Table 2.

Ontologies Used in ZFIN

Ontology	Description	Link	Citation
Zebrafish Anatomy Ontology (ZFA)	Ontology that represents the anatomy of Danio rerio	http://www.berkeleybop.org/ontologies/zfa.obo	(Van Slyke et al., 2014)
Zebrafish Stage Ontology (ZFS)	Ontology that describes the developmental stages of Danio rerio	http://www.berkeleybop.org/ontologies/zfs.obo	(Van Slyke et al., 2014)
Biological Spatial ontology (BSPO)	Ontology that provides standardized description of spatial and topological relationships	https://biological-spatial-ontology.googlecode.com	(Dahdul et al., 2014)
Phenotypic Quality ontology (PATO)	Ontology of phenotypic qualities	http://wiki.obofoundry.org/wiki/index.php/PATO:Main_Page	(Mabee et al., 2007)
Disease Ontology (DO)	Ontology of human diseases	http://disease-ontology.org/	(Kibbe et al. 2014)
Mouse Pathology ontology (MPATH)	Ontology describing the phenotype or pathology of rodent disease. ZFIN uses the Neoplasm subset.	http://www.berkeleybop.org/ontologies/mpath.owl	(Schofield et al., 2013)
Gene Ontology (GO)	Ontology representing gene product properties covering three domains: Cellular Component – the parts of a cell; Molecular Function-activities of gene products at the molecular level; Biological Process – sets of molecular events pertinent to the functioning of an integrated living unit that have a defined beginning and end.	http://geneontology.org/	(Ashburner et al., 2000)
Sequence Ontology (SO)	Ontology representing sequence features	http://www.sequenceontology.org/	(Eilbeck et al., 2005)