As a software product for use by researchers in several domains, Bioscholar is intended to serve as a vehicle for collaboration with biologists and with fellow bioinformatics developers. At present, the system has been applied to the following biomedical domains via collaboration with the following communities.
- Systems Biology Cancer Pathways (The DARPA 'Big Mechanisms' community including Peter Sorger at Harvard, Larry Hunter at Colorado, Andrey Rzhetsky at Chicago)
- Systems level neuroscience (Larry Swanson and Rick Thompson at USC, Arshad Khan at UTEP)
- Funcational Magenetic Resonance Imaging (Jessica Turner at the MIND Research Network)
- Primate HIV Activation Studies (Robert Murnane at U. Washington, Brian Foley at Los Alamos National Laboratory)
- MRI Infusion Studies (Ken Kubota peviously at the Kinetics Foundation, now at Michael J Fox Foundation)
KEfED modeling within the BioScholar system provides a point of interaction with colleagues in bioinformatics groups (necessary for interoperability and shared tool construction)
- The ISA-Tab format is an emerging de-facto standard for management of experimental metadata, developed and used by a growing number of communities, under the isacommons.org. We are actively collaborating with core ISA team to link the two modeling approaches to foster methods of data sharing and ontology development.
- The Ontology for Biomedical Investigation (OBI) is a community effort to develop a detailed OBO-foundry ontology for descriptions of experimental methods. We aim to make KEfED consistent with the OBI model (and even have the goal of BioScholar providing a curation methodology for OBI).
- Yogo is a no-SQL data repository for scientific data under development by Gwen Jacobs' group at U. Montana. We have developed the KEfED editor as an HTML plugin for the Yogo system.
- Dataverse is a data sharing architecture that we are investigating as a platform that could support the KEfED modeling system as a plugin for use by Dataverse users.