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|FISH & CHIPS|
Dear Zebrafish Community,
This column, “Fish & Chips”, will provide updates about current events at the zebrafish model organism database (ZFIN, zfin.org), and the Zebrafish International Resource Center (ZIRC, zebrafish.org). We will update you periodically on news, developments, projects and other matters from ZFIN or ZIRC that will hope will be interesting for you and useful for your research.
ZIRC and ZFIN are both located on the University of Oregon campus in Eugene, Oregon. Although both organizations work closely and frequently with each other, they are distinct and have separate funding and distinct aims.
Zebrafish Information Network (ZFIN)
ZFIN is the NIH funded community database resource for laboratory use of zebrafish established in 1995. ZFIN develops and supports integrated zebrafish genetic, genomic, developmental, and physiological information, and maintains the definitive reference data sets of zebrafish research data. A combination of automated processes and expert curation from the published literature done by professional curators produces data sets which are extensively cross-linked to corresponding data in other model organism and human databases. Line designations are officially registered with ZFIN to help keep the large volume of new mutants organized and avoid conflicts. ZFIN curators are available (firstname.lastname@example.org) to handle inquiries about data in ZFIN, nomenclature of genes, mutants, and transgenic lines, as well as provide support for direct data loads from your lab into ZFIN.
ZFIN is an international research resource used by researchers in over 200 countries annually. Currently, nearly 2500 publication records are being added to the ZFIN database annually. All the publications we can obtain PDFs for (~80%) are associated with genes, alleles, genotypes, antibodies, etc. in a process called indexing. ZFIN curators then extract more detailed information such as gene expression patterns, phenotypes, disease models, and gene function annotations from approximately 50% of the indexed publications annually. Publications are prioritized for full curation based on their content, with publications including new alleles, phenotypes, gene expression, or human disease models given top priority. Without a PDF, nothing can be added to ZFIN. For this reason, open access publishing is strongly encouraged.
ZFIN includes nearly 100,000 images and over 63,000 mutants and transgenic lines. Of those mutants, nearly 30,000 are available through ZIRC, over 18,000 are available from the European Zebrafish Resource Center (EZRC), and over 160 are available from the China Zebrafish Resource Center (CZRC). ZFIN collaborates with each of these resource centers to provide access to ordering information when alleles are available from one of these sources.
Zebrafish International Resource Center (ZIRC).
ZIRC was established in 1999 and serves the biomedical research community as a central repository for wild-type, transgenic, and mutant zebrafish lines. We acquire, maintain, and re-distribute these to laboratories in the US and to more than 40 countries abroad. ZIRC also provides other resources such as monoclonal antibodies, cDNA/EST probes, and paramecia for larval food cultures. In addition, the ZIRC provides diagnostic health services for fish facilities, which include zebrafish histopathology for disease diagnosis or sentinel testing, bacteriology, and necropsy exams, usually followed by husbandry and health consultations.
To fulfill its function, ZIRC imports live males or cryopreserved sperm and amplifies the resource before making it available to the research community. Particularly when resources are imported from large-scale genetic screens, ZIRC and ZFIN data acquisition is closely coordinated between the two organizations and the provider. Once lines have been imported at ZIRC, they are backed up as cryopreserved sperm samples, and the most frequently requested lines are also maintained live. Requests for fish lines can be placed via the ZIRC web site (zebrafish.org), which links to the corresponding ZFIN pages. This helps users to locate and review up-to-date research information before they place an order. In addition, the internal ZIRC inventory databases for line maintenance and identification are also linked to ZFIN pages, supporting the characterization of fish lines by molecular genotyping, reporter gene expression, or phenotype. Nightly data exchanges between ZFIN and ZIRC ensure that the cross-linked pages are up to date and display accurate “Order This” links on ZFIN’s Gene and Genomic Feature pages for resources that are available for distribution by ZIRC. As of August 2017, ZIRC’s collection consists of over 36,000 alleles, representing approximately 10,500 cryopreserved and live lines. Dozens of laboratories contributed to the ZIRC collection, particularly, large-scale genetic screens such as the Boston and Tübingen screens, the Hopkins Laboratory/MIT (Boston) screen of retroviral insertion mutants, Sanger Institute Zebrafish Mutation Project (ZMP, http://www.sanger.ac.uk/resources/zebrafish/zmp/ ), the Zebrafish Insertion Collection (ZInC, http://research.nhgri.nih.gov/ZInC/ ), and the International Zebrafish Protein Trap Consortium (http://zfishbook.org/ ).
ZIRC also collaborates closely with its European counterpart, the European Zebrafish Resource Center (EZRC, http://www.ezrc.kit.edu/) located at the Karlsruhe Institute of Technology KIT, in Germany. The resource centers are currently coordinating a release of approximately 4000 – 6000 alleles from the Sanger ZMP collection in September 2017 that were previously not available to the public. We hope that access to these alleles will support and aid your research!
Doug Howe (University of Oregon)
Zoltan M. Varga (University of Oregon)