The Apache Software Foundation Announces Apache® cTAKES™ v4.0

[Sally Khudairi <sk...@apache.org>]

[ this announcement is available online at https://s.apache.org/OJJw ]

Widely adopted Open Source biomedical data extraction, annotation, and
clinical information management platform now faster and easier to use.

Forest Hill, MD —25 April 2017— The Apache Software Foundation (ASF),
the all-volunteer developers, stewards, and incubators of more than 350
Open Source projects and initiatives, announced today the availability
of Apache® cTAKES™ v4.0, the latest version of the Open Source natural
language processing system for information extraction from
health-related free-text.

Apache cTAKES (clinical Text Analysis Knowledge Extraction System) is a
natural-language processing based information extraction platform for
health-related text that identifies signals important for the biomedical
domain including types of clinical named entities mapped to various
biomedical terminologies/ontologies such as the Unified Medical Language
System (UMLS) -- drugs, diseases/disorders, signs/symptoms, anatomical
sites and procedures along with their associated attributes such as
negation, uncertainty, and more.

"Apache cTAKES has helped considerably advance biomedical data
extraction and clinical information management over the last several
years," said Pei Chen, Vice President of Apache cTAKES. "We are proud to
lead the development of a widely adopted, interoperable,
community-driven solution for clinical decision support systems and
clinical research. The improvements in v4 makes cTAKES easier to use,
thereby benefiting the greater medical community."

cTAKES originated in 2006 by a team of physicians, computer scientists,
and software engineers at Mayo Clinic, and was submitted to the Apache
Incubator in June 2012. cTAKES was built using the Apache UIMA
(Unstructured Information Management Architecture) framework and Apache
OpenNLP machine-learning based toolkit for the processing of
health-related natural language text. Apache cTAKES components create
rich linguistic and semantic annotations that have been utilized for a
variety of biomedical use cases including clinical decision support
systems and clinical research. 

Highlights of Apache cTAKES v4 include:
Dictionary Builder Graphical user interface (GUI) for easy dictionary
selection and build-up;
Pipe Bits to be used to describe cTAKES modules for programs that help
users create pipelines such as document descriptions of components, and
inputs, outputs, parameters, dependencies implemented as Java
annotations simplifies pipeline builders indicates whether a component
is a Collection Reader, Annotator, or a Cas Consumer (Writer);
Piper files, allowing fast and easy creation and modification of custom
pipelines with many capabilities;
Graphical user interface (GUI) for easy pipeline creation to select
cTAKES components, view descriptions of the components, and inputs,
outputs, parameters, dependencies implemented using the new Pipe Bits;
Example Clinical Documents with manual expert annotations of clinical
narratives (mock ups). The narratives were annotated using the Open
Source Anafora annotation tool (https://github.com/weitechen/anafora);
Temporal module for extraction of events, time expressions, and temporal
relations; and
Numerous bug fixes that resulted in a more stable, much faster and
robust release

"Apache cTAKES v4 release is a pivotal milestone that incorporates
state-of-the-art methods for some of the most difficult tasks in
clinical narrative processing and information extraction, namely
coreference resolution and temporality. Integrating novel user friendly
interfaces and a scaled up optimization of its core concept mapper, v4
provides the open-source and medical communities a stable, industrial
strength tool to mine clinical text," said Prof. Guergana Savova, ASF
Member and Apache cTAKES Project Management Committee member, and
Principal Investigator of the Natural Language Processing Lab at the
Computational Health Informatics Program, Boston Children’s Hospital and
faculty at Harvard Medical School. "The world-wide community involvement
is exactly what we envisioned when we started cTAKES back in 2006. We
are grateful to the community for its many contributions and are greatly
appreciative of the efforts of Sean Finan and James Masanz, members of
the Apache cTAKES Project Management Committee for leading this
milestone release."

"We are using Apache cTAKES v4 to link phenotypic and genomic/genetic
data for the Boston Children’s Hospital Precision Link Biobank," said
Kenneth D. Mandl, Director of the Computational Health Informatics
Program at Boston Children’s Hospital.
"We are using cTAKES to help identify people with multiple sclerosis
from the electronic health records and investigate disease trajectory
and treatment response in this chronic neurological disorder," said
Zongqi Xia, MD, PhD, an Assistant Professor of Neurology and Biomedical
Informatics at University of Pittsburgh.

"We have been using cTAKES in the VA Radiology Reports to look for word
tokens that correlate with lung, liver and other findings," said Dr. Joe
Erdos, faculty at Yale School of Medicine and associated scientist at
the Veterans Affairs (VA) in Connecticut.

"We have been frequent users of cTAKES since the 3.x days, and are
excited by the cTAKES release," said Chris Mattmann, Principal Data
Scientist in the Engineering & Science Directorate at NASA Jet
Propulsion Laboratory, and member of the Apache cTAKES Project
Management Committee. "Our Shangridocs tool that allows for interactive
text extraction and analysis from science research papers in the
bioinformatics/clinical domain is built around Apache cTAKES and Apache
OpenNLP. We plan on upgrading ASAP to cTAKES 4.0 and contributing to the
platform. cTAKES scalability is something we are very interested in -
and in the ability to extend the existing UMLS taxonomy with custom
medical metadata and information and cTAKES 4.0 (and beyond) is the
perfect platform for growth in this area."

Availability and Oversight
Apache cTAKES software is released under the Apache License v2.0 and is
overseen by a self-selected team of active contributors to the project.
A Project Management Committee (PMC) guides the Project's day-to-day
operations, including community development and product releases. For
downloads, documentation, and ways to become involved with Apache
cTAKES, visit http://ctakes.apache.org/

About The Apache Software Foundation (ASF)
Established in 1999, the all-volunteer Foundation oversees more than 350
leading Open Source projects, including Apache HTTP Server --the world's
most popular Web server software. Through the ASF's meritocratic process
known as "The Apache Way," more than 620 individual Members and 6,000
Committers successfully collaborate to develop freely available
enterprise-grade software, benefiting millions of users worldwide:
thousands of software solutions are distributed under the Apache
License; and the community actively participates in ASF mailing lists,
mentoring initiatives, and ApacheCon, the Foundation's official user
conference, trainings, and expo. The ASF is a US 501(c)(3) charitable
organization, funded by individual donations and corporate sponsors
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© The Apache Software Foundation. "Apache", "cTAKES", "Apache cTAKES",
and "ApacheCon" are registered trademarks or trademarks of the Apache
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