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254      <a href="../../system_requirements/" class="md-nav__link">
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258    System Requirements
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305            
306  
307  <span class="md-ellipsis">
308    Building a Database (Nextflow)
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310  
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313          </label>
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318            Building a Database (Nextflow)
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321            
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324  
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326  
327  
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329      <a href="../../nextflow/installation/" class="md-nav__link">
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332  <span class="md-ellipsis">
333    Installation
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338    </li>
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349    <li class="md-nav__item">
350      <a href="../../nextflow/inputs/" class="md-nav__link">
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354    Inputs
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360  
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371      <a href="../../nextflow/parameters/" class="md-nav__link">
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375    Parameters
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392      <a href="../../nextflow/outputs/" class="md-nav__link">
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396    Outputs
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409  
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412    <li class="md-nav__item">
413      <a href="../../nextflow/running_the_pipeline/" class="md-nav__link">
414        
415  
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417    Running the Workflow
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419  
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429  
430  
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433    <li class="md-nav__item">
434      <a href="../../nextflow/examples/" class="md-nav__link">
435        
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438    Examples
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443    </li>
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466            
467  
468  <span class="md-ellipsis">
469    Advanced
470  </span>
471  
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474          </label>
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479            Advanced
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490      <a href="../../nextflow/docker_images/" class="md-nav__link">
491        
492  
493  <span class="md-ellipsis">
494    Docker Images
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499    </li>
500  
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537          
538          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
539            
540  
541  <span class="md-ellipsis">
542    Nodes and Relationships
543  </span>
544  
545
546            <span class="md-nav__icon md-icon"></span>
547          </label>
548        
549        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
550          <label class="md-nav__title" for="__nav_5">
551            <span class="md-nav__icon md-icon"></span>
552            Nodes and Relationships
553          </label>
554          <ul class="md-nav__list" data-md-scrollfix>
555            
556              
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558  
559  
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562  
563  
564    <li class="md-nav__item md-nav__item--active">
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567      
568      
569      
570        <label class="md-nav__link md-nav__link--active" for="__toc">
571          
572  
573  <span class="md-ellipsis">
574    Identifiers
575  </span>
576  
577
578          <span class="md-nav__icon md-icon"></span>
579        </label>
580      
581      <a href="./" class="md-nav__link md-nav__link--active">
582        
583  
584  <span class="md-ellipsis">
585    Identifiers
586  </span>
587  
588
589      </a>
590      
591        
592
593<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
594  
595  
596  
597  
598    <label class="md-nav__title" for="__toc">
599      <span class="md-nav__icon md-icon"></span>
600      Table of contents
601    </label>
602    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
603      
604        <li class="md-nav__item">
605  <a href="#uids" class="md-nav__link">
606    <span class="md-ellipsis">
607      UIDs
608    </span>
609  </a>
610  
611</li>
612      
613        <li class="md-nav__item">
614  <a href="#proteins" class="md-nav__link">
615    <span class="md-ellipsis">
616      Proteins
617    </span>
618  </a>
619  
620</li>
621      
622        <li class="md-nav__item">
623  <a href="#assemblies" class="md-nav__link">
624    <span class="md-ellipsis">
625      Assemblies
626    </span>
627  </a>
628  
629</li>
630      
631        <li class="md-nav__item">
632  <a href="#nucleotides" class="md-nav__link">
633    <span class="md-ellipsis">
634      Nucleotides
635    </span>
636  </a>
637  
638</li>
639      
640    </ul>
641  
642</nav>
643      
644    </li>
645  
646
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651  
652  
653  
654  
655    <li class="md-nav__item">
656      <a href="../schema/" class="md-nav__link">
657        
658  
659  <span class="md-ellipsis">
660    Schema
661  </span>
662  
663
664      </a>
665    </li>
666  
667
668              
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670          </ul>
671        </nav>
672      
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674  
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1278<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
1279  
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1288      
1289        <li class="md-nav__item">
1290  <a href="#uids" class="md-nav__link">
1291    <span class="md-ellipsis">
1292      UIDs
1293    </span>
1294  </a>
1295  
1296</li>
1297      
1298        <li class="md-nav__item">
1299  <a href="#proteins" class="md-nav__link">
1300    <span class="md-ellipsis">
1301      Proteins
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1308  <a href="#assemblies" class="md-nav__link">
1309    <span class="md-ellipsis">
1310      Assemblies
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1315      
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1317  <a href="#nucleotides" class="md-nav__link">
1318    <span class="md-ellipsis">
1319      Nucleotides
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1336                
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1338
1339  
1340    <a href="https://github.com/socialgene/socialgene.github.io/edit/main/docs/nodes_and_relationships/about_the_database.md" title="Edit this page" class="md-content__button md-icon">
1341      
1342      <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 20H6V4h7v5h5v3.1l2-2V8l-6-6H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h4zm10.2-7c.1 0 .3.1.4.2l1.3 1.3c.2.2.2.6 0 .8l-1 1-2.1-2.1 1-1c.1-.1.2-.2.4-.2m0 3.9L14.1 23H12v-2.1l6.1-6.1z"/></svg>
1343    </a>
1344  
1345  
1346
1347
1348  <h1>Identifiers</h1>
1349
1350<h2 id="uids">UIDs</h2>
1351<p>Most nodes have a "uid" property which stand for unique identifier. It is unique, but only within the same Node label; e.g. only one uid will be present across all "protein" nodes.</p>
1352<h2 id="proteins">Proteins</h2>
1353<p>For proteins the uid is the sha512t24u hash of the protein sequence, this means proteins with identical amino acid sequences are stored only once and referenced by this uid.</p>
1354<p>Protein nodes also have a CRC64 hash which can be used to cross-reference UniProt. The original protein ID from the input FASTA/Genome is found not on the redundant protein nodes but on the relationship between the node representing the nucleotide sequence the protein was found on, and the non-redundant protein.</p>
1355<p>An example of retrieving an input protein's original ID:</p>
1356<div class="tabbed-set tabbed-alternate" data-tabs="1:1"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><div class="tabbed-labels"><label for="__tabbed_1_1">Cypher</label></div>
1357<div class="tabbed-content">
1358<div class="tabbed-block"></div>
1359</div>
1360</div>
1361<div class="highlight"><pre><span></span><code><span class="k">MATCH</span><span class="w"> </span><span class="p">()</span><span class="o">-[</span><span class="n">e1</span><span class="p">:</span><span class="n">ENCODES</span><span class="o">]-&gt;</span><span class="p">(</span><span class="n">p1</span><span class="p">:</span><span class="n">protein</span><span class="w"> </span><span class="p">{</span><span class="n">uid</span><span class="p">:</span><span class="s">&quot;bnI__-NwnuHiyLRDrRcUdrPyYyIjfONy&quot;</span><span class="p">})</span><span class="w"> </span>
1362<span class="k">RETURN</span><span class="w"> </span><span class="n">e1</span><span class="p">.</span><span class="n">protein_id</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="n">protein_id</span><span class="p">,</span><span class="w"> </span><span class="n">p1</span><span class="p">.</span><span class="n">uid</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="n">uid</span>
1363<span class="k">LIMIT</span><span class="w"> </span><span class="m">2</span>
1364</code></pre></div>
1365<p>Results in:</p>
1366<table>
1367<thead>
1368<tr>
1369<th>protein_id</th>
1370<th>protein_uid</th>
1371</tr>
1372</thead>
1373<tbody>
1374<tr>
1375<td>ALC45_RS09175</td>
1376<td>bnI__-NwnuHiyLRDrRcUdrPyYyIjfONy</td>
1377</tr>
1378<tr>
1379<td>ALT75_RS12645</td>
1380<td>bnI__-NwnuHiyLRDrRcUdrPyYyIjfONy</td>
1381</tr>
1382</tbody>
1383</table>
1384<h2 id="assemblies">Assemblies</h2>
1385<p>For assemblies  SocialGene tries to assign a uid in preference of:</p>
1386<p>1) extract the <code>
1386Assembly:</code> identifier from the <code>dbxrefs</code> section of a genbank file and use it as the uid</p>
1387<p>2) use the name of the input file as the uid (assumption that a single file contains a single assembly/genome)</p>
1388<p>3) assign a random string as the uid</p>
1389<div class="admonition note">
1390<p class="admonition-title">Note</p>
1391<p>If a FASTA file was used as input the nucleotide and assembly node uids will be the FASTA file's name.</p>
1392</div>
1393<h2 id="nucleotides">Nucleotides</h2>
1394<p>Nucleotide sequences ("Locus" in GBK files) are assigned a unique id by hashing the assembly uid they come from, and the external nucleotide identifier. See the example below. The original nucleotide identifier is stored on the nucleotide node as the property <code>external_id</code>. </p>
1395<div class="tabbed-set tabbed-alternate" data-tabs="2:1"><input checked="checked" id="__tabbed_2_1" name="__tabbed_2" type="radio" /><div class="tabbed-labels"><label for="__tabbed_2_1">Cypher</label></div>
1396<div class="tabbed-content">
1397<div class="tabbed-block"></div>
1398</div>
1399</div>
1400<div class="highlight"><pre><span></span><code><span class="k">MATCH</span><span class="w"> </span><span class="p">(</span><span class="n">n1</span><span class="p">:</span><span class="n">nucleotide</span><span class="w"> </span><span class="p">{</span><span class="n">external_id</span><span class="p">:</span><span class="s">&quot;NZ_CXED01000052.1&quot;</span><span class="p">})</span>
1401<span class="k">RETURN</span><span class="w"> </span><span class="n">n1</span>
1402<span class="k">LIMIT</span><span class="w"> </span><span class="m">1</span>
1403</code></pre></div>
1404<p>Returns the node and its properties:</p>
1405<div class="highlight"><pre><span></span><code>{
1406  &quot;identity&quot;: 43109979,
1407  &quot;labels&quot;: [
1408    &quot;nucleotide&quot;
1409  ],
1410  &quot;properties&quot;: {
1411    &quot;strain&quot;: &quot;20051272_1361367&quot;,
1412    &quot;collection_date&quot;: &quot;2005-01-01&quot;,
1413    &quot;country&quot;: &quot;Egypt&quot;,
1414    &quot;db_xref&quot;: &quot;taxon:624&quot;,
1415    &quot;uid&quot;: &quot;zzGRoTd7WPwP8XCrEzdEmnbWtvJvCsap&quot;,
1416    &quot;serovar&quot;: &quot;NA&quot;,
1417    &quot;external_id&quot;: &quot;NZ_CXED01000052.1&quot;,
1418    &quot;mol_type&quot;: &quot;genomic DNA&quot;,
1419    &quot;isolation_source&quot;: &quot;feces&quot;
1420  },
1421  &quot;elementId&quot;: &quot;43109979&quot;
1422}
1423</code></pre></div>
1424<p>In this case the uid of the nucleotide node is <code>zzGRoTd7WPwP8XCrEzdEmnbWtvJvCsap</code>, which is the hash of assembly uid "GCF_001246015.1" and the nucleotide external_id "NZ_CXED01000052.1".</p>
1425<p>This can be verified in the SocialGene python library:</p>
1426<div class="tabbed-set tabbed-alternate" data-tabs="3:1"><input checked="checked" id="__tabbed_3_1" name="__tabbed_3" type="radio" /><div class="tabbed-labels"><label for="__tabbed_3_1">Python</label></div>
1427<div class="tabbed-content">
1428<div class="tabbed-block"></div>
1429</div>
1430</div>
1431<div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">socialgene.hashing.hashing</span> <span class="kn">import</span> <span class="n">hasher</span>
1432<span class="n">hasher</span><span class="p">(</span><span class="s2">&quot;GCF_001246015.1___NZ_CXED01000052.1&quot;</span><span class="p">)</span>
1433
1434<span class="c1"># &#39;zzGRoTd7WPwP8XCrEzdEmnbWtvJvCsap&#39;</span>
1435</code></pre></div>
1436<div class="admonition note">
1437<p class="admonition-title">Note</p>
1438<p>If a FASTA file was used as input the nucleotide and assembly node uids will be the FASTA file's name.</p>
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