From c8473a3a4dcf3d6438d982092fc3c95d3225ca7d Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Thu, 9 Apr 2026 15:21:26 -0400 Subject: [PATCH 1/8] gpt suggestion --- docs/getting_started/index.md | 114 +++++++++++++++++++++------------- docs/index.md | 107 ++++++++++++++++++------------- 2 files changed, 135 insertions(+), 86 deletions(-) diff --git a/docs/getting_started/index.md b/docs/getting_started/index.md index b585f766..dd45c61a 100644 --- a/docs/getting_started/index.md +++ b/docs/getting_started/index.md @@ -2,78 +2,106 @@ title: Re-Search made simple --- -

With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.

+# Search cancer data across multiple NCI data commons—instantly +Cancer data is distributed across multiple systems—CDA brings it together. -
+Find subjects, files, and studies using harmonized terms across repositories. No coding required. -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ +```{admonition} +:class: important - --- +👉 **[Start exploring data](interactive.html)** +Try interactive search or view the API docs. +
+ 👉 Start exploring data
+ Try interactive search · + View API docs +
+``` + +--- + +## 🔎 Find what you need—your way + +### 🔍 Explore (No coding) +Search and filter cancer datasets in a visual interface +👉 [Open interactive search](interactive.html) + +--- + +### 📓 Analyze (Low code) +Run queries and explore results in a ready-to-use notebook +👉 [Launch notebook in the cloud](notebooks.html) - Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website. -Head to our interactive page to try it out. -

+--- -- :material-clock-fast:{ .lg .middle } __Low code, no install__ +### ⚙️ Build (API) +Integrate CDA into pipelines and applications +👉 [View API documentation](api.html) - --- +--- - Fill in the blanks in our pre-built queries to find the data you need without installing a thing.

Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*

-Launch CDA in the cloud -

+## 🖥️ See it in action -- :fontawesome-brands-python:{ .lg .middle } __Power users__ +Search across datasets with one query: - --- +- Filter by disease type, demographics, or study +- View harmonized results across repositories +- Export data for downstream analysis - Install `cdapython` with `pip` and get up - and running in no time +👉 **Try a sample search:** +[Find adenocarcinoma subjects across datasets](interactive.html) - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +--- - ```python - from cdapython import * - ``` +## 💡 Why use CDA? -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ +CDA removes the hardest parts of finding cancer data: - --- +- 🔗 **Search multiple data commons at once** + No need to query each repository separately - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab -

+- 🧠 **Harmonized data model** + Use consistent terms across datasets -- :simple-swagger:{ .lg .middle } __Developers__ +- ⚡ **From exploration to analysis quickly** + Move from search → notebook → pipeline - --- +- 🧪 **Flexible for all users** + Works for researchers, analysts, and developers - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?

Whatever your use case, CDA can help. +--- - [:octicons-arrow-right-24:**API documentation**](../documentation/developers/index.md) +## 🧭 What you can find -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ +Use CDA to discover: - --- +- Subjects across studies +- Clinical and genomic data files +- Metadata across CRDC repositories +- Cohorts matching specific criteria - Recently Updated Pages: +--- - - [Data Release](../release_notes/data_updates.md) - - [Code Release](../release_notes/cdapython.md) +## 🚀 Start in 10 seconds -- :simple-mysql:{ .lg .middle } __Need even more data?__ +Not sure where to begin? - --- +👉 [Open interactive search with a pre-built example](interactive.html) +Explore adenocarcinoma datasets across repositories. - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! +--- - :material-email: cancerdataaggregator `@` gmail +## 📚 Learn more +- [About CDA](about_us.html) +- [Data model](data_model.html) +- [Tutorials](tutorials.html) +- [API reference](api.html) +--- -

+## 🔬 Developed by +The National Cancer Institute’s Cancer Research Data Commons (CRDC) \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 58d7815f..41645984 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,79 +1,100 @@ --- title: Re-Search made simple --- +# Search cancer data across multiple NCI data commons—instantly -

With CDA you search by harmonized, common language terms. Using simple language you can get information about the subjects, files, or specimens that you care about in a standard dataframe format (tsv) that you can open in Excel, integrate into a pipeline or upload to your favorite cloud resource.

+Cancer data is distributed across multiple systems—CDA brings it together. +Find subjects, files, and studies using harmonized terms across repositories. No coding required. -
+
+ 👉 Start exploring data
+ Try interactive search · + View API docs +
+ +--- -- :material-clock-fast:{ .lg .middle } __Don't code? No problem!__ +## 🔎 Find what you need—your way - --- +### 🔍 Explore (No coding) +Search and filter cancer datasets in a visual interface +👉 [Open interactive search](interactive.html) - Browse through a curated dataset of all subjects that have data at multiple data centers using an intuitive filtering tool right in this website. -Head to our interactive page to try it out. -

+--- + +### 📓 Analyze (Low code) +Run queries and explore results in a ready-to-use notebook +👉 [Launch notebook in the cloud](notebooks.html) + +--- -- :material-clock-fast:{ .lg .middle } __Low code, no install__ +### ⚙️ Build (API) +Integrate CDA into pipelines and applications +👉 [View API documentation](api.html) - --- +--- - Fill in the blanks in our pre-built queries to find the data you need without installing a thing.

Send your results to [Broad Institute FireCloud:octicons-link-external-16:](https://datacommons.cancer.gov/analytical-resource/broad-institute-firecloud){:target="_blank"} or [Velsera Cancer Genomics Cloud:octicons-link-external-16:](https://www.cancergenomicscloud.org/){:target="_blank"} for a complete cloud experience. Find the data you need, fetch all the files, and run your favorite bioinformatics pipeline *all without ever leaving your web browser.*

-Launch CDA in the cloud -

+## 🖥️ See it in action -- :fontawesome-brands-python:{ .lg .middle } __Power users__ +Search across datasets with one query: - --- +- Filter by disease type, demographics, or study +- View harmonized results across repositories +- Export data for downstream analysis - Install `cdapython` with `pip` and get up - and running in no time +👉 **Try a sample search:** +[Find adenocarcinoma subjects across datasets](interactive.html) - ```bash - pip3 uninstall -y cdapython; pip3 install git+https://github.com/CancerDataAggregator/cdapython.git@develop - python3 - ``` +--- - ```python - from cdapython import * - ``` +## 💡 Why use CDA? -- :fontawesome-brands-python:{ .lg .middle } __Code in the Cloud__ +CDA removes the hardest parts of finding cancer data: - --- +- 🔗 **Search multiple data commons at once** + No need to query each repository separately - Bring lists of files or subjects found with CDA to the [ISB Cancer Gateway in the Cloud (ISB-CGC):octicons-link-external-16:](https://isb-cgc.org/){:target="_blank"} to instantly access both associated derived data and raw files, for use in cloud processing pipelines -- either in your own preferred environment or using ISB-CGC's free Google Cloud Platform credits program. - Test it out on Google Colab -

+- 🧠 **Harmonized data model** + Use consistent terms across datasets -- :simple-swagger:{ .lg .middle } __Developers__ +- ⚡ **From exploration to analysis quickly** + Move from search → notebook → pipeline - --- +- 🧪 **Flexible for all users** + Works for researchers, analysts, and developers - Are you building a metadata microservice? Connecting even more databases? Hosting a computational resource?

Whatever your use case, CDA can help. +--- - [:octicons-arrow-right-24:**API documentation**](documentation/developers/) +## 🧭 What you can find -- :material-bell-alert-outline:{ .lg .middle } __What's new?__ +Use CDA to discover: - --- +- Subjects across studies +- Clinical and genomic data files +- Metadata across CRDC repositories +- Cohorts matching specific criteria - Recently Updated Pages: +--- - - [Data Release](release_notes/data_updates.md) - - [Code Release](release_notes/cdapython.md) +## 🚀 Start in 10 seconds -- :simple-mysql:{ .lg .middle } __Need even more data?__ +Not sure where to begin? - --- +👉 [Open interactive search with a pre-built example](interactive.html) +Explore adenocarcinoma datasets across repositories. - Do you dream of having a CDA database instance of your very own? Or CDA but bigger somehow? - We can make those dreams come true. Let's chat! +--- - :material-email: cancerdataaggregator `@` gmail +## 📚 Learn more +- [About CDA](about_us.html) +- [Data model](data_model.html) +- [Tutorials](tutorials.html) +- [API reference](api.html) +--- -

+## 🔬 Developed by +The National Cancer Institute’s Cancer Research Data Commons (CRDC) \ No newline at end of file From d091be8412cc3a723e7faf87c9704bee49419e3a Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Thu, 9 Apr 2026 15:27:08 -0400 Subject: [PATCH 2/8] don't need to render --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 81914456..0c8c41ac 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -44,7 +44,7 @@ plugins: remove_input_tags: - hide_code include_source: True - execute: True + execute: False allow_errors: False ignore: ["documentation/cdapython/vignettes/005_TCIA.ipynb"] From b73cb614e31efa01e466a768c19ee6c8b9bcb651 Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Fri, 10 Apr 2026 13:14:12 -0400 Subject: [PATCH 3/8] Create google.html --- docs/interactive/google.html | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 docs/interactive/google.html diff --git a/docs/interactive/google.html b/docs/interactive/google.html new file mode 100644 index 00000000..7424b35a --- /dev/null +++ b/docs/interactive/google.html @@ -0,0 +1,19 @@ + + + From 15b94512071bda264335d68a5273cec91e81028f Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Fri, 10 Apr 2026 13:15:01 -0400 Subject: [PATCH 4/8] Update mkdocs.yml --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 0c8c41ac..8358d297 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -93,6 +93,7 @@ extra_css: nav: - Getting Started: - getting_started/index.md + - google search: interactive/google.html - Interactive Search: interactive/index.ipynb - getting_started/no-install.md - getting_started/install.md From 5fccd87fa8e5f40feb7d3f3db9e79833359a74d4 Mon Sep 17 00:00:00 2001 From: Amanda Charbonneau Date: Fri, 10 Apr 2026 15:02:41 -0400 Subject: [PATCH 5/8] Update google.html --- docs/interactive/google.html | 33 +++++++++++++++++++-------------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/docs/interactive/google.html b/docs/interactive/google.html index 7424b35a..4023f782 100644 --- a/docs/interactive/google.html +++ b/docs/interactive/google.html @@ -1,19 +1,24 @@ - + + + +

 
 

From 5bfbf0add68e146da0a2a53364c82f3aa021d148 Mon Sep 17 00:00:00 2001
From: Amanda Charbonneau 
Date: Fri, 10 Apr 2026 15:47:10 -0400
Subject: [PATCH 6/8] Update google.html

---
 docs/interactive/google.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/interactive/google.html b/docs/interactive/google.html
index 4023f782..d62064cc 100644
--- a/docs/interactive/google.html
+++ b/docs/interactive/google.html
@@ -7,7 +7,7 @@
 async function searchCDA() {
   const query = document.getElementById("searchBox").value;
 
-  const response = await fetch("https://cda.datacommons.cancer.gov/api/v1/subjects", {
+  const response = await fetch("https://cda.datacommons.cancer.gov/summary/subject", {
     method: "POST",
     headers: {
       "Content-Type": "application/json"

From b72ededd58edfd77b9bffb7bbe83108afd3ae1a8 Mon Sep 17 00:00:00 2001
From: Amanda Charbonneau 
Date: Fri, 10 Apr 2026 15:50:50 -0400
Subject: [PATCH 7/8] Update google.html

---
 docs/interactive/google.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/interactive/google.html b/docs/interactive/google.html
index d62064cc..016498ac 100644
--- a/docs/interactive/google.html
+++ b/docs/interactive/google.html
@@ -13,7 +13,7 @@
       "Content-Type": "application/json"
     },
     body: JSON.stringify({
-      search_list: [query]
+      SEARCH_LIST: [query]
     })
   });
 

From 2754653d8154c55daa722fe39f9f036f9002663f Mon Sep 17 00:00:00 2001
From: Amanda Charbonneau 
Date: Fri, 10 Apr 2026 16:08:30 -0400
Subject: [PATCH 8/8] Update google.html

---
 docs/interactive/google.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/interactive/google.html b/docs/interactive/google.html
index 016498ac..637c5eb5 100644
--- a/docs/interactive/google.html
+++ b/docs/interactive/google.html
@@ -7,7 +7,7 @@
 async function searchCDA() {
   const query = document.getElementById("searchBox").value;
 
-  const response = await fetch("https://cda.datacommons.cancer.gov/summary/subject", {
+  const response = await fetch("https://cda-dev.datacommons.cancer.gov/summary/subject", {
     method: "POST",
     headers: {
       "Content-Type": "application/json"