I. INTRODUCTION

The Zebrafish Anatomy Ontology (ZFA) [1,2] is an OBO Foundry [3] ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) [4] to describe the developmental progression of the gross and cellular anatomy of the zebrafish, Danio rerio, from single cell zygote to adult. Zebrafish share many anatomical and physiological characteristics with other vertebrates, including humans, and have emerged as a premiere organism to study vertebrate development and genetics. The Zebrafish Model Organism Database (ZFIN) [5] uses the ZFA and ZFS to annotate zebrafish phenotype and gene expression data from the primary literature and from contributed data sets. By using the ZFA and ZFS to annotate gene expression and phenotypic data, ZFIN is able to provide efficient querying and analysis across ZFIN data as well as cross-species inference [6].

II. CURRENT STATUS

The ZFA and ZFS are developed utilizing OBO Foundry principles [7] to ensure orthogonality, accessibility, and interoperability. The ZFA is designed to model anatomy using a largely structure-based subclass hierarchy, featuring a strong partonomy (using the part_of relation) and developmental hierarchy (using the develops_from relation). Each anatomical class in ZFA is defined using these relationships to other classes in ZFA as well as to stage classes in ZFS. The relations used between the ZFA and ZFS are start_stage and end_stage. The start_stage utilized is equivalent to Relation Ontology (RO) [8] The changes to the neural crest branch better reflect the development of neural crest and its constituent cells from the neural plate border, their gross location along the axis, as well as differentiation of pre-migratory and migratory populations (14 classes). To effectively model the neural crest there was coordination with appropriate CL classes [9] to allow for proper cross referencing with in the ZFA. The hierarchy implemented in ZFA should be applicable for all vertebrates and is intended to be in a format UBERON [10,11] can generalize across species.

Additional development of ZFA classes has been varied and driven by the focus of research in the zebrafish community. Active development has focused on structures that develop in older fish as adult processes are being increasingly investigated by the zebrafish community. To support this research discrete updating across the ontology was done to reflect adult structures and includes the adult surface structures: maxillary barbels, with supporting vasculature (10 classes) [12]; breeding tubercles (11 classes) [13,14]; adult fin musculature ( 12 classes) [15]; heart muscles (4 classes) [16]. To better extend the developmental modeling of larval and juvenile fish to adult stages, we extended the vasculature branch by centering on vasculature development of organs with a particular attention on the lymph vasculature. To that end we added branchial, facial and visceral lymph vasculature classes (22 classes ) [17] and blood vasculature (8 classes) [12,18]. In addition, updates to the nervous system (21 classes) and modelling of replacement teeth were implemented. Overall the ZFA has expanded the hierarchical modeling of the zebrafish anatomy by 121 classes.

IV. FUTURE WORK

The ZFA will continue to be built to meet the needs of the zebrafish research community. ZFIN curators are actively involved in the zebrafish and ontology research communities to improve the ZFA through addition of classes, definitions, relations, and the continued support for interoperable ontologies. The neural crest branch will undergo continued development to model the various migratory streams and their development contributions to defined structures.