GITBOOK-433: change request with no subject merged in GitBook

Author: fedorov

SUMMARY.md

@@ -25,18 +25,19 @@
 
 * [Introduction](data/introduction.md)
 * [Data model](data/data-model.md)
-* [Data versioning](data/data-versioning.md)
 * [Organization of data](data/organization-of-data/README.md)
   * [Files and metadata](data/organization-of-data/files-and-metadata.md)
+  * [BigQuery tables](data/organization-of-data/bigquery-tables.md)
   * [DICOM stores](data/organization-of-data/dicom-stores.md)
   * [Clinical data](data/organization-of-data/clinical.md)
-  * [Resolving CRDC Globally Unique Identifiers (GUIDs)](data/organization-of-data/guids-and-uuids.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-index and 3D Slicer](data/downloading-data/downloading-data.md)
   * [s5cmd](data/downloading-data/downloading-data-with-s5cmd.md)

api/getting-started.md

@@ -1,6 +1,8 @@
 # Getting Started
 
-<mark style="color:red;">Note: 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.</mark>
+{% hint style="danger" %}
+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).
 

data/data-versioning.md

@@ -42,7 +42,7 @@ In order to reproduce the result of such analysis, it must be possible to precis
 
 Because an IDC version exactly defines the set of data against which the filter/query is applied, and because all versions of all data, except data removed due to PHI/PII concerns, should continue to be available, a cohort is therefore persistent over the course of the evolution of IDC data.
 
-## DICOM Entities are versioned
+
 
 There are various reasons that can cause modification of the existing collections in IDC:
 

data/organization-of-data/README.md

@@ -1,15 +1,13 @@
 # Organization of data
 
-This section describes the current organization of IDC data. The organization of data was static from IDC Version 2  through IDC Version 13 except that [clinical data](organization-of-data-v2-through-v13-deprecated/clinical.md) was added in Version 11. Development of the clinical data resource is an ongoing project. From IDC v14, our data [became available](https://registry.opendata.aws/nci-imaging-data-commons/) from the Amazon AWS Open Data Registry, and the files in storage buckets were organized into series-level folders.
+IDC provides a variety of interfaces to access both the data (as files) and metadata (to subset files and build cohorts). The flow of data and the relationship between the various components IDC uses is summarized in the following figure.
 
-### IDC data model
+{% embed url="https://docs.google.com/presentation/d/1UVpNVyVy3xIYLDnm4rtgAUmSu-uKQo5krekI9DSMT8o/edit?usp=sharing" %}
 
-### [Files and metadata](files-and-metadata.md)
+We maintain the following resources to enable access to IDC data:
 
-### [GA4GH DRS objects](https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids)
-
-### [Clinical Data](organization-of-data-v2-through-v13-deprecated/clinical.md)
-
-### [Organization of data, v1 through V13 (deprecated)](./#organization-of-data-v1-through-v13-deprecated)
-
-### [Organization of data in v1 (deprecated)](organization-of-data-v1.md)
+* [Cloud storage buckets](./#files-and-metadata): files maintained by IDC are mirrored between Google and AWS public storage buckets that provide fee-free egress without requiring login. The buckets organize files by DICOM series, each series stored in a separate folder. Given the large overall size of data in IDC, you will likely need to use one of the search interfaces to identify relevant series first.
+* BigQuery tables: collection-level metadata, DICOM metadata, [clinical data tables](clinical.md) available via SQL query interface.
+* Python API: pip-installable [idc-index package](https://idc-index.readthedocs.io/en/latest/) provides programmatic interface and command-line tools to search IDC data using most important metadata attributes, and to download files corresponding to the selected cohorts from the cloud buckets
+* [REST API](broken-reference): alternative language-independent API for selecting subsets of data
+* [DICOMweb](dicom-stores.md): DICOM files and metadata queries available from Google Healthcare DICOM stores