BioScholar
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 scientific literature. This project is funded by NIGMS from 2008-2012 under grant RO1-GM083871. Aspects of the project work are also supported by : the Biomedical Informatics Research Network (1 U24 RR025736).
More information »NeuARt - NeuARt III
The adage: 'all data is spatial' is especially pertinent in the field of neuroscience, since neuronal data must be indexed by the neuroanatomical location of phenomena or entities under study. Brain atlases are very widely used as laboratory tools, being some of the most highly cited publications in science. This project seeks to use brain atlases as a method for indexing data from the literature in a neuroinformatics system. This data includes both textual and graphical information, ranging from highly detailed maps constructed from vector-based spatial primitives, histological photographs and drawings, to textual reports of experimental findings in the literature (which we will analyze on a large scale). This project will develop a collaborative environment to enable neuroscientists to use these valuable maps within the community as a whole by contributing data to a shared system with an open-source system that permits querying, overlaying, viewing and annotating such data in an integrated manner. This project is funded by NIMH from 2009-2014 (RO1-MH079068-01A2).
More information »SciKnowMine
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).
More information »Crux
Within this project, we are using the KEfED approach to provide the basis for developing a data-managment system for a funding agency that is attempting to (a) understand where it's money is going and (b) directly plan it's scientific efforts by being able to plan what its research strategy is. This project is in its second year after having been seeded by funding from the Michael J Fox and Kinetics foundations for Parkinson's research. We are very grateful to Michael Rogan and Ken Kubota from the Kinetics Foundation for their continued support in this project. Going forward, this project is a collaborative effort between BMKEG, the Kinetics Foundation and the ISATab group in Oxford.
More information »ooevv - The Ontology of Experimental Variables and Value
This is an ontology design pattern destined for the straightforwrd curation of experimental variables and a description of the values that each variable may use. We focus on providing a framework for curation by domain experts based on Excel workbooks.
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