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© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop EXPERIBASE C. Forbes Dewey, Jr. Massachusetts Institute of Technology
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Intelligent data repositories Intelligent query and optimization Find key facts in the forest Have knowledge available in real time Biological pathways and models Bedside application of information What’s exciting in biomedical information technology?
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop The biomedical information platform Clinical Complexity Computational Complexity Biological Complexity Systems Complexity
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Systems Knowledge Pathways & Models Data Normalization Experimental Curated & Derived Clinical Applied Use Cases Drug Trials Standards Interoperability Data Integrity Curation Platform Knowledge Representation Interface Semantic Web Access & Query Creation & Sharing The biomedical information platform
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Archival data storage and retrieval (e.g. FDA) Collaboration between different biological experiments Multiple data types: images, microarrays, mass spec, FACS Facilitate analysis using existing paradigms Create new paradigms that can provide unique information and lead to unique discoveries Intelligent Biological Archives... Why do we need them???
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Don’t reinvent the wheel What similar problems have people faced in other fields? What existing technologies are consistent with the target environment? DICOM
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Object model of DICOM standard Image Overlay Curve... Patient Study Series Study Series
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop ExperiBase Based on ontology standards Conceptual consistency between different experimental methods Reuse of concepts between different experimental methods Portable platform independent of OS “DICOM for Biology” “Good” DICOM
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop “Stove-piped” data objects
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Normalized data object model
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop ExperiBase object model Single experiment
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Gel Electrophoresis Western Blot 1D Gel (Converted from HUPo) 2D Gel Flow Cytometry / FACS Microarray Experiments Mass Spectrometry Microscope Images Current support by ExperiBase CompleteIn progressPreliminary
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Fluorescence Activated Cell Sorter (FACS) (Flow cytometry) Quantitative, multiple parameter analysis of large numbers of individual cells Cell surface markers Intracellular proteins Ca++ mobilization 12 colors and 15 parameters Sorting: 60,000 cell/second Ref.: Jianmin Chen, MIT, 2005
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Classes of information for FACS experiments Sample information Source Description Instrument description Manufacturer & model Settings – time, gel, voltage, etc. Preconditioning Sample process methods Process materials Process duration Raw image data Post-processing protocols Derived data from image
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop CytometryML --Robert C. Leif, Suzanne B. Leif, etc, XML_Med, a Division of Newport Instruments
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop FACS IOD Ref: Leif, Leif, and Leif, Cytometry 54A (2003)
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop FACS IOD (Expanded Portion)
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop FACS IOD (Expanded Portion)
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop CREATE TYPE detector_desc_t UNDER detector_info_t AS (detector varchar(64), detector_setting real, detector_unit_pref REF(unit_prefix_t), detector_unit REF(unit_t), measurement varchar(64)) MODE DB2SQL; CREATE TYPE beam_splitter_t UNDER detector_info_t AS (beam_splitter varchar(64), low_cut_off_1 real, high_cut_off_1 real, low_cut_off_2 real, high_cut_off_2 real, low_cut_off_3 real, high_cut_off_3 real, unit_prefix REF(unit_prefix_t), unit REF(unit_t), description varchar(64), item_info REF(item_info_t)) MODE DB2SQL; PMT 600 Flourescence Dichroic_Reflect_Low DRLP Omega Optical XF2010 Band_Block unknown AF45 Omega Optical XF3084 Object-Relational Database Schema XML Schema PMT 600 Flourescence Dichroic_Reflect_Low DRLP Omega Optical XF2010 Band_Block unknown AF45 Omega Optical XF3084 XML Document
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Next Step – Addressing Reality Complex experiments Sample complexity Experimental complexity Multiple analysis methods Revisit original data many times Derived data may exceed original data Derived data may not be exposed Archival issues Search over large data collections Data integrity and consistency Local modifications
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop XML Object Model OWL Ontology XML is hierarchical XML has limited definitions XML has loose structure XML is not easily modified OWL uses triples OWL has many types of relationships OWL has a formal structure definition OWL files can be combined and separated easily
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Owl Structure Classes Properties Types Meta-Data
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Protégé
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop What’s Next? LSID and Unit integration Showing the ability to merge and compare databases Creating a correct SQL translation mechanism Creating a web site for people to visit the progress of the ontology Seeking consensus
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Merging Different Versions Barry Smith: ” “Could you tell me how the capabilities of RDF would enable the exchange of data between two ontologies in a single repository, where the ontologies use different namespaces?”
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop SQL Integration
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop A classic use case arising from clinical trials Successive images in time of plaques caused by multiple sclerosis. Surgical Planning Laboratory, Brigham and Women’s Hospital, Boston
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Medicine is an information science and a healing art Our objective is to create information systems that serve the development of biology and medicine. In the end, we want to make this information available in the treatment of human disease and the enhancement of life. ExperiBase r d z m p e u k b s q w a j g x h
© © cfdewey 2006 EXPERIBASE at the NCBO Image Ontology Workshop Thanks to... Richard Kitney Peter Hunter Judith Blake Mark Wilkinson Paul Matsudaira NIH My lab collaborators Ngon DaoPat McCormick Shixin ZhangEric Osborn Alex RabodzeyKurt Stihl Yu YaoKaori Hagihara Shiva AyyaduraiHoward Chou Jim McGrathCatherine Howell Jia Har NCBO: Mark Musen Daniel Rubin (Barry Smith) (Michael Ashburner)
© © cfdewey 2004 A Unique Opportunity in Biological Information Standards C. Forbes Dewey, Jr. Massachusetts Institute of Technology ExperiBase.
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