Biomedical Knowledge Engineering Group



BioScholar is a Knowledge Engineering and Management system to support a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group by curating and processing knowledge from the biomedical scientific literature. In particular, we use BioScholar as the platform for our work in the DARPA Big Mechanisms program.

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We seek to provide a service for experimental neuroscientists by providing made-to-order, modular, principled, open-source knowledge engineering neuroinformatics software based on an agile, rapid-deployment model. 

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The Knowledge Engineering from Experimental Design methodology provides a concrete general computational approach to modeling, capturing and publishing research findings based on observations. Here we describe preliminary implementations, the underlying theoretical rationale and validation studies in multiple domains.  

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The Portable Document Format (PDF) is the almost universally used file format for online scientific publications. It is also notoriously difficult to read and handle computationally, presenting challenges for developers of biomedical text mining or biocuration informatics systems that use the published literature as an information source. To facilitate the effective use of scientific literature in such systems we introduce Layout-Aware PDF Text Extraction (LA-PDFText).

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Here, we focus on using the KEfED approach to provide a data management system (either for an individual laboratory, for a research community or even for a funding agency). 

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We propose to create a framework to support biocuration called SciKnowMine (after 'Scientific Knowledge Mine'), cyberinfrastructure that supports biocuration through the automated mining of text, images, and other amenable media at the scale of the entire literature. We will initially address at least one million documents as the primary testing ground, and grow from there. Our current work is centered on supporting the processes of the Mouse Genome Informatics system at Jackson Laboratory and are based on a community effort in collaboration with Larry Hunter, Karin Verspoor, Kevin Cohen and Ellen Rilloff. This project is funded by NSF from 2009-2012 (#0849977).

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VPDMf - View-Primitive-DataModel framework

The VPDMf stands for 'View Primitive Data Model framework' and is a scaffolding framework for developing knowledge-engineering systems based on a simple frame-oriented conceptual design. The system uses a encapsulation mechanism to capture schema elements into views in the design phase of developing a system. It is implemented in Java and uses a simplified representation of UML class diagrams to provide the basic architecture for the system. From this base, it is possible to generate source code for a variety of elements that are useful for biomedical knowledge engineering systems. 

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