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier</td>
<td style="text-align:left">The taxid of the molecule (e.g. taxid:9606) should always be provided. In parenthesis, it is recommended to add the common name/scientific name of the organism.</td>
<td style="text-align:left"><code>taxid:9606</code><br> <code>taxid:9606(human)</code> <br> <code>taxid:9606(Homo sapiens)</code></td>
</tr>
<tr>
<td style="text-align:left">Interactor checksums (columns 33 and 34)</td>
<td style="text-align:left">Use <strong>rogid</strong> and <strong>crogid</strong></td>
<td style="text-align:left"><code>rogid:UcdngwpTSS6hG/pvQGgpp40u67I9606</code> <br> <code>crogid:UcdngwpTSS6hG/pvQGgpp40u67I9606</code></td>
</tr>
</tbody>
</table>
<p><strong>What is a ROGID ?</strong></p>
<p>ROGID (Redundant Object Group Identifier) is a SHA-1 digest of the protein interactor's primary amino acid sequence concatenated with the NCBI taxonomy identifier. The first 27 character of a ROGID is always the hash value (SEGUID) to which is appended the taxid. Please refer to the <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573892" target="_blank">iRefIndex paper</a> for more details.</p>
<p><strong>What is a CROGID ?</strong></p>
<p>This is similar to ROGID but allows the description of <em>Canonical</em> Redundant Object Group. See below how a canonical sequence should be chosen.</p>
<h4 id="3-small-molecules">3. Small Molecules</h4>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data required</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">Unique identifier</td>
<td style="text-align:left">use the <strong>standard inchi key</strong> if not ambiguous, otherwise use a non ambiguous identifier (Chebi recommended). As the standard inchi key is not a database identifier but more a checksum, a unique Chebi identifier would be recommended. The standard inchi key should only be used as identifier for enrichment purposes and it may be moved to the checksum columns after data enrichment. If the standard inchi key is used as an identifier, the database is unknown and we should write standard inchi key in parenthesis</td>
<td style="text-align:left"><code>unknown:"KTUFNOKKBVMGRW-UHFFFAOYSA-N"(standard inchi key)</code></td>
</tr>
<tr>
<td style="text-align:left">Alternative identifier</td>
<td style="text-align:left">use cross references to <strong>chebi</strong> or other small molecule database that can identify without ambiguity the small molecule.</td>
<td style="text-align:left"><code>chebi:"CHEBI:45783"</code></td>
</tr>
<tr>
<td style="text-align:left">Interactor Xrefs</td>
<td style="text-align:left">Use cross references to databases that can give more information about the small molecule but cannot be used as identifier. This columns can also contain secondary identifiers that are ambiguous (can be shared by two different small molecules for instance) and that cannot be used to identify a single molecule.</td>
<td style="text-align:left"><code>pubchem:26697112</code></td>
</tr>
<tr>
<td style="text-align:left">Alias</td>
<td style="text-align:left">add a <strong>standard inchi</strong>, <strong>smile</strong>, <strong>Chebi name</strong>, <strong>drug name</strong></td>
<td style="text-align:left"><code>unknown:"1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)"(standard inchi)</code><br><code>chebi:imatinib(chebi name)</code></td>
</tr>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier</td>
<td style="text-align:left">it should be '-' if undefined, taxid:-3(unknown), taxid:-2(chemical synthesis) or a specific taxid if known</td>
<td style="text-align:left"></td>
</tr>
<tr>
<td style="text-align:left">Interactor checksums (columns 33 and 34)</td>
<td style="text-align:left">Use <strong>standard inchi key</strong></td>
<td style="text-align:left"><code>standard inchi key:"KTUFNOKKBVMGRW-UHFFFAOYSA-N"</code></td>
</tr>
</tbody>
</table>
<p>Should the Standard InCHI Key not describe unambiguously a molecule, the data provider should use an other cross reference and keep the Standard InCHI Key as a checksum only.</p>
<p><strong>What is a Standard InChI ?</strong></p>
<p>IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.</p>
<p><strong>What is a Standard InChI Key ?</strong></p>
<p>The standard InChI Key is a condensed, 27 character identifier that is a hashed version of the full standard InChI (using the SHA-256 algorithm), designed to allow for easy web searches of chemical compounds.</p>
<p>The <a href="http://www.inchi-trust.org/?q=node/3" target="_blank">InChI Trust</a> has more information and software support for InChI related matters.</p>
<h4 id="4-nucleic-acids">4. Nucleic Acids</h4>
<table>
<thead>
<tr>
<th><strong>Column</strong></th>
<th><strong>Data required</strong></th>
<th><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td>Unique identifier</td>
<td>use a single cross references to <strong>embl/genebank/ddbj</strong></td>
<td><code>ddbj/embl/genbank:U41813</code></td>
</tr>
<tr>
<td>Alternative identifier</td>
<td>use other cross references to other nucleotide sequence databases such as Refseq nucleotides</td>
<td></td>
</tr>
<tr>
<td>NCBI Taxonomy identifier</td>
<td>The taxid of the molecule (e.g. taxid:9606) should be provided when available. In parenthesis, it is recommended to add the common name/scientific name of the organism. It should be '-' if undefined, taxid:-3(unknown) or taxid:-2(chemical synthesis) otherwise.</td>
<td>.</td>
</tr>
</tbody>
</table>
<h4 id="5-gene">5. Gene</h4>
<p>This case is differentiated from 'Nucleic Acid' as not all nucleic acid sequence result in genes. Furthermore genes can be references to with set of public databases that differs from other Nucleic Acid based molecules.</p>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data required</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">Unique identifier</td>
<td style="text-align:left">use <strong>a unique</strong> cross references to <strong>entrez gene/locuslink</strong>, <strong>ensembl</strong>, or <strong>ensemblGenome</strong></td>
<td style="text-align:left"><code>entrez gene/locuslink:84665</code><br><code>ensembl:X63509</code><br><code>ensemblgenomes:AT1G66140</code></td>
</tr>
<tr>
<td style="text-align:left">Alternative identifier</td>
<td style="text-align:left">use cross references to <strong>entrez gene/locuslink</strong>, <strong>ensembl</strong> and <strong>ensemblGenome</strong> that could not be used in 'unique identifier' columns.</td>
<td style="text-align:left"></td>
</tr>
<tr>
<td style="text-align:left">Interactor Xrefs</td>
<td style="text-align:left">use other cross references to other databases that can add more information about the gene but cannot be used as identifier</td>
<td style="text-align:left"></td>
</tr>
<tr>
<td style="text-align:left">Alias</td>
<td style="text-align:left">use gene names, ORF, locus names and/or gene synonyms</td>
<td style="text-align:left"></td>
</tr>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier</td>
<td style="text-align:left">The taxid of the molecule (e.g. taxid:9606) should always be provided. In parenthesis, the common name and/or scientific name should be given</td>
<td style="text-align:left"><code>taxid:9606(Homo sapiens)</code><br><code>taxid:9606(human)</code></td>
</tr>
</tbody>
</table>
<h3 id="b-describing-the-publication">B. Describing the publication</h3>
<p>Currently, the publication can be described using up to 2 columns in MITAB. The publication information should be provided because can be used for PSICQUIC queries, clustering, scoring and linking to the original publication.</p>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data required</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">identifier of the publication (col 8)</td>
<td style="text-align:left">use <strong>a unique</strong> cross references to pubmed or doi. If an IMEx id has been assigned to the publication, it should be added as well. If no pubmed id or DOI number can be used, another publication identifier could be used</td>
<td style="text-align:left"><code>pubmed:10655498</code><br><code>pubmed:16980971</code><br><code>imex:IM-1</code></td>
</tr>
<tr>
<td style="text-align:left">First Author</td>
<td style="text-align:left">use the first author surname in the publication and the publication date in parenthesis</td>
<td style="text-align:left"><code>Ciferri et al.(2005)</code></td>
</tr>
</tbody>
</table>
<h3 id="c-describing-the-organism">C. Describing the organism</h3>
<p>In MITAB 2.7, three columns can describe organisms.</p>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data required</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier for interactor A (col 10 and 11)</td>
<td style="text-align:left">use <strong>a unique</strong> taxId and in parenthesis gives the common name and/or scientific name. This information should always be provided for genes and proteins. For nucleic acids and small molecules, the column can be empty if the information is not relevant, -2 to indicate "chemical synthesis" and -3 to indicate "unknown"</td>
<td style="text-align:left"><code>taxid:9606(human)</code><br><code>taxid:9606(human)</code><br><code>taxid:9606(Homo sapiens)</code></td>
</tr>
<tr>
<td style="text-align:left">NCBI Taxonomy identifier for the host organism</td>
<td style="text-align:left">use the taxId of the host organism only. -3 for unknown, -2 for chemical synthesis, -4 for in vivo and -5 for in sillico are allowed. In parenthesis, give the common name and/or scientific name of the organism. Cell types and tissues cannot be represented in this column. This information is recommended for MIMIx</td>
<td style="text-align:left"><code>taxid:9606(human)</code><br><code>taxid:9606(human)</code><br><code>taxid:9606(Homo sapiens)</code></td>
</tr>
</tbody>
</table>
<h3 id="d-describing-controlled-vocabularies">D. Describing controlled vocabularies</h3>
<p>In MITAB 2.7, 12 columns are controlled vocabulary columns :</p>
<ul>
<li>MIMIx : interaction detection method (col 7), biological roles (col 17 and 18), experimental roles (col 19 and 20) and participant identification methods (col 41 and 42).</li>
<li>Complex expansion should always be provided in column 16 when the binary interaction has been expanded and was originally part of a n-ary interaction</li>
<li>IMEx : interaction type which can be used for scoring (col 12), interactor types which can be used to filter interactions (col 21 and 22)</li>
<li>source databases should always be provided in column 13</li>
</ul>
<table>
<thead>
<tr>
<th style="text-align:left"><strong>Column</strong></th>
<th style="text-align:left"><strong>Data format</strong></th>
<th style="text-align:left"><strong>Example(s)</strong></th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left">columns 7, 12, 16, 17, 18, 19, 20, 21, 22, 41 and 42,</td>
<td style="text-align:left">use <strong>a unique</strong> cross references to the PSI-MI ontology. In parenthesis, it should be the name of the MI term in the ontology</td>
<td style="text-align:left"><code>psi-mi:"MI:0914"(association)</code></td>