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

Melissa H Little, Jane Brennan, Kylie Georgas, Jamie A Davies, Duncan R Davidson, Richard A Baldock, Annemiek Beverdam, John Frederick Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Anne Cullen-McEwen, Jean S Fleming, Thierry Gilbert, Derek Houghton, Matt H Kaufman, Elena Kleymenova, Peter Anthony Koopman, Alfor G Lewis, Andrew P McMahon & 8 others Cathy L Mendelsohn, Eleanor Katherine Mitchell, Bree A Rumballe, Derina E Sweeney, M Todd Valerius, Gen Yamada, Yiya Yang, Jing Yu

Research output: Contribution to journalArticleResearchpeer-review

87 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)680 - 699
Number of pages20
JournalGene Expression Patterns
Volume7
Issue number6
Publication statusPublished - 2007

Cite this

Little, M. H., Brennan, J., Georgas, K., Davies, J. A., Davidson, D. R., Baldock, R. A., ... Yu, J. (2007). A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expression Patterns, 7(6), 680 - 699.
Little, Melissa H ; Brennan, Jane ; Georgas, Kylie ; Davies, Jamie A ; Davidson, Duncan R ; Baldock, Richard A ; Beverdam, Annemiek ; Bertram, John Frederick ; Capel, Blanche ; Chiu, Han Sheng ; Clements, Dave ; Cullen-McEwen, Luise Anne ; Fleming, Jean S ; Gilbert, Thierry ; Houghton, Derek ; Kaufman, Matt H ; Kleymenova, Elena ; Koopman, Peter Anthony ; Lewis, Alfor G ; McMahon, Andrew P ; Mendelsohn, Cathy L ; Mitchell, Eleanor Katherine ; Rumballe, Bree A ; Sweeney, Derina E ; Valerius, M Todd ; Yamada, Gen ; Yang, Yiya ; Yu, Jing. / A high-resolution anatomical ontology of the developing murine genitourinary tract. In: Gene Expression Patterns. 2007 ; Vol. 7, No. 6. pp. 680 - 699.
@article{0c17131d066546ea913f0b7a1d506582,
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.",
author = "Little, {Melissa H} and Jane Brennan and Kylie Georgas and Davies, {Jamie A} and Davidson, {Duncan R} and Baldock, {Richard A} and Annemiek Beverdam and Bertram, {John Frederick} and Blanche Capel and Chiu, {Han Sheng} and Dave Clements and Cullen-McEwen, {Luise Anne} and Fleming, {Jean S} and Thierry Gilbert and Derek Houghton and Kaufman, {Matt H} and Elena Kleymenova and Koopman, {Peter Anthony} and Lewis, {Alfor G} and McMahon, {Andrew P} and Mendelsohn, {Cathy L} and Mitchell, {Eleanor Katherine} and Rumballe, {Bree A} and Sweeney, {Derina E} and Valerius, {M Todd} and Gen Yamada and Yiya Yang and Jing Yu",
year = "2007",
language = "English",
volume = "7",
pages = "680 -- 699",
journal = "Gene Expression Patterns",
issn = "1567-133X",
publisher = "Elsevier",
number = "6",

}

Little, MH, Brennan, J, Georgas, K, Davies, JA, Davidson, DR, Baldock, RA, Beverdam, A, Bertram, JF, Capel, B, Chiu, HS, Clements, D, Cullen-McEwen, LA, Fleming, JS, Gilbert, T, Houghton, D, Kaufman, MH, Kleymenova, E, Koopman, PA, Lewis, AG, McMahon, AP, Mendelsohn, CL, Mitchell, EK, Rumballe, BA, Sweeney, DE, Valerius, MT, Yamada, G, Yang, Y & Yu, J 2007, 'A high-resolution anatomical ontology of the developing murine genitourinary tract', Gene Expression Patterns, vol. 7, no. 6, pp. 680 - 699.

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 Frederick; Capel, Blanche; Chiu, Han Sheng; Clements, Dave; Cullen-McEwen, Luise Anne; Fleming, Jean S; Gilbert, Thierry; Houghton, Derek; Kaufman, Matt H; Kleymenova, Elena; Koopman, Peter Anthony; Lewis, Alfor G; McMahon, Andrew P; Mendelsohn, Cathy L; Mitchell, Eleanor Katherine; Rumballe, Bree A; Sweeney, Derina E; Valerius, M Todd; Yamada, Gen; Yang, Yiya; Yu, Jing.

In: Gene Expression Patterns, Vol. 7, No. 6, 2007, p. 680 - 699.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - A high-resolution anatomical ontology of the developing murine genitourinary tract

AU - Little, Melissa H

AU - Brennan, Jane

AU - Georgas, Kylie

AU - Davies, Jamie A

AU - Davidson, Duncan R

AU - Baldock, Richard A

AU - Beverdam, Annemiek

AU - Bertram, John Frederick

AU - Capel, Blanche

AU - Chiu, Han Sheng

AU - Clements, Dave

AU - Cullen-McEwen, Luise Anne

AU - Fleming, Jean S

AU - Gilbert, Thierry

AU - Houghton, Derek

AU - Kaufman, Matt H

AU - Kleymenova, Elena

AU - Koopman, Peter Anthony

AU - Lewis, Alfor G

AU - McMahon, Andrew P

AU - Mendelsohn, Cathy L

AU - Mitchell, Eleanor Katherine

AU - Rumballe, Bree A

AU - Sweeney, Derina E

AU - Valerius, M Todd

AU - Yamada, Gen

AU - Yang, Yiya

AU - Yu, Jing

PY - 2007

Y1 - 2007

N2 - 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.

AB - 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.

UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17452023

M3 - Article

VL - 7

SP - 680

EP - 699

JO - Gene Expression Patterns

JF - Gene Expression Patterns

SN - 1567-133X

IS - 6

ER -

Little MH, Brennan J, Georgas K, Davies JA, Davidson DR, Baldock RA et al. A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expression Patterns. 2007;7(6):680 - 699.