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<h2 class="hd hd-2 unit-title">Introduction</h2>
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<p>In order to allow the secondary analysis of electronic health records and <span style="font-size: 1em;">apply the techniques discussed previously,</span><span style="font-size: 1em;"> a number of different prerequisites and structural elements are needed, for example:</span></p>
<ol>
<li>Electronic health records/registries</li>
<li>Databases</li>
<li>A programming language to navigate through these databases</li>
</ol>
<p>These embody some of the core elements without which the secondary analysis of electronic health records (and thus medical data as a whole) could not be deployed. Hence, they embody the pillars of modern data science.</p>
<p>In this subsection, we introduce these different elements and highlight useful examples.</p>
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<p><strong>Learning Objectives</strong></p>
<p>In the following section you will learn about:</p>
<ul>
<li>The function and individual characteristics of electronic health records and registries</li>
<li>The progression of databases and their usage</li>
<li>SQL as an example of a query language and some basic commands</li>
<li>The MIMIC III Database, its structure and other important databases for critical care research</li>
<li>The challenge of interpreting heterogeneous data</li>
</ul>
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<h2 class="hd hd-2 unit-title">EHRs and Registries</h2>
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<h4 style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">What are EHRs and registries? What is the difference between them?</h4>
<p style="color: #313131; margin: 0px 0px 1.41575em;"><span style="color: inherit; font-style: inherit; font-variant: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em;">While both EHRs (Electronic Health Records) and registries use clinical information at the patient level, registries are typically population focused, purpose driven, and designed to derive information on health outcomes defined before the data are collected and analyzed. On the other hand, EHRs are focused on the collection and use of an individual patient's health-related information. While in practice there may be some overlap in functionality between EHRs and registries, their roles are distinct, and both are very important to the health care system.</span></p>
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<h4 style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">Electronic Health Records</h4>
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<p style="color: #313131; margin: 0px 0px 1.41575em;">An electronic health record (EHR) refers to the systemic collection of electronic health information of an individual patient or population. EHRs can be comprehensive systems that manage both clinical and administrative data; for example, an EHR may collect medical histories, demographics, laboratory data, and physician notes, and may assist with billing, interpractice referrals, appointment scheduling, and prescription refills. The system is designed to represent data that captures the state of the patient at all times. It is possible to view an entire patient history without the need to track down the patient’s previous medical record volume, and EHRs assist in ensuring data is accurate, appropriate and legible.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">According to the Institute of Medicine (IOM), an EHR has four core functionalities: health information and data, results management, order entry and support, and decision support. Due to all the information being in a single system, it makes it much more effective when extracting medical data for the examination of possible trends and long-term changes in the patient.</p>
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<h4 style="text-rendering: optimizelegibility; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 16px; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">Registries</h4>
<p style="text-rendering: optimizelegibility; margin: 0px 0px 1.41575em; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">A registry is an organized system that uses observational study methods to collect uniform data (clinical and other) to evaluate specified outcomes for a population defined by a particular disease, condition, or exposure, and that serves one or more predetermined scientific, clinical, or policy purposes. Registries are focused on populations and are designed to fulfill specific purposes defined before the data are collected and analyzed. EHRs are patient centric and are designed to collect, share, and use that information for the benefit of that individual.</p>
<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">Other terms also used to refer to patient registries include clinical registries, clinical data registries, disease registries, and outcomes registries.</p>
<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">A patient registry can be a powerful tool to observe the course of disease; to understand variations in treatment and outcomes; to examine factors that influence prognosis and quality of life; to describe care patterns, including appropriateness of care and disparities in the delivery of care; to assess effectiveness; to monitor safety and harm; and to measure quality of care. Through functionalities such as feedback of data, registries are also being used to study quality improvement.</p>
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<h3>Source</h3>
<p>Gliklich RE, Dreyer NA, Leavy MB, editors. Registries for Evaluating Patient Outcomes: A User's Guide [Internet]. 3rd edition. Rockville (MD): Agency for Healthcare Research and Quality (US); 2014 Apr. 15, Interfacing Registries With Electronic Health Records. Available from: https://www.ncbi.nlm.nih.gov/books/NBK208625/</p>
<p>Gliklich RE, Dreyer NA, Leavy MB, editors. Registries for Evaluating Patient Outcomes: A User's Guide [Internet]. 3rd edition. Rockville (MD): Agency for Healthcare Research and Quality (US); 2014 Apr. 1, Patient Registries. Available from: https://www.ncbi.nlm.nih.gov/books/NBK208643/</p>
<p></p>
<p></p>
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<h2 class="hd hd-2 unit-title">Databases</h2>
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<h5 style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;"><font color="#313131" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif">What is a Database?</font></h5>
<p style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">Databases, organized collections of data, were first proposed in the 1960s with the advent of random access storage. They were originally used only for very specialized applications due to their cost and complexity, but have now become ubiquitous in all aspects of our daily interactions with computer systems. Whether we are doing banking, checking social media, reading articles, or even playing a game, we are interacting with a database, which stores and manages our data.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 16px;">Today’s databases are significantly larger and faster than anything imagined at that time. The rate of data growth and size has exceeded most expectations. Therefore, database technology has continued to grow and expand to accommodate new forms of data and the different requirements these systems place on the databases.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 16px;">The first databases were navigational databases, which then evolved into hierarchical databases. These databases required significant custom coding and were difficult to analyze. The advancement of relational databases introduced more functionality into the database, creating an explosion of database technology. These systems maintain the integrity and access to complex data in a multi-user environment. They handle the complex task of data management so that developers can handle the higher-level systems. Today, there exists greater variety of databases tailored to a greater variety of problems.</p>
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<h3>Source:</h3>
<p>MITx: HST.936x, Designing Health Information Systems, Part 2: Introduction to Health Information Technology, 2.3: Databases and Registries, Introduction</p>
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<h2 class="hd hd-2 unit-title">SQL</h2>
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<h4 style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em;">An Introduction to SQL </h4>
<p style="color: #313131; margin: 0px 0px 1.41575em;">Structured Query Language (SQL) is a special purpose programming language for interacting with and extracting data from relational databases. Due to the popularity of relational database systems, SQL has become the most popular data query language in the world. In 1986, SQL became a standard of the American National Standards Institute (ANSI). Although SQL is an ANSI standard, in practice SQL syntax differs mildly across database systems. </p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">Tables and relationships define the core data in a relational database. Each table comprises multiple columns, with each row typically representing a record. Each column has a defined data type and set of attributes, which helps to maintain data integrity and ensures that contents of the column are correctly represented. SQL data types support multiple data formats, including exact and approximate numeric data, date and time, character or string data, and binary large objects (often referred to as BLOBs). Along with the data type, attributes are associated with the data such as default value, uniqueness, and length. The entirety of this information comprises the database metadata and helps to maintain integrity and efficient operation of the database.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">SQL is an interpreted language with relatively few commands that can be executed directly or embedded in an application or website. It extends the work by Edgar F. Codd’s relational model published in 1970 with a foundation in relational algebra. Donald D. Chamberlin and Raymond F. Boyce originally developed SQL in the 1970s while at IBM. The language is easy to learn but hard to master. It provides the core commands to perform all CRUD operations. CRUD stands for Create, Read, Update and Delete. The standard SQL commands to interact with relational DBs are create, select, insert, update, delete, and drop. These commands can be classified into groups based on their core functions. The data definition language groups of commands include create, which is used to build new tables, views, and other objects; alter, which changes existing database objects; and drop, which deletes database tables, views, or other structures. These commands are very powerful and generally not reversible, so extreme caution should be exercised with their use.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><span face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">The data manipulation commands are used to interact with data within the database instead of the structure itself. </span><span style="font-family: monospace, serif;">SELECT</span><span face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;"> retrieves certain records from one or more tables, </span><span face="monospace, serif" style="font-family: monospace, serif;">INSERT</span><span style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 1em;"> is used to create a record, </span><span style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 1em;"><span style="font-family: monospace, serif;">UPDATE</span></span><span style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 1em;"> changes an existing record, and </span><span style="font-size: 1em;"><span style="font-family: monospace, serif;">DELETE </span></span><span style="font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 1em;">removes one or more records. There are also data control commands that are beyond the scope of this course.</span></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">A SQL expression is constructed by a unique set of rules and guidelines to make the command unambiguous and easily understandable by the DBMS. The command is constructed similar to an English sentence with a verb, expression, predicate, and joining elements. In addition, SQL operators allow relatively complex Boolean or arrhythmic functions.</p>
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<h4 style="color: #313131; font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 1em; line-height: 1.4em;">Select Statement</h4>
<p style="color: #313131; margin: 0px 0px 1.41575em;">The most frequently used SQL statement is the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">select</code> statement. Select statements are used to query or retrieve data from a table in the database. A query may retrieve information from specified columns or from all of the columns in a table. Select statements are typically structured as follows:</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><code style="font-size: 1em; line-height: 1.4em; color: #313131;">SELECT columns</code><br style="line-height: 1.4em;" /><code style="font-size: 1em; line-height: 1.4em; color: #313131;">FROM table</code><br style="line-height: 1.4em;" /><code style="font-size: 1em; line-height: 1.4em; color: #313131;">[WHERE conditions]</code><br style="line-height: 1.4em;" /><code style="font-size: 1em; line-height: 1.4em; color: #313131;">[ORDER BY columns];</code></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">where <span style="font-family: monospace, serif;">table</span><span style="font-size: 1em;"> is the name of the table from which the information is retrieved, and </span><span style="font-family: monospace, serif;">columns</span><span style="font-size: 1em;"> list includes one or more columns from which data is retrieved, separated by commas. The clauses within the brackets are optional, and the entire query is generally terminated with a semicolon.</span></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">We can select all of the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">subject_id</code> and date of birth (<code style="font-size: 1em; line-height: 1.4em; color: #313131;">dob</code>) corresponding to female subjects as follows:</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><code style="font-size: 1em; line-height: 1.4em; color: #313131;">SELECT subject_id, dob<br style="line-height: 1.4em;" />FROM patients<br style="line-height: 1.4em;" />WHERE gender = 'F';</code></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">This query returns the entire <code style="font-size: 1em; line-height: 1.4em; color: #313131;">subject_id</code> and <code style="font-size: 1em; line-height: 1.4em; color: #313131;">dob</code> columns from the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">patients</code> table where the patient <code style="font-size: 1em; line-height: 1.4em; color: #313131;">gender</code> is "<code style="font-size: 1em; line-height: 1.4em; color: #313131;">F</code>". <code style="font-size: 1em; line-height: 1.4em; color: #313131;">WHERE</code> clauses can be combined with standard logical operators <code style="font-size: 1em; line-height: 1.4em; color: #313131;">AND</code>, <code style="font-size: 1em; line-height: 1.4em; color: #313131;">OR</code>:</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><code style="font-size: 1em; line-height: 1.4em; color: #313131;">SELECT subject_id, dob<br style="line-height: 1.4em;" />FROM patients<br style="line-height: 1.4em;" />WHERE subject_id = 109<br style="line-height: 1.4em;" />OR subject_id = 117;</code></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">The <code style="font-size: 1em; line-height: 1.4em; color: #313131;">ORDER BY</code> keyword is relatively straightforward: it will sort the data in the order you specify. The query below orders the results by the patient <code style="font-size: 1em; line-height: 1.4em; color: #313131;">subject_id</code>, for example:</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><code style="font-size: 1em; line-height: 1.4em; color: #313131;">SELECT subject_id, dob<br style="line-height: 1.4em;" />FROM patients<br style="line-height: 1.4em;" />ORDER BY subject_id</code></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">Complex questions can be answered by joining multiple tables to create a composite result. Often we need information coming from multiple tables. This can be achieved using the SQL <code style="font-size: 1em; line-height: 1.4em; color: #313131;">JOIN</code> keyword. There are several types of join, including <code style="font-size: 1em; line-height: 1.4em; color: #313131;">INNER JOIN</code>, <code style="font-size: 1em; line-height: 1.4em; color: #313131;">LEFT JOIN</code>, and <code style="font-size: 1em; line-height: 1.4em; color: #313131;">RIGHT JOIN</code>. It is important to understand the difference between these joins because their usage can significantly impact query results. Detailed guidance on joins is widely available on the web. We provide a single example here, to illustrate how joins are used.</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">Using the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">INNER JOIN</code> keyword, we will select a list of patients from the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">patients</code> table along with dates of birth, and join to the <code style="font-size: 1em; line-height: 1.4em; color: #313131;">admissions</code> table to get the admission time for each hospital admission. We use <code style="font-size: 1em; line-height: 1.4em; color: #313131;">INNER JOIN</code> to indicate that two or more tables should be combined based on a common attribute, which in our case is <code style="font-size: 1em; line-height: 1.4em; color: #313131;">subject_id</code>:</p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;"><code style="font-size: 1em; line-height: 1.4em; color: #313131;">-- INNER JOIN will only return rows where subject_id<br style="line-height: 1.4em;" />-- appears in both the patients table and the admissions table<br style="line-height: 1.4em;" />SELECT p.subject_id, p.dob, a.hadm_id, a.admittime<br style="line-height: 1.4em;" />FROM patients p<br style="line-height: 1.4em;" />INNER JOIN admissions a<br style="line-height: 1.4em;" />ON p.subject_id = a.subject_id<br style="line-height: 1.4em;" />ORDER BY subject_id, hadm_id;</code></p>
<p style="color: #313131; margin-right: 0px; margin-bottom: 1.41575em; margin-left: 0px;">There are multiple online resources to learn about SQL, so we will not go into further depth here. Several free courses are available, such as Database Systems at MIT Open Courseware and Introduction to Databases from Stanford University.</p>
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<h3>Source:</h3>
<p>MITx: HST.936x, Designing Health Information Systems, Part 2: Introduction to Health Information Technology, 2.3: Databases and Registries, SQL overview</p>
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<h2 class="hd hd-2 unit-title">Databases: An Example</h2>
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<h4><span style="color: #313131; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; letter-spacing: normal;">MIMIC-III</span></h4>
<p><span style="color: #313131; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; letter-spacing: normal;">MI</span><span color="#313131" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" style="color: #313131; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">MIC-III is an openly available dataset developed by the MIT Lab for Computational Physiology, comprising deidentified health data associated with ~60,000 hospital stays. Spanning 2001-2012, it includes demographics, vital signs, laboratory tests, medications, and more. A paper describing MIMIC-III is available from: </span><a href="http://www.nature.com/articles/sdata201635" style="text-rendering: optimizelegibility; background: transparent; margin: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline; transition: color 0.25s ease-in-out 0s; text-decoration-line: none; color: #0075b4;">http://www.nature.com/articles/sdata201635</a></p>
<p>The dataset is provided as a collection of comma-separated value (CSV) files, which can be loaded into a database system such as PostgreSQL. A list of tables is provided on the MIMIC website: <a href="http://mimic.physionet.org/mimictables/admissions/" style="text-rendering: optimizelegibility; background: transparent; margin: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline; transition: color 0.25s ease-in-out 0s; text-decoration-line: none; color: #0075b4;">http://mimic.physionet.org/mimictables/admissions/</a></p>
<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">We have highlighted some of the key tables below:</p>
<ul style="text-rendering: optimizelegibility; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; line-height: 1.4em; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">
<li style="text-rendering: optimizelegibility; margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline;"><code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">patients</code>: a list of patients covered in MIMIC-III, each identified by a unique <code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">subject_id</code>.</li>
<li style="text-rendering: optimizelegibility; margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline;"><code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">admissions</code>: a list of hospital admissions, each identified by a unique <code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">hadm_id</code>.</li>
<li style="text-rendering: optimizelegibility; margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline;"><code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">icustays</code>: a list of ICU stays, each identified by a unique <code style="text-rendering: optimizelegibility; font-size: inherit; margin: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; line-height: 1.4em; vertical-align: baseline; border-radius: 3px; color: #313131;">icustay_id</code>.</li>
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<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;">Querybuilder (<a href="https://mimic.physionet.org/gettingstarted/querybuilder/" target="[object Object]" style="text-rendering: optimizelegibility; background: transparent; margin: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline; transition: color 0.25s ease-in-out 0s; text-decoration-line: none; color: #0075b4;">https://mimic.physionet.org/gettingstarted/querybuilder/</a>) allows you to explore MIMIC-III with simple queries. For detailed analysis, we recommend that you build MIMIC-III in a Postgres database on your local computer by following the instructions on the MIMIC website (<a href="https://mimic.physionet.org/tutorials/install-mimic-locally-ubuntu/" target="[object Object]" style="text-rendering: optimizelegibility; background: transparent; margin: 0px; padding: 0px; border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: 1.4em; font-family: inherit; vertical-align: baseline; transition: color 0.25s ease-in-out 0s; text-decoration-line: none; color: #0075b4;">https://mimic.physionet.org/tutorials/install-mimic-locally-ubuntu/</a>).</p>
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<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif; vertical-align: baseline; color: rgb(49, 49, 49);">Alistair Johnson PhD<br />Laboratory for Computational Physiology<br />Massachusetts Institute of Technology</p>
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<h3 class="hd hd-2">Introduction to MIMIC-III</h3>
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<h2 class="hd hd-2 unit-title">Other Intensive Care Databases</h2>
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<h4>Other databases for critical care research:<br /><br /></h4>
<p><a href="https://eicu-crd.mit.edu/" target="[object Object]">eICU Collaborative Research Database<br /></a>The eICU Collaborative Research Database is a large multi-center critical care database made available by Philips Healthcare in partnership with the MIT Laboratory for Computational Physiology.<a href="https://eicu-crd.mit.edu/" target="[object Object]"><br /></a></p>
<p><a href="https://amsterdammedicaldatascience.nl/" target="[object Object]">AmsterdamUMCdb<br /></a>The first freely accessible intensive care database from within the European Union. It contains de-identified health data related to tens of thousands of European intensive care unit admissions, including demographics, vital signs, laboratory tests and medications.</p>
<p><a href="https://mimic-cxr.mit.edu/" target="[object Object]">MIMIC-CXR<br /></a>The MIMIC Chest X-ray (MIMIC-CXR) Database is a large publicly available dataset of chest radiographs with free-text radiology reports.</p>
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<h2 class="hd hd-2 unit-title">The Prerequisite for High-Quality Data Analytics</h2>
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<p style="text-rendering: optimizelegibility; margin-right: 0px; margin-left: 0px; padding: 0px; border: 0px; outline: 0px; font-variant-numeric: inherit; font-variant-east-asian: inherit; font-stretch: inherit; font-size: 16px; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif; vertical-align: baseline; color: #313131;"><span color="#313131" face="Open Sans, Helvetica Neue, Helvetica, Arial, sans-serif" style="color: #313131; font-family: 'Open Sans', 'Helvetica Neue', Helvetica, Arial, sans-serif;">John D. Halamka<br /></span>Professor of Medicine, Harvard Medical School<br />Chief Information Officer, Beth Israel Deaconess Medical Center</p>
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<h3 class="hd hd-2">The Prerequisite for High-Quality Data Analytics</h3>
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<h3 class="hd hd-4 downloads-heading sr" id="video-download-transcripts_2ec1a4f945f24447936d15e9cea5db29">Downloads and transcripts</h3>
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<div class="wrapper-download-transcripts">
<h4 class="hd hd-5">Transcripts</h4>
<ul class="list-download-transcripts">
<li class="transcript-option">
<a class="btn btn-link" href="/courses/course-v1:MITx+HST.953x+3T2020/xblock/block-v1:MITx+HST.953x+3T2020+type@video+block@2ec1a4f945f24447936d15e9cea5db29/handler/transcript/download" data-value="srt">Download SubRip (.srt) file</a>
</li>
<li class="transcript-option">
<a class="btn btn-link" href="/courses/course-v1:MITx+HST.953x+3T2020/xblock/block-v1:MITx+HST.953x+3T2020+type@video+block@2ec1a4f945f24447936d15e9cea5db29/handler/transcript/download" data-value="txt">Download Text (.txt) file</a>
</li>
</ul>
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</div>
</div>
</div>
</div>
<div class="vert vert-2" data-id="block-v1:MITx+HST.953x+3T2020+type@html+block@a81c7469ae7e488dbfd761af7bfbfb7f">
<div class="xblock xblock-public_view xblock-public_view-html xmodule_display xmodule_HtmlBlock" data-block-type="html" data-has-score="False" data-runtime-class="LmsRuntime" data-runtime-version="1" data-init="XBlockToXModuleShim" data-request-token="dfd204ec43c311efaedb16ffcfe1c469" data-graded="False" data-usage-id="block-v1:MITx+HST.953x+3T2020+type@html+block@a81c7469ae7e488dbfd761af7bfbfb7f" data-course-id="course-v1:MITx+HST.953x+3T2020">
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<p>Key Points:</p>
<ul>
<li>Heterogeneous data can be very challenging to analyze and interpret (e.g. due to a lack of consistency, missing data, etc.)</li>
<ul>
<ul>
<li>For example, different clinical staff might record a given observation very differently or accidentally enter the wrong number/unit/medication, etc. </li>
</ul>
</ul>
<li>Homogeneous data is not only easier to analyze but also allows for more reliable and robust interpretation when there is certainty about the correctness of inputs</li>
</ul>
</div>
</div>
</div>
</div>
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<h2 class="hd hd-2 unit-title">End of Subsection 1.3: Quiz</h2>
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Question 1
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<legend id="69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1-legend" class="response-fieldset-legend field-group-hd">Which of the following is NOT a core function of an EHR?</legend>
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<input type="radio" name="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1" id="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1-choice_1-label" for="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1"> Results management
</label>
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<div class="field">
<input type="radio" name="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1" id="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1-choice_2-label" for="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1"> Merging previously siloed data
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<div class="field">
<input type="radio" name="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1" id="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1-choice_3-label" for="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1"> Order entry and support
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<input type="radio" name="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1" id="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_4" class="field-input input-radio" value="choice_4"/><label id="69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1-choice_4-label" for="input_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1_choice_4" class="response-label field-label label-inline" aria-describedby="status_69ce8c1f6f524cdab2c0d7f2d908dfa0_2_1"> Decision support
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Question 2
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<legend id="2a5a330a246b4df2be4df9f1b3d4cb0e_2_1-legend" class="response-fieldset-legend field-group-hd">Which of the following only applies to registries, not EHRs?</legend>
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<input type="radio" name="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1" id="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="2a5a330a246b4df2be4df9f1b3d4cb0e_2_1-choice_0-label" for="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1"> Usage of clinical information at the patient level
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<input type="radio" name="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1" id="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="2a5a330a246b4df2be4df9f1b3d4cb0e_2_1-choice_2-label" for="input_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_2a5a330a246b4df2be4df9f1b3d4cb0e_2_1"> Population focused
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Question 3
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<legend id="a517a11401434d888307b54643fd7f64_2_1-legend" class="response-fieldset-legend field-group-hd">The first databases were of which type?</legend>
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<input type="radio" name="input_a517a11401434d888307b54643fd7f64_2_1" id="input_a517a11401434d888307b54643fd7f64_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="a517a11401434d888307b54643fd7f64_2_1-choice_1-label" for="input_a517a11401434d888307b54643fd7f64_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_a517a11401434d888307b54643fd7f64_2_1"> Navigational
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<input type="radio" name="input_a517a11401434d888307b54643fd7f64_2_1" id="input_a517a11401434d888307b54643fd7f64_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="a517a11401434d888307b54643fd7f64_2_1-choice_2-label" for="input_a517a11401434d888307b54643fd7f64_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_a517a11401434d888307b54643fd7f64_2_1"> Relational
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<input type="radio" name="input_a517a11401434d888307b54643fd7f64_2_1" id="input_a517a11401434d888307b54643fd7f64_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="a517a11401434d888307b54643fd7f64_2_1-choice_3-label" for="input_a517a11401434d888307b54643fd7f64_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_a517a11401434d888307b54643fd7f64_2_1"> Integrational
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Question 4
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><p>Which output will be returned when the following query would be executed on MIMIC-III?</p>
<p>SELECT subject_id, dob</p>
<p>FROM patients</p>
<p>WHERE gender = 'F';</p>
<div class="choicegroup capa_inputtype" id="inputtype_9d02fcd31012433bb423ad6b217b1ee7_2_1">
<fieldset aria-describedby="status_9d02fcd31012433bb423ad6b217b1ee7_2_1">
<div class="field">
<input type="radio" name="input_9d02fcd31012433bb423ad6b217b1ee7_2_1" id="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="9d02fcd31012433bb423ad6b217b1ee7_2_1-choice_0-label" for="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_9d02fcd31012433bb423ad6b217b1ee7_2_1"> Only Male patients
</label>
</div>
<div class="field">
<input type="radio" name="input_9d02fcd31012433bb423ad6b217b1ee7_2_1" id="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="9d02fcd31012433bb423ad6b217b1ee7_2_1-choice_1-label" for="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_9d02fcd31012433bb423ad6b217b1ee7_2_1"> Only Female patients
</label>
</div>
<div class="field">
<input type="radio" name="input_9d02fcd31012433bb423ad6b217b1ee7_2_1" id="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="9d02fcd31012433bb423ad6b217b1ee7_2_1-choice_2-label" for="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_9d02fcd31012433bb423ad6b217b1ee7_2_1"> All patients, including the subject ID and the date of birth of only female patients
</label>
</div>
<div class="field">
<input type="radio" name="input_9d02fcd31012433bb423ad6b217b1ee7_2_1" id="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="9d02fcd31012433bb423ad6b217b1ee7_2_1-choice_3-label" for="input_9d02fcd31012433bb423ad6b217b1ee7_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_9d02fcd31012433bb423ad6b217b1ee7_2_1"> Only Female patients, including the subject ID and the date of birth of only male patients
</label>
</div>
<span id="answer_9d02fcd31012433bb423ad6b217b1ee7_2_1"/>
</fieldset>
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Question 5
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><div class="choicegroup capa_inputtype" id="inputtype_48b57d1e0b10414189a4e81240835c1d_2_1">
<fieldset aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1">
<legend id="48b57d1e0b10414189a4e81240835c1d_2_1-legend" class="response-fieldset-legend field-group-hd">Which of the following is not a feature of MIMIC-III?</legend>
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<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_0-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Publicly available
</label>
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<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_1-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Contains patient data from Beth Israel Deaconess Medical Center
</label>
</div>
<div class="field">
<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_2-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Contains deidentified patient level health data
</label>
</div>
<div class="field">
<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_3-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Collected within the years 2010-2020
</label>
</div>
<div class="field">
<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_4" class="field-input input-radio" value="choice_4"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_4-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_4" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Associated with ~60,000 hospital stays
</label>
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<div class="field">
<input type="radio" name="input_48b57d1e0b10414189a4e81240835c1d_2_1" id="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_5" class="field-input input-radio" value="choice_5"/><label id="48b57d1e0b10414189a4e81240835c1d_2_1-choice_5-label" for="input_48b57d1e0b10414189a4e81240835c1d_2_1_choice_5" class="response-label field-label label-inline" aria-describedby="status_48b57d1e0b10414189a4e81240835c1d_2_1"> Includes demographics, vital signs, laboratory tests, medications
</label>
</div>
<span id="answer_48b57d1e0b10414189a4e81240835c1d_2_1"/>
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Question 6
</h3>
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><p>Complete the following sentence:</p>
<div id="inputtype_d616aecd056c43d3bc66238d2d34de11_2_1" class=" capa_inputtype textline">
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