Brief introduction to NeuroLex. Stephen D. Larson NeuroML 3 rd Annual Workshop London - 3/31/11
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1 Brief introduction to NeuroLex Stephen D. Larson NeuroML 3 rd Annual Workshop London - 3/31/11
2 Overview Brief introduction to linked data Value of ontologies for neuroscience Neuroscience information framework: Using ontologies to index online neuroscience databases NeuroLex.org: Collaborative online management of neuroscience ontologies
3 Programmatic resources NIF maintains the NIF vocabularies in different forms for different purposes Neurolex Wiki: Lexicon for community review and comment NIFSTD: set of modular OWL files normalized under BFO and available for download NCBO Bioportal for visibility and mapping services
4 BRIEF INTRODUCTION TO LINKED DATA
5 Open Linked Data Graph
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10 Biological Linked Data
11 World Wide Web Consortium s Health Care and Life Sciences Interest Group Working now on a Translational Medicine Ontology & Knowledge Base!!!
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15 What is a "triple"?: 1) subject + 2) relation + 3) object = triple! Rat triple store to GPi from STN STN GPi species Rat
16 VALUE OF ONTOLOGIES FOR NEUROSCIENCE
17 Shared ontologies for neuroscience provide a structured way to organize concepts Cerebellum Granule Cell Is a Cerebellum Stellate Cell Is a Cerebellum Basket Cell Cell Neuroepithelial cell Is a Is a Is a Neuron Is a Is a Is a Cerebellum Lugaro Cell Cerebellum Golgi Cell Cerebellum Purkinje Cell Ontologies provide a formalism for the conceptual bridge between data Goal: represent terminological knowledge in a machine analyzable form o Taxonomy o Relationships o Supports reasoning and inference
18 Value of ontologies for neuroscience We need a parts catalog for the brain Society for Neuroscience Keynote lecture, 2009 Larry Swanson, University of Southern California
19 Confocal image stacks Masako Terada, Eric Bushong, Fred Gage, Mark Ellisman Amira
20 Value of ontologies for neuroscience: structuring data
21 Electron microscopy Eric Bushong, Mark Ellisman Amira
22 Value of ontologies for neuroscience: structuring data
23 Shared building blocks Calbindin Calbindin Cerebellum Purkinje cell axon Has part Cerebellum Purkinje neuron Has part Has part Cerebellum Purkinje cell dendrite Is part of Cerebellum granule cell layer Has part Cerebellar cortex Has part Cerebellum Purkinje cell soma Is part of Cerebellum Purkinje cell layer Is part of Cerebellum molecular layer Has part
24 NEUROSCIENCE INFORMATION FRAMEWORK: USING ONTOLOGIES TO INDEX ONLINE NEUROSCIENCE DATABASES
25 NIF in action (
26 NIF searches across multiple sources of information NIF data federation Independent databases registered with NIF or through web services NIF registry: catalog NIF Web: custom web index (work in progress) NIF literature: neuroscience-centered literature corpus (Textpresso)
27 NEUROLEX.ORG: COLLABORATIVE ONLINE MANAGEMENT OF NEUROSCIENCE ONTOLOGIES
28 An online ontology for neuroscience Built using the same open source software that runs Wikipedia Extra functionality to create ontologies Allows anyone to edit or create new concepts 16,000 concepts NeuroLex.org 800 Visitors, September, 2010 to March, 2011
29 NeuroLex is being found spontanously online
30 Categories linked through explicit relationships
31 Who makes sure the data is reliable? Curators with the NIH-funded Neuroscience Information Framework and volunteers with the International Neuroinformatics Coordinating Facility YOU!!!
32 Flexibility NIF maintains the NIF vocabularies in different forms for different purposes Neurolex Wiki: Lexicon for community review and comment NIFSTD: set of modular OWL files normalized under BFO and available for download NCBO Bioportal for visibility and mapping services
Defined versus Asserted Classes: Working with the OWL Ontologies. NIF Webinar February 9 th 2010
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