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???