Current Active Projects

These projects have current funding support and are ongoing.

It's primary purpose is to provide software for experimental biomedical scientists that would permit 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 derived on a local store of PDF files. This project is funded by NIGMS from 2008-2012 ( RO1-GM083871).

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).

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).

Here, we leverage the KEfED approach to design and build data repositories for use by funding agencies. The Michael J Fox and Kinetics foundations need to keep track of the primary data generated by their fundees. This project is a collaborative effort between the BMKEG, the Yogo Toolkit group (run by Gwen Jacobs from MSU) and Alan Ruttenberg from ScienceCommons. This project is jointly funded by the Michael J. Fox and Kinetics Foundations.

This project is concerned with developing a curation and documentation system for information integration in collaboration with the II Group at ISI as part of the BIRN.
This project is concerned with building a graphical browser of the contents of NIH's Reporter system. This work was started within BMKEG and is now hosted on BIRN servers. The majority of work involved in the development of the new mapping capabilities is being performed by a commercial development house (Chalklabs) and NLP research driving the underlying data processing is being performed by Andrew MacCallum's group at UMass. This is documented extensively on the project's website:

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