Biomedical Knowledge Engineering Group

Older legacy organization for Knowledge Engineering work by Gully Burns at the Information Sciences Institute (USC). See @GullyBurns

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

    Jupyter Notebook 2 5 Apache-2.0 Updated Jan 17, 2019
  • UimaBioC-based pipelines to drive sciDT analysis.

    Java Apache-2.0 Updated Sep 15, 2018
  • This is where we manage maven dependencies, versions and repositories for all our development projects. This serves as the parent for all subsequent work.

    24 Updated Jun 30, 2018
  • Offshoot of vpdmfCore, extracting all code generation capabilities to provide better delineated system.

    Java Updated Jun 30, 2018
  • The core components of the VPDMf system including tools to build and manage linked systems in MySQL, Java and Flex.

    Java 1 Updated Jun 30, 2018
  • 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 Updated Jun 30, 2018
  • Implementations of the Domain Insight Graph (DIG, http://dig.isi.edu) formalism applied to advanced, complex scientific subjects (systems level neuroscience, systems biology, etc.).

    2 Updated Jun 27, 2018
  • Semantic Web Constructs for ERuDIte

    2 Updated Jun 22, 2018
  • The BioScholar web application.

    JavaScript 1 Apache-2.0 Updated May 9, 2018
  • The VPDMf-driven library for all functionality pertaining to literature citations and documents.

    Java 1 Updated May 4, 2018
  • Updated May 3, 2018
  • VPDMf model for the digital library system

    Updated May 3, 2018
  • The BioPAX Object Model, API and utilities implemented in Java

    Java 4 Updated Mar 6, 2018
  • 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 52 51 GPL-3.0 Updated Mar 2, 2018
  • 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 2 Apache-2.0 Updated Feb 9, 2018
  • The BioScholar web application, as described in Russ et al. 2011 (http://www.biomedcentral.com/1471-2105/12/351).

    Common Lisp 2 Updated Aug 10, 2017
  • 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 Updated May 15, 2017
  • 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 1 Apache-2.0 Updated May 15, 2017
  • High-level build project for all VPDMf submodules

    1 Updated Apr 7, 2017
  • Utilities for bmkeg libraries (includes file, zip, spring and other miscellaneous tools).

    Java 4 Updated Apr 7, 2017
  • An open-source CRF Reference String Parsing Package

    Perl 42 LGPL-3.0 Updated Feb 10, 2017
  • NeuARt is an open source brain atlas viewer with data overlays.

    Updated Jan 25, 2017
  • Source to www.draw.io

    JavaScript 2,206 GPL-3.0 Updated Dec 28, 2016
  • 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 Updated Dec 19, 2016
  • VPDMf model for terminology (from ontologies)

    Updated Dec 20, 2016
  • VPDMf model for people

    Updated Dec 20, 2016
  • VPDMf model for full text documents (designed to work with lapdftext)

    Updated Dec 19, 2016
  • VPDMf-based data access object for the Ontology of Experimental Variables and Values (OoEVV)

    Web Ontology Language 1 Updated Dec 19, 2016
  • All the components needed to build a Flex module for the Digital Library subsystem.

    ActionScript 1 Updated Dec 19, 2016
  • JavaScript Apache-2.0 Updated Dec 19, 2016

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