PUBLICATION
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio
- Authors
- Van Slyke, C.E., Bradford, Y.M., Westerfield, M., Haendel, M.A.
- ID
- ZDB-PUB-140513-468
- Date
- 2014
- Source
- Journal of Biomedical Semantics 5: 12 (Journal)
- Registered Authors
- Bradford, Yvonne, Haendel, Melissa A., Van Slyke, Ceri E., Westerfield, Monte
- Keywords
- none
- MeSH Terms
- none
- PubMed
- 24568621 Full text @ J Biomed Semantics
Citation
Van Slyke, C.E., Bradford, Y.M., Westerfield, M., Haendel, M.A. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. Journal of Biomedical Semantics. 5:12.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping