LexGrid

A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime

Jyotishman Pathak, Harold Solbrig, James D. Buntrock, Thomas M. Johnson, Christopher Chute

Research output: Contribution to journalArticle

Abstract

Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.

Original languageEnglish (US)
Pages (from-to)305-315
Number of pages11
JournalJournal of the American Medical Informatics Association
Volume16
Issue number3
DOIs
StatePublished - May 2009
Externally publishedYes

Fingerprint

Vocabulary
Terminology
Systematized Nomenclature of Medicine
Current Procedural Terminology
Controlled Vocabulary
Gene Ontology
Informatics
International Classification of Diseases
Penicillins
Language
Delivery of Health Care

ASJC Scopus subject areas

  • Health Informatics

Cite this

LexGrid : A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime. / Pathak, Jyotishman; Solbrig, Harold; Buntrock, James D.; Johnson, Thomas M.; Chute, Christopher.

In: Journal of the American Medical Informatics Association, Vol. 16, No. 3, 05.2009, p. 305-315.

Research output: Contribution to journalArticle

@article{0fa28f5c6f724db09548f7e984c31267,
title = "LexGrid: A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime",
abstract = "Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.",
author = "Jyotishman Pathak and Harold Solbrig and Buntrock, {James D.} and Johnson, {Thomas M.} and Christopher Chute",
year = "2009",
month = "5",
doi = "10.1197/jamia.M3006",
language = "English (US)",
volume = "16",
pages = "305--315",
journal = "Journal of the American Medical Informatics Association : JAMIA",
issn = "1067-5027",
publisher = "Oxford University Press",
number = "3",

}

TY - JOUR

T1 - LexGrid

T2 - A Framework for Representing, Storing, and Querying Biomedical Terminologies from Simple to Sublime

AU - Pathak, Jyotishman

AU - Solbrig, Harold

AU - Buntrock, James D.

AU - Johnson, Thomas M.

AU - Chute, Christopher

PY - 2009/5

Y1 - 2009/5

N2 - Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.

AB - Many biomedical terminologies, classifications, and ontological resources such as the NCI Thesaurus (NCIT), International Classification of Diseases (ICD), Systematized Nomenclature of Medicine (SNOMED), Current Procedural Terminology (CPT), and Gene Ontology (GO) have been developed and used to build a variety of IT applications in biology, biomedicine, and health care settings. However, virtually all these resources involve incompatible formats, are based on different modeling languages, and lack appropriate tooling and programming interfaces (APIs) that hinder their wide-scale adoption and usage in a variety of application contexts. The Lexical Grid (LexGrid) project introduced in this paper is an ongoing community-driven initiative, coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics, designed to bridge this gap using a common terminology model called the LexGrid model. The key aspect of the model is to accommodate multiple vocabulary and ontology distribution formats and support of multiple data stores for federated vocabulary distribution. The model provides a foundation for building consistent and standardized APIs to access multiple vocabularies that support lexical search queries, hierarchy navigation, and a rich set of features such as recursive subsumption (e.g., get all the children of the concept penicillin). Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services.

UR - http://www.scopus.com/inward/record.url?scp=65349189781&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=65349189781&partnerID=8YFLogxK

U2 - 10.1197/jamia.M3006

DO - 10.1197/jamia.M3006

M3 - Article

VL - 16

SP - 305

EP - 315

JO - Journal of the American Medical Informatics Association : JAMIA

JF - Journal of the American Medical Informatics Association : JAMIA

SN - 1067-5027

IS - 3

ER -