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114 changes: 71 additions & 43 deletions docs/getting_started/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,78 +2,106 @@
title: Re-Search made simple
---

<div class="center" markdown> <p>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.</p></div>
# Search cancer data across multiple NCI data commons—instantly

Cancer data is distributed across multiple systems—CDA brings it together.

<div class="grid cards" markdown>
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.
<div style="margin-top: 1em; margin-bottom: 2em;">
<a href="interactive.html"><strong>👉 Start exploring data</strong></a><br>
<a href="interactive.html">Try interactive search</a> ·
<a href="api.html">View API docs</a>
</div>
```

---

## 🔎 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.
<a href="../interactive/" title="interactive search" class="md-button md-button">Head to our interactive page to try it out.
</a></p>
---

- :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. <p>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.*<p>
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/Welcome.ipynb" title="Try it now" class="md-button md-button">Launch CDA in the cloud
</a></p>
## 🖥️ 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.
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/010_isbcgc.ipynb" title="isbcgcusecase" class="md-button md-button">Test it out on Google Colab
</a></p>
- 🧠 **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? <p>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)

---

</div>
## 🔬 Developed by

The National Cancer Institute’s Cancer Research Data Commons (CRDC)
107 changes: 64 additions & 43 deletions docs/index.md
Original file line number Diff line number Diff line change
@@ -1,79 +1,100 @@
---
title: Re-Search made simple
---
# Search cancer data across multiple NCI data commons—instantly

<div class="center" markdown> <p>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.</p></div>
Cancer data is distributed across multiple systems—CDA brings it together.

Find subjects, files, and studies using harmonized terms across repositories. No coding required.

<div class="grid cards" markdown>
<div style="margin-top: 1em; margin-bottom: 2em;">
<a href="interactive.html"><strong>👉 Start exploring data</strong></a><br>
<a href="interactive.html">Try interactive search</a> ·
<a href="api.html">View API docs</a>
</div>

---

- :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.
<a href="interactive/" title="interactive search" class="md-button md-button">Head to our interactive page to try it out.
</a></p>
---

### 📓 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. <p>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.*<p>
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/Welcome.ipynb" title="Try it now" class="md-button md-button">Launch CDA in the cloud
</a></p>
## 🖥️ 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.
<a href="https://colab.research.google.com/github/CancerDataAggregator/Community-Notebooks/blob/main/Tutorials/010_isbcgc.ipynb" title="isbcgcusecase" class="md-button md-button">Test it out on Google Colab
</a></p>
- 🧠 **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? <p>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)

---

</div>
## 🔬 Developed by

The National Cancer Institute’s Cancer Research Data Commons (CRDC)
24 changes: 24 additions & 0 deletions docs/interactive/google.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
<input id="searchBox" placeholder="Search cancer data (e.g. lung cancer)" />
<button onclick="searchCDA()">Search</button>

<pre id="results"></pre>

<script>
async function searchCDA() {
const query = document.getElementById("searchBox").value;

const response = await fetch("https://cda-dev.datacommons.cancer.gov/summary/subject", {
method: "POST",
headers: {
"Content-Type": "application/json"
},
body: JSON.stringify({
SEARCH_LIST: [query]
})
});

const data = await response.json();
document.getElementById("results").textContent =
JSON.stringify(data, null, 2);
}
</script>
3 changes: 2 additions & 1 deletion mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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"]

Expand Down Expand Up @@ -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
Expand Down
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