The zebrafish anatomy and stage ontologies: Representing the anatomy and development of Danio rerio

Ceri E. van Slyke, Yvonne M. Bradford, Monte Westerfield, Melissa A. Haendel

Research output: Contribution to journalArticle

27 Scopus citations

Abstract

Background: The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Danio rerio, from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets.Results: The ZFA models anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development.Conclusions: The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease.

Original languageEnglish (US)
Article number12
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
StatePublished - Feb 25 2014

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications

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