Connecting ontologies for the representation of biological pathways

Anna Maria Masci, Mikhail Levin, Alan Ruttenberg, Lindsay G. Cowell

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.

Original languageEnglish (US)
Title of host publicationCEUR Workshop Proceedings
Pages387-392
Number of pages6
Volume833
StatePublished - 2011
Event2nd International Conference on Biomedical Ontology, ICBO 2011 - Buffalo, NY, United States
Duration: Jul 26 2011Jul 30 2011

Other

Other2nd International Conference on Biomedical Ontology, ICBO 2011
CountryUnited States
CityBuffalo, NY
Period7/26/117/30/11

Fingerprint

Ontology
Foundries
Signal transduction

Keywords

  • OBO foundry
  • Ontology
  • OWL
  • Semantic web
  • Signal transduction pathway

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Masci, A. M., Levin, M., Ruttenberg, A., & Cowell, L. G. (2011). Connecting ontologies for the representation of biological pathways. In CEUR Workshop Proceedings (Vol. 833, pp. 387-392)

Connecting ontologies for the representation of biological pathways. / Masci, Anna Maria; Levin, Mikhail; Ruttenberg, Alan; Cowell, Lindsay G.

CEUR Workshop Proceedings. Vol. 833 2011. p. 387-392.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Masci, AM, Levin, M, Ruttenberg, A & Cowell, LG 2011, Connecting ontologies for the representation of biological pathways. in CEUR Workshop Proceedings. vol. 833, pp. 387-392, 2nd International Conference on Biomedical Ontology, ICBO 2011, Buffalo, NY, United States, 7/26/11.
Masci AM, Levin M, Ruttenberg A, Cowell LG. Connecting ontologies for the representation of biological pathways. In CEUR Workshop Proceedings. Vol. 833. 2011. p. 387-392
Masci, Anna Maria ; Levin, Mikhail ; Ruttenberg, Alan ; Cowell, Lindsay G. / Connecting ontologies for the representation of biological pathways. CEUR Workshop Proceedings. Vol. 833 2011. pp. 387-392
@inproceedings{cf8ddf25f19c462cb81c59e6b12abdc3,
title = "Connecting ontologies for the representation of biological pathways",
abstract = "Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.",
keywords = "OBO foundry, Ontology, OWL, Semantic web, Signal transduction pathway",
author = "Masci, {Anna Maria} and Mikhail Levin and Alan Ruttenberg and Cowell, {Lindsay G.}",
year = "2011",
language = "English (US)",
volume = "833",
pages = "387--392",
booktitle = "CEUR Workshop Proceedings",

}

TY - GEN

T1 - Connecting ontologies for the representation of biological pathways

AU - Masci, Anna Maria

AU - Levin, Mikhail

AU - Ruttenberg, Alan

AU - Cowell, Lindsay G.

PY - 2011

Y1 - 2011

N2 - Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.

AB - Significant effort has been put into the creation of a multitude of large, publicly available pathway databases. Most make their content available in at least one of several standard representation formats, but there are limitations to existing pathway representation formats, including underutilization of a common set of biomedical ontologies. To address this limitation, we developed an approach to representing biological pathways that relies on the use of ontologies from the Open Biomedical Ontologies (OBO) Foundry, including the Relation Ontology (RO), and adheres to the logical principles of ontology development advocated by the Foundry. To demonstrate the utility of this representation approach, we have curated comprehensive pathway representations for the signal transduction pathways initiated by seven of the mouse Toll-like receptors (TLR). Current efforts include the development of approaches for utilizing these representations for pathway analysis.

KW - OBO foundry

KW - Ontology

KW - OWL

KW - Semantic web

KW - Signal transduction pathway

UR - http://www.scopus.com/inward/record.url?scp=84891919985&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84891919985&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84891919985

VL - 833

SP - 387

EP - 392

BT - CEUR Workshop Proceedings

ER -