=Paper=
{{Paper
|id=Vol-1747/IP20_ICBO2016
|storemode=property
|title=Growth of the Zebrafish Anatomy Ontology: Expanded to Support Adult Morphology and Dynamic Changes in the Early Embryo
|pdfUrl=https://ceur-ws.org/Vol-1747/IP20_ICBO2016.pdf
|volume=Vol-1747
|authors=Ceri Van Slyke,Yvonne Bradford,Christian Pich
|dblpUrl=https://dblp.org/rec/conf/icbo/SlykeBP16
}}
==Growth of the Zebrafish Anatomy Ontology: Expanded to Support Adult Morphology and Dynamic Changes in the Early Embryo ==
https://ceur-ws.org/Vol-1747/IP20_ICBO2016.pdf
Growth of the Zebrafish Anatomy Ontology
Expanded to support adult morphology and dynamic changes in the early embryo
Ceri E. Van Slyke*, Yvonne M. Bradford, and Christian Pich
ZFIN, 5291University of Oregon
Eugene, Oregon 97403 USA
van_slyke@zfin.org
Abstract—The Zebrafish Anatomy Ontology (ZFA) is an it develops from, and during which stages it exists. The ZFA
application ontology used by ZFIN to support curation of has 2977 classes, 85% with text definitions, representing
expression and phenotype. The research community also uses anatomical structures from different anatomical systems across
the ontology to support annotation of high throughput studies. the zebrafish developmental series.
As the research focus of the zebrafish community evolves it
drives changes in the ZFA. Here we provide an update on the
changes made to support research carried out in adult fish and III. CURRENT WORK
describe the changes in modeling of the neural crest in the The current focus of development of the ZFA has been
ontology in order to bring the structure of the ontology into extending the tree as new research on anatomy is published and
closer accordance with the morphological changes that occur to build an extensible framework for future work. Improved
during development. modelling of transient structures present for only a short period
early in zebrafish development has been an area of active
Keywords—ZFA; ZFS; anatomy; neural crest development. Toward this end, work has been done to
improve modeling of neural crest based on outcomes of the
I. INTRODUCTION Neural Crest Workshop held at the National Evolutionary
The Zebrafish Anatomy Ontology (ZFA)[1, 2] is an OBO Synthesis Center (NESCent) during the Phenotype RCN
Foundry [3] ontology that is used in conjunction with the meeting 2012 (http://www.phenotypercn.org/?page_id=54 ).
Zebrafish Stage Ontology (ZFS) [4] to describe the The changes to the neural crest branch better reflect the
developmental progression of the gross and cellular anatomy of development of neural crest and its constituent cells from the
the zebrafish, Danio rerio, from single cell zygote to adult. neural plate border, their gross location along the axis, as well
Zebrafish share many anatomical and physiological as differentiation of pre-migratory and migratory populations
characteristics with other vertebrates, including humans, and (14 classes). To effectively model the neural crest there was
have emerged as a premiere organism to study vertebrate coordination with appropriate CL classes[9] to allow for proper
development and genetics. The Zebrafish Model Organism cross referencing with in the ZFA. The hierarchy implemented
Database (ZFIN) [5] uses the ZFA and ZFS to annotate in ZFA should be applicable for all vertebrates and is intended
zebrafish phenotype and gene expression data from the primary to be in a format UBERON[10, 11] can generalize across
literature and from contributed data sets. By using the ZFA and species.
ZFS to annotate gene expression and phenotypic data, ZFIN is Additional development of ZFA classes has been varied
able to provide efficient querying and analysis across ZFIN and driven by the focus of research in the zebrafish
data as well as cross-species inference[6]. community. Active development has focused on structures that
develop in older fish as adult processes are being increasingly
II. CURRENT STATUS investigated by the zebrafish community. To support this
The ZFA and ZFS are developed utilizing OBO Foundry research discrete updating across the ontology was done to
principles[7] to ensure orthogonality, accessibility, and reflect adult structures and includes the adult surface structures:
interoperability. The ZFA is designed to model anatomy using maxillary barbels, with supporting vasculature (10 classes)
a largely structure-based subclass hierarchy, featuring a strong [12]; breeding tubercles (11 classes) [13, 14]; adult fin
partonomy (using the part_of relation) and developmental musculature ( 12 classes) [15]; heart muscles (4 classes) [16].
hierarchy (using the develops_from relation). Each anatomical To better extend the developmental modeling of larval and
class in ZFA is defined using these relationships to other juvenile fish to adult stages, we extended the vasculature
classes in ZFA as well as to stage classes in ZFS. The relations branch by centering on vasculature development of organs with
used between the ZFA and ZFS are start_stage and end_stage. a particular attention on the lymph vasculature. To that end we
The start_stage utilized is equivalent to Relation Ontology added branchial, facial and visceral lymph vasculature classes
(RO) [8] ‘starts_during’ and end_stage is equivalent to RO (22 classes ) [17] and blood vasculature (8 classes)[12, 18]. In
‘ends_during’. In this way, each anatomical entity can be addition, updates to the nervous system (21 classes) and
defined in terms of what it is a type of, what it is a part of, what modelling of replacement teeth were implemented. Overall
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ACKNOWLEDGMENT [12] E. A. Binelli, A. N. Luna, and E. E. LeClair, “Anatomy and ontogeny of
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