Skip to main content
SpringerLink
Log in

Using ZFIN: Data Types, Organization, and Retrieval

  • Protocol
  • First Online:
Eukaryotic Genomic Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1757))

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.

*The members of the ZFIN Staff are listed in the Acknowledgments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.00
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Westerfield M, Doerry E, Kirkpatrick AE et al (1997) An on-line database for zebrafish development and genetics research. Semin Cell Dev Biol 8:477–488. https://doi.org/10.1006/scdb.1997.0173

    Article  PubMed  CAS  Google Scholar 

  2. Howe DG, Bradford YM, Eagle A et al (2017) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic Acids Res 45:D758–D768. https://doi.org/10.1093/nar/gkw1116

    Article  PubMed  CAS  Google Scholar 

  3. Howe DG, Bradford YM, Conlin T et al (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res 41:D854–D860. https://doi.org/10.1093/nar/gks938

    Article  PubMed  CAS  Google Scholar 

  4. Sprague J, Bayraktaroglu L, Bradford Y et al (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 36:D768–D772. https://doi.org/10.1093/nar/gkm956

    Article  PubMed  CAS  Google Scholar 

  5. Van Slyke CE, Bradford YM, Westerfield M, Haendel MA (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics 5:12. https://doi.org/10.1186/2041-1480-5-12

    Article  PubMed  PubMed Central  Google Scholar 

  6. Howe DG, Bradford YM, Eagle A et al (2016) A scientist’s guide for submitting data to ZFIN. Methods Cell Biol 135:451–481. https://doi.org/10.1016/bs.mcb.2016.04.010

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  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 

  8. Barrett T, Wilhite SE, Ledoux P et al (2013) NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res 41:D991–D995. https://doi.org/10.1093/nar/gks1193

    Article  PubMed  CAS  Google Scholar 

  9. Schriml LM, Mitraka E (2015) The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. Mamm Genome 26:584–589. https://doi.org/10.1007/s00335-015-9576-9

    Article  PubMed  PubMed Central  Google Scholar 

  10. Schriml LM, Arze C, Nadendla S et al (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res 40:D940–D946. https://doi.org/10.1093/nar/gkr972

    Article  PubMed  CAS  Google Scholar 

  11. Bradford YM, Toro S, Ramachandran S et al (2017) Zebrafish models of human disease: gaining insight into human disease at ZFIN. ILAR J 58(1):4–15. https://doi.org/10.1093/ilar/ilw040

    Article  PubMed  PubMed Central  Google Scholar 

  12. Gaudet P, Livstone MS, Lewis SE, Thomas PD (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform 12:449–462. https://doi.org/10.1093/bib/bbr042

    Article  PubMed  PubMed Central  Google Scholar 

  13. Huntley RP, Sawford T, Mutowo-Meullenet P et al (2015) The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res 43:D1057–D1063. https://doi.org/10.1093/nar/gku1113

    Article  CAS  PubMed  Google Scholar 

  14. Chibucos MC, Mungall CJ, Balakrishnan R et al (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) 2014:bau075. https://doi.org/10.1093/database/bau075

    Article  Google Scholar 

  15. Chibucos MC, Siegele DA, JC H, Giglio M (2017) The evidence and conclusion ontology (ECO): supporting GO annotations. Methods Mol Biol 1446:245–259. https://doi.org/10.1007/978-1-4939-3743-1_18

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  16. Finn RD, Attwood TK, Babbitt PC et al (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45:D190–D199. https://doi.org/10.1093/nar/gkw1107

    Article  PubMed  CAS  Google Scholar 

  17. Sigrist CJA, de Castro E, Cerutti L et al (2013) New and continuing developments at PROSITE. Nucleic Acids Res 41:D344–D347. https://doi.org/10.1093/nar/gks1067

    Article  PubMed  CAS  Google Scholar 

  18. Finn RD, Coggill P, Eberhardt RY et al (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285. https://doi.org/10.1093/nar/gkv1344

    Article  PubMed  CAS  Google Scholar 

  19. Artimo P, Jonnalagedda M, Arnold K et al (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res 40:W597–W603. https://doi.org/10.1093/nar/gks400

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Kamens J (2015) The Addgene repository: an international nonprofit plasmid and data resource. Nucleic Acids Res 43:D1152–D1157. https://doi.org/10.1093/nar/gku893

    Article  PubMed  CAS  Google Scholar 

  21. Csályi K, Fazekas D, Kadlecsik T et al (2016) SignaFish: a Zebrafish-specific signaling pathway resource. Zebrafish 13:541–544. https://doi.org/10.1089/zeb.2016.1277

    Article  PubMed  Google Scholar 

  22. Howe K, Clark MD, Torroja CF et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503. https://doi.org/10.1038/nature12111

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Ruzicka L, Bradford YM, Frazer K et al (2015) ZFIN, The zebrafish model organism database: updates and new directions. Genesis 53:498–509. https://doi.org/10.1002/dvg.22868

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Nasevicius A, Ekker SC (2000) Effective targeted gene “knockdown” in zebrafish. Nat Genet 26:216–220. https://doi.org/10.1038/79951

    Article  PubMed  CAS  Google Scholar 

  25. Hwang WY, Fu Y, Reyon D et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227–229. https://doi.org/10.1038/nbt.2501

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Sander JD, Cade L, Khayter C et al (2011) Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 29(8):697. https://doi.org/10.1038/nbt.1934

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. https://doi.org/10.1186/gb-2009-10-3-r25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Sprague J, Bayraktaroglu L, Clements D et al (2006) The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res 34:D581–D585. https://doi.org/10.1093/nar/gkj086

    Article  PubMed  CAS  Google Scholar 

  29. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29. https://doi.org/10.1038/75556

    Article  PubMed  PubMed Central  CAS  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, OR

    Google 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, OR

    Google Scholar 

  32. Sullivan J, Karra K, Moxon SAT et al (2013) InterMOD: integrated data and tools for the unification of model organism research. Sci Rep 3:1802. https://doi.org/10.1038/srep01802

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Lyne R, Sullivan J, Butano D et al (2015) Cross-organism analysis using InterMine. Genesis 53:547–560. https://doi.org/10.1002/dvg.22869

    Article  PubMed  PubMed Central  Google Scholar 

  34. Smith B, Ashburner M, Rosse C et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251–1255. https://doi.org/10.1038/nbt1346

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Stein LD, Mungall C, Shu S et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610. https://doi.org/10.1101/gr.403602

    Article  PubMed  PubMed Central  CAS  Google 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

Download references

Acknowledgments

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].

Author information

Authors and Affiliations

  1. The Zebrafish Information Network, University of Oregon, Eugene, OR, USA

    Ceri E. Van Slyke, Yvonne M. Bradford, Douglas G. Howe, David S. Fashena, Sridhar Ramachandran & Leyla Ruzicka

Authors
  1. Ceri E. Van Slyke
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yvonne M. Bradford
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Douglas G. Howe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David S. Fashena
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sridhar Ramachandran
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Leyla Ruzicka
    View author publications

    You can also search for this author in PubMed Google Scholar

Consortia

ZFIN Staff*

Corresponding author

Correspondence to Ceri E. Van Slyke .

Editor information

Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

    Martin Kollmar

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Van Slyke, C.E. et al. (2018). Using ZFIN: Data Types, Organization, and Retrieval. In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7737-6_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7736-9

  • Online ISBN: 978-1-4939-7737-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation