A high-resolution anatomical ontology of the developing murine genitourinary tract

Little, Melissa H., Brennan, Jane, Georgas, Kylie, Davies, Jamie A., Davidson, Duncan R., Baldock, Richard A., Beverdam, Annemiek, Bertram, John F., Capel, Blanche, Chiu, Han Sheng, Clements, Dave, Cullen-McEwen, Luise, Fleming, Jean, Gilbert, Thierry, Herzlinger, Doris, Houghton, Derek, Kaufman, Matt H., Kleymenova, Elena, Koopman, Peter A., Lewis, Alfor G., McMahon, Andrew P., Mendelsohn, Cathy L., Mitchell, Eleanor K., Rumballe, Bree A., Sweeney, Derina E., Valerius, M. Todd, Yamada, Gen, Yang, Yiya and Yu, Jing (2007) A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expression Patterns, 7 6: 680-699. doi:10.1016/j.modgep.2007.03.002

Author Little, Melissa H.
Brennan, Jane
Georgas, Kylie
Davies, Jamie A.
Davidson, Duncan R.
Baldock, Richard A.
Beverdam, Annemiek
Bertram, John F.
Capel, Blanche
Chiu, Han Sheng
Clements, Dave
Cullen-McEwen, Luise
Fleming, Jean
Gilbert, Thierry
Herzlinger, Doris
Houghton, Derek
Kaufman, Matt H.
Kleymenova, Elena
Koopman, Peter A.
Lewis, Alfor G.
McMahon, Andrew P.
Mendelsohn, Cathy L.
Mitchell, Eleanor K.
Rumballe, Bree A.
Sweeney, Derina E.
Valerius, M. Todd
Yamada, Gen
Yang, Yiya
Yu, Jing
Title A high-resolution anatomical ontology of the developing murine genitourinary tract
Journal name Gene Expression Patterns   Check publisher's open access policy
ISSN 1567-133X
Publication date 2007-06-01
Sub-type Article (original research)
DOI 10.1016/j.modgep.2007.03.002
Open Access Status DOI
Volume 7
Issue 6
Start page 680
End page 699
Total pages 20
Place of publication Amsterdam
Publisher Elsevier Science
Language eng
Subject 270205 Genetic Development (incl. Sex Determination)
780105 Biological sciences
Abstract Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided. (c) 2007 Elsevier B.V. All rights reserved.
Keyword Developmental Biology
Genetics & Heredity
genitourinary development
Renal development
Kidney development
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID U01 DK092983
R01 DK085242
R01 DK095044
R56 DK078158
R01 DK078158
U01 DK094523
K01 DK083425
R01 ES017099
U54 DK104309
U01 DK070219
U01 DK094479
UO1 DK094479
U01 DK094530
U01 DK070136
U01 DK101038
Institutional Status UQ
Additional Notes Erratum: Gene Expression Patterns Volume 8 Issue 1 pp 47-50

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Created: Tue, 19 Feb 2008, 03:34:52 EST