ImagingDataCommons · fedorov · May 6, 2026 · May 4, 2026 · May 6, 2026 · May 6, 2026
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/workflows/urlchecker.yml b/.github/workflows/urlchecker.yml
@@ -1,64 +1,40 @@
-# This is a basic workflow to help you get started with Actions
-
 name: CI
 
-# Controls when the workflow will run
 on:
-  # Triggers the workflow on push or pull request events but only for the prod branch
   push:
     branches: [ prod ]
   pull_request:
     branches: [ prod ]
-
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
+  linkcheck:
     runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-
-      - name: urlchecker-action
-        # You may pin to the exact commit or the version.
-        # uses: urlstechie/urlchecker-action@34deb4cef759f25e661415f3597a1ad1d0e7a4c6
-        uses: urlstechie/urlchecker-action@0.0.25
+      - uses: actions/checkout@v4
+
+      - name: Link Checker
+        uses: lycheeverse/lychee-action@v2
         with:
-          # A project to clone. If not provided, assumes already cloned in the present working directory.
-          git_path: # optional
-          # A subfolder to parse instead of the root directory.
-          subfolder: # optional
-          # Force pass of checking, regardless of the result.
-          force_pass: # optional
-          # If a project (git_path) is defined, use this branch. Defaults to master
-          branch: prod
-          # Cleanup (delete) repository to check after doing so (appropriate for when clone is done)
-          cleanup: # optional
-          # A comma seperated list of paths or patterns to include.
-          include_files: # optional, default is 
-          # A comma-separated list of file types to cover in the URL checks
-          file_types: # optional, default is .md,.py,.rst,.html
-          # Choose whether to include file with no URLs in the prints.
-          print_all: false # optional
-          # Choose whether to print a more verbose end summary with files and broken URLs.
-          verbose: true # optional
-          # If a request fails, retry this number of times. Defaults to 1
-          retry_count: # optional, default is 1
-          # A csv file path to save the results to.
-          save: # optional, default is 
-          # The timeout (seconds) to provide to requests to wait for a response.
-          timeout: # optional, default is 5
-          # A comma seperated links to exclude during URL checks.
-          exclude_urls: # optional, default is 
-          # A comma seperated patterns to exclude during URL checks.
-            http://localhost:6080/vnc.html?autoconnect=true,https://www.linkedin.com/in/fabian-seidl-390147a4/,https://storage.googleapis.com
-          exclude_patterns: # optional, default is 
-          # A comma seperated list of paths or patterns to exclude during URL checks.
-            viewer.imaging.datacommons.cancer.gov,dx.doi.org
-          exclude_files: # optional, default is 
+          args: >-
+            --no-progress
+            --exclude 'localhost'
+            --exclude 'linkedin\.com'
+            --exclude 'storage\.googleapis\.com'
+            --exclude 'viewer\.imaging\.datacommons\.cancer\.gov'
+            --exclude 'proxy\.imaging\.datacommons\.cancer\.gov'
+            --exclude 'doi\.org'
+            --exclude 'dicom\.nema\.org'
+            --exclude 'console\.cloud\.google\.com'
+            --exclude 'cloud\.google\.com'
+            --exclude 'docs\.google\.com'
+            --exclude 'scholar\.google\.com'
+            --exclude 'mayo\.edu'
+            --exclude 'cancer\.gov'
+            --exclude 'access-ci\.org'
+            --exclude 'towardsai\.net'
+            '**/*.md'
+            '**/*.py'
+            '**/*.rst'
+            '**/*.html'
+          fail: true
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ IDC is as much about data as it is about what you can do with the data! We maint
 * **programmatic access**: use [`idc-index` python package](https://github.com/ImagingDataCommons/idc-index) to perform search, download and other operations programmatically
 * **cohort building**: use rich and extensive metadata to build subsets of data programmatically using `idc-index` or BigQuery SQL
 * **download**: use your favorite S3 API client or `idc-index` to efficiently fetch any of the IDC files from our public buckets
-* **analysis**: conveniently access IDC files and metadata from the tools that are cloud-native, such as Google Colab or Looker; fetch IDC data directly into 3D Slicer using [SlicerIDCBrowser extension](https://github.com/ImagingDataCommons/SlicerIDCBrowser/)
+* **analysis**: conveniently access IDC files and metadata from the tools that are cloud-native, such as Google Colab; fetch IDC data directly into 3D Slicer using [SlicerIDCBrowser extension](https://github.com/ImagingDataCommons/SlicerIDCBrowser/)
 
 {% hint style="info" %}
 The overview of IDC is available in this open access publication. If you use IDC, please acknowledge us by citing it!

diff --git a/SUMMARY.md b/SUMMARY.md
@@ -31,12 +31,6 @@
   * [DICOM stores](data/organization-of-data/dicom-stores.md)
   * [Clinical data](data/organization-of-data/clinical.md)
   * [UUIDs and GUIDs](data/organization-of-data/guids-and-uuids.md)
-  * [Deprecated functionality](data/organization-of-data/deprecated-functionality/README.md)
-    * [Organization of data in v1 (deprecated)](data/organization-of-data/organization-of-data-v1.md)
-    * [Organization of data, v2 through V13 (deprecated)](data/organization-of-data/organization-of-data-v2-through-v13-deprecated/README.md)
-      * [Files and metadata](data/organization-of-data/organization-of-data-v2-through-v13-deprecated/files-and-metadata.md)
-      * [Resolving CRDC Globally Unique Identifiers (GUIDs)](data/organization-of-data/organization-of-data-v2-through-v13-deprecated/guids-and-uuids.md)
-      * [Clinical data](data/organization-of-data/organization-of-data-v2-through-v13-deprecated/clinical.md)
 * [Data versioning](data/data-versioning.md)
 * [Downloading data](data/downloading-data/README.md)
   * [IDC Portal](data/downloading-data/idc-portal.md)
@@ -89,24 +83,21 @@
 * [Manifests](api/manifests.md)
 * [Accessing the API](api/accessing-the-api.md)
 * [Endpoint Details](api/endpoint-details.md)
-* [V1 API](api/v1-api/README.md)
-  * [Getting Started](api/v1-api/getting-started.md)
-  * [IDC Data Model Concepts](api/v1-api/idc-data-model-concepts.md)
-  * [Accessing the API](api/v1-api/accessing-the-api.md)
-  * [Endpoint Details](api/v1-api/endpoint-details.md)
-  * [Release Notes](api/v1-api/release-notes.md)
 
 ## Cookbook
 
 * [Colab notebooks](cookbook/notebooks.md)
 * [BigQuery](cookbook/bigquery.md)
-* [Looker dashboards](cookbook/data-studio/README.md)
+* [Data Studio dashboards](cookbook/data-studio/README.md)
   * [Dashboard for your cohort](cookbook/data-studio/cohort-dashboard.md)
   * [More dashboard examples](cookbook/data-studio/more-dashboard-examples.md)
 * [ACCESS allocations](cookbook/access-allocations.md)
 * [Compute engine](cookbook/virtual-machines/README.md)
   * [3D Slicer desktop VM](cookbook/virtual-machines/idc-desktop.md)
-  * [Using a BQ Manifest to Load DICOM Files onto a VM](cookbook/virtual-machines/using-a-bq-manifest-to-load-dicom-files-onto-a-vm.md)
   * [Using VS Code with GCP VMs](cookbook/virtual-machines/using-vs-code-with-gcp-vms.md)
   * [Security considerations](cookbook/virtual-machines/security-considerations.md)
 * [NCI Cloud Resources](cookbook/nci-data-commons-cloud-resources.md)
+
+## Archive
+
+* [Archive](archive.md)
diff --git a/analysis/untitled.md b/analysis/untitled.md
diff --git a/api/README.md b/api/README.md
@@ -1,2 +1,3 @@
 # API
 
+This section documents the IDC REST API, which provides programmatic access to IDC collections, series, and manifests. The API requires authentication via an OAuth2 token. See [Getting Started](getting-started.md) for setup instructions.
diff --git a/api/accessing-the-api.md b/api/accessing-the-api.md
@@ -62,7 +62,7 @@ We expect that most API access will be programmed access, and, moreover, that mo
 In Python, we can issue the following request to obtain a list of the collections in the current IDC version:
 
 <pre><code><strong>response = requests.get("https://api.imaging.datacommons.cancer.gov/v2/collections")
-</strong><strong>collections = response.json['collections']
+</strong><strong>collections = response.json()['collections']
 </strong></code></pre>
 
 ## Paged queries

diff --git a/api/getting-started.md b/api/getting-started.md
@@ -4,7 +4,7 @@
 As of 15-July-2025, support for user defined cohorts has been removed from the both the IDC API V1 and the IDC API V2. The API documentation has been revised accordingly.
 {% endhint %}
 
-This section describes version 2 of the IDC REST API . The documentation for the version 1 API will be found [here](https://learn.canceridc.dev/api/v1-api).
+This section describes version 2 of the IDC REST API.
 
 This API is designed for use by developers of image analysis and data mining tools to directly query the public resources of the IDC and retrieve information into their applications. The API complements the IDC web application but eliminates the need for users to visit the IDC web pages to perform manifest export, and transfer of image data to some local file system.
 

diff --git a/api/manifests.md b/api/manifests.md
@@ -649,7 +649,7 @@ If the fields list is as above, then this is a fragment of the _collection granu
       {
         "Modality": "CT",
         "SliceThickness": null,
-        "collection_id": "tcga_luad"
+        "collection_id": "tcga_luad",
         "instance_count": "212",
         "patient_count": "1",
         "series_count": "2",
@@ -687,7 +687,7 @@ If the fields list is as above, then this is a fragment of the _collection granu
     ],
     "rowsReturned": 88,
     "totalFound": 88
-  }
+  },
   "next_page": "",
 }
 ```
@@ -782,7 +782,7 @@ then this is a fragment of the _version granularity_ manifest of our example coh
     ],
     "rowsReturned": 87,
     "totalFound": 87
-  }
+  },
   "next_page": "",
 }
 ```

diff --git a/api/v1-api/README.md b/api/v1-api/README.md
diff --git a/api/v1-api/accessing-the-api.md b/api/v1-api/accessing-the-api.md
diff --git a/api/v1-api/endpoint-details.md b/api/v1-api/endpoint-details.md
diff --git a/api/v1-api/getting-started.md b/api/v1-api/getting-started.md
Original file line number	Diff line number	Diff line change
		@@ -1,2 +1,3 @@
		# API

		This section documents the IDC REST API, which provides programmatic access to IDC collections, series, and manifests. The API requires authentication via an OAuth2 token. See [Getting Started](getting-started.md) for setup instructions.