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new 35294bc Gave README .md extension. Updated readme to have a bit more
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commit 35294bc731b99b223c900af16f93df6b341b7bea
Author: Sean Finan <[email protected]>
AuthorDate: Sat Dec 23 16:12:02 2023 -0500
Gave README .md extension. Updated readme to have a bit more information -
resembles the wiki landing page. Should sync the two when ready.
---
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-
-Apache cTAKES
-==================================
-
-Apache cTAKES<sup>TM</sup> is a natural language processing system for
extraction of information from electronic medical record clinical free-text.
-
-Requirements
----------------------------------------
-Java 1.8 is required to run cTAKES
-Maven 3 is required to build cTAKES
-
-A license for the [Unified Medical Language System
(UMLS)](https://www.nlm.nih.gov/research/umls/index.html) is required to use
the named entity recognition module (dictionary lookup) with the default
dictionary.
-
-Information can be found in the [wiki](https://github.com/apache/ctakes/wiki)
concerning:
-- Developer installation.
-- User installation.
-- Running the system and its tools.
-- Example pipelines.
-- The application programming interface (API).
-- Example code.
-- Extending the system.
-- Incorporating Apache cTAKES<sup>TM</sup> in a maven project.
-
-* Documentation is currently in progress.
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+# Apache cTAKES™
+
+## Introduction
+
+
+The Apache™ clinical Text Analysis and Knowledge Extraction System (cTAKES™)
focuses on extracting knowledge
+from clinical text through Natural Language Processing (NLP) techniques.
+
+cTAKES is engineered in a modular fashion and employs leading-edge rule-based
and machine learning methods.
+
+cTAKES has standard features for biomedical text processing software,
+including the ability to extract concepts such as symptoms, procedures,
diagnoses, medications and anatomy
+with attributes and standard codes.
+
+More powerful components can perform tasks as complex as identifying temporal
events,
+dates and times – resulting in placement of events in a patient timeline.
+
+Components are trained on gold standards from the biomedical as well as the
general domain.
+This affords usability across different types of clinical narrative (e.g.
radiology reports,
+clinical notes, discharge summaries) in various institution formats as well as
other types of
+health-related narrative (e.g. twitter feeds), using multiple data standards
(e.g. Health Level 7 (HL7),
+Clinical Document Architecture (CDA), Fast Healthcare Interoperability
Resources (FHIR), SNOMED-CT, RxNORM).
+
+cTAKES is the NLP platform for many initiatives across the world covering a
variety of research purposes
+and large datasets.
+Contributors include professionals at medical and commercial institutions, NLP
and Machine Learning researchers,
+Medical Doctors, and students of many disciplines and levels.
+We encourage people from all backgrounds to get involved! (link)
+
+
+<br>
+
+## Supported Environments
+1. **Java 1.8** is required to run cTAKES. Run this command to check your Java
version:
+```
+$ java -version
+```
+2. **Maven 3** is required to build cTAKES. Run this to command to check your
Maven version:
+```
+$ mvn -version
+```
+3. A license for the [Unified Medical Language System
(UMLS)](https://www.nlm.nih.gov/research/umls/index.html)
+ is required to use the named entity recognition module (dictionary lookup)
with the default dictionary.
+4. **Python 3** is required to use cTAKES [Python Bridge to Java
(PBJ)](https://github.com/apache/ctakes/wiki/pbj_intro).
+Run this to command to check your Python version:
+```
+$ python -V
+```
+
+
+<br/>
+
+
+## Getting Started
+
+### New Users
+
+The easiest way for new users to get a jump start running cTAKES is to use the
[Standard Pipeline Installation Facility](artifacts).
+The Standard Pipeline Installation Facility is a tool that can install cTAKES
configured to run the most popular cTAKES pre-built pipelines.
+You can then use the [Piper File
Submitter](https://github.com/apache/ctakes/wiki/Piper+File+Submitter) GUI to
submit jobs or submit them from the command line.
+
+For access to all cTAKES capabilities, download a [zip]() or [tar.z]() file
containing a fully-built installation of the most recent cTAKES release.
+Then, after obtaining a UMLS license, use the [UMLS Package
Fetcher](https://github.com/apache/ctakes/wiki/cTAKES+UMLS+Package+Fetcher) GUI
to install a copy of the
+default dictionary for Named Entity Recognition (NER) using cTAKES Fast
Dictionary Lookup.
+
+### New Developers
+
+All source code for cTAKES versions 5+ is available from the [cTAKES GitHub
repository](https://github.com/apache/ctakes).
+1. Clone this repository
+```
+$ git clone https://github.com/apache/ctakes.git
+```
+2. Open your local copy of the repository in an IDE of your choice.
+3. Run directly from the code (link).
+ or
+4. Build a binary installation (link), and
+5. Run a binary installation (link).
+
+
+## More information
+
+Much more information can be found on the [cTAKES
wiki](https://github.com/apache/ctakes/wiki).
+
+You can also write to the cTAKES user and developer mailing lists: user at
ctakes.apache.org and dev at apache.ctakes.org
+and find answers to previously asked questions by searching the
[user](https://lists.apache.org/[email protected])
+and [developer](https://lists.apache.org/[email protected])
mail archives.
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