Using ZFIN: Data Types, Organization, and Retrieval
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.
Key wordsZFIN Zebrafish Information Network Danio rerio Database Genetics Genomics
The ZFIN staff who build, maintain, and add data to ZFIN: Ken Frazer, Holly Paddock, Amy Singer, Sabrina Toro, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Moxon, Christian Pich, Kevin Schapher, Xiang Shao, Ruben Lancaster, Anne Eagle, Jonathan Knight; who helped format the figures for this publication. Funding provided to Monte Westerfield, ZFIN’s Principal Investigator by National Human Genome Research Institute of the National Institutes of Health [HG002659].
- 7.Degrave, Agnes, Fürthauer, Maximilian, Heyer, Vincent, Loppin, Benjamin, Obrecht-Pflumio, Sophie, Steffan, Tania, Thisse, Bernard, Thisse, Christine, Woehl R (2001) Expression of the zebrafish genome during embryogenesis (NIH R01 RR15402). ZFIN on-line Publ.Google Scholar
- 30.Westerfield M (2007) The zebrafish book : a guide for the laboratory use of zebrafish (Danio rerio), 5th edn. University of Oregon Press, Eugene, ORGoogle Scholar
- 31.Westerfield M (2000) The zebrafish book: a guide for the laboratory use of zebrafish (Danio rerio), 4th edn. University of Oregon Press, Eugene, ORGoogle Scholar
- 36.Bradford, Yvonne, Van Slyke, Ceri, Toro, Sabrina, Ramachandran, Sridhar (2016) The Zebrafish Experimental Conditions Ontology Systemizing Experimental Descriptions in ZFIN. CEUR Workshop Proceedings 1747. http://ceur-ws.org/Vol-1747/IP25_ICBO2016.pdf