# Presentation: 531058

- Margaret Haber, RN, OCN** **
- Frank Hartel, PhD
** **Enterprise Vocabulary Services
- National Cancer Institute

**NCI **
**Enterprise Vocabulary Services (EVS) **
**and Semantic Integration at NCI**** **

## NCI EVS Goal – Integration by Meaning

-  **Clinical, translational, and basic research terminology have overlapping but specialized needs, therefore EVS assists to:**
- Integrate different conceptual frameworks
- Create terminological and taxonomic conventions across systems
-  **Vocabulary Products**
- NCI Thesaurus – an ontology-like terminology
- NCI Metathesaurus – maps vocabularies
- External vocabularies maintained and served: MedDRA, HL7, NDF-RT, LOINC, etc.

## In caBIG, NCI EVS Goal

-  **Support vCDE efforts to deploy clinical, translational, and basic research terminology**
- That supports each frame of reference
- Assure that widely used terminological and taxonomic conventions are followed
-  **Support Workspace terminology needs**
- Help find and use relevant existing terminology
- Incorporate needed terminology in EVS
- Provide liaison between NCI and caBIG Workspaces
- Example: Lara Fournier and Lakshmi Grama regarding CT study type in CTMS, CDISC, CTGOV and PDQ

## caCORE SDK – An EVS-enabled Semantic Tool in caBIG

**caCORE SDK – An EVS-enabled Semantic Tool in caBIG**

## NCI Thesaurus (NCIt)

**Reference Terminology for NCI, Partners**
**A Federal Standard Terminology**
**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**

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

## NCI Thesaurus (2)

**Published Monthly**
**Public domain, open content license**
**Available on-line and by download ****(OWL, Ontylog XML, flat files)**
**48,000+ “Concepts” hierarchically organized**
**Description-logic based**
** “****Roles” establish machine readable semantic relationships between Concepts, ex.:**
** *****“******Carcinoma” Clinically_associated_with “Lytic Bone Lesions,” ***
***“******TP53” Gene_associated_with_Disease “Breast Carcinoma****”*

**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)

## NCI Thesaurus is Deployed:

**NCI Thesaurus is Deployed**:
- _http://nciterms.nci.nih.gov_
- _http://www.nci.nih.gov/EVS_
-  (full documentation)
- API: caCORE public access
- Fulfills NCI and collaborators’ needs for controlled vocabulary
- Public domain, open content license

## Example Concept Details 

- 				**Concept Details**
**URI: ****	****  ****	****http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C42887**
**Version: ****	****July 2005 (05.07d)**
**	****	****Aerosol Dosage Form**
**Identifiers:**
**  ****	****name ****	****  ****	****  ****	****Aerosol_Dosage_Form**
**  ****	****code ****	****  ****	****  ****	****C42887**
**Information about this concept:**
**  ****	****Synonym with source data ****	****Aerosol Dosage Form|PT|NCI**
**  ****	****Synonym ****	****	****	****AER**
**  ****	****Synonym ****	****	****	****Aerosol**
**  ****	****Synonym with source data ****	****Aerosol Dose Form|SY|NCI**
**  ****	****Synonym ****	****	****	****Aerosol Dosage Form**
**  ****	****DEFINITION ****	****	****FDA|A product that is packaged under pressure and contains therapeutically active ****	****	****	****ingredients that are released upon activation of an appropriate valve system; it ****	****	****	****is intended for ****	****topical application to the skin as well as local application into the ****	****	****	****nose (nasal aerosols), mouth (lingual aerosols), or lungs (inhalation aerosols).**
**  ****	****FDA_Table ****	****	****Dosage Form (C-DRG-00201)**
**  ****	****Synonym with source data ****	****Aerosol****|PT|FDA|246**
**  ****	****Preferred_Name ****	****	****Aerosol Dosage Form**
**  ****	****Synonym with source data ****	****AER|AB|FDA|246**
**  ****	****Semantic_Type ****	****	****Manufactured Object**
**  ****	****Synonym ****	****	****	****Aerosol Dose Form**
**Superconcepts:**
**	****Gas Dosage Form**
**	****Topical Dosage Form**
**Subconcepts:**
**	****Aerosol Foam Dosage Form**
**	****Aerosol Spray Dosage Form**
**	****Metered Aerosol Dosage Form**
**	****Powder Aerosol Dosage Form**

- This indicates the concept is an FDA concept used in the SPL

- This indicates the FDA table in which the concept occurs

## NCI Metathesaurus:

**Filtered UMLS Metathesaurus extended with additional required vocabularies**
**930,000+ concepts, 2,200,000 terms and phrases with definitions**
**Mappings among over 50 vocabularies**
**Extensive synonymy: Over 40,000 terms for neoplasms mapped to 7,000 concepts**
**Used as online dictionary and thesaurus, for mapping and document indexing**

**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	

## NCI Metathesaurus (2)

- Minor releases monthly, Major releases twice a year
-  Provides a mapped overlap and partial inter-relation of current versions of NCI and partner required vocabularies, ex. The ICD’s, MedDRA, SNOMED, MeSH (NLM Medical Subject Headings), HCPCS (procedures), LOINC (lab values), drug terminologies (VA NDF-RT, AOD, RxNORM, Multum, NCI Thesaurus drugs, etc.)

## FDA (Terminology for Drugs, Devices, and Clinical Trial Terminology Initiatives)
VA (Drugs, Common Clinical Trials Semantics, Terminology Operations)
CDC (Cancer Incidence and Prevention, Terminology Operations)
Cancer Centers (Clinical Trials, Experimental Organism Terminology, Micro- nutrients, Open Terminology Servers, other (caBIG))
CDISC/HL7 RCRIM (Clinical Research Data Standards)

- FDA (Terminology for Drugs, Devices, and Clinical Trial Terminology Initiatives)
- VA (Drugs, Common Clinical Trials Semantics, Terminology Operations)
- CDC (Cancer Incidence and Prevention, Terminology Operations)
- Cancer Centers (Clinical Trials, Experimental Organism Terminology, Micro- nutrients, Open Terminology Servers, other (caBIG))
- CDISC/HL7 RCRIM (Clinical Research Data Standards)

## NCI EVS will maintain and provide access to FDA SPL Terminology
NCI Thesaurus will be the namespace used
Access Via 
Download at ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
Public, open API http://ncicb.nci.nih.gov/core/caBIO)
Web Servlet at http://nciterms.nci.nih.gov

- NCI EVS will maintain and provide access to FDA SPL Terminology
- NCI Thesaurus will be the namespace used
- Access Via
- Download at _[ftp://ftp1.nci.nih.gov/pub/cacore/EVS/](ftp://ftp1.nci.nih.gov/pub/cacore/EVS/)_
- Public, open API http://ncicb.nci.nih.gov/core/caBIO)
- Web Servlet at http://nciterms.nci.nih.gov

## CDISC terminology group has established an independent working environment at NCI for the specification and development of broad based clinical trials standard terminology, based on CDISC models (SDTM)
CDISC is using the NCI Data Standards Repository (caDSR metadata repository), and controlled terminology from NCI EVS, including but not limited to NCI Thesaurus resources for novel terminology development
These open CDISC standards, developed in collaboration with FDA, NIH, HL7 and others, can provide the basis for a controlled terminology set to be broadly adopted as standard in the clinical trials community

- CDISC terminology group has established an independent working environment at NCI for the specification and development of broad based clinical trials standard terminology, based on CDISC models (SDTM)
- CDISC is using the NCI Data Standards Repository (caDSR metadata repository), and controlled terminology from NCI EVS, including but not limited to NCI Thesaurus resources for novel terminology development
- These open CDISC standards, developed in collaboration with FDA, NIH, HL7 and others, can provide the basis for a controlled terminology set to be broadly adopted as standard in the clinical trials community

## The opportunity to develop shared models, metadata standards, and core semantics drawn from standard terminology, such as NCIt and other EVS hosted vocabularies, in order to:
Ensure the validity of cross study data comparison and analysis
Improve the efficiency, evaluation of safety and efficacy, and time to approval for treatments (increased patient safety and reduced cost)
Improve the links between primary healthcare delivery systems and clinical research and trials

**The opportunity to develop shared models, metadata standards, and core semantics drawn from standard terminology, such as NCIt and other EVS hosted vocabularies, in order to:**
- Ensure the validity of cross study data comparison and analysis
- Improve the efficiency, evaluation of safety and efficacy, and time to approval for treatments (increased patient safety and reduced cost)
- Improve the links between primary healthcare delivery systems and clinical research and trials

## NCI Thesaurus Browser: CDISC tagged concepts

## NCI Thesaurus Browser: concept-“Race”

## Contact:Margaret W. Haber, RN, OCNNCI Office of Communicationsmhaber@mail.nih.govFrank Hartel, PhDNCI Center for Bioinformaticshartel@mail.nih.gov