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    32 repositories

    • UimaBioC

      Public
      Simple interaction code to define the 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 23, 2020Feb 23, 2020

    • ske-utils

      Public
      Utilities for bmkeg libraries (includes file, zip, spring and other miscellaneous tools).
      Java
      •4•1•0•0•Updated Feb 11, 2020Feb 11, 2020

    • SciKnowEngine.github.io

      Public
      Website for USC ISI Scientific Knowledge Engineering group
      HTML
      •
      Apache License 2.0
      •13•1•0•0•Updated Jan 21, 2020Jan 21, 2020

    • fastai

      Public
      Demonstration / test code to run fastai models
      MIT License
      •0•0•0•0•Updated Aug 18, 2019Aug 18, 2019

    • 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•15•0•0•Updated Mar 21, 2019Mar 21, 2019

    • ske-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•0•Updated Mar 20, 2019Mar 20, 2019

    • sciknowmap

      Public
      Python
      •0•2•0•0•Updated Jan 28, 2019Jan 28, 2019

    • ro-biocuration2019

      Public
      Research Object describing source code and data for Burns et al (2019)
      MIT License
      •1•0•0•0•Updated Jan 3, 2019Jan 3, 2019

    • Molecular_Interaction_Evidence_Fragment_Corpus

      Public
      Other
      •1•0•0•0•Updated Nov 8, 2018Nov 8, 2018

    • evidx-figureAnalysis

      Public
      Frameworks for the analysis of figures from scientific papers expressed as PDF files.
      0•0•0•0•Updated Sep 25, 2018Sep 25, 2018

    • docker-bioscholar

      Public
      Docker image of the BioScholar web application. Permits the system to be deployed anywhere.
      Java
      •54•0•0•0•Updated Aug 3, 2018Aug 3, 2018

    • ro-semSci2018

      Public
      MIT License
      •0•0•0•0•Updated Jul 23, 2018Jul 23, 2018

    • etk

      Public
      Extraction Toolkit
      Julia
      •
      MIT License
      •48•0•0•0•Updated Jul 18, 2018Jul 18, 2018

    • ro-semSci2017

      Public
      Research Object Implementation for submission to ISWC 2017
      MIT License
      •0•0•0•0•Updated Jul 18, 2018Jul 18, 2018

    • SciKnowGraph

      Public
      Scientific Knowledge Graphs are applications of Knowledge Graph methods (driven currently from the work of DIG group at ISI, http://dig.isi.edu/). We cover methods for multiple domains: systems level neuroscience, systems biology, etc.
      semantic-webontologyontology-design-patternsscientific-knowledge-engineering
      3•1•0•0•Updated Jun 27, 2018Jun 27, 2018

    • kefed.io

      Public
      Knowledge Engineering from Experimental Design
      JavaScript
      •
      MIT License
      •0•2•13•0•Updated Jun 26, 2018Jun 26, 2018

    • docker_bioscholar

      Public
      Docker image of the BioScholar web application. Permits the system to be deployed anywhere.
      Apache License 2.0
      •0•0•0•0•Updated May 31, 2018May 31, 2018

    • evidx-alignment

      Public
      MIT License
      •5•0•0•0•Updated Mar 29, 2018Mar 29, 2018

    • dig-alignment

      Public
      Code to do feature alignment in dig
      PHP
      •
      Apache License 2.0
      •17•0•0•0•Updated Jan 11, 2018Jan 11, 2018

    • vpdmf-bioc

      Public
      Apache License 2.0
      •0•0•0•0•Updated Dec 8, 2017Dec 8, 2017

    • PyBioC

      Public
      Python library for work with BioCreative files
      Python
      •
      Other
      •14•0•0•0•Updated Nov 29, 2017Nov 29, 2017

    • TextAnnotationGraphs

      Public
      A modular annotation system that supports complex, interactive annotation graphs embedded on top of sequences of text.
      JavaScript
      •
      MIT License
      •18•0•0•0•Updated Nov 11, 2017Nov 11, 2017

    • kefedEditor

      Public
      The original KEfED editor 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 30, 2017Aug 30, 2017

    • corex_topic

      Public
      Hierarchical topic models for sparse count data with CorEx.
      Python
      •
      Apache License 2.0
      •120•0•0•0•Updated Aug 4, 2017Aug 4, 2017

    • bioc-ld

      Public
      A Linked Data implementation of the National Library of Medicine's BioC format.
      MIT License
      •0•0•0•0•Updated Jul 22, 2017Jul 22, 2017

    • skeDigitalLibrary

      Public
      Currently, this is the legacy 'BioScholar' system encapsulated into a single project. We will evolve this tool to work within the DIG architecture.
      Java
      •0•0•0•0•Updated Jul 1, 2017Jul 1, 2017

    • CorEx

      Public
      CorEx or "Correlation Explanation" constructs a hierarchy of maximally informative representations of complex data.
      Python
      •
      GNU General Public License v2.0
      •54•0•0•0•Updated Jun 2, 2017Jun 2, 2017

    • kefedProject

      Public
      Organizing project for work on the Knowledge Engineering from Experimental Design (KEfED) methodology.
      JavaScript
      •0•0•0•0•Updated Jun 1, 2017Jun 1, 2017

    • digapp-ht

      Public
      Copy of dig-polymer for new data set
      HTML
      •
      Apache License 2.0
      •9•0•0•0•Updated Mar 22, 2017Mar 22, 2017

    • ooevvTools

      Public
      VPDMf-based data access object for the Ontology of Experimental Variables and Values (OoEVV)
      Java
      •1•0•0•0•Updated Dec 19, 2016Dec 19, 2016