PGRN Ontology Network Resource

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22 Οκτ 2013 (πριν από 3 χρόνια και 5 μήνες)

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Consistent

and

standardized

common

model

to

support

large
-
scale

vocabulary

use

and

adoption




Robust, scalable, and common API to reduce
variation in clinical description attributable to
interface dependencies




HL7 ANSI and ISO Standard


















Collection of programmable interfaces to access
controlled terminologies and ontologies




Supports deferred query resolution, payload
optimization, defining and querying value sets




Provides HL7 CTS 2 interface (future)

PGRN Ontology Network Resource


Jyotishman Pathak, PhD Robert R. Freimuth, PhD Christopher G. Chute, MD, DrPH

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN

Email: chute@mayo.edu

Background and Aims



Data sharing requires transformation of clinical
data into comparable consistent formats




In practice, clinical data and provider
information is unstructured and non
-
standard




Overall Aim: Develop an open
-
source,
dynamically configurable services framework for
standards
-
conforming, comparable, and
consistent phenotypic data representation




Specific Aims:



Adapt LexEVS as terminology/ontology
infrastructure for PGRN



Establish globally available resource for
biomedical ontologies and value sets
relevant to PGRN



Develop infrastructure for phenotype
representation referencing LexEVS



Act as intermediary between PGRN
investigators and standards bodies






Ontologies provide a formal specification of
how to represent objects, concepts, and
relationships among them




Ontologies can be used for:



Naming “things” (annotation)



Modeling a domain of interest



Computational reasoning over data



Driving Natural Language Processing



Semantic information integration




Ontologies in the biomedical domain:



Genotype: Gene Ontology



Diseases/Findings: SNOMED
-
CT, ICD



Laboratory Measurements: LOINC



Drugs: RxNorm, NDF
-
RT



Domain
-
Specific: NCI Thesaurus, RadLex




Multiple representations available:



Open Biomedical Ontologies (OBO)



Web Ontology Language (OWL)



Rich Release Format (RRF)


Clinical Data Normalization

Personnel

Value Sets Creation and Querying

Enterprise Vocabulary Services (EVS)

LexEVS Infrastructure

Standardized Phenotype Representation

Biomedical Ontologies



Value Set Definition

with in the LexGrid logical model defines
the contents of Value Set




Possible forms of Value Set Definitions



Containing just the reference to Code System



Containing just the reference to other Value Set



Includes all the concept codes defined in the referencing
Value Set Definition



Reference to Code System plus concept codes, optionally
with relationship plus additional rules



Includes concept codes from the referencing code system
that satisfies the rule set defined in the definition



Combinations




Value Set services provided by EVS



Load, Create, Remove, Modify



List all the Value Set Definitions loaded in the system



Dynamically resolve Value Set Definition



Check if one Value Set is sub set of other Value Set



Check if a concept code is part of given Value Set






Value Set Definition
: Find the SNOMED
-
CT term GLIOMA
and its immediate children, remove the root node




Value Set Demo Example



Study PhenX templates on consensus measures for
phenotypes and environmental exposures




Investigate HL7 and ISO templates and archetypes for
disease or observation description




Apply natural language processing techniques where
applicable for phenotype extraction and representation



Christopher G. Chute

Robert R. Freimuth

Jyotishman Pathak

Lexical Grid Project (LexGrid)