A high-resolution anatomical ontology of the developing murine genitourinary tract.
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.
Little
Melissa H
MH
Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia. M.Little@imb.uq.edu.au
Brennan
Jane
J
Georgas
Kylie
K
Davies
Jamie A
JA
Davidson
Duncan R
DR
Baldock
Richard A
RA
Beverdam
Annemiek
A
Bertram
John F
JF
Capel
Blanche
B
Chiu
Han Sheng
HS
Clements
Dave
D
Cullen-McEwen
Luise
L
Fleming
Jean
J
Gilbert
Thierry
T
Herzlinger
Doris
D
Houghton
Derek
D
Kaufman
Matt H
MH
Kleymenova
Elena
E
Koopman
Peter A
PA
Lewis
Alfor G
AG
McMahon
Andrew P
AP
Mendelsohn
Cathy L
CL
Mitchell
Eleanor K
EK
Rumballe
Bree A
BA
Sweeney
Derina E
DE
Valerius
M Todd
MT
Yamada
Gen
G
Yang
Yiya
Y
Yu
Jing
J
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*