BIRN Knowledge Engineering Working Group Chair: Gully APC Burns
Jan 20, 2016
BIRN Knowledge Engineering Working
Group
Chair: Gully APC Burns
Core Capabilities
• Knowledge Representation and Reasoning Services within BIRN specifically geared towards applications
• Development of a knowledge engineering application development framework
• Support for ontology development within BIRN (but collaboration rather than competition with existing ontology tech. groups)
• Text mining tools and applications
Constituencies
• Users– Scientific Consortia +
Communities(BIRN testbeds, NRPCs, CVRG, AlzForum, etc.)
– Publishers(Elsevier, etc.)
– Professional Societies(Society for Neuroscience, etc.)
– Govt. Funding Agencies(NIH, NSF, etc.)
– Disease Foundations(M. J. Fox Foundation, Kinetics Foundation, etc.)
• Partners– Ontology infrastructure
developers(NIF, NCBO, GO, ScienceCommonns, OBI, SNOMED, IUPHAR, etc.)
– Biocurators(Model Organism Databases, MGI, UniProt, etc.)
– BioNLP specialists and developers(BioCREATIVE group, Andrey Rhzetsky, Larry Hunter, etc.)
– Companies...(Chalklabs, etc)
We are closely aligned with the Data Integration Working Group
Required Knowledge Engineering Elements
Knowledge Engineering from Experimental Design (KE-f-ED)
“Novel neurotrophic factor CDNF protects midbrain dopamine neurons in vivo”
Lindholm, P. et al. (2007), Nature, 448(7149): p. 73-7
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Data and Relations underlying the statement: “CDNF protects nigral dopaminergic neurons in vivo”
derived from Figure 3 of derived from Lindholm, P. et al. (2007), Nature, 448(7149): p. 73-7
labeling-density [CDNF (10ug)][4 weeks][cells] = 96 ± 3 % lesion vs. intact side
labeling-density [CDNF (10ug)][4 weeks][fibers] = 74 ± 3 % lesion vs. intact side
behavior-count [vehicle][4 weeks] >[CDNF (10ug)][4 weeks]
Topic Mapping CRISP datahttp://www.nihmaps.org/
Ned Talley, Program Director for Channels, Synapses and Circuits at NINDS.
Much interest across all institutes of NIH.
Team + Collaborators
Existing BIRNCC Team– Jose Luis Ambite (ISI) – Naveen Ashish (UCI)– Gully Burns (ISI)– Hans Chalupsky (ISI)– Ed Hovy (UCI)– Tommy Ingulfsen (ISI)– Craig Knoblock (ISI) – Thomas Russ (ISI)– Jessica Turner (UCI)
Invited to participate– Seth Ruffins (UCLA)– Alan Ruttenberg
(ScienceCommons)
Would like to invite...Lots of people!!!You???