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

    Author(s)
    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
    Griffith University Author(s)
    Fleming, Jean S.
    Year published
    2007
    Metadata
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    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 ...
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    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.
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    Journal Title
    Gene Expression Patterns
    Volume
    7
    Issue
    6
    Publisher URI
    http://www.elsevier.com/wps/find/journaldescription.cws_home/628039/description#description
    Subject
    Genetics
    Clinical sciences
    Publication URI
    http://hdl.handle.net/10072/15105
    Collection
    • Journal articles

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