Dataset Information

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.

SUBMITTER: Little MH

PROVIDER: S-EPMC2117077 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature

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

Little Melissa H MH 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

Gene expression patterns : GEP 20070323 6

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. Th ...[more]

PMID: 17452023

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Project description:Gold-standard annotated corpora have become important resources for the training and testing of natural-language-processing (NLP) systems designed to support biocuration efforts, and ontologies are increasingly used to facilitate curational consistency and semantic integration across disparate resources. Bringing together the respective power of these, the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of full-length, open-access biomedical journal articles with extensive manually created syntactic, formatting and semantic markup, was previously created and released. This initial public release has already been used in multiple projects to drive development of systems focused on a variety of biocuration, search, visualization, and semantic and syntactic NLP tasks. Building on its demonstrated utility, we have expanded the CRAFT Corpus with a large set of manually created semantic annotations relying on Uberon, an ontology representing anatomical entities and life-cycle stages of multicellular organisms across species as well as types of multicellular organisms defined in terms of life-cycle stage and sexual characteristics. This newly created set of annotations, which has been added for v2.1 of the corpus, is by far the largest publicly available collection of gold-standard anatomical markup and is the first large-scale effort at manual markup of biomedical text relying on the entirety of an anatomical terminology, as opposed to annotation with a small number of high-level anatomical categories, as performed in previous corpora. In addition to presenting and discussing this newly available resource, we apply it to provide a performance baseline for the automatic annotation of anatomical concepts in biomedical text using a prominent concept recognition system. The full corpus, released with a CC BY 3.0 license, may be downloaded from http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml. Database URL: http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

Dataset Information

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

Publications

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

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