Name: Biomedical Knowledge Engineering Group
Type: Organization
Bio: Older legacy organization for Knowledge Engineering work by Gully Burns at the Information Sciences Institute (USC). See @GullyBurns
Location: Information Sciences Institute, Marina del Rey
Blog: http://bmkeg.github.io
Biomedical Knowledge Engineering Group's Projects
VPDMf data access object (dao) library to support the Knowledge Engineering from Experimental Design (KEfED) approach.
The BioScholar web application, as described in Russ et al. 2011 (http://www.biomedcentral.com/1471-2105/12/351).
LA-PDFText is a system for extracting accurate text from PDF-based research articles (and an interface to be able to improve performance where needed). The system is open-source and provides a simple baseline function for extracting text from primary research articles using rules that developers can customize. This means that the system works quite well for most applications (and might occasionally make mistakes and extract the wrong text), but it is always possible to 'hack' your own rules and improve performance.
Systems to drive the development of rule files for LA-PDFText
All the components needed to build a Flex module for the Digital Library subsystem.
High-level build project for all LAPDF-Text submodules
A web application resource (*.war) file for the digital library client.
Library to provide VPDMf support for the LAPDF-Text text extraction system. This is used by VPDMf systems to access the LAPDF-Text functionality.
NeuARt is an open source brain atlas viewer with data overlays.
NLM .nxml to text format conversion
Simple standalone utilities for online literature repositories (Pubmed, PMC, Elsevier, Wiley)
VPDMf-based data access object for the Ontology of Experimental Variables and Values (OoEVV)
An open-source CRF Reference String Parsing Package
The BioPAX Object Model, API and utilities implemented in Java
A little python script that converts files and whole directory trees from one RDF serialization into another.
Relocated to https://github.com/BMKEG/sciDP-pipeline
LSTM based sequence labeling model for scientific discourse tagging. This work was created by Pradeep Dasigi @ CMU
UimaBioC-based pipelines to drive sciDT analysis.
Web application for Knowledge Engineering from Experimental Design (KEfED).
High-level build project to develop KEfED + OoEVV formulisms in isolation from the literature.
Full client application for the Knowledge Engineering from Experimental Design system.
This is the codebase for the SciKnowMine web application. This codebase generates a *.war file that can be deployed in a tomcat server or run from the command line using Maven's implementation of the Jetty server.
All libraries and components relevant to the SciKnowMine triage application.
API used to create and manage HDF5-based SDCubes