# Presentation: 523867

## - EVS Overview -Biomedical Terminology and Ontology Resources

**Frank Hartel, Ph.D.**
**Director, Enterprise Vocabulary Services**
**NCI Center for Bioinformatics**

## EVS Goal – Integration by Meaning

-  Clinical, translational, and basic research have overlapping but specialized needs
- Inconsistent conceptual frameworks
- Terminology and taxonomic conventions
- May conflict
- Evolve at different rates
-  Knowledge model or terminology?
- Reasoning: inference about data
- Tagging data: store/transfer/archive for future analysis

##  Enterprise Vocabulary Services

**Services and resources that address NCI's needs for controlled vocabulary ****http://ncicb.nci.nih.gov/core/EVS **
**An NCI collaboration**
**NCI Office of Communications**
**Cancer Information Products and Systems**
**PDQ and Cancer.gov**
**NCI Center for Bioinformatics**
**caCORE (built on EVS terminology)**
**Community portals**

**Notes:**
OC using EVS and working to integrate EVS terminology into PDQ and cancer.gov. 

##  EVS - concluded

**Vocabulary Products**
**NCI Thesaurus – an ontology-like terminology**
**NCI Metathesaurus – maps vocabularies**
**External vocabularies maintained and served**
**Current Collaborations**
**Federal Collaboration**
**MAGE Ontology**
**Human Anatomy**
**Cancer Classification **
**MMHCC**
**HL7, CHI**

**Notes:**
Quality control, mappings, and collaborations all strengthen the quality and usefulness of the content.  

Includes:
Including Drug :NLM’s RxNORM, VA National Drug File Reference Terminology, FDA and our own ThesaurusRx for drug thesaurus in our space
CDC shared terminology technology, process best practices, etc
VA share NCI extensions to TDE/DTS software
external reviews by CAP,
anatomy review/collaboration, and 
participation in various standards efforts 

## NCI Thesaurus

- Reference Terminology for NCI
- Public domain, open content license
- Broad coverage of cancer domain
**Neoplastic disease**
**Findings and Abnormalities**
**Anatomy**
**Agents, drugs, chemicals **
**Oncogenes, gene products**
**Cancer models - mouse**
**Research techniques, management**

**Notes:**
Neoplastic disease – clinical goes to the 
Molecular – findings and abnormalities

## NCI Thesaurus - concluded

- Description-logic based (AL-)
- 34,000+ “Concepts” hierarchically organized
-  20 hierarchies, 19 “Kinds”
-  “Roles” establish semantic relationships between Concepts
- “Properties” state facts about Concept
- Concept history

**Notes:**
Kind==(disjoint classes)
Terms	    Concepts	Category	
1,691,850  783,158	NCI Metathesaurus	
  100,000	34,000	NCI Thesaurus	
		10,521	Disease, Abnormality, Finding	
		(5,901)	  ...Neoplasm (within Disease)	
		 3,531	Drug	
		 2,773	Chemotherapy Regimens	
		 4,320	Anatomy	
		 1,767	Gene	
		 2,200	Protein (Gene Product)

## Slide 7

## NCI Thesaurus Production Environment

## NCI Thesaurus access 

**MGED Ontology uses DAML+OIL**
**daml+oil allows inclusion of external ontology content via RDF**
**NCI DTS server, servlet enhanced with URI **
**Enables MGED Ontology to specify NCI content via reference**

**Notes:**
Mention:
OWL
Flat File
And other means of access independent of caCORE and caBIO API

## MAGE Ontology points to NCI Thesaurus

## Future: Protégé/OWL ?

## NCI Metathesaurus

**UMLS Metathesaurus extended with cancer-oriented vocabularies**
**780,000+ concepts, 1,700,000 terms and phrases**
**Mappings among over 50 vocabularies**
**Rich synonymy: Over 40,000 terms for “cancer” mapped to 7,000 concepts**
**Used as online dictionary, thesaurus, for mapping and document indexing**
**Accessible via caBIO APIs**

**Notes:**
The current numbers are a little lower than this, 1.6 M, but they will be somewhat higher after our next build (will include CT)

1,691,850  783,158	NCI Metathesaurus	

## Slide 13

## Publication Cycle

- NCI Thesaurus
- Monthly
- History applies to published concepts
- Formats
- Ontylog XML
- OWL
- Flat file

- NCI Metathesaurus
- Minor releases monthly
- Major releases twice a year
- Format
- MR+

## EVS Team

**EVS**
- NCI OC – oncology, pathology, pharmacy
- Margaret Haber
- Larry Wright
- NCI CB – biology, operations
- Sherri Coronado
- Gilberto Fragoso
- Frank Hartel
*Apelon, Inc. **	**	**Northup Grumman, Inc.*
*Aspen, Inc.**	**	**Kevric Corporation*
*Jim Oberthaler Consulting*

## Structure of History Tables

- TDE

- DTS

***TOC***

## Server API extensions (DTSRPC)

- Client

- DTS-RPC
- Server

- DTS
- Server

- DTS
- Database

- XMLRPC

- DTS API
- (Apelon)

- caBIO
- API

***Server API extensions (DTSRPC)***

- NCI
- Extensions

- User
- Application

## NCICB builds on EVS via caCORE Infrastructure 

## Encoding NCI content in MAGE

- Biomaterials
- Cell Type
- Organism_part

**...**
**<!-- The cell type of AD145: Epithelial Cell.  **
** **
**	****The term was obtained from the NCI Thesaurus, has "Somatic Cell" as parent **
**	****concept.  For purpose of example coding only, prefer using MO:CellType.**
**-->**
**     ****<OntologyEntry category="Somatic Cell" value="Epithelial Cell">**
**      ****<OntologyReference_assn>**
**       ****<DatabaseEntry accession="C12578"**
**URI="http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=**
**NCI+Thesaurus&#38;code=C12578">**
**        ****<Database_assnref>**
**         ****<Database_ref identifier="DB:nci_thesaurus" />**
**        ****</Database_assnref>**
**       ****</DatabaseEntry>**
**      ****</OntologyReference_assn>**
**     ****</OntologyEntry>**
**...**

## Slide 20