TY - JOUR
T1 - The zebrafish anatomy and stage ontologies
T2 - Representing the anatomy and development of Danio rerio
AU - van Slyke, Ceri E.
AU - Bradford, Yvonne M.
AU - Westerfield, Monte
AU - Haendel, Melissa A.
N1 - Funding Information:
This work was funded by NIH HG002659, NIH HG004838, and NSF BDI-0641025. We acknowledge Christian Pich for extensive technical help in updating the load of the ZFA into ZFIN, Perian Song for providing technical support for integrating CL terms into ZFA, Brock Sprunger for data integrity checks, Erik Segerdell for editing the Zebrafish Anatomical Dictionary initially, Chris Mungall for design advice, feedback, and quality assurance mechanisms, Wasila Dahdul Paula Mabee, and John Lundberg for their anatomical expertise, and the entire ZFIN staff for their instrumental work on the expression and phenotype annotation system.
Publisher Copyright:
© 2014 Van Slyke et al.; licensee BioMed Central Ltd.
PY - 2014/2/25
Y1 - 2014/2/25
N2 - 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.
AB - 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.
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U2 - 10.1186/2041-1480-5-12
DO - 10.1186/2041-1480-5-12
M3 - Article
AN - SCOPUS:84907961999
SN - 2041-1480
VL - 5
JO - Journal of Biomedical Semantics
JF - Journal of Biomedical Semantics
IS - 1
M1 - 12
ER -