title: A high-resolution anatomical ontology of the developing murine genitourinary tract.
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.
authors: Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia. M.Little@imb.uq.edu.au
authors: Melissa H
authors: MH
authors: Little
authors: Jane
authors: J
authors: Brennan
authors: Kylie
authors: K
authors: Georgas
authors: Jamie A
authors: JA
authors: Davies
authors: Duncan R
authors: DR
authors: Davidson
authors: Richard A
authors: RA
authors: Baldock
authors: Annemiek
authors: A
authors: Beverdam
authors: John F
authors: JF
authors: Bertram
authors: Blanche
authors: B
authors: Capel
authors: Han Sheng
authors: HS
authors: Chiu
authors: Dave
authors: D
authors: Clements
authors: Luise
authors: L
authors: Cullen-McEwen
authors: Jean
authors: J
authors: Fleming
authors: Thierry
authors: T
authors: Gilbert
authors: Doris
authors: D
authors: Herzlinger
authors: Derek
authors: D
authors: Houghton
authors: Matt H
authors: MH
authors: Kaufman
authors: Elena
authors: E
authors: Kleymenova
authors: Peter A
authors: PA
authors: Koopman
authors: Alfor G
authors: AG
authors: Lewis
authors: Andrew P
authors: AP
authors: McMahon
authors: Cathy L
authors: CL
authors: Mendelsohn
authors: Eleanor K
authors: EK
authors: Mitchell
authors: Bree A
authors: BA
authors: Rumballe
authors: Derina E
authors: DE
authors: Sweeney
authors: M Todd
authors: MT
authors: Valerius
authors: Gen
authors: G
authors: Yamada
authors: Yiya
authors: Y
authors: Yang
authors: Jing
authors: J
authors: Yu
mesh_terms: D000818:Animals; D002987:Clitoris / Q000254:growth & development; D004707:Endoderm / Q000502:physiology; D005260:Female; D018507:Gene Expression Regulation, Developmental; D008297:Male; D008648:Mesoderm / Q000502:physiology; D051379:Mice / Q000196:embryology / Q000235:genetics* / Q000254:growth & development; D009399:Nephrons / Q000196:embryology / Q000254:growth & development; D010413:Penis / Q000254:growth & development; D012611:Scrotum / Q000254:growth & development; D012741:Sexual Maturation; D014566:Urogenital System / Q000033:anatomy & histology / Q000254:growth & development*