Semantic Media Wiki Open Terminology Development - Initial Steps - Frank Hartel, Ph.D. Associate Director, Enterprise Vocabulary Services National Cancer.

Slides:



Advertisements
Similar presentations
Introduction The cancerGrid metadata registry (cgMDR) has proved effective as a lightweight, desktop solution, interoperable with caDSR, targeted at the.
Advertisements

1 Open Ontology Repository Planning Meeting for Ontology repositories: approaches, technologies, collaboration Ken Baclawski June 15, 2009.
Upper Ontology Summit Tuesday March 14 The BFO perspective Barry Smith Department of Philosophy, University at Buffalo National Center.
Experiences from the NCBO OBO-to-OWL Mapping Effort Dilvan A. Moreira, University of São Paulo Mark A. Musen, Stanford University.
CVRG Presenter Disclosure Information Tahsin Kurc, PhD Center for Comprehensive Informatics Emory University CardioVascular Research Grid Core Infrastructure.
11 caGrid adoption at the NCRI Informatics Initiative in the UK ONIX use of caGrid technology Edward Zukowski July, 2009.
Consistent and standardized common model to support large-scale vocabulary use and adoption Robust, scalable, and common API to reduce variation in clinical.
Common Terminology Criteria for Adverse Events (CTCAE) v.4: Updating a Cancer Research Standard Ann Setser 1, Ranjana Srivastava 2, Lawrence Wright 1,
IPY and Semantics Siri Jodha S. Khalsa Paul Cooper Peter Pulsifer Paul Overduin Eugeny Vyazilov Heather lane.
LexGrid for cBIO Division of Biomedical Informatics Mayo Clinic Rochester, MN.
© Copyright 2008, Mayo Clinic College of Medicine Mayo Clinic Open Health Tools Application for Membership OHT Board Meeting, Birmingham, UK July 1, 2008.
LexWiki Framework & Use Cases SMW for Distributed Terminology Development Guoqian Jiang, PhD, Robert Freimuth, PhD, Haorld Solbrig Mayo Clinic NCI caBIG.
Who am I Gianluca Correndo PhD student (end of PhD) Work in the group of medical informatics (Paolo Terenziani) PhD thesis on contextualization techniques.
 Goals Unambiguous description of how the investigation was performed Consistent annotation, powerful queries and data integration  Details NOT model.
Information and Business Work
National Cancer Institute U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health NCI Perspective on Informatics and Clinical Decision.
National center for ontological research. Part One: The History of NCOR and ECOR Part Two: How to Establish JCOR: The Japanese Consortium.
Mayo LexWiki: A Prototype of Collaborative Platform for Terminology/Ontology Content Development Guoqian Jiang, Ph.D. Division of Biomedical Informatics,
Measurable Interoperability for Archival Data Lewis J. Frey, PhD
Implementing Metadata Marjorie M K Hlava, President Access Innovations, Inc. Albuquerque, NM
Semantic Web Technologies Lecture # 2 Faculty of Computer Science, IBA.
Development Principles PHIN advances the use of standard vocabularies by working with Standards Development Organizations to ensure that public health.
The Health Ontology Mapper (HOM) Method Clinical & Translational Science Ontology Workshop (NCBO/CTSA) April 24, 2012 Rob Wynden - Chief Scientist, Ketty.
Limning the CTS Ontology Landscape Barry Smith 1.
Mike Conlon Here’s Mike on a conference call from his home. Mike spends a lot of time on conference calls from his home, and from coffee shops in and around.
Cancer Bioinformatics Grid (caBIG) CANS 2006 Chicago, Illinois Shannon Hastings Department of Biomedical Informatics Ohio State University.
Environmental Terminology Research in China HE Keqing, HE Yangfan, WANG Chong State Key Lab. Of Software Engineering
A Case Study of ICD-11 Anatomy Value Set Extraction from SNOMED CT Guoqian Jiang, PhD ©2011 MFMER | slide-1 Division of Biomedical Statistics & Informatics,
CaBIG Semantic Infrastructure 2.0: Supporting TBPT Needs Dave Hau, M.D., M.S. Acting Director, Semantic Infrastructure NCI Center for Biomedical Informatics.
LexEVS Overview Mayo Clinic Rochester, Minnesota June 2009.
Imports, MIREOT Contributors: Carlo Torniai, Melanie Courtot, Chris Mungall, Allen Xiang.
Using the Open Metadata Registry (openMDR) to create Data Sharing Interfaces October 14 th, 2010 David Ervin & Rakesh Dhaval, Center for IT Innovations.
Key Foundational Layers Classification, Vocab, Web Stds –Classification Content Model (Taxonomy) –Web Std Tech Requirements W3C, cloud, online, offline.
H Using the Open Metadata Registry (OpenMDR) to generate semantically annotated grid services Rakesh Dhaval, MS, Calixto Melean,
Briefing: HL7 Working Group Meeting Update for the VCDE Community Dianne M. Reeves Associate Director, Biomedical Data Standards NCI CBIIT VCDE Meeting.
Clinical Data Interchange Standards Consortium (CDISC) uses NCIt for its Study Data Tabulation Model (SDTM) and other global data standards for medical.
Open Terminology Portal (TOP) Frank Hartel, Ph.D. Associate Director, Enterprise Vocabulary Services National Cancer Institute, Center for Biomedical Informatics.
A School of Information Science, Federal University of Minas Gerais, Brazil b Medical University of Graz, Austria, c University Medical Center Freiburg,
Alan Ruttenberg PONS R&D Task force Alan Ruttenberg Science Commons.
Food and Agriculture Organization of the UN Library and Documentation Systems Division Margherita Sini July 2005 Managing domain ontologies within the.
10/24/09CK The Open Ontology Repository Initiative: Requirements and Research Challenges Ken Baclawski Todd Schneider.
Use Cases / Requirements Notes from 6/12/2007 Rockville, MD meeting.
LexEVS Semantic Tooling Advancements Kevin Peterson Mayo Clinic Mayo 2009.
SKOS. Ontologies Metadata –Resources marked-up with descriptions of their content. No good unless everyone speaks the same language; Terminologies –Provide.
Pediatric Terminology Harmonization Initiative Introduction October2014 National Cancer Institute EVS.
This material was developed by Duke University, funded by the Department of Health and Human Services, Office of the National Coordinator for Health Information.
-KHUSHBOO BAGHADIYA.  Introduction  System Description  iCAT in use  Evolution of the system  Evolution of modeling  Evolution of features  Evolution.
- EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics.
Protégé 3.4 Plug-in for Editing and Maintaining the NCI Thesaurus Protégé Conference June 23, 2009 Amsterdam Sherri de Coronado, Gilberto Fragoso.
2007 Mouse All Hands Meeting BIRN Ontology Day Jeff Grethe & Bill Bug (BIRN OTF) - March 7th, 2007.
Big Data that might benefit from ontology technology, but why this usually fails Barry Smith National Center for Ontological Research 1.
EcoInformatics Initiative 04/18/2007 Terminology and the Semantic MediaWikiEcoterm IV – Vienna 17 – 18 April 2007 Terminology Curation with the Semantic.
Sherri de Coronado Enterprise Vocabulary Services NCI Center for Bioinformatics and Information Technology March 11, 2009 A Terminology.
Supporting Collaborative Ontology Development in Protégé International Semantic Web Conference 2008 Tania Tudorache, Natalya F. Noy, Mark A. Musen Stanford.
Semantics and the EPA System of Registries Gail Hodge IIa/ Consultant to the U.S. Environmental Protection Agency 18 April 2007.
LexWiki Framework & Use Cases SMW for Distributed Terminology Development Guoqian Jiang, PhD, Harold Solbrig Mayo Clinic Meeting with Dr. Jakob (WHO) May.
Welcome to the caBIG Community! The cancer Biomedical Informatics Grid (caBIG ® ) offers more than 120 open source tools, technologies and infrastructure.
National Cancer Institute caCORE Software Developers Meeting Agenda and meeting notes July 26, 2007.
National Cancer Institute caDSR Briefing for Small Scale Harmonication Project Denise Warzel Associate Director, Core Infrastructure caCORE Product Line.
WE TRAIN PARTNERS. ZeroWIN Knowledge Community Management Implementation plan for Task 9.3.
Dream of Medical Grid in Korea What can we do for it? Global Grid Forum13 Workshop 13 th Mar 2005 Young-Woo Kim, MD, PhD Center for Gastric Cancer, National.
CPR Ontology: Issues Encountered Using BFO Chimezie Ogbuji.
Cancer Bioinformatics Grid (caBIG) CANS 2006 Chicago, Illinois
The UMLS and the Semantic Web
Agenda Federated Enterprise Architecture Vision
TRSS Terminology Registry Scoping Study
CCNT Lab of Zhejiang University
Stanford Medical Informatics
Networking and Health Information Exchange
OBI – Standard Semantic
Presentation transcript:

Semantic Media Wiki Open Terminology Development - Initial Steps - Frank Hartel, Ph.D. Associate Director, Enterprise Vocabulary Services National Cancer Institute, Center for Biomedical Informatics 10th Open Forum on Metadata Registries July 10, 2007

2 Biomedical Grid Terminology ( BiomedGT© ) BiomedGT© is a project of the National Cancer Institute Initially an effort of the NCI Center for Biomedical Informatics and Information Technology Transition rapidly to biomedical community partnership BiomedGT© features Open content development by biomedical community volunteers Federated ontology structure Infrastructure support by NCI Free, open license Coverage of translational research domain Clear distinction between ontology and thesaurus components

3 Why Open Content Development ? Open content development by members of the community using the terminology has been proven to work, maturing rapidly Gene Ontology (GO) Ontology for Biomedical Investigations (OBI) And many others – see Open Biomedical Ontologies Organization National Center for Biomedical Ontology Advantages Community acceptance, content is relevant to community needs Fast publication cycle Disadvantages Development tools vs representational sophistication Long term viability of purely voluntary efforts

4 Why Federation? Biomedicine is a huge domain Coverage in a single ontology isn’t in the cards Overwhelms tools, editorial and production techniques Slows production cycles, runs up costs (partially due to redundant modeling) Complexity, size overwhelm users Federation should help Ontologies scoped reflect scientific domains Scales better to tools, editorial and production techniques Easier to structure and extent, easier for users to understand More attractive to subject matter experts (SMEs) Many fine ontologies exist: reuse should help control costs Easier to federate (in theory) Federation is an active area of research and development OBO Foundry has one approachOBO Foundry Alan Rector and the Manchester Group has anotherAlan Rector W3C Health Care and Life Sciences Special Interest Group (HCLSIG) is working on another

5 Open Content Development in BiomedGT Semantic Media Wiki and NCI Protégé/OWL Wiki supports biomedical SMEs Easy to learn tool Registration for SMEs who wish to edit View current BiomedGT content (from LexBIG) Make changes that are stored in Wiki database Anonymous read only access for others Protégé used by ontologists Renders SME input as OWL DL 1.1 Protégé Workflow is it the touch point SME input “harvested” from Wiki database Incorporated into work assignments to ontologists Wiki and BiomedGT GForge Project supports SME, ontologist dialogGForge Project Publication via caCORE/LexBIG services NCBO Portal-based NCI Portal supports download & interactive search/displayNCBO Portal-basedNCI Portal

6 Open Collaboration Infrastructure and Process

7 Context of Open Development – NCI Enterprise Vocabulary Services

8 BiomedGT Collaborators and Preparations All biomedical communities will be welcome Initial collaboration is with UK Cancer Grid (Clinical Trials Ontology) Additional early collaborations within the cancer Biomedical Informatics Grid Completion of ongoing development of collaboration infrastructure will precede large scale open development Semantic Media Wiki modifications Protégé Workflow Integration of Wiki database and workflow tool Meanwhile preliminary conversion of NCI Thesaurus data are occurring Provides structural basis for subject matter domains within BiomedGT Provides basis to distinguish ontological (class representing real-world entity/process) from thesaurus classes (class provides browsing/navigation support)

9 Initial Construction of BiomedGT timeline NCIT Seed BiomedGT Beta - upper level ontology - initial binning of NCIT top concepts - initial tagging: thesaurus vs ontology publish to Media Wiki worklists to Protégé Community developmentDL Modeling baselines BiomedGT

10 Reusing Terminology Components – Federation in Protégé 3.x owl:imports of both terminologies into the Protégé editor GO NCIT

11 DL Modeling in BiomedGT with Gene Ontology Terms/Concepts

12 DL Modeling in BiomedGT with Gene Ontology Terms/Concepts

13 Q & A