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BIRN Knowledge Engineering Working Group

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

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BIRN Knowledge Engineering Working Group

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  1. BIRN Knowledge Engineering Working Group Chair: Gully APC Burns

  2. 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

  3. 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) Constituencies

  4. We are closely aligned with the Data Integration Working Group

  5. Required Knowledge Engineering Elements

  6. Knowledge Engineering from Experimental Design (KE-f-ED)

  7. “Novel neurotrophic factor CDNF protects midbrain dopamine neurons in vivo” * * * Lindholm, P. et al. (2007), Nature, 448(7149): p. 73-7

  8. Data and Relations underlying the statement: “CDNF protects nigral dopaminergic neurons in vivo” labeling-density [CDNF (10ug)][4 weeks][cells] = 96 ± 3 % lesion vs. intact side behavior-count [vehicle][4 weeks] > [CDNF (10ug)][4 weeks] labeling-density [CDNF (10ug)][4 weeks][fibers] = 74 ± 3 % lesion vs. intact side derived from Figure 3 of derived from Lindholm, P. et al. (2007), Nature, 448(7149): p. 73-7

  9. 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.

  10. 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??? Team + Collaborators

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