Using ZFIN: Data Types, Organization, and Retrieval

Abstract

The Zebrafish Model Organism Database (ZFIN; zfin.org) was established in 1994 as the primary genetic and genomic resource for the zebrafish research community. Some of the earliest records in ZFIN were for people and laboratories. Since that time, services and data types provided by ZFIN have grown considerably. Today, ZFIN provides the official nomenclature for zebrafish genes, mutants, and transgenics and curates many data types including gene expression, phenotypes, Gene Ontology, models of human disease, orthology, knockdown reagents, transgenic constructs, and antibodies. Ontologies are used throughout ZFIN to structure these expertly curated data. An integrated genome browser provides genomic context for genes, transgenics, mutants, and knockdown reagents. ZFIN also supports a community wiki where the research community can post new antibody records and research protocols. Data in ZFIN are accessible via web pages, download files, and the ZebrafishMine (zebrafishmine.org), an installation of the InterMine data warehousing software. Searching for data at ZFIN utilizes both parameterized search forms and a single box search for searching or browsing data quickly. This chapter aims to describe the primary ZFIN data and services, and provide insight into how to use and interpret ZFIN searches, data, and web pages.

Keywords: Danio rerio; Database; Genetics; Genomics; ZFIN; Zebrafish Information Network.

Fig. 1

ZFIN is an extensively crosslinked gene-centric resource. Many data pages in ZFIN share reciprocal hyperlinks between related records. The gene record and corresponding gene page provide the central hub around which much of the data and zfin.org website are organized, respectively. Gene web pages (center) share reciprocal hyperlinks with pages for 12 major related data types (peripheral). Many of these data type pages are also linked to pages other than the gene page. For clarity, those links are not represented

Fig. 2

Gene page for cxcr4b

Fig. 3

Genomic feature page for hu3393

Fig. 4

Genotype page for vu119Tg

Fig. 5

Fish page for vu119Tg + MO3-pkd2 + MO9-pkd2

Fig. 6

Sequence targeting reagent page for CRISPR1-tyr

Fig. 7

Antibody page for Ab1-crb2a

Fig. 8

Construct page for Gene Trap Gt(GBT-P9)

Fig. 9

Example of a ZFIN publication page for ZDB-PUB-970210-31

Fig. 10

Zebrafish Anatomy Ontology term page for margin

Fig. 11

Disease Ontology term page for Diamond-Blackfan anemia

Fig. 12

ZFIN home page

Fig. 13

Two examples of Single Box Search using two different search strategies to converge on the same data. (A) Selecting the Gene/Transcript category, then specific facet values for Type = Gene and Expression Anatomy = “Purkinje cell” produces a list of 24 genes that have curated gene expression in Purkinje cells. (B) Searching for expression in Purkinje cells using the text search. A search for Purkinje cell in the “Expression” category, then limit results to zebrafish genes and expression in Purkinje cells. Both methods produce genes and expression data for Purkinje cells

Fig. 14

ZebrafishMine Templates—Human Disease. (A) Templates are preset queries against the ZebrafishMine data warehouse. Filtering templates for “disease” returns 5 templates. Selecting “Human Disease → Zebrafish Model (mutants)”brings up the template. (B) “Human Disease → Zebrafish Model (mutants)” allows queries by Disease Ontology terms and returns disease models that consist of mutant fish in standard environmental conditions. The query can be edited using the “Edit Query” button on the bottom right that takes users to the QueryBuilder interface. The bottom bar contains links to the web service URL for the specific query as well as links to download the query in a variety of scripting languages or in XML format

Fig. 15

File dependencies “Expression data for Wildtype Fish” compared with “ZFIN Genes with Expression Assay Records” using a concept map. “Expression data for Wildtype Fish” refers to only one ontology, the Zebrafish Anatomy Ontology, and one additional download file “ZFIN Bibliography”. In contrast “ZFIN Genes with Expression Assay Records” references five files in addition to “ZFIN Bibliography” The set of files refer to eight separate ontologies to provide the complete picture of the Fish, environmental conditions or treatments present during the expression measurements and the structures where the expression occurs

Fig. 16

ZFIN GBrowse integration. Information about gene expression, phenotype, knockdown reagents (STRs) along with Ensembl transcripts is provided via GBrowse. The Knockdown Reagent track is generated by ZFIN using bowtie analysis and is a unique resource provided by ZFIN. On the left side of every track name there is a set of icons that allows users to customize their browsing experience; hiding, expanding, removing the track from the display, sharing or saving a track of interest, and configuring the track display, color, number of features