Create a new project in the database

The project creation app in the Clinical Knowledge Graph was designed to make the process straightforward and user-friendly. To create a project, please follow the steps below.

Neo4j

  1. Open neo4j desktop

  2. Start the database

Terminal

  1. In one terminal window:

  • Start a redis-server (Unix only):

$ redis-server

  1. In another terminal windows:

  • Activate the virtual environment (if created beforehand) and run ckg_app

$ conda activate ckgenv
$ ckg_app

The ckg_app will start the Dash app, and 3 Celery queues:

Creation queue

Creates a queue to synchronize the project creation.

Update queue

This queue can be used to update the graph database in the background. Note: A full update will take longer than running through the command line.

Compute queue - Report generation

Queue used for the generation of project reports.

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Browser

  1. Copy the url http://localhost:5000/ into a web browser and you will be directed to a login page.

  2. Enter your username and password

This action will redirect you to the CKG home page app. From here, you can navigate to different applications, including the “Project Creation” app.

Note

Username and password will be authenticated in the CKG database. For this reason, you should have been created as a new user in the database before this step.

Project creation

From the CKG app home page, you can navigate to the project creation app by clicking PROJECT CREATION or pasting the url http://localhost:5000/apps/projectCreationApp in the browser.

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Project Creation App

Once you have been redirected, please fill in all the information needed to create a project. This includes all the fields marked with * (mandatory). (1) After all fields are filled in, please revise all the information and press Create Project. (2) The page will refresh and once finished, the project identifier will be depicted in front of the Project information header. (3) Use this identifier to search for data related to your project.

At this stage, and if your project has been successfully created in the database, a new button will appear and the message will instruct you to download a compressed file with the experimental design and clinical data template files. To do so, please press the button “Download Clinical Data template”. (4)

Note

Each field, with the exception of Project name, Project Acronym, Number of subjects, Project Description, Starting Date and Ending Date, can take multiple values. Select the most appropriate ones for your specific project.

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Experimental Design file example

Fill in the ExperimentalDesign_Pxxxxxxx.xlsx file with your subject, biological sample and analytical sample identifiers. Please double-check they are correct, this information is essential to map the results correctly in the database.

The ClinicalData_Pxxxxxxx.xlsx file needs to be filled in with all the relevant clinical data and sample information. For more instructions on how to fill in the file, please see Upload project experimental data.

To check your project in the neo4j database interface:

  • Open the Neo4j desktop app

  • Find the graph database in use and click Manage, followed by Open Browser (opens a new window).

  • In the new Neo4j window, click on the database symbol (top left corner) and, under Node Labels, click Project

At this point, you should be able to see all the nodes corresponding to projects loaded in the database. To expand your project information, click on your project node and in the bottom of the window press the < symbol. Here you will find all the attributes of the project, including the project identifier (typically “P000000xx”).