Leif Neve

The Yale cTAKES Extensions (YTEX) is a set of UIMA annotation engines and utilites that complement the Clinical Text Analysis and Knowledge Extraction System (cTAKES). These include: Semantic Search Engine: A web service that enables users to find doc ...

Weka Machine Learning Project An exciting and potentially far-reaching development in computer science is the invention and application of methods of machine learning. These enable a computer program to automatically analyse a large body of data and deci ...

Category Classification

The purpose of NLM's Unified Medical Language System® (UMLS) is to facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health. To that end, NLM produces and distributes the UMLS ...

This package consists of Perl modules along with supporting Perl programs that implement the semantic similarity and relatedness measures described by Leacock & Chodorow (1998), Wu & Palmer (1994), Nguyen and Al-Mubaid (2006), Rada, et. al. 1989, ...

This package provides a Perl interface to the Unified Medical Language System (UMLS). The UMLS is a knowledge representation framework encoded designed to support broad scope biomedical research queries. There exists three major sources in the UMLS. The M ...

UMLS Visualizer

This is a link to a java based UMLS visualizer. Your comments are most welcome.  It takes 30-60 seconds to load when first invoked.  Instructions:  Select the databases to search on the right. Type in a particular term at the bottom and press return.  Th ...

The Online Registry of Biomedical Informatics Tools (ORBIT) Project is the result of a collaboration of more than 30 researchers, developers, informaticians, etc. across more than a dozen academic and federal research organizations. It was created to prov ...

The MITRE Identification Scrubber Toolkit (MIST) is a suite of tools for identifying and redacting personally identifiable information (PII) in free-text medical records. MIST helps you replace these PII either with obscuring fillers, such as [NAME], or w ...

 "DrugDDI: an annotated corpus for drug-drug interactions" submitted for publication.   The DrugDDI corpus is part of a larger study about automatic Drug-Drug Interaction Extraction. The corpus provides data for the development and automatic evaluatio ...

Category Human Annotated
The Arrowsmith Project Home Page

 Arrowsmith Two Node Search tool,  Anne O'Tate value-added PubMed search tool,  Author-ity Author Name Disambiguation tools, ADAM abbreviation database,    WETLAB prototype electronic lab notebook,   Compendium of Biomedical Text Mining tools,   ...

What is SOCR? The Statistics Online Computational Resource (SOCR) designs, validates and freely disseminates knowledge. Specifically, SOCR provides portable online aids for probability and statistics education, technology based instruction and statistica ...

SenseClusters is a suite of Perl programs that supports unsupervised clustering of similar contexts. It relies on it's own native methodology, and also provides support for Latent Semantic Analysis. SenseClusters is a complete system that takes users from ...

SemRep is a program that extracts semantic predications (subject-predicate-object triples) from biomedical free text. Elements of a semantic predications are drawn from the UMLS knowledge sources; the subject and object pair corresponds to UMLS Metathesau ...

SecTag

Clinical notes are often divided into sections, or segments, such as "history of present illness" or "past medical history." These sections often have subsections as well, such as the "cardiovascular exam" section of the "physical exam." One can gain grea ...

Category Sectionizer

The Resource Discovery System (RDS) is a system for discovering research resources.  RDS has many partnerning institutions which to date include the Clinical and Translational Science Award (CTSA) sites, the National Centers for Biomedical Computing Excel ...

Category Bioinformatics

RapidMiner is an environment for machine learning and data mining experiments. It allows experiments to be made up of a large number of arbitrarily nestable operators, described in XML files which are created with RapidMiner's graphical user interface. Ra ...

PMC Parser can be used to parse PMC open access articles' XML files. Create an object of PmcArticle and call various methods to obtain relevant data.

Category Other
Tags
PheWAS - phenome-wide association studies

Current methods to identify gene-disease associations primarily rely on clinical trials or observational cohorts to identify patients.  At Vanderbilt, we have used an EMR-linked DNA biobank called BioVU to derive case and controls populations using data w ...

Category Genome Analysis
NER-based semantic classifier for diseases in discharge summaries

The system performs identification of disease mentions in discharge summaries also assessing uncertainty and negation. Evaluated at the i2b2 Obesity Challenge ranking 1st and 2nd in the textual (explicit) and intuitive (implicit) subtasks respectively. ...

Category Sectionizer

The MIMIC-II research database (Multiparameter Intelligent Monitoring in Intensive Care) is notable for three factors:  it is publicly and freely available; it encompasses a diverse and very large population of ICU patients; and it contains high temporal ...

Category Relational