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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.

Pubmed ID: 17452023 RIS Download

Mesh terms: Animals | Clitoris | Endoderm | Female | Gene Expression Regulation, Developmental | Male | Mesoderm | Mice | Nephrons | Penis | Scrotum | Sexual Maturation | Urogenital System

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Associated grants

  • Agency: NIDDK NIH HHS, Id: R01 DK061459-02
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-04
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-08
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-05
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-07S1
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-09
  • Agency: NIDDK NIH HHS, Id: R01 DK061459
  • Agency: NIDDK NIH HHS, Id: R56 DK082963-01
  • Agency: NIDDK NIH HHS, Id: U01 DK070136-02
  • Agency: NIDDK NIH HHS, Id: U01 DK070181-03
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-06
  • Agency: NIDDK NIH HHS, Id: DK070181
  • Agency: NIDDK NIH HHS, Id: R56 DK082963
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-03
  • Agency: Medical Research Council, Id: MC_U127527203
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-07
  • Agency: NIDDK NIH HHS, Id: DK07020001
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-01A1S1
  • Agency: NIDDK NIH HHS, Id: U01 DK070136
  • Agency: NIDDK NIH HHS, Id: R01 DK061459-01A1
  • Agency: NIDDK NIH HHS, Id: U01 DK070181
  • Agency: NIDDK NIH HHS, Id: U01 DK070200-01

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GenitoUrinary Development Molecular Anatomy Project

International consortium providing a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; a high resolution molecular anatomy highlighting development of the GU system; mouse strains to facilitate developmental and functional studies within the GU system; experimental protocols and standard specifications; tutorials describing GU organogenesis and primary data via the database. The data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system.

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