Knowledge Engineering from Experimental Design (KEfED) is a design methodology for experimental data that is based on the idea that it should be possible to develop a generative model for data based on the experimental protocol that created it. This work was originally described in Russ et al 2011, where we describe a prototype editing system written in the Flex language (see https://github.com/BMKEG/kefedEditor). Since Flex is now deprecated, that system is now obselete.
We here develop kefed.io: an ontology-enabled, Javascript tool based on JGraph's MxGraph software. This is commercial-grade software that has recently been released as open source. It is a graph-drawing web-application that can be repackaged and repurposed to provide an high-quality user interface for composing diagrams that represent experimental protocols. This core functionality provides the basis for the kefed.io system.
This is currently implemented as a Spring Boot application, and can be downloaded, built and run with the following commands:
$ git clone https://github.com/SciKnowEngine/kefed.io
$ cd kefed.io
$ mvn clean package spring-boot:run
This is an early prototype developed directly from the mxGraph package, using the grapheditor demo (found at https://github.com/jgraph/mxgraph/tree/master/javascript/examples/grapheditor). The JGraph developers recently changed the license of their more complete and feature-rich draw.io editor to the Apache 2 license (which makes that a suitable target for our eventual adoption).
The previous implementation of the KEfED Editor was initially developed as part of the BioScholar project (RO1-GM083871) and was funded by the Michael J. Fox Foundation.
Current work is partially funded by a subcontract from the Immune Epitope Database (http://iedb.org) to develop KEfED as a vehicle for biocuration. It is also supported under the 'EvidX' project for information extraction [wiki], [NIH Reporter].