Introduction for Clinical Database 陳勁辰2003/06/02

Introduction  Database management system (DBMS)  Actual study information  Administrative information  Relational database model

Relational database model  Multiple tables  Entities: rows  Attributes: columns  Primary key  Foreign key  Principle of table normalization

Relational database model  Example: Infant Jaundice Study: whether neonatal jaundice affects neuropsychiatric scores at five years of age  Table relations: one-to-many, many- to-many, and one-to-one  Need for a multi-table: repeated measurements on individual subjects.

Jaundice vs non-jaundice: t-test p=0.46

One-to-many One-to-many

Normal Form Violation  Repeating columns: violate the First Normal Form (1NF)  Redundancy in column values: violates the Second Normal Form (2NF)

Many-to-many

One-to-one

Referential integrity  Referential Integrity in a normalized, relational database  Not allow creation of an exam record for a subject who does not already exist in the “ Baby ” table, and it will not allow assigning an exam to a doctor who does not already exist in the “ Doctor ” table.  A subject may not be deleted unless and until all that subject ’ s examinations have also been deleted.  One-to-many: parent-children  Forbids the creation of “ orphans ”

Undesirability of Storing Calculated Values  Inconsistencies result if one of the “ raw-data ” fields is updated without updating the calculated field  Solution: recalculating the value in a query  Storing calculated values such as “ AgeInMonths ” : violate the Third Normal Form (3NF)

Data Dictionaries, Data Types, and Domains  Data dictionary: a table of information about the database itself  “ Metadata ”  Data types: text, number, dates, etc.  Domain: range of allowed values  Object data type: BLOB (Binary Large Object), eg. photo (*.jpeg); cannot be sorted or sought

Extracting Data from the Database (Queries)  Structured Query Language or SQL  A query can join data from two or more tables, display only selected fields, and filter for records that meet certain criteria  SQL has 3 sublanguages: DDL – Data Definition Language, DML – Data Manipulation Language, and DCL – Data Control Language

SQL SELECT Baby.SubjectID, Baby.DOB, Exam.ExDate FROM Baby INNER JOIN Exam ON Baby.SubjectID = Exam.SubjectID WHERE Exam.ExDate Between #1/1/2010# And #2/28/2010# ORDER BY Exam.ExDate;

Guidelines for Database Management for Clinical Research 1. Establish the database tables, their rows and columns, and their relationships correctly at the outset. 2. Establish and follow naming conventions for columns and tables. 3. Obtain baseline demographic and clinical information about members of the study population from existing computer databases. 4. Minimize the extent to which study measurements are recorded on paper forms. 5. Follow standard data entry conventions. 6. Back up the database regularly.

Guidelines for Database Management for Clinical Research  Establish the database tables, their rows and columns, and their relationships correctly at the outset.  A poorly organized database makes data maintenance and retrieval nearly impossible. Make sure the data are normalized. Avoid data structures that require duplicate data entry or redundant storage.

Guidelines for Database Management for Clinical Research  Establish and follow naming conventions for columns and tables.  Short field names without spaces or underscores are convenient for programming, querying, and other manipulations. Instead of spaces or underscores, use “ IntraCaps ” (upper case letters within the variable name) to distinguish words, e.g. “ StudyID ”, “ FName ”, or “ ExamDate ”. Table names should be singular, e.g. “ Baby ” instead of “ Babies ”, “ Exam ” instead of “ Exams ”.

Guidelines for Database Management for Clinical Research  Obtain baseline demographic and clinical information about members of the study population from existing computer databases.  Avoid re-entering data which are already available (in digital format) from other sources. In the Infant Jaundice Study, the patient demographic data and contact information are obtained from the hospital database. Computer systems can almost always produce character- delimited or fixed-column-width text files that the database management system can import.

Guidelines for Database Management for Clinical Research  Minimize the extent to which study measurements are recorded on paper forms.  Enter data directly into the computer database or move data from paper forms into the computer database as close to the data collection time as possible. When you define a variable in a computer database, you specify both its format and its domain or range of allowed values. Using these format and domain specifications, computer data entry forms give immediate feedback about improper formats and values that are out of range. The best time to receive this feedback is when the study subject is still on site.

Guidelines for Database Management for Clinical Research Follow standard data entry conventions. Follow standard data entry conventions. Several conventions for data entry and display have developed over time. Although most users of screen forms are not aware of these conventions, they have come to expect them subconsciously. For example, a series of mutually exclusive, collectively exhaustive choices is usually displayed as an “ option group ” consisting of several different “ radio buttons ”, whereas choices which are not mutually exclusive are displayed as check boxes Several conventions for data entry and display have developed over time. Although most users of screen forms are not aware of these conventions, they have come to expect them subconsciously. For example, a series of mutually exclusive, collectively exhaustive choices is usually displayed as an “ option group ” consisting of several different “ radio buttons ”, whereas choices which are not mutually exclusive are displayed as check boxes

Guidelines for Database Management for Clinical Research Back up the database regularly and check the adequacy of the back up procedure by periodically restoring a file from the back up medium. Back up the database regularly and check the adequacy of the back up procedure by periodically restoring a file from the back up medium.