Clinical Text Analysis and Knowledge Extraction System (cTAKES) is a system through which one creates one or more pipelines to process clinical notes and to identify clinical named entities. For example, a pipeline can identify mentions of drugs; diseases and disorders; signs and symptoms; and anatomical sites and procedures. Each named entity that is found is given attributes for the text span, the ontology mapping code, the context (probable/possible, family history of, or history of), and negated/not negated.
cTAKES is built on the UIMA framework. cTAKES 1.2 does not provide a GUI of its own for installation or processing. The documentation shows how to use the GUIs provided by the UIMA framework, and how to run cTAKES from a command line.
Before using cTAKES you need to know that cTAKES does not provide any mechanisms of its own to handle patient data securely. It is assumed that cTAKES is installed on a system that can process patient data, or that any data being processed by cTAKES has already been through a deidentification step in order to comply with any applicable laws.
Download and Install
There are two kinds of cTAKES users. One is the user that wishes to utilize the tool, without any compile steps or use of development environments. The goal is primarily to get the tool up and running and to apply it to clinical documents. These users will install the software like any other product that you might buy or download. Note that there still may be file configuration required by using an editor.
The second is a developer that will be taking the cTAKES software to extend or modify it here and there to suit project needs. More parameters and such can be customized in this kind of environment for fine tuned control, but it does require that you have an integrated development environment in which to modify, build and deploy the code.
There is a third install path, but this is for developers, so it does not count as a third user type. It is possible to build a back-end server out of the software. That is, there will be no graphical user interface available. The developer will have only application programming interfaces (APIs) available with which to interact. These instructions are embedded into the Developer install instructions. At one point during the install pay attention to the Important icon. These will mark steps not required if you don't want a back-end server.
cTAKES release 1.2 includes a new annotator (beta version) called SideEffect, which extracts physician-asserted drug side effects from clinical notes. This release also introduces icTAKES, which provides an integrated version of Mayo Clinic's cTAKES for end users and developers. To distinguish them, cTAKES (downloadable from sourceforge) is distributed as cTAKES 1.2.1 and _i_cTAKES (also downloadable from sourceforge) is distributed as cTAKES 1.2.2. The table below links to the proper download and install instructions depending on the user. Consideration is also given to the install environment you wish to use. The latest release is recommended, which has a simple install mechanism.
cTAKES download and install selection
Forums and Contact Information
We encourage use of our forums as the first line for inquiries. There are separate forums for discussion by user type:
Consortium General Discussion
cTAKES End User Discussions
cTAKES Developer Discussions
If you have an issue that can not be placed into public forums, we also have an email address for you to use: firstname.lastname@example.org
Conventions in the guide.
Glossary of terms.