info/tutorials/modality/accessing-clinical-records.md

Accessing clinical records using almirah

This tutorial will guide you through the process of accessing clinical records from the CALM Brain Resource using the almirah Python library.

Connecting to the Database

First, we'll import the necessary library and connect to the database.

from almirah import Database

Create a database instance with the specified name, host, and backend:

db = Database(name="calm-brain", host="https://calm-brain.ncbs.res.in/db-request/", backend="request")
db

This should output:

<Database url: 'request:calm-brain@https://calm-brain.ncbs.res.in/db-request/'>

Querying the Database

Next, we connect to the database using credentials:

db.connect("username", "password")

Now, let's query a specific table, such as presenting_disorders, and display some of the data:

df = db.query(table="presenting_disorders")
df[["subject", "session", "addiction"]].head()

This displays the first few rows of the queried table in a DataFrame format:

	subject	session	addiction
0	D0019	101	0
1	D0019	111	0
2	D0020	101	0
3	D0020	111	<NA>
4	D0021	101	0

We can also get the total number of records in the table:

len(df)

This returns the total number of records:

2561

Lastly, let's find the number of records where addiction is noted:

len(df[df["addiction"] == 1])

This gives us the count of records with addiction:

522

This concludes the tutorial. You've learned how to connect to a database, query its tables, and analyze the data using the almirah library.