KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration

Yongqun He; Becky Steck; Edison Ong; Laura Mariani; Chrysta Lienczewski; Ulysses Balis; Matthias Kretzler; Jonathan Himmelfarb; John F. Bertram; Evren Azeloglu; Ravi Iyengar; Deborah Hoshizaki; Sean D. Mooney

KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration

Yongqun He, Becky Steck, Edison Ong, Laura Mariani, Chrysta Lienczewski, Ulysses Balis, Matthias Kretzler, Jonathan Himmelfarb, John F. Bertram, Evren Azeloglu, Ravi Iyengar, Deborah Hoshizaki, Sean D. Mooney

Anatomy & Developmental Biology

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Research

1 Citation (Scopus)

Abstract

The human kidney has a complex structure and diverse interactions among its cells and cell components, both during homeostasis and in its diseased states. To better understand the kidney, it is critical to systematically classify, represent, and integrate kidney gene activities, cell types, cell states, and interstitial components. Toward this goal, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology. KTAO also generates new semantic axioms to logically link terms of entities in different domains. As a first study, KTAO represents over 200 known kidney gene markers and their profiles in different cell types in kidney patients. Such a representation supports kidney knowledge base generation, query, and data integration.

Original language	English
Title of host publication	Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018)
Editors	Pankaj Jaiswal, Laurel Cooper, Melissa A. Haendel, Christopher J. Mungall
Place of Publication	Aachen, Germany
Publisher	RWTH Aachen University
Number of pages	6
Volume	2285
Publication status	Published - 22 Dec 2018
Event	International Conference on Biological Ontology - Corvallis, United States of America Duration: 7 Aug 2018 → 10 Aug 2018 Conference number: 9th

Publication series

Name	CEUR Workshop Proceedings
Publisher	Rheinisch-Westfaelische Technische Hochschule, Aachen
ISSN (Print)	1613-0073

Conference

Conference	International Conference on Biological Ontology
Abbreviated title	ICBO 2018
Country/Territory	United States of America
City	Corvallis
Period	7/08/18 → 10/08/18

Keywords

AKI
Atlas
CKD
Disease
Gene marker
Kidney
KTAO
Ontology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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http://ceur-ws.org/Vol-2285/

Cite this

He, Y., Steck, B., Ong, E., Mariani, L., Lienczewski, C., Balis, U., Kretzler, M., Himmelfarb, J., Bertram, J. F., Azeloglu, E., Iyengar, R., Hoshizaki, D., & Mooney, S. D. (2018). KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration. In P. Jaiswal, L. Cooper, M. A. Haendel, & C. J. Mungall (Eds.), Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018) (Vol. 2285). (CEUR Workshop Proceedings). RWTH Aachen University. http://ceur-ws.org/Vol-2285/

He, Yongqun ; Steck, Becky ; Ong, Edison et al. / KTAO : A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration. Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018). editor / Pankaj Jaiswal ; Laurel Cooper ; Melissa A. Haendel ; Christopher J. Mungall. Vol. 2285 Aachen, Germany : RWTH Aachen University, 2018. (CEUR Workshop Proceedings).

@inproceedings{bc72f35e03cb432fac95bfee32d73ce3,

title = "KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration",

abstract = "The human kidney has a complex structure and diverse interactions among its cells and cell components, both during homeostasis and in its diseased states. To better understand the kidney, it is critical to systematically classify, represent, and integrate kidney gene activities, cell types, cell states, and interstitial components. Toward this goal, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology. KTAO also generates new semantic axioms to logically link terms of entities in different domains. As a first study, KTAO represents over 200 known kidney gene markers and their profiles in different cell types in kidney patients. Such a representation supports kidney knowledge base generation, query, and data integration.",

keywords = "AKI, Atlas, CKD, Disease, Gene marker, Kidney, KTAO, Ontology",

author = "Yongqun He and Becky Steck and Edison Ong and Laura Mariani and Chrysta Lienczewski and Ulysses Balis and Matthias Kretzler and Jonathan Himmelfarb and Bertram, {John F.} and Evren Azeloglu and Ravi Iyengar and Deborah Hoshizaki and Mooney, {Sean D.}",

year = "2018",

month = dec,

day = "22",

language = "English",

volume = "2285",

series = "CEUR Workshop Proceedings",

publisher = "RWTH Aachen University",

editor = "Pankaj Jaiswal and Cooper, {Laurel } and Haendel, {Melissa A.} and Mungall, {Christopher J.}",

booktitle = "Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018)",

note = "International Conference on Biological Ontology, ICBO 2018 ; Conference date: 07-08-2018 Through 10-08-2018",

}

He, Y, Steck, B, Ong, E, Mariani, L, Lienczewski, C, Balis, U, Kretzler, M, Himmelfarb, J, Bertram, JF, Azeloglu, E, Iyengar, R, Hoshizaki, D & Mooney, SD 2018, KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration. in P Jaiswal, L Cooper, MA Haendel & CJ Mungall (eds), Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018). vol. 2285, CEUR Workshop Proceedings, RWTH Aachen University, Aachen, Germany, International Conference on Biological Ontology, Corvallis, Oregon, United States of America, 7/08/18. <http://ceur-ws.org/Vol-2285/>

KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration. / He, Yongqun; Steck, Becky; Ong, Edison et al.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018). ed. / Pankaj Jaiswal; Laurel Cooper; Melissa A. Haendel; Christopher J. Mungall. Vol. 2285 Aachen, Germany: RWTH Aachen University, 2018. (CEUR Workshop Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference Paper › Research

TY - GEN

T1 - KTAO

T2 - International Conference on Biological Ontology

AU - He, Yongqun

AU - Steck, Becky

AU - Ong, Edison

AU - Mariani, Laura

AU - Lienczewski, Chrysta

AU - Balis, Ulysses

AU - Kretzler, Matthias

AU - Himmelfarb, Jonathan

AU - Bertram, John F.

AU - Azeloglu, Evren

AU - Iyengar, Ravi

AU - Hoshizaki, Deborah

AU - Mooney, Sean D.

N1 - Conference code: 9th

PY - 2018/12/22

Y1 - 2018/12/22

N2 - The human kidney has a complex structure and diverse interactions among its cells and cell components, both during homeostasis and in its diseased states. To better understand the kidney, it is critical to systematically classify, represent, and integrate kidney gene activities, cell types, cell states, and interstitial components. Toward this goal, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology. KTAO also generates new semantic axioms to logically link terms of entities in different domains. As a first study, KTAO represents over 200 known kidney gene markers and their profiles in different cell types in kidney patients. Such a representation supports kidney knowledge base generation, query, and data integration.

AB - The human kidney has a complex structure and diverse interactions among its cells and cell components, both during homeostasis and in its diseased states. To better understand the kidney, it is critical to systematically classify, represent, and integrate kidney gene activities, cell types, cell states, and interstitial components. Toward this goal, we developed a Kidney Tissue Atlas Ontology (KTAO). KTAO reuses and aligns with existing ontologies such as the Cell Ontology, UBERON, and Human Phenotype Ontology. KTAO also generates new semantic axioms to logically link terms of entities in different domains. As a first study, KTAO represents over 200 known kidney gene markers and their profiles in different cell types in kidney patients. Such a representation supports kidney knowledge base generation, query, and data integration.

KW - AKI

KW - Atlas

KW - CKD

KW - Disease

KW - Gene marker

KW - Kidney

KW - KTAO

KW - Ontology

UR - http://www.scopus.com/inward/record.url?scp=85059869285&partnerID=8YFLogxK

M3 - Conference Paper

AN - SCOPUS:85059869285

VL - 2285

T3 - CEUR Workshop Proceedings

BT - Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018)

A2 - Jaiswal, Pankaj

A2 - Cooper, Laurel

A2 - Haendel, Melissa A.

A2 - Mungall, Christopher J.

PB - RWTH Aachen University

CY - Aachen, Germany

Y2 - 7 August 2018 through 10 August 2018

ER -

He Y, Steck B, Ong E, Mariani L, Lienczewski C, Balis U et al. KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration. In Jaiswal P, Cooper L, Haendel MA, Mungall CJ, editors, Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018). Vol. 2285. Aachen, Germany: RWTH Aachen University. 2018. (CEUR Workshop Proceedings).

KTAO: A kidney tissue atlas ontology to support community-based kidney knowledge base development and data integration

Abstract

Publication series

Conference

Keywords

UN SDGs

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