Van Slyke Ceri E, Bradford Yvonne M, Howe Douglas G, Fashena David S, Ramachandran Sridhar, Ruzicka Leyla
The Zebrafish Information Network, University of Oregon, Eugene, OR, USA.
Methods Mol Biol. 2018;1757:307-347. doi: 10.1007/978-1-4939-7737-6_11.
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.
斑马鱼模式生物数据库（ZFIN；zfin.org）成立于1994年，是斑马鱼研究界的主要遗传和基因组资源。ZFIN中一些最早的记录是关于人员和实验室的。从那时起，ZFIN提供的服务和数据类型有了显著增长。如今，ZFIN提供斑马鱼基因、突变体和转基因的官方命名，并整理多种数据类型，包括基因表达、表型、基因本体论、人类疾病模型、直系同源关系、基因敲低试剂、转基因构建体和抗体。本体论在整个ZFIN中用于构建这些经过专业整理的数据。一个集成的基因组浏览器为基因、转基因、突变体和基因敲低试剂提供基因组背景。ZFIN还支持一个社区维基，研究社区可以在上面发布新的抗体记录和研究方案。ZFIN中的数据可通过网页、下载文件以及ZebrafishMine（zebrafishmine.org）获取，ZebrafishMine是InterMine数据仓库软件的一个安装版本。在ZFIN中搜索数据既可以使用参数化搜索表单，也可以使用单个搜索框快速搜索或浏览数据。本章旨在描述ZFIN的主要数据和服务，并深入介绍如何使用和解读ZFIN的搜索、数据及网页。
