The zebrafish anatomy and stage ontologies: Representing the anatomy and development of Danio rerio

Journal of Biomedical Semantics

Volumn 5, Issue 1, 2014, Pages

  van Slyke, Ceri E ^a   Bradford, Yvonne M ^a   Westerfield, Monte ^a   Haendel, Melissa A ^b  

^a UNIVERSITY OF OREGON   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84907961999     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-5-12     Document Type: Article

References (81)

1. Medeiros DM, Crump JG. New perspectives on pharyngeal dorsoventral patterning in development and evolution of the vertebrate jaw. Dev Biol 2012, 371:121-135. 10.1016/j.ydbio.2012.08.026, 3466404, 22960284.
2. Solnica-Krezel L, Schier AF, Driever W. Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics 1994, 136:1401-1420. 1205920, 8013916.
3. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RHA, Cuppen E. Efficient target-selected mutagenesis in zebrafish. Genome Res 2003, 13:2700-2707. 10.1101/gr.1725103, 403812, 14613981.
4. Amsterdam A, Yoon C, Allende M, Becker T, Kawakami K, Burgess S, Gaiano N, Hopkins N. Retrovirus-mediated insertional mutagenesis in zebrafish and identification of a molecular marker for embryonic germ cells. Cold Spring Harb Symp Quant Biol 1997, 62:437-450.
5. Nasevicius A, Ekker SC. Effective targeted gene " knockdown" in zebrafish. Nat Genet 2000, 26:216-220. 10.1038/79951, 11017081.
6. Sander JD, Cade L, Khayter C, Reyon D, Peterson RT, Joung JK, Yeh J-RJ. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat Biotechnol 2011, 29:697-698. 10.1038/nbt.1934, 3154023, 21822241.
7. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh J-RJ, Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013, 31:227-229. 10.1038/nbt.2501, 3686313, 23360964.
8. Balciunas D, Davidson AE, Sivasubbu S, Hermanson SB, Welle Z, Ekker SC. Enhancer trapping in zebrafish using the sleeping beauty transposon. BMC Genomics 2004, 5:62. 10.1186/1471-2164-5-62, 520745, 15347431.
9. Kotani T, Nagayoshi S, Urasaki A, Kawakami K. Transposon-mediated gene trapping in zebrafish. Methods 2006, 39:199-206. 10.1016/j.ymeth.2005.12.006, 16814563.
10. ZFIN. http://zfin.org.
11. Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res 2003, 31:241-243. 10.1093/nar/gkg027, 165474, 12519991.
12. Sprague J, Bayraktaroglu L, Clements D, Conlin T, Fashena D, Frazer K, Haendel M, Howe DG, Mani P, Ramachandran S, Schaper K, Segerdell E, Song P, Sprunger B, Taylor S, Van Slyke CE, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res 2006, 34(Database issue):D581-D585. 1347449, 16381936.
13. Owl version ZFA. http://purl.obolibrary.org/obo/zfa.owl.
14. Zebrafish Develomental Stage Ontology. http://purl.obolibrary.org/obo/zfs.obo.
15. 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:e1000247. 10.1371/journal.pbio.1000247, 2774506, 19956802.
16. Relations Ontology (RO). http://purl.obolibrary.org/obo/ro.owl.
17. Anatomy Dictionary Meeting May 10th-11th 1999. http://zfin.org/zf_info/anatomy/dict/meeting_sum.html.
18. Haendel MA, Neuhaus F, Osumi-Sutherland DS, Mabee PM, Mejino JLV, Mungall CJ, Smith B. CARO- The Common Anatomy Reference Ontology. Anat Ontol Bioinforma Princ Pract 2008, 327-350. London: Springer, Burger A, Davidson D, Baldock R.
19. EMAP. http://www.obofoundry.org/cgi-bin/detail.cgi?id=emap.
20. Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA. EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. J Biomed Semantics 2013, 4:15. 10.1186/2041-1480-4-15, 3851555, 23972281.
21. Drosophila gross anatomy (FBbt). http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy.
22. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25:1251-1255. 10.1038/nbt1346, 2814061, 17989687.
23. OBO Foundry Principles. 2008, http://obofoundry.org/wiki/index.php/OBO_Foundry_Principles_2008.
24. Uberon-ZFA. http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl.
25. Cell Ontology (CL). http://purl.obolibrary.org/obo/cl.owl.
26. Ghazvinian A, Noy NF, Musen MA. How orthogonal are the OBO foundry ontologies?. J Biomed Semantics 2011, 2(Suppl 2):S2.
27. OBO Flat File Format 1.4 Syntax and Semantics. http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html.
28. Zon LI, Traver D, Davidson AJ, Van Slyke CE. ZFIN Anatomy Working Group: Blood 2006,
29. Mabee PM, Haendel MA, Arratia G, Coburn MM, Hilton E, Lundberg J, Mayden RL. ZFIN Anatomy Working Group: Skeletal System 2006,
30. Chen X, Moorman SJ, Wallace KN, Pack M, Haendel MA. ZFIN Anatomy Working Group: Digestive System 2007,
31. Sive H, Mueller T, Wullimann MF, Kuwada JY, Moorman SJ, Haendel MA. ZFIN Anatomy Working Group: Nervous System 2006,
32. UDoc - the Uberon documentation system. https://github.com/obophenotype/uberon/wiki/About-documentation.
33. Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One 2012, 7:e51070. 10.1371/journal.pone.0051070, 3519498, 23251424.
34. Tracker, ZFA. https://sourceforge.net/tracker/?group_id=76834&atid=994726.
35. Hu N, Yost HJ, Clark EB. Cardiac morphology and blood pressure in the adult zebrafish. Anat Rec 2001, 264:1-12. 10.1002/ar.1111, 11505366.
36. Poon K-L, Liebling M, Kondrychyn I, Garcia-Lecea M, Korzh V. Zebrafish cardiac enhancer trap lines: new tools for in vivo studies of cardiovascular development and disease. Dev Dyn 2010, 239:914-926. 10.1002/dvdy.22203, 20063419.
37. Pattern Formation in Zebrafish. Volume 40. 2002, Berlin, Heidelberg, New York: Springer-Verlag, Solnica-Krezel L.
38. Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG, Hughes SM. Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evol Dev 2006, 8:101-110. 10.1111/j.1525-142X.2006.05079.x, 3360970, 16409387.
39. Windner SE, Bird NC, Patterson SE, Doris RA, Devoto SH. Fss/Tbx6 is required for central dermomyotome cell fate in zebrafish. Biol Open 2012, 1:806-814. 10.1242/bio.20121958, 3507223, 23213474.
40. Yaniv K, Isogai S, Castranova D, Dye L, Hitomi J, Weinstein BM. Live imaging of lymphatic development in the zebrafish. Nat Med 2006, 12:711-716. 10.1038/nm1427, 16732279.
41. Küchler AM, Gjini E, Peterson-Maduro J, Cancilla B, Wolburg H, Schulte-Merker S. Development of the zebrafish lymphatic system requires VEGFC signaling. Curr Biol 2006, 16:1244-1248. 10.1016/j.cub.2006.05.026, 16782017.
42. Developmental Staging Series. http://www.obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_stages.
43. Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn 1995, 203:253-310. 10.1002/aja.1002030302, 8589427.
44. Lowery LA, Sive H. Strategies of vertebrate neurulation and a re-evaluation of teleost neural tube formation. Mech Dev 2004, 121:1189-1197. 10.1016/j.mod.2004.04.022, 15327780.
45. Zebrafish Atlas. http://zfatlas.psu.edu/index.php.
46. Spatial. http://www.obofoundry.org/cgi-bin/detail.cgi?id=spatia.
47. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology: the gene ontology consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
48. Gene Ontology. http://purl.obolibrary.org/obo/go.obo.
49. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the gene ontology. J Biomed Inform 2011, 44:80-86. 10.1016/j.jbi.2010.02.002, 2910209, 20152934.
50. Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007, 22:345-350. 10.1016/j.tree.2007.03.013, 17416439.
51. PATO. http://purl.obolibrary.org/obo/pato.owl.
52. MPATH. http://purl.obolibrary.org/obo/mpath.owl.
53. Simmons T, Appel B. Mutation of pescadillo disrupts oligodendrocyte formation in zebrafish. PLoS One 2012, 7:e32317. 10.1371/journal.pone.0032317, 3285679, 22384214.
54. Washington NL, Mungall CJ, Abdulla A, Lewis SE, Harris N, Gibson M. Phenote. 2012, http://www.phenote.org/.
55. Medaka Fish anatomy and development ontology (MFO). http://www.obofoundry.org/cgi-bin/detail.cgi?id=medaka_anatomy_development.
56. Xenopus anatomy and development ontology (XAO). http://www.obofoundry.org/cgi-bin/detail.cgi?id=xenopus_anatomy.
57. Segerdell E, Bowes JB, Pollet N, Vize PD. An ontology for Xenopus anatomy and development. BMC Dev Biol 2008, 8:92. 10.1186/1471-213X-8-92, 2561031, 18817563.
58. Teleost anatomy ontology (TAO). http://www.obofoundry.org/cgi-bin/detail.cgi?id=teleost_anatomy.
59. Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM. The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol 2010, 59:369-383. 10.1093/sysbio/syq013, 2885267, 20547776.
60. Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One 2010, 5:e10708. 10.1371/journal.pone.0010708, 2873956, 20505755.
61. Haendel MA, Balhoff JP, Bastian F, Blackburn DC, Blake JA, Comte A, Dahdul WM, Dececchi T, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno P, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology. J Biomed Semantics 2014, Accepted(in revision).
62. Courtot M, Gibson F, Lister A, Malone J, Schober D, Brinkman R, Ruttenberg A. MIREOT: the minimum information to reference an external ontology term. Nat Preced 2009, 1.
63. Vertebrate Skeletal Anatomy Ontology. http://www.obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_skeletal_anatomy.
64. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012, 13:R5. 10.1186/gb-2012-13-1-r5, 3334586, 22293552.
65. Phenotype RCN. http://www.phenotypercn.org/.
66. Bradford YM, Dahdul WM, Dececchi A, Haendel MA, Hall BK, Hayamizu T, Hochheiser H, Lewis SE, Mabee PM, McCarthy F, Mungall CJ, Olsson L, Ponferrada V, Pulikanti R, Ruffins S, Segerdell E, Wall C, Zorn C. Phenotype RCN Neural Crest Meeting 2012, Durham, NC.
67. Bgee. http://bgee.unil.ch/bgee/bgee.
68. Bastian F, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M. Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. Data Integr Life Sci 2008, 124-131. France: Evry, Bairoch A, Cohen-Boulakia S, Froidevaux C.
69. Phenoscape Knowledgebase. http://kb.phenoscape.org/.
70. Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2014, 2-30.
71. Smedley D, Oellrich A, Köhler S, Ruef B, Westerfield M, Robinson P, Lewis S, Mungall C. PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford) 2013, 2013:bat025. 3649640, 23660285.
72. Chen C-K, Mungall CJ, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield PN, Smedley D. MouseFinder: candidate disease genes from mouse phenotype data. Hum Mutat 2012, 33:858-866. 10.1002/humu.22051, 3327758, 22331800.
73. Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech 2013, 6:358-372. 10.1242/dmm.010322, 3597018, 23104991.
74. Becker TS, Rinkwitz S. Zebrafish as a genomics model for human neurological and polygenic disorders. Dev Neurobiol 2012, 72:415-428. 10.1002/dneu.20888, 21465670.
75. LAMHDI. http://www.lamhdi.org/.
76. Monarch Initiative. http://monarchinitiative.org/.
77. Anatomy Dictionary Meeting December 10, 1999. http://zfin.org/zf_info/anatomy/dict/mtg2.html.
78. Day-Richter J, Harris MA, Haendel MA, Lewis SE, . The Gene Ontology OBO-Edit Working Group OBO-Edit-an ontology editor for biologists. Bioinformatics 2007, 23:2198-2200. 10.1093/bioinformatics/btm112, 17545183, The Gene Ontology OBO-Edit Working Group.
79. Zebrafish Anatomy and Development Ontology (ZFA) foundry page. http://www.obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy.
80. Zebrafish-anatomical-ontology. http://code.google.com/p/zebrafish-anatomical-ontology/.
81. OORT. http://code.google.com/p/owltools/wiki/OortIntro.