# Presentation: 759434

## Enhancing Quality of Retrieval Through Concept Edit History -- EVS Update

**Enhancing Quality of Retrieval Through Concept Edit History -- EVS Update**

**Frank Hartel**
**Sherri De Coronado**
**Gilberto Fragoso**
**Iris Guo **
**Kim Ong**

- NCICB Jamboree

- February 26, 2003

## Outline

- Terminology development -- concept creation, modification, split, merge, retirement
- Edit history Usage
- TDE Ontylog editor extension
- Next steps
- Summary

- NCICB Jamboree

- February 26, 2003

## Elementary Edit Actions In Terminology Development

***Version 1***

- Create

- Split

- Retire

- Merge

- Modify

***Version 2***

- Create

- Split

- Retire

- Merge

- Modify

***Version 3***

- Create

- Split

- Retire

- Merge

- Modify

***Version 4***

- Create

- Split

- Retire

- Merge

- Modify

- (Create,  Modify,  Split,  Merge,  Retire)

- Evolution of versions/baseline over time

- NCICB Jamboree

- February 26, 2003

## 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.

- NCICB Jamboree

- February 26, 2003

**Notes:**
slide 4 on ras looks at least approximately correct to me.  It looks like H-ras was discovered about 1 year earlier than K-ras (and was called Ha-ras).  They were discovered from different viruses - the Harvey virus, and the Kirsten murine sarcoma viruses. They both code for p21 proteins. I don't see anything where it was just called ras, but I remember from the days in the lab that in the very early 80s there were people working on plain old ras oncogene. 

Yes, the nomenclature from back then is sort of fuzzy, p21 ras, p21 sarc,
I don't remember when exactly it became ras but it was referred to as
c-ras & p21 ras before the distinction between h-ras & k-ras was established.  It 
should raise less concerns if the reference to HUMAN in the slide is eliminated.
Gilberto

## Scientific Reasons for 

- 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***

- NCICB Jamboree

- February 26, 2003

## Concept Based Retrieval

- D1<C1, C2>

- D2<C1, C3,  C4 >

- Document

- Indexing terms

- Concepts used for retrieval

- C2

- C1

- Search
- Engine

- Relevant documents

- User

- NCICB Jamboree

- February 26, 2003

## 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

- R1

- R2

- R3

- R4

- Edit History

- NCICB Jamboree

- February 26, 2003

## Edit History Storage

***Edit History Storage***

- NCICB Jamboree

- February 26, 2003

## Terminology Development Environment

- NCICB Jamboree

- February 26, 2003

## 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.

- NCICB Jamboree

- February 26, 2003

## 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

- NCICB Jamboree

- February 26, 2003

## Extend Ontylog Editor With Plug-Ins

**Use *****Concept Edit Tree***** widget to build plug-ins**

- NCICB Jamboree

- February 26, 2003

## 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.**

- NCICB Jamboree

- February 26, 2003

## TDE Extension - Merge Panel

**Edit action is explicitly logged in the TDE History database as a merge event.**

- Concept to stay

- Concept to retire

**Non-redundant roles and properties are transferred**
**from the retiring concept to the resultant merged **
**concept. **

- NCICB Jamboree

- February 26, 2003

## 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.**

- NCICB Jamboree

- February 26, 2003

## 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.**

- NCICB Jamboree

- February 26, 2003

## 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

- NCICB Jamboree

- February 26, 2003

## 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

- NCICB Jamboree

- February 26, 2003

**Notes:**
About 6 weeks...
Extent ion is a wrapper –
De-granularization
With some new methods – retrieve information in a vector or data structure, and to get old concept info from retired concept list

## 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)

- NCICB Jamboree

- February 26, 2003

## 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

- NCICB Jamboree

- February 26, 2003

## Contact

- Dr. Francis W. Hartel
- Center for Bioinformatics
- National Cancer Institute
- 6116 Executive Blvd.
- Rockville, MD  20892-8335
- Phone: (301) 435-3869
- Fax: (301) 480-4222
- Email: hartel@mail.nih.gov

- NCICB Jamboree

- February 26, 2003