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<title>Data Management</title>
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</head>
<body id="_relational_database_management_systems" class="article toc2 toc-left">
<div id="header">
<h1>Data Management</h1>
<div class="details">
<span id="author" class="author">Jan Aerts</span><br>
<span id="email" class="email"><a href="mailto:jan.aerts@kuleuven.be">jan.aerts@kuleuven.be</a></span><br>
</div>
<div id="toc" class="toc2">
<div id="toctitle">Table of Contents</div>
<p><span class="toc-root"><a href="index.html">Data Management</a></span></p><ul class="sectlevel1">
<li><a href="_relational_database_management_systems.html"><span class="toc-current">1. Relational Database Management Systems</span></a>
<ul class="sectlevel2">
<li><a href="_relational_database_management_systems.html#_examples_of_data">1.1. Examples of data</a>
</li>
<li><a href="_relational_database_management_systems.html#_relational_databases">1.2. Relational databases</a>
</li>
<li><a href="_relational_database_management_systems.html#_database_schema_and_normalisation">1.3. Database schema and normalisation</a>
</li>
<li><a href="_relational_database_management_systems.html#_sql_structured_query_language">1.4. SQL - Structured Query Language</a>
</li>
<li><a href="_relational_database_management_systems.html#_drawbacks_of_relational_databases">1.5. Drawbacks of relational databases</a>
</li>
<li><a href="_relational_database_management_systems.html#_python_api_to_sqlite">1.6. Python API to sqlite</a>
</li>
</ul>
</li>
<li><a href="_nosql_an_introduction.html">2. NoSQL: an introduction</a>
</li>
<li><a href="_keyvalue_stores.html">3. Key/value stores</a>
</li>
<li><a href="_document_oriented_databases.html">4. Document-oriented databases</a>
</li>
<li><a href="_graph_databases.html">5. Graph databases</a>
</li>
<li><a href="_arangodb.html">6. ArangoDB</a>
</li>
<li><a href="_arangodb_interfaces.html">7. ArangoDB interfaces</a>
</li>
</ul>
</div>
</div>
<div id="content">
<div class="sect1">
<h2 id="_relational_database_management_systems">1. Relational Database Management Systems</h2>
<div class="sectionbody">
<div class="paragraph">
<p>This is a <em>practical</em> introduction to relational database management systems and SQL. The text is written focussing on how you can get things done, and does not go into the theoretical and technical backgrounds. The online version of this text is available at <a href="http://vda-lab.github.io/data-management" class="bare">http://vda-lab.github.io/data-management</a></p>
</div>
<div class="paragraph">
<p>Working with data almost invariably involves working with relational databases and SQL (Structured Query Language). They have a decades-old history and are very established. In this section, we go over the why and how of this type of database.</p>
</div>
<div class="paragraph">
<p>Let’s look at some example life science fields where we collect data to make the rest of the session a bit more concrete.</p>
</div>
<div class="sect2">
<h3 id="_examples_of_data">1.1. Examples of data</h3>
<div class="sect3">
<h4 id="_microbiome_data">1.1.1. Microbiome data</h4>
<div class="paragraph">
<p>Microbiome data offer a window into the complex world of microbial communities and their interactions with their environment. This can be in the human or animal body, soil, or other ecosystems. By measuring and analyzing this data, we can gain insights into a lot of processes: in humans and animals, it can illuminate aspects of health, disease, and nutrition; in agriculture, it can enhance our understanding of soil health, plant growth, and crop resilience.</p>
</div>
<div class="paragraph">
<p>Microbiome data typically consist of OTU (operational taxonomic unit) or ASV (amplicon sequence variant) tables, which can be considered large tables where the columns represent the OTUs/ASVs, the rows represent different samples, and the cells indicate the amount of that OTU/ASV found in a particular sample.</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 16.6666%;">
<col style="width: 16.6666%;">
<col style="width: 16.6666%;">
<col style="width: 16.6666%;">
<col style="width: 16.6666%;">
<col style="width: 16.667%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">sample</th>
<th class="tableblock halign-left valign-top">SRS024625.570280</th>
<th class="tableblock halign-left valign-top">SRS018102.573993</th>
<th class="tableblock halign-left valign-top">SRS017304.575372</th>
<th class="tableblock halign-left valign-top">SRS024151.575546</th>
<th class="tableblock halign-left valign-top">…​</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">963239</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">12</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">2</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">15</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">4431292</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">5</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">3</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">4480529</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">7</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">4345640</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">0</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">3</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">8</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
</tbody>
</table>
<div class="paragraph">
<p>Both samples and OTUs/ASVs themselves can contain metadata. For the samples, these can include the sampling device, the age of the subject, the location of the sample (e.g. skin vs gut vs …​), etc. For the OTUs, these are e.g. consensus sequences and taxonomy.</p>
</div>
</div>
<div class="sect3">
<h4 id="_dna_sequencing_and_genotyping">1.1.2. DNA sequencing and genotyping</h4>
<div class="paragraph">
<p>The importance of DNA sequencing and genotyping is steadily increasing within research and health care. In genotyping, one reads the nucleotides at specific positions in the genome to check if the patient has an allele that for example constitutes a higher risk to certain diseases, or that indicates higher or lower sensitivity to certain medication.</p>
</div>
<div class="paragraph">
<p>For example, mutations in the BRCA1 and BRCA2 genes change a person’s chance of getting breast cancer (see <a href="http://arup.utah.edu/database/BRCA/Variants/BRCA2.php" class="bare">http://arup.utah.edu/database/BRCA/Variants/BRCA2.php</a> for a list of possible mutations in BRCA2 and their pathogenicity). One of the many harmful mutations is a mutation at position 32,316,517 on chromosome 13 (in exon 2 of BRCA2) that changes a C to an A, resulting in a stop codon.</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="assets/brca2.png" alt="brca2"></span></p>
</div>
<div class="paragraph">
<p>Genotyping results therefore contain information on:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>the individual</p>
</li>
<li>
<p>the polymorphism (i.e. identifying what nucleotide is changed) position in the genome (i.e. chr13 position 32,316,517)</p>
</li>
<li>
<p>the allele (i.e. C or A)</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>For each, additional information can be recorded:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>for the individual: their name, ethnicity</p>
</li>
<li>
<p>for the polymorphism: the unique identifier in a central database (in this case: rs878853592), the chromosome (chr13), the position (32,316,517), the allele that occurs in healthy individuals (i.e. C)</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>An example genotype table:</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="assets/genotype_table.png" alt="genotype table"></span></p>
</div>
<div class="paragraph">
<p>This table contains the information for 3 polymorphisms (called rs12345, rs98765 and rs28465) for 2 individuals (individual_A and individual_B). Typically, thousands of polymorphisms are recorded for thousands of individuals.
A particular type of polymorphism is the single nucleotide polymorphism (SNP), which will be why tables below will be called <code>snps</code>.</p>
</div>
</div>
<div class="sect3">
<h4 id="_epidemiological_studies">1.1.3. Epidemiological studies</h4>
<div class="paragraph">
<p>Epidemiology is described as "the study of the occurrence and distribution of health-related states or events in specified populations, including the study of determinants influencing such states, and the application of this knowledge to control the health problems" (Dictionary of Epidemiology, Porta 2008). It covers a very broad and diverse line of research:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>experimental vs observational studies</p>
</li>
<li>
<p>within the observational studies:</p>
<div class="ulist">
<ul>
<li>
<p>exploratory vs descriptive</p>
</li>
<li>
<p>exposure vs outcome oriented</p>
</li>
</ul>
</div>
</li>
</ul>
</div>
<div class="paragraph">
<p>The collected data can also be very diverse, and include questionnaires, forms, medical device outcomes, biological data, etc.</p>
</div>
<div class="paragraph">
<p>Epidemiological studies are generally done in one of two settings: primary (based on newly collected data) or secondary (using existing databases).</p>
</div>
<div class="paragraph">
<p>Generally a codebook or data dictionary that describes all data sources (collected, derived, transformed, …​). An example of a data dictionary is provided below (taken from Ahrens, W. et al. (2014): Handbook of epidemiology. Table 27.2).</p>
</div>
<div class="paragraph">
<p><span class="image"><img src="assets/datadictionary.png" alt="datadictionary"></span></p>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_relational_databases">1.2. Relational databases</h3>
<div class="paragraph">
<p>There is a wide variety of database systems to store data, but the most-used in the relational database management system (RDBMS). These basically consist of tables that contain rows (which represent instance data) and columns (representing properties of that data). Any table can be thought of as an Excel-sheet.</p>
</div>
<div class="paragraph">
<p>Relational databases are the most wide-spread paradigm used to store data. They use the concept of tables with each <strong>row</strong> containing an <strong>instance of the data</strong>, and each <strong>column</strong> representing different <strong>properties</strong> of that instance of data. Different implementations exist, include ones by Oracle and MySQL. For many of these (including Oracle and MySQL), you need to run a database server in the background. People (or you) can then connect to that server via a client. In this session, however, we’ll use <strong>SQLite3</strong>. SQLite is used by Firefox, Chrome, Android, Skype, …​</p>
</div>
<div class="sect3">
<h4 id="_sqlite">1.2.1. SQLite</h4>
<div class="paragraph">
<p>The relational database management system (RDBMS) that we will use is <strong>SQLite</strong>. It is very lightweight and easy to set up.</p>
</div>
<div class="sect4">
<h5 id="_using_sqlite_on_the_linux_command_line">Using SQLite on the linux command line</h5>
<div class="paragraph">
<p>To create a new database that you want to give the name 'new_database.sqlite', just call <code>sqlite3</code> with the new database name. <code>sqlite3 new_database.sqlite</code> The name of that file does not have to end with <code>.sqlite</code>, but it helps you to remember that this is an SQLite database. If you add tables and data in that database and quit, the data will automatically be saved.</p>
</div>
<div class="paragraph">
<p>There are two types of commands that you can run within SQLite: <strong>SQL commands</strong> (the same as in any other relational database management system), and <strong>SQLite-specific commands</strong>. The latter start with a period, and do <strong>not</strong> have a semi-colon at the end, in contrast to SQL commands (see later).</p>
</div>
<div class="paragraph">
<p>Some useful commands:</p>
</div>
<div class="ulist">
<ul>
<li>
<p><code>.help</code> ⇒ Returns a list of the SQL-specific commands</p>
</li>
<li>
<p><code>.tables</code> ⇒ Returns a list of tables in the database</p>
</li>
<li>
<p><code>.schema</code> ⇒ Returns the schema of all tables</p>
</li>
<li>
<p><code>.header on</code> ⇒ Add a header line in any output</p>
</li>
<li>
<p><code>.mode column</code> ⇒ Align output data in columns instead of output as comma-separated values</p>
</li>
<li>
<p><code>.quit</code></p>
</li>
</ul>
</div>
</div>
<div class="sect4">
<h5 id="_using_db_browser_for_sqlite">Using DB Browser for SQLite</h5>
<div class="paragraph">
<p>If you like to use a graphical user interface (or don’t work on a linux or OSX computer), you can use the DB Browser for SQLite which you can download <a href="https://sqlitebrowser.org/">here</a>.</p>
</div>
<div class="paragraph">
<p>Note: In all code snippets that follow below, the <code>sqlite></code> at the front represents the sqlite prompt, and should <strong>not</strong> be typed in…​</p>
</div>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_database_schema_and_normalisation">1.3. Database schema and normalisation</h3>
<div class="paragraph">
<p>We’ll look into two examples to guide us through developing a good database schema. The database schema is basically the description of what the database looks like: what are the names of the tables, what are the columns in those tables, and how are these connected between tables?</p>
</div>
<div class="sect3">
<h4 id="_a_student_database">1.3.1. A student database</h4>
<div class="sect4">
<h5 id="_the_simplest_version">The simplest version</h5>
<div class="paragraph">
<p>Let’s say we want to store which students follow the G0R72A course ("Data Visualisation in Data Science"). We want to keep track of their first name, last name, student ID, and whether or not they follow the course. This should allow for some easy queries, such as listing all people who take the course, or returning the number of people who do so.
In this case, a <em>flat database</em> would suffice; i.e. a <em>single</em> table can hold all information.</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 25%;">
<col style="width: 25%;">
<col style="width: 25%;">
<col style="width: 25%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">first_name</th>
<th class="tableblock halign-left valign-top">last_name</th>
<th class="tableblock halign-left valign-top">student_id</th>
<th class="tableblock halign-left valign-top">takes_course</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0U29A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0P18A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">H09B7A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">E02N3A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Sarah</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Smith</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0002</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0U29A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
</tbody>
</table>
</div>
<div class="sect4">
<h5 id="_a_slightly_less_simple_setting">A slightly less simple setting</h5>
<div class="paragraph">
<p>Consider that we want to store which students follow which courses in MSc Statistics. So we’d like to keep:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>first name, last name, student ID</p>
</li>
<li>
<p>courses a student takes (E02N3A, G0R72A, …​)</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>This should allow for queries e.g. to find out which people follow a particular course, the average number of courses a student takes, etc.</p>
</div>
<div class="paragraph">
<p>Let’s take the same approach as above, and we simply add a column for each course.</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 14.2857%;">
<col style="width: 14.2857%;">
<col style="width: 14.2857%;">
<col style="width: 14.2857%;">
<col style="width: 14.2857%;">
<col style="width: 14.2857%;">
<col style="width: 14.2858%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">first_name</th>
<th class="tableblock halign-left valign-top">last_name</th>
<th class="tableblock halign-left valign-top">student_id</th>
<th class="tableblock halign-left valign-top">takes_I0U29A</th>
<th class="tableblock halign-left valign-top">takes_G0R72A</th>
<th class="tableblock halign-left valign-top">…​</th>
<th class="tableblock halign-left valign-top">takes_E02N3A</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">N</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Sarah</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Smith</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0002</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">N</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Mary</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Kopals</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0003</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">N</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Y</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
</tbody>
</table>
<div class="paragraph">
<p>This way of working (called the <em>wide format</em>) does present some issues, though.</p>
</div>
<div class="ulist">
<ul>
<li>
<p>We will end up with a huge table. Imagine there are 20 courses at KU Leuven and 80 at other universities in Flanders that the student can follow. In addition, suppose there are 50 students. This would mean that we need (3 + 100)*50 = 5,150 cells to store this data.</p>
</li>
<li>
<p>There can be a lot of wasted space, for example courses that nobody takes.</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>An alternative is to use the <em>long format</em>:</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 25%;">
<col style="width: 25%;">
<col style="width: 25%;">
<col style="width: 25%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">first_name</th>
<th class="tableblock halign-left valign-top">last_name</th>
<th class="tableblock halign-left valign-top">student_id</th>
<th class="tableblock halign-left valign-top">takes_course</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0U29A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0P18A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">H09B7A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">E02N3A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Sarah</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Smith</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0002</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0U29A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">…​</p></td>
</tr>
</tbody>
</table>
<div class="paragraph">
<p>This solves the issue of not having to store the information when a course is <em>not</em> taken, decreasing the number of cells needed from 5,150 to 2,000.</p>
</div>
<div class="paragraph">
<p>This is still not ideal though, as this design still suffers from a lot of redundancy: the first name, last name and student ID are provided over and over again. Imagine that we’d keep home address (street, street number, zip code, city, country) as well, that would look like this:</p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
<col style="width: 12.5%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">first_name</th>
<th class="tableblock halign-left valign-top">last_name</th>
<th class="tableblock halign-left valign-top">student_id</th>
<th class="tableblock halign-left valign-top">street</th>
<th class="tableblock halign-left valign-top">number</th>
<th class="tableblock halign-left valign-top">zip</th>
<th class="tableblock halign-left valign-top">city</th>
<th class="tableblock halign-left valign-top">takes_course</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Some Street</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1234</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">MajorCity</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0U29A</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Martin</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Van Deun</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">S0001</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Some Street</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">1234</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">MajorCity</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">I0P18A</p></td>
</tr>