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kefeddao

VPDMf data access object (dao) library to support the Knowledge Engineering from Experimental Design (KEfED) approach.

kefeddataeditorapp

kefededitor

The BioScholar web application, as described in Russ et al. 2011 (http://www.biomedcentral.com/1471-2105/12/351).

kefedmodeleditorapp

lapdftext

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.

lapdftext-rules

Systems to drive the development of rule files for LA-PDFText

lapdftextclientapp

lapdftextclientcomponents

All the components needed to build a Flex module for the Digital Library subsystem.

lapdftextproject

High-level build project for all LAPDF-Text submodules

lapdftextserver

A web application resource (*.war) file for the digital library client.

lapdftextvpdmf

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

NeuARt is an open source brain atlas viewer with data overlays.

nxml2txt

NLM .nxml to text format conversion

onlineliteratureresources

Simple standalone utilities for online literature repositories (Pubmed, PMC, Elsevier, Wiley)

ooevvdao

VPDMf-based data access object for the Ontology of Experimental Variables and Values (OoEVV)

parscit

An open-source CRF Reference String Parsing Package

paxtools

The BioPAX Object Model, API and utilities implemented in Java

rdfconvert

A little python script that converts files and whole directory trees from one RDF serialization into another.

scidp-preprocessing

Relocated to https://github.com/BMKEG/sciDP-pipeline

scidt

LSTM based sequence labeling model for scientific discourse tagging. This work was created by Pradeep Dasigi @ CMU

scidt-pipeline

UimaBioC-based pipelines to drive sciDT analysis.

sciknowlab

Web application for Knowledge Engineering from Experimental Design (KEfED).

sciknowlabproject

High-level build project to develop KEfED + OoEVV formulisms in isolation from the literature.

sciknowlabsystem

Full client application for the Knowledge Engineering from Experimental Design system.

sciknowmine

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.

sciknowmineproject

All libraries and components relevant to the SciKnowMine triage application.

sciknowminesystem

sdcube_api

API used to create and manage HDF5-based SDCubes

skmcore

skmtopicmodeling