/data-models

Versioned history of the MC2 Center data model

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MC2 Center Data Models

Data models and standard terms used by MC2 Center


GitHub release (latest by date) GitHub Release Date GitHub

🔎 Data Models Explorer: https://mc2-center.github.io/data-models/

📊 Data Curator App: https://dca.app.sagebionetworks.org/

Overview

This project contains the released versions of the JSON-LD schemas for the Cancer Complexity Knowledge Portal (CCKP), and more broadly, MC2 Center. You can learn more about the schemas/data models and other aspects of this project in our portal documentation - coming soon! The MC2 Center data model is in both CSV and JSON-LD format.

Folder Structure

.
├── dca_config/
├── docs/
├── modules/
├── scripts/
└── templates/

DCA Configuration

MC2 Center's configurations for the DCA is located in ./dca_config.

Documentation

All docs are located in the ./docs directory and are written in Markdown format. Some docs are generated before the site is built, which is handled by the hooks.py script in ./scripts.

Valid Values

Valid values are separated into modules (located in ./modules), where various pieces of the data model can be updated, including the standard terms/valid values.

Add a new valid value

When a new valid value needs to be added to the data model:

  1. Research the term and make sure we do not already have a synonym for it that exists. Using NCIt is excellent for this, though sometimes looking outside of NCIt is necessary. If we do currently have a synonym in use, add the valid value as a "non preferred term" in the applicable attribute CSV in ./modules. If not:

  2. Add the valid value in the "attribute" column of the applicable csv in the appropriate module folder. E.g. if a new tumor type needs to be added go to tumorType.csv and add the new term in the attribute column). Fill out the rest of the columns as completely as possible, this includes the description, the required column, parent column, source column, non-preferred terms column, the ontology identifier, url, NCIt Code, and any notes. Please make a note of who added it and the date.

  3. Be sure to look up any synonyms and add to the "non preferred terms" column. This will make annotating easier in the future.

Update a valid value

Please open a ticket and let the MC2 Center internal data team know the reasoning behind why a valid value should be updated/removed.

Annotation Templates

A collection of ready-for-use templates are available in ./templates, that can be used with the Data Curator App (DCA) to add/update entities on the CCKP.

How to Contribute

Thank you helping us continuously improve the MC2 Center data models! To contribute, please read our contributing guidelines on the docs site.