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DeepPhe-Release

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Public release of the DeepPhe analytic software

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DeepPhe
=======

# Cancer Deep Phenotype Extraction (DeepPhe) Project

This repository is the home of the [**public source code** releases](https://github.com/DeepPhe/DeepPhe-Release/releases)
of the DeepPhe Cancer Phenotype Extraction System. 
For an installation GUI of the DeepPhe system, please download our **Installation Tool** 
for [Windows](https://github.com/DeepPhe/DeepPhe-Dist/releases/download/main/DeepPhe_windows.exe) 
or [Linux](https://github.com/DeepPhe/DeepPhe-Dist/releases/download/main/DeepPhe.dmg).

DeepPhe uses combines natural language processing built on the [Apache cTAKES](https://github.com/apache/ctakes?tab=readme-ov-file#apache-ctakes) clinical NLP framework with an extensive domain information model to:
* extract information from plaintext documents    
* summarize information for Cancers and Tumors across multiple documents
* visualize results at patient and cohort levels using our [DeepPhe Viz](https://github.com/DeepPhe/DeepPhe-Viz-v2) tool.

The system has been tested using documents from five cancer domains:
* Breast Cancer
* Ovarian Cancer
* Malignant Melanoma
* Prostate Cancer
* Childhood brain cancer

There are two different products associated with DeepPhe:

* __DeepPhe-XN__: a full suite of tools, designed to support cohort discovery for cancer clinical research.
Instructions for our installation tool are available on our [Wiki](https://github.com/DeepPhe/DeepPhe-Release/wiki) for [Windows](https://github.com/DeepPhe/DeepPhe-Release/wiki/Windows-Installation-Instructions), 
[MacOS](https://github.com/DeepPhe/DeepPhe-Release/wiki/Mac-Installation-Instructions),
or [Linux](https://github.com/DeepPhe/DeepPhe-Release/wiki/Linux-Installation-Instructions)
* __DeepPhe-CR__: separate web-service based software similar in some ways to DeepPhe, but designed to support cancer registries. 
It uses a different ontology, extracts only top-confidence attributes pertinent to Cancer-Registries, and processes single documents instead of a patient's entire record.
Installation instructions are available in the [DeepPhe-CR release repository](https://github.com/DeepPhe/DeepPhe-CR-Release).

## Licensing
* DeepPhe is provided under an [Apache 2 software license](LICENSE).

* DeepPhe includes portions of the [HemOnc.org](https://hemonc.org/wiki/Ontology) ontology.

* DeepPhe includes portions of the [NCI Thesaurus](https://ncit.nci.nih.gov/ncitbrowser/).

* DeepPhe includes portions of the [NLM UMLS](https://www.nlm.nih.gov/research/umls/index.html).

* DeepPhe uses the [Apache cTAKES](https://github.com/apache/ctakes?tab=readme-ov-file#apache-ctakes) clinical NLP framework.

* DeepPhe uses the [Neo4j](https://neo4j.com/) graph database platform.

## Contact / Help
If you'd like to drop us a note, or have technical questions, please post on [the issue tracker](https://github.com/DeepPhe/DeepPhe-Release/issues).

Metrics on downloads and usage could help us with funding future enhancements.

DeepPhe-Release

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