- evs overview - biomedical terminology and ontology resources frank hartel, ph.d. director,...

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- EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

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Page 1: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

- EVS Overview -Biomedical Terminology and

Ontology Resources

Frank Hartel, Ph.D.Director, Enterprise Vocabulary

ServicesNCI Center for Bioinformatics

                                 

Page 2: - 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

Page 3: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

Enterprise Vocabulary ServicesServices 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

Page 4: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

EVS - concludedVocabulary 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

Page 5: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

NCI ThesaurusReference Terminology for NCIPublic domain, open content licenseBroad coverage of cancer domain Neoplastic disease Findings and Abnormalities Anatomy Agents, drugs, chemicals Oncogenes, gene products Cancer models - mouse Research techniques, management

Page 6: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

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

Page 7: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics
Page 8: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

NCI Thesaurus Production Environment

ProductionRelease

ExternalTesting

NCI ThesaurusTest DTSServers

NCI ThesaurusEditing Environment

NCI ThesaurusWorkflow

Conflict Detectionand Resolution

Work ListGeneration

Classification

HxValidation

Hx

Baseline

Schema

Schema

Schema

Individual Editors’ TDE Workflow Client Editing Application DB Schema - Current NCI Baseline - Local History

Lead Editor TDE Work Manager Client Editing Application Conflict Detection/Resolution DB Schema - Master NCI Baseline - Master History

ChangeSet

WorkAssignment

CandidateRelease

Hx

NCI ThesaurusProduction

DTS Servers

Hx

Release

Page 9: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

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

NCI DTSServer

NCI DTSServlet, Tomcat

MGEDOntology

...RDF: to

NCIcontent

Microarray MAGECoding

URI

caBIOEVS Object

XML/RPCAPI

Run-timeaccess to

NCI Concepts

caBIO-basedEnvironments

Page 10: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

MAGE Ontology points to NCI Thesaurus

Page 11: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

Future: Protégé/OWL ?

Page 12: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

NCI MetathesaurusUMLS Metathesaurus extended with cancer-oriented vocabularies 800,000+ concepts, 2,000,000+ 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

Page 13: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics
Page 14: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

Publication CycleNCI 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+

Page 15: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

EVS TeamEVS

NCI OC – oncology, pathology, pharmacy Margaret HaberLarry Wright

NCI CB – biology, operationsSherri CoronadoGilberto FragosoFrank Hartel

Apelon, Inc. Northup Grumman, Inc.Aspen, Inc. Kevric CorporationJim Oberthaler Consulting

Page 16: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

Structure of History Tables

Column Name Description

History_ID Record Number

Concept_Code Concept Code

Concept_ Name Preferred Name of Concept

Action Edit Action

Reference_Code Referenced Concept Code

Edit_Date Timestamp

Edit_Name Name of edited NCI Thesaurus™ schema

Host IP address of editor's workstation

Published Publication state of history entry

TDE

Column Name Description

History_ID Record Number

Concept_Code Concept Code

Action Edit Action

Baseline_Date Date of NCI Thesaurus™ Baseline

Reference_Code Referenced Concept Code

DTS

TOC

Page 17: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

DTS-RPCClient

DTS-RPCServer

DTSServer

DTSDatabase

XMLRPC DTS API

(Apelon)

caBIOAPI

Server API extensions (DTSRPC)

NCIExtensions

UserApplication

Page 18: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

NCICB builds on EVS and caCORE Infrastructure

caCOREcaBIO API

EVS Package EVS ProductionServers

Thesaurus

Release

Metathesaurus

caBIO

caBIOservers

caBIORepository

NCICB Portals caImage CGAP caMOD MycaBIO

Hx

ReleaseXML/RPC

RMI

EVS-dependentApplication

s

Other caBIOPackages

caDSR

caDSRserver

caDSRRepository

caBIO APIEVS PAckage

Page 19: - EVS Overview - Biomedical Terminology and Ontology Resources Frank Hartel, Ph.D. Director, Enterprise Vocabulary Services NCI Center for Bioinformatics

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>…