February 26, 2003NCICB Jamboree1 Enhancing Quality of Retrieval Through Concept Edit History -- EVS Update Frank Hartel Sherri De Coronado Gilberto Fragoso Iris Guo Kim Ong

February 26, 2003NCICB Jamboree2 Outline Terminology development -- concept creation, modification, split, merge, retirement Edit history Usage TDE Ontylog editor extension Next steps Summary

February 26, 2003NCICB Jamboree3 Elementary Edit Actions In Terminology Development Version 1 CreateSplit RetireMerge Modify Version 2 CreateSplit RetireMerge Modify Version 3 CreateSplit RetireMerge Modify Version 4 CreateSplit RetireMerge Modify (Create, Modify, Split, Merge, Retire) Evolution of versions/baseline over time

February 26, 2003NCICB Jamboree4 Scientific Reasons for Concept Splits Oncogene ras discovered based on sequence homology (hybridization) to the v-onc gene of the Harvey strain of murine sarcoma virus. Subsequently, it was discovered that there were multiple related ras genes, Ha-ras, and Ki-ras. Later on, a new ras, N-ras, was found.

February 26, 2003NCICB Jamboree5 BCL1 gene discovered in the vicinity of a t(11;14) translocation, involved in the malignant transformation of B cells. PRAD1 gene found in parathyroid adenomas bearing chromosomal abnormalities. CCND1 codes for one of a set of proteins, cyclins, that regulate cell cycle progression. Scientific Reasons for Concept Merges

February 26, 2003NCICB Jamboree6 Concept Based Retrieval D 1 D 2 DocumentIndexing terms Concepts used for retrieval C2C2 C1C1 Search Engine Relevant documents User

February 26, 2003NCICB Jamboree7 Edit History Usage Thesaurus version new retire split merge modify Version 1 Version 2 Version 3 Version 4 Concepts used for retrieval Document are often indexed using different versions of terminology. Re-indexing document to keep in pace with changes made to the terminology is impractical and can be very costly. Edit history can greatly enhance precision and recall. pre-indexed documents Search Engine R1R1 R2R2 R3R3 R4R4 Edit History

February 26, 2003NCICB Jamboree8 Edit History Storage

February 26, 2003NCICB Jamboree9 Terminology Development Environment

February 26, 2003NCICB Jamboree10 Terminology Development Environment Previously, only three types of edit action are logged – add, modify, and delete. Concepts created through split actions are confounded by newly created concepts. Concepts merged into other concepts are indistinguishable from retired concepts. Failure to explicitly track merge and split edit actions may result in a low recall rate in information retrieval. * Recall defines the number of relevant documents retrieved as fraction of all relevant documents.

February 26, 2003NCICB Jamboree11 Approach Taken to Extend TDE Create reusable concept edit tree Java bean Develop user interface for processing split, merge, and retirement edit actions Log edit events in TDE history database with clarity and precision

February 26, 2003NCICB Jamboree12 Extend Ontylog Editor With Plug-Ins Use Concept Edit Tree widget to build plug-ins

February 26, 2003NCICB Jamboree13 TDE Extension - Split Panel Edit action is explicitly logged in the TDE History database as a split event. A concept is created as a result of a split. Roles and properties may be transferred from one concept to another using drag & drop.

February 26, 2003NCICB Jamboree14 TDE Extension - Merge Panel Edit action is explicitly logged in the TDE History database as a merge event. Concept to stayConcept to retire Non-redundant roles and properties are transferred from the retiring concept to the resultant merged concept.

February 26, 2003NCICB Jamboree15 TDE Extension - Preretirement Concept to retire Sub-concepts are re-treed. Role relationships targeted (i.e., pointing) to the retiring concept are either removed or re-targeted. Concept can be retired only if all preconditions are met.

February 26, 2003NCICB Jamboree16 TDE Extension - Retire Panel Edit action is explicitly logged in the TDE History database as a retire event. A non-editable tree shows concept definition information pertinent to the retiring concept.

February 26, 2003NCICB Jamboree17 Next Steps Consolidate edit history logged by individual modelers in terminology development environment (TDE) into concept history data useful to Distributed Terminology System (DTS) users

February 26, 2003NCICB Jamboree18 Next Steps Extend caBIO and DTS Server capability to facilitate high quality information retrieval End User Applications caBIO.jar DTS History API DTS Extension DTS Server XMLRPC Client XMLRPC Server Edit history database EVS Repositories of Indexed Document to be developed )( External Databases Concepts used for retrieval

February 26, 2003NCICB Jamboree19 Summary Tracking explicit edit actions in TDE is absolutely essential to terminology and concept based information retrieval. We have successfully extend TDE Ontylog editor to explicitly track split, merge, and retirement edit events. Concept history data and supporting APIs will soon become available to DTS users and developers through caBIO. caBIO (Cancer Bioinformatics Infrastructure Objects)

February 26, 2003NCICB Jamboree20 EVS Team Frank Hartel Sherri De Coronado Gilberto Fragoso Margaret Haber Larry Wright Jim Oberthaler Northrop Grumman, Inc. Kevric Corporation Aspen Inc. Apelon, Inc. Kim Ong Iris Guo Bob Dione

February 26, 2003NCICB Jamboree21 Contact Dr. Francis W. Hartel Center for Bioinformatics National Cancer Institute 6116 Executive Blvd. Rockville, MD Phone: (301) Fax: (301)