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adding references to TCIA and VPODC nbs #231

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adding references to TCIA and VPODC nbs
DanBiber Jul 17, 2025
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Merge branch 'master' into add-citation
DanBiber Jul 18, 2025
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32 changes: 30 additions & 2 deletions jupyter-prometheus/combined_demos/TCIA_notebook.ipynb
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Expand Up @@ -927,11 +927,39 @@
"With these extensions the notebook evolves from a showcase into a\n",
"production-ready radiogenomic analysis scaffold.\n"
]
},
{
"cell_type": "markdown",
"id": "c8ae151d",
"metadata": {},
"source": [
"## 📚 References & Recommended Resources\n",
"\n",
"1. **Do, N., Grossman, R. L., Feldman, T., _et al._ (2019).** “The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology.” *Seminars in Oncology* **46**(4-5), 314–320. <https://pubmed.ncbi.nlm.nih.gov/31629530/>\n",
"\n",
"2. **Clark, K., Vendt, B., Smith, K., _et al._ (2013).** “The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository.” *Journal of Digital Imaging* **26**, 1045–1057. <https://doi.org/10.1007/s10278-013-9622-7>\n",
"\n",
"3. **VA Precision Oncology Data Commons Portal.** Accessed July 2025. <https://vpodc.data-commons.org/>\n",
"\n",
"4. **The Cancer Imaging Archive (TCIA) Portal.** Accessed July 2025. <https://www.cancerimagingarchive.net/>\n",
"\n",
"---\n",
"\n",
"### 🔗 Helpful How‑Tos & Client Tools\n",
"\n",
"* **Gen3 Client Documentation:** <https://gen3.org/resources/user/gen3-client/>\n",
"* **Gen3 Commons Portal:** <https://gen3.datacommons.io/>\n",
"* **VPODC Project Overview:** <https://vpodc.data-commons.org/>\n",
"\n",
"> **Tip:** If you encounter HTTP 403 errors when downloading data, verify that your Gen3 credentials JSON is present in `~/.gen3/credentials.json` and that your account has the proper access policies.\n",
"\n",
"For additional assistance, contact your program’s system administrator or open a ticket with Gen3 Support."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -945,7 +973,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.6.10"
}
},
"nbformat": 4,
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30 changes: 23 additions & 7 deletions jupyter-prometheus/combined_demos/VPODC_data_download_guide.ipynb
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Expand Up @@ -2111,20 +2111,36 @@
"metadata": {},
"source": [
"---\n",
"## 📚 References and Next Steps\n",
"- [Gen3 Client Documentation](https://gen3.org/resources/user/gen3-client/)\n",
"- [Gen3 Commons Portal](https://gen3.datacommons.io/)\n",
"## 📚 References\n",
"\n",
"\n",
"\n",
"1. **Do N, Grossman RL, Feldman T, et al. (2019)**. “The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology.” *Seminars in Oncology* **46**(4–5):314–320. DOI: [10.1053/j.seminoncol.2019.09.002](https://doi.org/10.1053/j.seminoncol.2019.09.002) \n",
"\n",
"2. **Elbers DC, Fillmore NR, Sung F‑C, et al. (2020)**. “The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database.” *Patterns* **1**:100083. DOI: [10.1016/j.patter.2020.100083](https://doi.org/10.1016/j.patter.2020.100083) \n",
"\n",
"3. **Cheng D, Ramos‑Cejudo J, Tuck D, et al. (2019)**. “External validation of a prognostic model for mortality among patients with non‑small‑cell lung cancer using the Veterans Precision Oncology Data Commons.” *Seminars in Oncology* **46**(4–5):327–333. DOI: [10.1053/j.seminoncol.2019.09.006](https://doi.org/10.1053/j.seminoncol.2019.09.006) \n",
"\n",
"\n",
"\n",
"---\n",
"\n",
"### 🔗 Useful Resources\n",
"\n",
"- [Gen3 Client Documentation](https://gen3.org/resources/user/gen3-client/) \n",
"- [Gen3 Commons Portal](https://gen3.datacommons.io/) \n",
"- [VPODC Project Overview](https://vpodc.data-commons.org/)\n",
"\n",
"If you encounter download errors (e.g., HTTP 403), ensure your Gen3 credentials are correctly configured and your profile has access permissions.\n",
"---\n",
"\n",
"For additional help, contact your system administrator or Gen3 support."
"> ⚠️ If you encounter download errors (e.g., HTTP 403), ensure your Gen3 credentials are correctly configured and your profile has appropriate access. \n",
"> For additional support, contact your system administrator or the Gen3 support team.\n"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -2138,7 +2154,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.6.10"
}
},
"nbformat": 4,
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