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This is where we manage maven dependencies, versions and repositories for all our development projects. This serves as the parent for all subsequent work.
Offshoot of vpdmfCore, extracting all code generation capabilities to provide better delineated system.
The core components of the VPDMf system including tools to build and manage linked systems in MySQL, Java and Flex.
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)
Implementations of the Domain Insight Graph (DIG, http://dig.isi.edu) formalism applied to advanced, complex scientific subjects (systems level neuroscience, systems biology, etc.).
Semantic Web Constructs for ERuDIte
The BioScholar web application.
The VPDMf-driven library for all functionality pertaining to literature citations and documents.
VPDMf model for the digital library system
LSTM based sequence labeling model for scientific discourse tagging. This work was created by Pradeep Dasigi @ CMU
The BioPAX Object Model, API and utilities implemented in Java
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…
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.
The BioScholar web application, as described in Russ et al. 2011 (http://www.biomedcentral.com/1471-2105/12/351).
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')
UimaBioC-based pipelines to drive sciDT analysis.
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
High-level build project for all VPDMf submodules
Utilities for bmkeg libraries (includes file, zip, spring and other miscellaneous tools).
An open-source CRF Reference String Parsing Package
NeuARt is an open source brain atlas viewer with data overlays.
Source to www.draw.io
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).
VPDMf model for terminology (from ontologies)
VPDMf model for people
VPDMf model for full text documents (designed to work with lapdftext)
VPDMf-based data access object for the Ontology of Experimental Variables and Values (OoEVV)
All the components needed to build a Flex module for the Digital Library subsystem.