=Paper=
{{Paper
|id=Vol-1747/IP25_ICBO2016
|storemode=property
|title=The Zebrafish Experimental Conditions Ontology Systemizing Experimental Descriptions in ZFIN
|pdfUrl=https://ceur-ws.org/Vol-1747/IP25_ICBO2016.pdf
|volume=Vol-1747
|authors=Yvonne Bradford,Ceri Van Slyke,Sabrina Toro,Sridhar Ramachandran
|dblpUrl=https://dblp.org/rec/conf/icbo/BradfordSTR16
}}
==The Zebrafish Experimental Conditions Ontology Systemizing Experimental Descriptions in ZFIN ==
https://ceur-ws.org/Vol-1747/IP25_ICBO2016.pdf
The Zebrafish Experimental Conditions Ontology
Systemizing Experimental Descriptions in ZFIN
Yvonne M. Bradford*, Ceri E. Van Slyke, Sabrina Toro, Sridhar Ramachandran
ZFIN, Institute of Neuroscience
University of Oregon
Eugene, Oregon
ybradford@zfin.org
Abstract— The Zebrafish Experimental Conditions Ontology
(ZECO) defines the major experimental conditions used in B. Design specifications
research studies that employ the zebrafish, Danio rerio. We are The ZECO hierarchy is developed according to the major
systematically building the ontology to encompass both standard types of experimental and environmental conditions used in
control conditions and experimental conditions and it is designed zebrafish research. The high level nodes include biological
to allow better data curation and more precise information treatment, chemical treatment, diet, housing conditions, in vitro
retrieval. culture, surgical manipulation, lighting conditions, temperature
exposure, radiation exposure and water quality. Biological
Keywords—zebrafish; Danio rerio; experimental conditions; treatments deal with experimental conditions where there is
ZECO either the addition or subtraction of another organism from the
fish and/or the environment and can be used to denote both
I. INTRODUCTION pathogenic and commensal interactions. The chemical
Zebrafish are an aquatic model organism utilized treatment branch of the ontology is designed to be post-
extensively for cellular, molecular, developmental, genetic, and composed [1] with the Chemical Entities of Biological
disease associated research. Zebrafish are easily manipulated Interest ontology (CHEBI) [2] to allow specification of the
research animals and as such are subjected to experimental exact chemicals used in the experiment. This design decision
conditions which range from amputation to chemical allows for the creation of needed experimental conditions on
application via food or tank water, to manipulation of lighting the fly without having to enumerate all possible chemicals used
conditions. To facilitate the annotation of experimental within the ontology. A similar design strategy can be used for
conditions used in zebrafish research the Zebrafish Model surgical manipulation, ablation and resection of particular
Organism Database (ZFIN) has developed the Zebrafish anatomical structures by post-composing with the Zebrafish
Experimental Conditions ontology (ZECO). Anatomical ontology (ZFA) [3], thus allowing more precise
enumeration of surgically manipulated entities. The other high
level nodes of housing conditions, lighting conditions,
II. RESULTS AND DISCUSSION temperature exposure and water quality are meant to allow for
the annotation of tank conditions that the zebrafish is exposed
A. An applied ontology
to during the course of the experiment.
ZECO is an applied ontology which will be deployed at
ZFIN to effectively annotate gene expression, phenotypes, and In its rudimentary form ZECO is a simple is_a hierarchy.
human disease models that are a result of the genetic and/or As development of the ontology proceeds certain classes will
experimental conditions applied to zebrafish. The concise have multiple inheritance either via declared or inferred
annotation of experimental conditions allows for the relationships. Additionally classes that inherently reference
differentiation of phenotypes and perturbations of gene either chemicals, like dietary fat, or anatomy, like retina
expression that result from genetic manipulation versus those puncture, will have a reference to the appropriate term from
resulting from environmental or experimental condition CHEBI or ZFA in the logical definition. The goal is to deposit
manipulation. Phenotypes influenced by environmental or ZECO at the Obo Foundry which requires ontologies to be
experimental treatment can be as diverse as a change in extensible and interoperable [4]. ZECO was developed due to
behavior or a change in disease state. For example, the lack of an existing ontology that effectively covered the
environmental conditions such as diet play a large part in unique experimental conditions applied to zebrafish. In the
human morbidity and mortality. Components of the zebrafish future ZECO could be rooted as the aquatic branch of a larger
diet such as sugar, fat, or protein can be altered to replicate environmental ontology, which could include the rat
observed human diet composition allowing for the exploration Experimental Conditions Ontology (XCO)[5] and the Plant
of how diet can affect the etiology of various phenotypes and Environment Ontology (EO)[6] which would cover all
human diseases. experimental conditions encountered by model organisms.
Steinbeck, “The ChEBI reference database and ontology for biologically
relevant chemistry: enhancements for 2013,” Nucleic Acids Res., vol.
41, no. Database, pp. D456–D463, 2013.
ACKNOWLEDGMENT [3] C. E. Van Slyke, Y. M. Bradford, M. Westerfield, and M. A. Haendel,
This work was supported by funds from the National “The zebrafish anatomy and stage ontologies: representing the anatomy
Institute of Health HG002659. and development of Danio rerio.,” J. Biomed. Semantics, vol. 5, no. 1, p.
12, Jan. 2014.
[4] “OBO Foundry Principles 2008.” [Online]. Available:
http://obofoundry.org/wiki/index.php/OBO_Foundry_Principles_2008.
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