ZFIN updates to support zebrafish environmental exposure data

Abstract

The Zebrafish Information Network (ZFIN, zfin.org) is the database resource for genetic, genomic, and phenotypic data from research using zebrafish, Danio rerio. ZFIN curates information about genetic perturbations, gene expression, phenotype, gene function, and human disease models from zebrafish research publications and makes these data available to researchers worldwide. Over the past 20 years, zebrafish have increasingly been used to investigate the effects of environmental exposures, becoming an ideal model to study toxicity, phenotypic outcomes, and gene-chemical interactions. Despite this, database resources supporting zebrafish toxicology and environmental exposure research are limited. To fill this gap, ZFIN has expanded functionality to incorporate and convey toxicology data better. ZFIN annotations for gene expression, phenotype, and human disease models include information about genotypes and experimental conditions used. One type of experimental condition the database captures is the application of chemicals to zebrafish. ZFIN annotates chemicals using the Chemical Entities of Biological Interest Ontology (ChEBI) along with the Zebrafish Experimental Conditions Ontology (ZECO) to denote route of exposure and other experimental conditions. These features allow researchers to search phenotypes and human disease models linked to chemicals more efficiently. Here, we discuss how experimental conditions are displayed on ZFIN web pages, the data displayed on chemical term pages, and how to search and download data associated with chemical exposure experiments.

Keywords: danio rerio; ZFIN; environmental exposure; expression; human disease model; model organism database; phenotype; zebrafish.

Fig. 1.

Zebrafish experimental conditions ontology (ZECO) describes a) Four routes of exposure of toxins/chemicals to zebrafish. b) Hierarchical structure of ZECO chemical exposure terms. Note that the parent term “chemical treatment” can be used when specific routes of exposure are unspecified by authors.

Fig. 2.

Multiple experimental conditions annotation. a) Example of phenotype annotation using multiple environmental conditions. Arrow denotes icon to access pop-up. b) The pop-up lists all terms used in the condition annotation with their definitions. https://zfin.org/ZDB-FIG-210103-23#phenotype-data.

Fig. 3.

Publication detail page. ZFIN publication page summary section with link to CTD publication page (red box). Clicking the link redirects to the corresponding page at CTD. https://zfin.org/ZDB-PUB-120117-13.

Fig. 4.

Pentetrazol chemical term page. a) Summary section of chemical term page. This provides term information such as synonyms and cross-references to other resources. Arrow denotes links to corresponding CTD page. b) First table of Phenotype section “Phenotype resulting from pentetrazol”. Table aggregates phenotypes inferred to be caused by pentetrazol. c) Second table of Phenotype section “Phenotypes where environments contain pentetrazol”. Table aggregates all phenotypes that have an experimental condition which is annotated with pentetrazol. d) Third table of Phenotype section “Phenotype modified by environments containing pentetrazol”. Table aggregates all phenotypes that have an experimental condition that is annotated with pentetrazol and are either ameliorated or exacerbated. e) Human disease section of chemical term page. This table lists human disease model annotations that have conditions containing pentetrazol. Evidence column lists either traceable author statement (TAS) or inferred by curator (IC) codes that indicate that there is evidence from a publication that directly supports the disease model annotation or the annotation was made on the basis of curatorial judgement, respectively. https://zfin.org/CHEBI:34910.

Fig. 5.

Ontology search. a) Ontology Search (red box) is available from the Research tab on the home page. Clicking the link redirects to the ontology search interface. b) Ontology search interface has a type ahead autocomplete text entry box to support searching ChEBI terms. https://zfin.org/action/ontology/search.

Fig. 6.

Faceted search results page. Phenotype search using faceted search. Facets on left allow users to select parameters to modify search results. Arrow denotes facet users can pick to refine phenotype search results to those annotations with a chemical condition. https://zfin.org/search?q=.

Fig. 7.

CTD facet in the publication category. The Publication category of faceted search has a CTD facet (arrow) to limit results to publications in ZFIN corpus that are linked to CTD. https://zfin.org/search?q=&fq=category%3A%22Publication%22&category=Publication&fq=has_ctd%3A%22true%22.