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

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Title A high-resolution anatomical ontology of the developing murine genitourinary tract
Author Little, Melissa H.; Brennan, Jane; Georgas, Kylie; Davies, Jamie A.; Davidson, Duncan R.; Baldock, Richard A.; Beverdam, Annemiek; Bertram, John F.; Capel, Blanch; Chiu, Han Sheng; Clements, Dave; Cullen-McEwen, Luise; Fleming, Jean S.; 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
Journal Name Gene Expression Patterns
Editor S. Aizawa, M. Leptin, N. Papalopulu, D. Stainier, C.D. Stern, P. Tam
Year Published 2007
Place of publication Netherlands
Publisher Elsevier BV
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) 1727 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.
Peer Reviewed Yes
Published Yes
Publisher URI http://www.elsevier.com/wps/find/journaldescription.cws_home/628039/description#description
Copyright Statement Copyright 2007 Elsevier. Please refer to the journal's website for access to the definitive, published version.
Volume 7
Issue Number 6
Page from 680
Page to 699
ISSN 1567-133X
Date Accessioned 2007-06-21
Language en_AU
Faculty Faculty of Science, Environment, Engineering and Technology
Subject Animal Anatomy and Histology
URI http://hdl.handle.net/10072/15105
Publication Type Journal Articles (Refereed Article)
Publication Type Code c1

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