remove the Allen CCF example from Lookup Tables.

Author: dimitri-yatsenko

book/20-concepts/00-databases.md

@@ -81,7 +81,7 @@ Modern databases typically separate data management from data use through distin
 ### Common Architectures
 
 **Server-Client Architecture** (most common): A database server program manages all data operations, while client programs (your scripts, applications, notebooks) connect to request data or submit changes. The server enforces all rules and access permissions consistently for every client. This is like a library where the librarian (server) manages the books and enforces checkout policies, while patrons (clients) request materials.
-The two most popular open-source relational database systems: MySQL and Postgres implement a server-client architecture.
+The two most popular open-source relational database systems: MySQL and PostgreSQL implement a server-client architecture.
 
 **Embedded Databases**: The database engine runs within your application itself—no separate server. This works for single-user applications like mobile apps or desktop software, but doesn't support multiple users accessing shared data simultaneously.
 SQLite is a common embedded database @10.14778/3554821.3554842.

book/20-concepts/03-relational-practice.md

@@ -67,7 +67,7 @@ erDiagram
     
     RESEARCHER {
         int researcher_id PK
-        string name
+        string researcher_name
         string email
         string lab_role
     }
@@ -89,16 +89,17 @@ erDiagram
     }
     
     RECORDING {
+        int experiment_id PK, FK
         int recording_id PK
-        int experiment_id FK
         datetime recording_time
         string file_path
         string recording_quality
     }
     
     NEURAL_UNIT {
+        int experiment_id PK, FK
+        int recording_id PK, FK        
         int unit_id PK
-        int recording_id FK
         float spike_rate
         float receptive_field_size
     }
@@ -118,55 +119,57 @@ The ER diagram translates almost directly to SQL table definitions:
 
 ```sql
 CREATE TABLE Researcher (
-    researcher_id INT PRIMARY KEY AUTO_INCREMENT,
+    researcher_id INT,
     name VARCHAR(100) NOT NULL,
     email VARCHAR(100) UNIQUE,
-    lab_role VARCHAR(50)
+    lab_role VARCHAR(50),
+    PRIMARY KEY(researcher_id)
 );
 
 CREATE TABLE AnimalSubject (
-    subject_id INT PRIMARY KEY AUTO_INCREMENT,
+    subject_id INT PRIMARY KEY,
     species VARCHAR(50) NOT NULL,
     date_of_birth DATE,
     sex ENUM('M', 'F', 'Unknown')
 );
 
 CREATE TABLE Experiment (
-    experiment_id INT PRIMARY KEY AUTO_INCREMENT,
+    experiment_id INT,
     researcher_id INT NOT NULL,
     subject_id INT NOT NULL,
     experiment_date DATE NOT NULL,
     description TEXT,
     protocol VARCHAR(100),
+    PRIMARY KEY (experiment_id),
     FOREIGN KEY (researcher_id) REFERENCES Researcher(researcher_id),
     FOREIGN KEY (subject_id) REFERENCES AnimalSubject(subject_id)
 );
 
 CREATE TABLE Recording (
-    recording_id INT PRIMARY KEY AUTO_INCREMENT,
     experiment_id INT NOT NULL,
+    recording_id INT NOT NULL,
     recording_time DATETIME NOT NULL,
     file_path VARCHAR(255) NOT NULL,
     recording_quality ENUM('excellent', 'good', 'fair', 'poor'),
+    PRIMARY KEY (experiment_id, recording_id),
     FOREIGN KEY (experiment_id) REFERENCES Experiment(experiment_id)
-        ON DELETE CASCADE
 );
 
 CREATE TABLE NeuralUnit (
-    unit_id INT PRIMARY KEY AUTO_INCREMENT,
+    experiment_id INT NOT NULL,
     recording_id INT NOT NULL,
-    spike_rate FLOAT,
-    receptive_field_size FLOAT,
-    FOREIGN KEY (recording_id) REFERENCES Recording(recording_id)
-        ON DELETE CASCADE
+    unit_id INT NOT NULL,
+    spike_rate FLOAT NOT NULL,
+    receptive_field_size FLOAT NOT NULL,
+    PRIMARY KEY (experiment_id, recording_id, unit_id),
+    FOREIGN KEY (experiment_id, recording_id) REFERENCES Recording(experiment_id, recording_id)
 );
 ```
 
 Note the key features:
 - **PRIMARY KEY**: Ensures each row has a unique identifier
 - **FOREIGN KEY**: Enforces referential integrity—you can't reference a non-existent entity
 - **NOT NULL**: Requires certain attributes to have values
-- **ON DELETE CASCADE**: Automatically removes dependent records when parent is deleted
 - **Data types**: Constrain what values can be stored (INT, VARCHAR, DATE, etc.)
 
 ### Populating with Sample Data
@@ -175,31 +178,31 @@ Let's add some sample data to see the database in action:
 
 ```sql
 -- Add researchers
-INSERT INTO Researcher (name, email, lab_role) VALUES
-    ('Dr. Sarah Chen', '[email protected]', 'Principal Investigator'),
-    ('Alex Martinez', '[email protected]', 'Postdoc'),
-    ('Jamie Park', '[email protected]', 'Graduate Student');
+INSERT INTO Researcher (researcher_id, name, email, lab_role) VALUES
+    (1, 'Dr. Sarah Chen', '[email protected]', 'Principal Investigator'),
+    (2, 'Alex Martinez', '[email protected]', 'Postdoc'),
+    (3, 'Jamie Park', '[email protected]', 'Graduate Student');
 
 -- Add animal subjects
-INSERT INTO AnimalSubject (species, date_of_birth, sex) VALUES
+INSERT INTO AnimalSubject (subject_id, aspecies, date_of_birth, sex) VALUES
     ('Mouse', '2024-01-15', 'M'),
     ('Mouse', '2024-01-20', 'F'),
     ('Mouse', '2024-02-03', 'M');
 
 -- Add an experiment
-INSERT INTO Experiment (researcher_id, subject_id, experiment_date, description, protocol) VALUES
-    (2, 1, '2024-08-15', 'Visual cortex recording during grating stimuli', 'Protocol-V1-001');
+INSERT INTO Experiment (experiment_id, researcher_id, subject_id, experiment_date, description, protocol) VALUES
+    (1, 2, 1, '2024-08-15', 'Visual cortex recording during grating stimuli', 'Protocol-V1-001');
 
 -- Add recordings from that experiment
-INSERT INTO Recording (experiment_id, recording_time, file_path, recording_quality) VALUES
-    (1, '2024-08-15 10:30:00', '/data/2024/08/15/rec001.dat', 'excellent'),
-    (1, '2024-08-15 11:45:00', '/data/2024/08/15/rec002.dat', 'good');
+INSERT INTO Recording (experiment_id, recording_id, recording_time, file_path, recording_quality) VALUES
+    (1, 1, '2024-08-15 10:30:00', '/data/2024/08/15/rec001.dat', 'excellent'),
+    (1, 2, '2024-08-15 11:45:00', '/data/2024/08/15/rec002.dat', 'good');
 
 -- Add neural units identified in first recording
-INSERT INTO NeuralUnit (recording_id, spike_rate, receptive_field_size) VALUES
-    (1, 15.3, 2.5),
-    (1, 8.7, 3.1),
-    (1, 22.4, 1.8);
+INSERT INTO NeuralUnit (experiment_id, recording_id, unit_id, spike_rate, receptive_field_size) VALUES
+    (1, 1, 1, 15.3, 2.5),
+    (1, 1, 2, 8.7, 3.1),
+    (1, 1, 3, 22.4, 1.8);
 ```
 
 ## Common Database Operations