Repositories list

• sciDT

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

  Jupyter Notebook

  •

  Apache License 2.0

  •5•2•0•0•Updated Jan 17, 2019Jan 17, 2019

• sciDT-pipeline

  Public
  UimaBioC-based pipelines to drive sciDT analysis.

  nlpuimapipeline+ 1bioc

  Java

  •

  Apache License 2.0

  •1•0•0•0•Updated Sep 14, 2018Sep 14, 2018

• bmkeg-parent

  Public
  This is where we manage maven dependencies, versions and repositories for all our development projects. This serves as the parent for all subsequent work.

  26•0•0•1•Updated Jun 30, 2018Jun 30, 2018

• vpdmfGenerator

  Public
  Offshoot of vpdmfCore, extracting all code generation capabilities to provide better delineated system.

  Java

  •1•0•1•0•Updated Jun 30, 2018Jun 30, 2018

• vpdmfCore

  Public
  The core components of the VPDMf system including tools to build and manage linked systems in MySQL, Java and Flex.

  Java

  •0•0•1•0•Updated Jun 30, 2018Jun 30, 2018

• uml

  Public
  This library manages all low-level interactions with our UML-based metamodel for the data schema of any given system. This includes systems to read various types of UML and other systems to auto-generate code for various languages (currently mainly java and actionscript)

  Java

  •2•0•0•0•Updated Jun 30, 2018Jun 30, 2018

• deepDIG

  Public
  Implementations of the Domain Insight Graph (DIG, http://dig.isi.edu) formalism applied to advanced, complex scientific subjects (systems level neuroscience, systems biology, etc.).

  3•1•0•0•Updated Jun 27, 2018Jun 27, 2018

• erudite-sw

  Public
  Semantic Web Constructs for ERuDIte

  2•0•0•0•Updated Jun 22, 2018Jun 22, 2018

• bioscholar

  Public
  The BioScholar web application.

  JavaScript

  •

  Apache License 2.0

  •1•0•0•0•Updated May 9, 2018May 9, 2018

• digitalLibraryDao

  Public
  The VPDMf-driven library for all functionality pertaining to literature citations and documents.

  Java

  •0•0•1•0•Updated May 4, 2018May 4, 2018

• vpdmf-parent

  Public
  0•0•0•0•Updated May 3, 2018May 3, 2018

• vpdmf-digitalLibrary

  Public
  VPDMf model for the digital library system

  0•0•0•0•Updated May 3, 2018May 3, 2018

• Paxtools

  Public
  The BioPAX Object Model, API and utilities implemented in Java

  Java

  •12•0•0•0•Updated Mar 6, 2018Mar 6, 2018

• lapdftext

  Public
  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 qu…

  Java

  •

  GNU General Public License v3.0

  •55•82•20•0•Updated Mar 2, 2018Mar 2, 2018

• UimaBioC

  Public
  Simple interaction code to define BioC as a UIMA type and provide support for it's use in text mining applications based on the CleartTk UIMA system.

  Java

  •

  Apache License 2.0

  •3•0•0•0•Updated Feb 8, 2018Feb 8, 2018

• kefedEditor

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

  Common Lisp

  •2•0•0•0•Updated Aug 10, 2017Aug 10, 2017

• cosid_linkage

  Public
  Python scripts to run evidence extraction pipelines from text annotated with discourse tags from SciDT. Methodology is based on the CoSID frames ('Cycles of Scientific Investigation in Discourse')

  Jupyter Notebook

  •0•0•4•0•Updated May 15, 2017May 15, 2017

• amr-ld

  Public
  A Python library for mapping AMRs to linked data formats (such as RDF and JSON-LD). This work is heavily derived from Naomi Saphra's 'AMRICA' library (https://github.com/nsaphra/AMRICA) and SMATCH

  Python

  •

  Apache License 2.0

  •0•4•0•0•Updated May 15, 2017May 15, 2017

• vpdmfProject

  Public
  High-level build project for all VPDMf submodules

  1•0•0•0•Updated Apr 7, 2017Apr 7, 2017

• bmkeg-utils

  Public
  Utilities for bmkeg libraries (includes file, zip, spring and other miscellaneous tools).

  Java

  •4•0•0•0•Updated Apr 7, 2017Apr 7, 2017

• ParsCit

  Public
  An open-source CRF Reference String Parsing Package

  Perl

  •

  GNU Lesser General Public License v3.0

  •47•0•0•0•Updated Feb 10, 2017Feb 10, 2017

• neuart

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

  0•0•0•0•Updated Jan 25, 2017Jan 25, 2017

• draw.io

  Public
  Source to www.draw.io

  JavaScript

  •

  GNU General Public License v3.0

  •7.7k•0•0•0•Updated Dec 28, 2016Dec 28, 2016

• bioscholarProject

  Public
  The overall project folder for the BioScholar system, described in Russ et al. 2011(http://www.biomedcentral.com/1471-2105/12/351). Version 1.0 of this project is the distribution associated with this paper from our Google Code site(https://code.google.com/p/bioscholar).

  MIT License

  •0•1•7•0•Updated Dec 19, 2016Dec 19, 2016

• vpdmf-terminology

  Public
  VPDMf model for terminology (from ontologies)

  0•0•0•0•Updated Dec 19, 2016Dec 19, 2016

• vpdmf-people

  Public
  VPDMf model for people

  0•0•0•0•Updated Dec 19, 2016Dec 19, 2016

• vpdmf-ftd

  Public
  VPDMf model for full text documents (designed to work with lapdftext)

  0•0•0•0•Updated Dec 19, 2016Dec 19, 2016

• ooevvDao

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

  Web Ontology Language

  •1•0•0•0•Updated Dec 19, 2016Dec 19, 2016

• lapdftextClientComponents

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

  ActionScript

  •1•0•0•0•Updated Dec 19, 2016Dec 19, 2016

• lapdftextClientApp

  Public
  JavaScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 19, 2016Dec 19, 2016