CoChat
Sign Up
Cited by 229Zebrafish Biomedical Research ApplicationsBiomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Zebrafish information network, the knowledgebase for Danio rerio research

Open access
Bradford, Yvonne M, Van Slyke, Ceri E, Ruzicka, Leyla, Singer, Amy, Eagle, Anne, Fashena, David, Howe, Douglas G, Frazer, Ken +5 more·2022·Genetics
DOI 10.1093/genetics/iyac016PMC PMC8982015

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/genetics/iyac016

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Cell type annotation was performed by verifying expression of established marker genes from ZFIN.

    “Cell type annotation was performed by verifying the expression of previously established marker genes using the Zebrafish Information Network (ZFIN, https://zfin.org/) (Bradford et al., 2022), resulting in the identification of 21 cell types:”

    From Deciphering the toxic effects of polystyrene nanoparticles on erythropoiesis at single-cell resolution (2025) · cites this paper as Bradford et al., 2022

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 41

  1. [1]Povey S, Lovering R, Bruford E, Wright M, Lush MWain, H. The HUGO Gene Nomenclature Committee (HGNC). Hum Genet. 2001; 109: 678– 680. 11810281
  2. [3]Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, et al Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Research. 2013; 2: 30. doi: 10.12688/f1000research.2-30.v1. 24358873 PMC3799545 · DOI
  3. [4]Van Slyke CE, Bradford YM, Howe DG, Fashena DS, Ramachandran S, Ruzicka L, ZFIN Staff. Using ZFIN: Data Types, Organization, and Retrieval. In: Methods in Molecular Biology, NIH Public Access; 2018. p. 307– 347. PMC6319390 29761463
  4. [6]Howe DG, Frazer K, Fashena D, Ruzicka L, Bradford Y, Ramachandran S Ruef BJ, Van Slyke C, Singer A, Westerfield W. Data extraction, transformation, and dissemination through ZFIN. Methods Cell Biol. 2011; 104: 311– 325. doi: 10.1016/B978-0-12-374814-0.00017-3. 21924170 PMC6322538 · DOI
  5. [7]Howe DG, Bradford YM, Eagle A, Fashena D, Frazer K, Kalit P, Mani P, Martin R, Moxon ST, Paddock H, et al A scientist’s guide for submitting data to ZFIN. Methods Cell Biol. 2016; 135: 451– 481. doi: 10.1016/bs.mcb.2016.04.010. 27443940 PMC6319372 · DOI
  6. [9]Laulederkind SJF, Hayman GT, Wang SJ, Smith JR, Petri V, Hoffman MJ, De Pons J, Tutaj MA, et al A primer for the rat genome database (RGD). Methods Mol Biol. 2018; 1757: 163– 209. 29761460 PMC6487669
  7. [10]Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C, et al WormBase 2017: molting into a new stage. Nucleic Acids Res. 2018; 46(D1): D869– D874. doi: 10.1093/nar/gkx998. 29069413 PMC5753391 · DOI
  8. [11]Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, et al; the FlyBase Consortium. FlyBase 2.0: the next generation. Nucleic Acids Res. 2019; 47(D1): D759– D765. doi: 10.1093/nar/gky1003. 30364959 PMC6323960 · DOI
  9. [12]Carbon S, Douglass E, Dunn N, Good B, Harris NL, Lewis SE, Mungall CJ, Basu S, Chisholm RL, Dodson RJ, et al The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 2019; 47: D330– D338. doi: 10.1093/nar/gky1055. 30395331 PMC6323945 · DOI · Paper page
  10. [13]Agapite J, Albou L-P, Aleksander S, Argasinska J, Arnaboldi V, Attrill H, Bello SM, Blake JA, Blodgett O, Bradford YM, et al; The Alliance of Genome Resources Consortium. Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 2020; 48(D1): D650– D658. doi: 10.1093/nar/gkz813. 31552413 PMC6943066 · DOI
  11. [14]Bult CJ, Blake JA, Calvi BR, Cherry JM, DiFrancesco V, Fullem R, Howe KL, Kaufman T, Mungall C, Perrimon N, et al The alliance of genome resources: building a modern data ecosystem for model organism databases. Genetics. 2019a; 213: 1189– 1196. 31796553 PMC6893393
  12. [15]Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, et al Model organism data evolving in support of translational medicine. Lab Anim. 2018; 47(10): 277– 289. doi: 10.1038/s41684-018-0150-4. PMC6322546 30224793 · DOI
  13. [16]Howe DG, Ramachandran S, Bradford YM, Fashena D, Toro S, Eagle A, Frazer K, Kalita P, Mani P, Martin R, et al The zebrafish information network: major gene page and home page updates. Nucleic Acids Res. 2021b; 49(D1): D1058– D1064. doi: 10.1093/nar/gkaa1010. 33170210 PMC7778988 · DOI
  14. [17]Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, et al Automated generation of gene summaries at the Alliance of Genome Resources. Database. 2020; 2020: baaa037. doi: 10.1093/database/baaa037. 32559296 PMC7304461 · DOI
  15. [19]Farnsworth DR, Saunders LM, Miller AC. A single-cell transcriptome atlas for zebrafish development. Dev Biol. 2020; 459(2): 100– 108. doi: 10.1016/j.ydbio.2019.11.008. 31782996 PMC7080588 · DOI
  16. [21]Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, et al Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med. 2017; 214(10): 2875– 2887. doi: 10.1084/jem.20170976. 28878000 PMC5626406 · DOI
  17. [22]Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018; 360(6392): 981– 987. doi: 10.1126/science.aar4362. 29700229 PMC6083445 · DOI · Paper page
  18. [23]Bradford YM, Van Slyke CE, Toro S, Ramachandran S. The zebrafish experimental conditions ontology: systemizing experimental descriptions in ZFIN. In: CEUR Workshop Proceedings; August 2016, Corvallis, OR.
  19. [24]Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics. 2014; 5(1): 12.doi: 10.1186/2041-1480-5-12. 24568621 PMC3944782 · DOI
  20. [25]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25: 25– 29. 10802651 PMC3037419
  21. [26]Carbon S, Douglass E, Good BM, Unni DR, Harris NL, Mungall CJ, Basu S, Chisholm RL, Dodson RJ, Hartline E, et al; The Gene Ontology Consortium. The gene ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021; 49(D1): D325– D334. doi: 10.1093/nar/gkaa1113. 33290552 PMC7779012 · DOI · Paper page
  22. [27]Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the biological spatial ontology. J Biomed Semantics. 2014; 5(1): 34– 13. doi: 10.1186/2041-1480-5-34. 25140222 PMC4137724 · DOI
  23. [28]Gkoutos GV, Green ECJ, Mallon AM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol. 2004; 6(1): R8.doi: 10.1186/gb-2004-6-1-r8. 15642100 PMC549069 · DOI
  24. [29]Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C, et al ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016; 44(D1): D1214– D1219. doi: 10.1093/nar/gkv1031. 26467479 PMC4702775 · DOI · Paper page
  25. [30]Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009; 7(11): e1000247. doi:10.1371/journal.pbio.1000247. 19956802 PMC2774506 · DOI
  26. [31]Matentzoglu N, Balhoff JP, Bello SM, Boerkoel CF, Bradford YM, Carmondy LC, Cooper LD, Grove CA, Harris NL, Kohler S, et al Phenotype Ontologies Traversing All the Organisms (POTATO) Workshop Aims to Reconcile Logical Definitions across Species; August, 2018, Corvallis, OR. doi: 10.5281/ZENODO.2382757. · DOI
  27. [32]Schriml LM, Mitraka E, Munro J, Tauber B, Schor M, Nickle L, Felix V, Jeng L, Bearer C, Lichenstein R, et al Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic Acids Res. 2019; 47(D1): D955– D962. doi: 10.1093/nar/gky1032. 30407550 PMC6323977 · DOI
  28. [33]Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: online Mendelian Inheritance in Man (OMIM®), an Online catalog of human genes and genetic disorders. Nucleic Acids Res. 2015; 43(D1): D789– D798. doi: 10.1093/nar/gku1205. 25428349 PMC4383985 · DOI · Paper page
  29. [34]Bradford YM, Toro S, Ramachandran S, Ruzicka L, Howe DG, Eagle A, Kalita P, Martin R, Taylor Moxon SA, Schaper K, et al Zebrafish models of human disease: gaining insight into human disease at ZFIN. ILAR J. 2017; 58(1): 4– 16. doi: 10.1093/ilar/ilw040. 28838067 PMC5886338 · DOI
  30. [35]Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, et al The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2007; 36(Database): D768– D72. doi: 10.1093/nar/gkm956. 17991680 PMC2238839 · DOI
  31. [36]Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, et al The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 2012; 40(D1): D565– D570. doi: 10.1093/NAR/GKR1048. 22123736 PMC3245010 · DOI
  32. [37]Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang H-Y, Dosztányi Z, El-Gebali S, Fraser M, et al InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017; 45(D1): D190– D199. doi: 10.1093/nar/gkw1107. 27899635 PMC5210578 · DOI
  33. [38]Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, et al Ensembl 2021. Nucleic Acids Res. 2021a; 49(D1): D884– D891. doi: 10.1093/nar/gkaa942. 33137190 PMC7778975 · DOI
  34. [39]Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister JR, Bryant SH, Canese K, et al; NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018; 46(D1): D8– D13. doi: 10.1093/nar/gkx1095. 29140470 PMC5753372 · DOI
  35. [40]Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003; 13(9): 2129– 2141. doi: 10.1101/gr.772403. 12952881 PMC403709 · DOI
  36. [41]Postlethwait J, Amores A, Cresko W, Singer A, Yan YL. Subfunction partitioning, the teleost radiation and the annotation of the human genome. Trends Genet. 2004; 20(10): 481– 490. doi: 10.1016/j.tig.2004.08.001. 15363902 · DOI
  37. [42]Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, et al The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021; 49(D1): D344– D354. doi: 10.1093/nar/gkaa977. 33156333 PMC7778928 · DOI · Paper page
  38. [43]Bateman A, Martin M-J, Orchard S, Magrane M, Agivetova R, Ahmad S, Alpi E, Bowler-Barnett EH, Britto R, Bursteinas B, et al The UniProt Consortium; UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021; 49(D1): D480– D489. doi: 10.1093/nar/gkaa1100. 33237286 PMC7778908 · DOI · Paper page
  39. [44]Csályi K, Fazekas D, Kadlecsik T, Türei D, Gul L, Horváth B, Módos D, Demeter A, Pápai N, Lenti K, et al SignaFish: a Zebrafish-specific signaling pathway resource. Zebrafish. 2016; 13(6): 541– 544. doi: 10.1089/zeb.2016.1277. 27097230 · DOI
  40. [45]Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stepan R, Sullivan J, Micklem G. InterMine: extensive web services for modern biology. Nucleic Acids Res. 2014; 42. doi: 10.1093/nar/gku301. PMC4086141 24753429 · DOI
  41. [46]Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, et al Databases and ontologies InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. 2012; 28(23): 3163– 3165. doi: 10.1093/bioinformatics/bts577. PMC3516146 23023984 · DOI

Cited by

Sorted by citations

Authors
Bradford, Y. M., Van Slyke, C. E., Ruzicka, L., Singer, A., Eagle, A., Fashena, D., Howe, D. G., Frazer, K., Martin, R., Paddock, H., Pich, C., Ramachandran, S., & Westerfield, M.
Affiliations
  • University of Oregon (US)
  • The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
Corresponding author
Bradford, Yvonne M
ORCID
Venue
Genetics
Publisher
Oxford University Press (OUP)
Published
2022-02-15
Volume
220
Issue
4
ISSN
  • 0016-6731 (ISSN-L)
  • 1943-2631
DOI
10.1093/genetics/iyac016
PMC
PMC8982015
OpenAlex
W4226172016
Cited by
229
References
4
Citations by year
2026: 41 · 2025: 61 · 2024: 65 · 2023: 48 · 2022: 13 · 2021: 1
FWCI
24.99
Type
journal article
Language
en
Open access
Licence
Locations
  • Genetics (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • National Human Genome Research Institute
  • National Institutes of Health (U41 HG002659, U24 HG010859)
  • Alliance of Genome Resources
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
zebrafish, genome annotation, single-cell RNA sequencing, Gene Ontology, human disease models, gene function, data integration, data interoperability
MeSH terms
Animals, Zebrafish, Genome, Genomics, Databases, Genetic, Gene Ontology

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review