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Protégé 3.4 Plug-in for Editing and Maintaining the NCI Thesaurus
Protégé ConferenceJune 23, 2009
AmsterdamSherri de Coronado, Gilberto Fragoso
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NCI Enterprise Vocabulary Services
Goal – Integration by Meaning
• EVS provides services and resources that assists to:– Integrate different conceptual frameworks for clinical, basic and
translational research, – Create terminological and taxonomic conventions across systems
• Controlled Terminology Products– NCI Thesaurus – an ontology-like cancer-centric controlled terminology– NCI Metathesaurus – maps biomedical vocabularies– BiomedGT (Biomedical Grid Terminology - new)– External vocabularies maintained and served: MedDRA, HL7, NDF-RT,
LOINC, GO, Zebrafish, RadLex, etc.
• Further info, see: https://wiki.nci.nih.gov/display/EVS/EVS+Wiki
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Products: NCI Thesaurus
• Reference Terminology for NCI, caBIG, Partners– Underpins caCORE, caGRID semantics
• A Federal Standard Terminology
• Public domain, open content license
• 80,000 “Concepts” hierarchically organized into domains
• Broad coverage of the cancer research and clinical domain including prevention and treatment trials– Neoplastic and other Diseases– Findings and Abnormalities– Anatomy, Tissues, Subcellular Structures– Agents, Drugs, Chemicals – Genes, Gene Products, Biological Processes– Animal Models – Mouse, other– Research techniques and management, apparatus, clinical and lab,
radiology, imagery
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Products: NCI Thesaurus (2)
• Description-logic based
• Concept History
• Published Monthly
• Accessible via API, web browsers, downloadable files
• Transition to OWL begun in ‘03
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Editing Tool Requirements
• Shared Data and Distributed Editing
• Reasoning
• GUI for Subject Matter Experts• search and reporting facilities
• Editing Consistency• basic content – preferred and alternative terms, definition
• Complex Operations• merge, split, retirement • tied to history tracking
• Rule Enforcement, Edit Checks• no duplicate restrictions, semantic type
• Support for Workflow, Editing Roles (manager, editor)
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Client – Server Environment
EditingHistory
Baseline
ExplanationServer
ProtegeServer
Prompt
Manager
Editor
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Edit Checks Configured into SW
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NCIEditTab Layout
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NCIEditTab – basic data
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NCIEditTab – editing definitions and terms
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NCIEditTab – relations subtab
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NCIEditTab – restrictions
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NCIEditTab – class expressions
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NCIEditTab – class expressions, editing
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NCIEditTab – other properties
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NCIEditTab – tree panel in copy, split, and merge
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NCIEditTab – retirement
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NCIEditTab – retirement
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NCIEditTab – reporting
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Lucene Query Tab
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Lucene Query Tab
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Lucene Query Tab
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NCI Workflow Tab
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Classification and Explanation Service
• Maturing the Pellet reasoner - NCIt Classification• Prior to initial work: non-terminating• Improving resource efficiency: 9 hours• Algorithmic optimizations: 5 minutes• Incremental updates: seconds
• Explanation Service• Improve the efficiency of editors by identifying problems and
causes
Modified from M. Smith, Clark&Parsia
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OWL Classes Tab – classification views
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Explanation Tab
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http://gforge.nci.nih.gov/frs/?group_id=174
Download site
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Acknowledgements
EVS Team• NCI staff
– Frank Hartel– Gilberto Fragoso– Sherri de Coronado– Margaret Haber– Larry Wright
• Protégé/ NCI Protégéprogrammers– Stanford BMIR staff– Dionne Associates– Clark & Parsia
• Production and QA staff– Steve Hunter (Ekagra)– M.A. Storey’s group (UVic)– Tracy Safran, Rob Wynne,
John Park