# Open Data Commons

## Open Data Commons

- [The Open Data Commons](https://fdilab.gitbook.io/open-data-commons/readme/readme.md)
- [Welcome to ODC-SCI](https://fdilab.gitbook.io/open-data-commons/readme/readme/welcome-to-odc-sci.md)
- [ODC-SCI Funding](https://fdilab.gitbook.io/open-data-commons/readme/readme/welcome-to-odc-sci/odc-sci-funding.md)
- [Welcome to ODC-TBI](https://fdilab.gitbook.io/open-data-commons/readme/readme/welcome-to-odc-tbi.md)
- [ODC-TBI Funding](https://fdilab.gitbook.io/open-data-commons/readme/readme/welcome-to-odc-tbi/odc-tbi-funding.md)
- [Principles of the ODC](https://fdilab.gitbook.io/open-data-commons/readme/readme/principles-of-the-odc.md)
- [The ODC Dataset](https://fdilab.gitbook.io/open-data-commons/readme/readme/elements-of-an-odc-dataset.md): This page explains what makes up a dataset on the ODC
- [Data Protection & Privacy in the ODC](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc.md)
- [Account Types](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc/account-types.md)
- [Verified Laboratories: The Lab Space](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc/verified-laboratories-the-lab-space.md)
- [Data Spaces](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc/data-spaces.md)
- [Uploading & Publishing Data](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc/uploading-and-publishing-data.md)
- [Who Can Use Data?](https://fdilab.gitbook.io/open-data-commons/readme/readme/data-protection-and-privacy-in-the-odc/who-can-use-data.md)
- [Benefits of Data Sharing](https://fdilab.gitbook.io/open-data-commons/readme/readme/benefits-of-data-sharing.md)
- [Publications](https://fdilab.gitbook.io/open-data-commons/readme/readme/publications.md)
- [Terms of Use & Policies](https://fdilab.gitbook.io/open-data-commons/readme/terms-of-use-and-policies.md)
- [ODC-SCI](https://fdilab.gitbook.io/open-data-commons/readme/terms-of-use-and-policies/odc-sci.md)
- [ODC-TBI](https://fdilab.gitbook.io/open-data-commons/readme/terms-of-use-and-policies/odc-tbi.md)
- [About ODC Standards](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/about-odc-standards.md): REFERENCE: overview of Data Specifications & Standards content in the ODC documentation
- [Metadata Standards](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/metadata-standards.md): REFERENCE: overview of Metadata Standards content in the ODC documentation
- [ODC Data Dictionary](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/metadata-standards/odc-data-dictionary.md): REFERENCE: identifies and describes the essential metadata content to be included in a Data Dictionary File. For file format and structure specifications, go to: Specs: Data Dictionary File
- [ODC Metadata Editor](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/metadata-standards/odc-narrative-and-metadata.md): REFERENCE: identifies and describes the essential metadata inputs and requirements of the Metadata Editor and how they are used to create a dataset's metadata homepage and citation
- [ODC Common Terminology](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/metadata-standards/common-terminology.md): REFERENCE: provides information on Common Terminology and resources to help researchers share and describe data using a common language
- [ODC-SCI CoDEs](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/metadata-standards/common-terminology/odc-sci-codes.md): REFERENCE: identifies and describes the ODC-SCI Community Data Elements (CoDEs) and provides a formatted ODC Data Dictionary Template containing all required variables (CoDEs)
- [Format & Structure Specifications](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications.md): REFERENCE: overview of Format & Structure Specifications content in the ODC documentation
- [Files & Accepted Formats](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications/files-and-accepted-formats.md): REFERENCE: technical information about accepted files and file formats
- [Tidy Data Format](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications/tidy-data-format.md): REFERENCE: learn the basics of Tidy Data format
- [Specs: Subject Data File](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications/specs-subject-data-file.md): REFERENCE: technical format and structure specifications for the Subject Data File
- [Specs: Data Dictionary File](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications/specs-data-dictionary-file.md): REFERENCE: technical format and structure specifications for the Data Dictionary File. For detailed information on metadata requirements and inputs, go to: ODC Data Dictionary
- [Minimum Upload Specifications](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/format-and-structure-specifications/minimum-upload-specifications.md): REFERENCE & TROUBLESHOOTING GUIDE: minimum required technical format and structure specifications for successful upload of Subject Data Files and Data Dictionary Files
- [ODC Publishing Standard](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard.md): REFERENCE: overview of ODC Publishing Standard content in the ODC documentation
- [SCI Required Variables](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard/sci-required-variables.md): REFERENCE: identifies and describes the 17 required variables that must be present to publish a dataset on ODC-SCI; see also: ODC-SCI CoDEs
- [TBI Required Variables](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard/tbi-required-variables.md): REFERENCE: identifies and describes the 9 required variables that must be present to publish a dataset on ODC-TBI
- [Editorial Review & Publication](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard/summary-of-review-process.md)
- [Narrative Summary (Abstract)](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard/summary-of-review-process/narrative-summary-abstract.md): REFERENCE: describes the content requirements and level of detail for the Narrative Summary (Abstract). For detailed information on all other metadata requirements go to: ODC Metadata Editor
- [Data Quality Checks for DOI](https://fdilab.gitbook.io/open-data-commons/data-specifications-and-standards/odc-publishing-standard/summary-of-review-process/data-quality-checks-for-doi.md): REFERENCE: describes the automated and manual Data Quality Checks performed by the ODC Data Team after a DOI Request has been made
- [Get Started](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here.md): New to the ODC? Here's a quick overview of how to get started. Pages containing step-by-step tutorials can be found in the left sidebar and are linked throughout this summary.
- [Create an Account](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/create-an-account.md): Follow these steps to create an account
- [Login](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/login.md): Follow these steps to login to your ODC account
- [Full Access](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/full-access.md): Follow these steps to unlock Full Access for your ODC account
- [Upgrade Account Type](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/full-access/upgrade-account-type.md): Started with a Basic Access Account? Follow these steps to upgrade to a Community Access Account
- [Manage a Lab Space](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/full-access/manage-a-lab-space.md)
- [Navigate the ODC](https://fdilab.gitbook.io/open-data-commons/tutorials/start-here/navigate-the-odc.md): Learn how to access user functions on the ODC
- [Update Profile](https://fdilab.gitbook.io/open-data-commons/tutorials/update-profile.md): Follow these steps to update the password or information associated with your user account profile
- [Upload to ODC](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc.md): In this page you will learn how to upload data to the ODC
- [Upload new data](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc/upload-new-data.md): This page will teach you how to upload a new dataset to the ODC
- [Upload a dictionary](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc/upload-a-dictionary.md)
- [Upload a Methodology file](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc/upload-a-methodology-file.md)
- [Supplementary files](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc/supplementary-files.md)
- [Common errors during upload](https://fdilab.gitbook.io/open-data-commons/tutorials/upload-to-odc/common-errors-during-upload.md)
- [Demo Lab](https://fdilab.gitbook.io/open-data-commons/tutorials/demo-lab.md)
- [Start Here](https://fdilab.gitbook.io/open-data-commons/how-to-guides/start-here.md)
- [Organise Data](https://fdilab.gitbook.io/open-data-commons/how-to-guides/organise-data.md): GUIDE: overview of Organise Data content guides in the ODC documentation
- [Lab Data & Project Management](https://fdilab.gitbook.io/open-data-commons/how-to-guides/organise-data/lab-data-and-project-management.md): GUIDE: best practices for Lab Data & Project Management, these strategies and templates can be adapted and implemented in any type of biomedical research laboratory
- [Unique Subject Identifiers](https://fdilab.gitbook.io/open-data-commons/how-to-guides/organise-data/unique-subject-identifiers.md): GUIDE: best practices for creating Unique Subject Identifiers
- [Naming Variables](https://fdilab.gitbook.io/open-data-commons/how-to-guides/organise-data/naming-variables.md): GUIDE: best practices for Naming Variables
- [Tidy Data Format](https://fdilab.gitbook.io/open-data-commons/how-to-guides/organise-data/tidy-data-format.md): GUIDE: learn the basics of Tidy Data format
- [Create a Dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/create-a-dataset.md): GUIDE: overview of Create a Dataset content in the ODC Documentation
- [Prepare to Publish](https://fdilab.gitbook.io/open-data-commons/how-to-guides/create-a-dataset/prepare-to-publish.md)
- [Prepare to Store/Archive](https://fdilab.gitbook.io/open-data-commons/how-to-guides/create-a-dataset/prepare-to-store-archive.md)
- [Manage a dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/manage-a-dataset.md)
- [Update a dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/manage-a-dataset/update-a-dataset.md)
- [Add metadata](https://fdilab.gitbook.io/open-data-commons/how-to-guides/manage-a-dataset/add-metadata.md)
- [Share data](https://fdilab.gitbook.io/open-data-commons/how-to-guides/manage-a-dataset/share-data.md)
- [Adding an experimental protocol to a dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/manage-a-dataset/adding-an-experimental-protocol-to-a-dataset.md): Experimental protocols provide important context for using and understanding data.
- [Publish a Dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/get-a-doi.md): GUIDE: overview of Publish a Dataset content in the ODC Documentation
- [Request a DOI](https://fdilab.gitbook.io/open-data-commons/how-to-guides/get-a-doi/request-a-doi.md)
- [Publish (Activate) a DOI](https://fdilab.gitbook.io/open-data-commons/how-to-guides/get-a-doi/request-a-doi-1.md)
- [How to cite ODC and dataset](https://fdilab.gitbook.io/open-data-commons/how-to-guides/how-to-cite-odc-and-dataset.md)
- [Get a reviewer token](https://fdilab.gitbook.io/open-data-commons/how-to-guides/get-a-reviewer-token.md): Getting access to private data
- [Lab Data Management](https://fdilab.gitbook.io/open-data-commons/downloadable-templates/lab-data-management.md)
- [ODC Data Templates](https://fdilab.gitbook.io/open-data-commons/downloadable-templates/odc-data-templates.md)
- [Estimating costs for data management and sharing](https://fdilab.gitbook.io/open-data-commons/data-fundamentals/estimating-costs-for-data-management-and-sharing.md): Information and tools for understanding and estimating costs involved in managing and sharing data
- [Sample DMS](https://fdilab.gitbook.io/open-data-commons/data-fundamentals/sample-dms.md): GUIDE: Sample language and hints for preparing an NIH data management and sharing (DMS) plan
- [Data Literacy](https://fdilab.gitbook.io/open-data-commons/data-fundamentals/data-literacy.md)
- [ODC Apps Toolbox](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox.md)
- [Advanced Search Dashboard (ODC-SCI)](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/advanced-search-dashboard-odc-sci.md): TOOL: Advanced Search Dashboard for exploring public datasets on ODC-SCI
- [ODC QCTool app](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/odc-quality-control-app.md)
- [ODC QCTool R package](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/odc-quality-control-app/odc-quality-control-package.md)
- [ODC QCTool API](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/odc-quality-control-app/odc-quality-control-api.md)
- [ODC Platform API](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/odc-sdk.md)
- [Dataset explorer app](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/eda-tool.md)
- [blotRig](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/blotrig.md)
- [syndRomics](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/syndromics.md)
- [Examples](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/examples.md)
- [Orange quick start](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/examples/orange-setup.md): Orange Data Mining setup and quick start
- [Orange demo](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/examples/orange-demo.md)
- [Jupyter notebook](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/examples/jupyter-notebook.md)
- [Historical checks](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/apps-toolbox/examples/historical-checks.md)
- [For developers](https://fdilab.gitbook.io/open-data-commons/odc-apps-toolbox/for-developers.md)
- [FAQ](https://fdilab.gitbook.io/open-data-commons/how-to-get-help/faq.md): WORK IN PROGRESS
- [Glossary](https://fdilab.gitbook.io/open-data-commons/how-to-get-help/glossary.md)
- [Contact Help Desk](https://fdilab.gitbook.io/open-data-commons/how-to-get-help/general-help.md)
- [Our Blogs](https://fdilab.gitbook.io/open-data-commons/extras/our-blogs.md)
- [Workshops and Outreach](https://fdilab.gitbook.io/open-data-commons/extras/workshops-and-outreach.md)
- [Community Feedback](https://fdilab.gitbook.io/open-data-commons/extras/community-feedback.md)
- [Documentation Updates](https://fdilab.gitbook.io/open-data-commons/extras/documentation-updates.md): Information on updates and revisions to the ODC Documentation
- [Getting your data ready](https://fdilab.gitbook.io/open-data-commons/hidden-content/getting-your-data-ready.md): GUIDE:
- [Data dictionary](https://fdilab.gitbook.io/open-data-commons/hidden-content/data-dictionary.md)
- [Mockup](https://fdilab.gitbook.io/open-data-commons/hidden-content/mockup.md)
- [Common errors for Dataset and Data Dictionary](https://fdilab.gitbook.io/open-data-commons/hidden-content/common-errors-for-dataset-and-data-dictionary.md)
- [Publication in ODC-SCI](https://fdilab.gitbook.io/open-data-commons/hidden-content/publication-in-odc-sci.md)
- [Publication in ODC-TBI](https://fdilab.gitbook.io/open-data-commons/hidden-content/publication-in-odc-tbi.md)
- [Data format](https://fdilab.gitbook.io/open-data-commons/hidden-content/data-format.md)
- [Terms of use and policies](https://fdilab.gitbook.io/open-data-commons/hidden-content/terms-of-use.md)


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on a page URL with the `ask` query parameter:
```
GET https://fdilab.gitbook.io/open-data-commons/readme/readme.md?ask=<question>
```
The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.