Open Source Java Medical Software

GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.

The GDL editor is multiplatform application that allows users to create, edit and run GDL files. GDL is a formal language designed to represent clinical knowledge for decision support. It is designed to be natural language- and reference terminology- agnostic by leveraging the designs of openEHR Reference Model and Archetype Model. The tool provides an editing and testing environment capable of generating forms based on the elements defined in the GDL. Requirements: Java Runtime Enviroment (JRE) 1.6 or higher

Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.

This is a functional prototype of automatic speech recognition system for medical reporting in Spanish using CMU Sphinx4 ASR toolkit. This ASR use pre-trained acoustic model and context dependent language model in nuclear medicine diagnostics.

A Java argumentation tool kit. Calculate the Dung acceptability of an argument given a source of conflicting arguments, with this library.

A java based neural network framework. The Auratus network is built around an XML messaging system, allowing for a complete MVC design. Additionally, Auratus networks are constructed and at the node/edge level, allowing for advanced topologies.

Evidence-based Guideline and Decision Support System. Provides patient specific point of care reminders in order to aid physicians provide high quality care. Input/output in the form of HL7 CDA Level 2 documents. Knowledge is encoded using Arden Syntax.

Application implements models described by classical mathematical equation for in vitro deposition prediction based on characteristics of formulation and assay conditions. This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012. Published article: https://www.dovepress.com/empirical-modeling-of-the-fine-particle-fraction-fornbspcarrier-based--peer-reviewed-fulltext-article-IJN

This project is a simulation of the behavior of the human immonological system. It does not intend, in this very first moment, to be a complete simulation but it's going to try to simulate the most important part that is the adaptative response.

This application allow user to predict microemulsion region based on algorithm consisted of artificial neural networks and random forests. Those techniques combined create Decision Support System. Application was created as a part of project K/DSC/000033 subsidy for young researchers from Polish Ministry of Higher Education.

This is a toolkit for medical natural language processing (NLP). The core engine is general enough to be used in a variety of text processing domains, though the toolkit includes specific support for medical reports and patient de-identification.

“Neurology Diagnosis System” is a web-based expert system for diagnosis of neurologic disorders or the disorders of our nervous system. Health assistants in remote areas can use the system to diagnose neurologic patients in the absence of neurolo

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.

OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework.

This ohnlp project has released "pipelines" that were contributed by members of the OHNLP Consortium. The pipelines are based on the Apache UIMA framework. medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0. MedTime is licensed under GNU General Public License version 3.0 (GPLv3). cTAKES development has moved to apache.org. See http://ctakes.apache.org/

A Trial Workbench for Facilitating Best Practices from Prospective to Acute Care in Respiratory Medicine. We aim to provide a set of information management toolboxes that facilitates decision support applications in medical information systems.

This application allow user to predict dissolution profile of solid dispersion systems based on algorithms like symbolic regression, deep neural networks, random forests or generalized boosted models. Those techniques can be combined to create expert system. Application was created as a part of project K/DSC/004290 subsidy for young researchers from Polish Ministry of Higher Education.

This software is related to ST-Guide project, an initiative arisen at the Institute of Computing of State University of Campinas (IC-UNICAMP) to solve the practice guideline formalization and implementation problems.

Semantic knowledge representation for analysis of microscopic images.

TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer maintained, as of 8/15/2019. You are free to continue to use this software under the license for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com

Genetic variants alter cellular behavior in a variety of ways, changing biochemical properties of DNA, mRNA, and proteins. Many large-scale sequencing projects are under way to detect human variation in health and disease. Although broad disease associations can be discovered by GWAS studies, the low-level impact of mutations is hardly available in structured form. The results of thousands of small-scale experiments, on the other hand, are present in the literature and discuss observations made ranging from alteration of active sites to changes in drug response resulting. Our aim is to bridge the gap between detection of genetic variants and their annotation with aforementioned observations. VarImpact extracts experimentally observed changes from the literature. This allows to annotate sequencing results with observed impacts, gather information about the mutational landscape observed in disease populations, and to study disease mechanisms. Check our Wiki for more!

The project is a J2EE-based decision support sytem designed to be used in healthcare scenarios.

Nengo is a suite for building and simulating models of large neural networks. It is based on Eliasmith & Anderson's Neural Engineering Framework, which provides a coherent theory of computation, representation, and dynamics in neural circuits.