The overall project folder for the BioScholar system, described in Russ et al. 2011( Version 1.0 of this project is the distribution associated with this paper from our Google Code site(
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bioscholar @ c4d0d6a
bioscholarSystem @ 6364277
bmkeg-as-parent @ c008f9a
bmkeg-parent @ de90310
digitalLibraryClientApp @ 8f1593e
digitalLibraryClientComponents @ 6a84e31
digitalLibraryDao @ babdcb1
kefedClientApp @ a508a5a
kefedClientComponents @ 65de833
kefedDao @ d5d1d04
kefedDataEditorApp @ 7efaed1
kefedModelEditorApp @ 2edabf8
lapdftext @ cc523a2
lapdftextClientApp @ b01b673
lapdftextClientComponents @ 588fb06
lapdftextVpdmf @ a85d24d
ooevvDao @ 1953888
vpdmf-bioscholar @ c65a6b2
vpdmf-digitalLibrary @ 1d46f28
vpdmf-ftd @ d1e2351
vpdmf-kefed @ 921e9f4
vpdmf-ooevv @ c04166f
vpdmf-parent @ da01a7a
vpdmf-people @ a5c26e9
vpdmf-terminology @ 3f83ec3

BioScholar System

The 'BioScholar' system was first described in our BMC Bioinformatics paper (Russ et al. 2011) as the first full implementation of a KEfED model. ('KEfED' stands for 'Knowledge Engineering from Experimental Design' and is our approach to represent experimental observations with little or no additional domain-specific interpretation). BioScholar itself, is intended to be an experimental knowledge management system curated from the scientific literature and specifically targeted to support early-stage biomedical researchers (graduate students and postdocs) in facing the very first research challenge that they face: making sense of the very large amount of existing knowledge in the literature.

Installing the BioScholar System source code.

This is a slightly involved process, since there are several dependencies that need to be installed in order using Maven.


For execution only

  • Maven (version 3+)
  • Git (naturally)
  • MySQL version 5+
  • Java 7
  • Flex 4.5.1

Installing the project

Note that in the current installation process we skip unit tests. This is less than ideal but reflects the 'alpha' nature of the current development version. Note that this process may take a long time.

1. git clone --recursive
2. cd bioscholarProject
3. mvn -DskipTests clean install

IMPORTANT Due to licensing restrictions of a subcomponent library, this build will currently fail with the kefedClientComponent submodule. We are working to switch out the offending library as a priority and will present a fully open source version as soon as possible.

Running the project

1. cd bioscholar
3. mvn jetty:start