update to idc-index- 0.11.9

Author: fedorov

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [1.3.0] - 2026-02-10
+
 ### Added
 
 - Digital pathology reference guide (`references/digital_pathology_guide.md`) with SM, ANN, and SEG query patterns, join examples, and pathology tool recommendations
@@ -23,13 +25,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
   - `references/use_cases.md` - End-to-end workflow examples
 - Quick Navigation section in SKILL.md with decision triggers for when to load each reference
 - `idc-data-version` field in frontmatter metadata
+- Documentation for new `contrast_index` table (contrast bolus metadata for CT, MR, PT, XA, RF series)
 
 ### Changed
 
+- Updated to idc-index 0.11.9 (IDC data version v23)
 - Reduced SKILL.md from 1,245 to 825 lines by extracting secondary content to reference files
 - Core Capabilities sections remain inline to ensure correct API pattern usage
 - Refactored detailed SM/ANN content from SKILL.md into `references/digital_pathology_guide.md`, keeping brief summaries with pointers in main skill
-- Updated to idc-index 0.11.8 (IDC data version v23)
 - Made IDC version (v23) more prominent in SKILL.md with verification guidance to prevent responses using older versions
 - Clarified distinction between `index_tables_guide.md` (structure/access) and `sql_patterns.md` (query examples)
 

SKILL.md

@@ -3,9 +3,9 @@ name: imaging-data-commons
 description: Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
 license: This skill is provided under the MIT License. IDC data itself has individual licensing (mostly CC-BY, some CC-NC) that must be respected when using the data.
 metadata:
-    version: 1.2.0
+    version: 1.3.0
     skill-author: Andrey Fedorov, @fedorov
-    idc-index: "0.11.8"
+    idc-index: "0.11.9"
     idc-data-version: "v23"
     repository: https://github.com/ImagingDataCommons/idc-claude-skill
 ---
@@ -122,6 +122,7 @@ The `idc-index` package provides multiple metadata index tables, accessible via
 | `seg_index` | 1 row = 1 DICOM Segmentation series | fetch_index() | Segmentation metadata: algorithm, segment count, reference to source image series |
 | `ann_index` | 1 row = 1 DICOM ANN series | fetch_index() | Microscopy Bulk Simple Annotations series metadata; references annotated image series |
 | `ann_group_index` | 1 row = 1 annotation group | fetch_index() | Detailed annotation group metadata: graphic type, annotation count, property codes, algorithm |
+| `contrast_index` | 1 row = 1 series with contrast info | fetch_index() | Contrast agent metadata: agent name, ingredient, administration route (CT, MR, PT, XA, RF) |
 
 **Auto** = loaded automatically when `IDCClient()` is instantiated
 **fetch_index()** = requires `client.fetch_index("table_name")` to load
@@ -140,7 +141,7 @@ The `idc-index` package provides multiple metadata index tables, accessible via
 | `source_DOI` | index, analysis_results_index | Link by publication DOI |
 | `crdc_series_uuid` | index, prior_versions_index | Link by CRDC unique identifier |
 | `Modality` | index, prior_versions_index | Filter by imaging modality |
-| `SeriesInstanceUID` | index, seg_index, ann_index, ann_group_index | Link segmentation/annotation series to its index metadata |
+| `SeriesInstanceUID` | index, seg_index, ann_index, ann_group_index, contrast_index | Link segmentation/annotation/contrast series to its index metadata |
 | `segmented_SeriesInstanceUID` | seg_index → index | Link segmentation to its source image series (join seg_index.segmented_SeriesInstanceUID = index.SeriesInstanceUID) |
 | `referenced_SeriesInstanceUID` | ann_index → index | Link annotation to its source image series (join ann_index.referenced_SeriesInstanceUID = index.SeriesInstanceUID) |
 
@@ -213,7 +214,7 @@ print(client.get_idc_version())  # Should return "v23"
 ```
 If you see an older version, upgrade with: `pip install --upgrade idc-index`
 
-**Tested with:** idc-index 0.11.8 (IDC data version v23)
+**Tested with:** idc-index 0.11.9 (IDC data version v23)
 
 **Optional (for data analysis):**
 ```bash

references/digital_pathology_guide.md

@@ -1,6 +1,6 @@
 # Digital Pathology Guide for IDC
 
-**Tested with:** IDC data version v23, idc-index 0.11.8
+**Tested with:** IDC data version v23, idc-index 0.11.9
 
 For general IDC queries and downloads, use `idc-index` (see main SKILL.md). This guide covers slide microscopy (SM) imaging, microscopy bulk simple annotations (ANN), and segmentations (SEG) in the context of digital pathology in IDC.
 

references/index_tables_guide.md

@@ -1,6 +1,6 @@
 # Index Tables Guide for IDC
 
-**Tested with:** idc-index 0.11.8 (IDC data version v23)
+**Tested with:** idc-index 0.11.9 (IDC data version v23)
 
 This guide covers the structure and access patterns for IDC index tables: programmatic schema discovery, DataFrame access, and join column references. For the overview of available tables and their purposes, see the "Index Tables" section in the main SKILL.md.
 
@@ -124,6 +124,7 @@ Use this table to identify join columns between index tables. Always call `clien
 | `index` | `ann_index` | `index.SeriesInstanceUID = ann_index.SeriesInstanceUID` |
 | `ann_index` | `ann_group_index` | `ann_index.SeriesInstanceUID = ann_group_index.SeriesInstanceUID` |
 | `index` | `clinical_index` | `index.collection_id = clinical_index.collection_id` (then filter by patient) |
+| `index` | `contrast_index` | `index.SeriesInstanceUID = contrast_index.SeriesInstanceUID` |
 
 For complete query examples using these joins, see `references/sql_patterns.md`.
 

references/sql_patterns.md

@@ -1,6 +1,6 @@
 # SQL Query Patterns for IDC
 
-**Tested with:** idc-index 0.11.8 (IDC data version v23)
+**Tested with:** idc-index 0.11.9 (IDC data version v23)
 
 Quick reference for common SQL query patterns when working with IDC data. For detailed examples with context, see the "Core Capabilities" section in the main SKILL.md.
 

references/use_cases.md

@@ -1,6 +1,6 @@
 # Common Use Cases for IDC
 
-**Tested with:** idc-index 0.11.8 (IDC data version v23)
+**Tested with:** idc-index 0.11.9 (IDC data version v23)
 
 This guide provides complete end-to-end workflow examples for common IDC use cases. Each use case demonstrates the full workflow from query to download with best practices.