WormBase 2016: Expanding to enable helminth genomic research

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D774-D780

  Howe, Kevin L ^a   Bolt, Bruce J ^a   Cain, Scott ^b   Chan, Juancarlos ^c   Chen, Wen J ^c   Davis, Paul ^a   Done, James ^c   Down, Thomas ^a   Gao, Sibyl ^b   Grove, Christian ^c   Harris, Todd W ^b   Kishore, Ranjana ^c   Lee, Raymond ^c   Lomax, Jane ^d   Li, Yuling ^c   Muller, Hans Michael ^c   Nakamura, Cecilia ^c   Nuin, Paulo ^b   Paulini, Michael ^a   Raciti, Daniela ^c   Schindelman, Gary ^c   Stanley, Eleanor ^d   Tuli, Mary Ann ^c   Van Auken, Kimberly ^c   Wang, Daniel ^c   Wang, Xiaodong ^c   Williams, Gary ^a   Wright, Adam ^b   Yook, Karen ^c   Berriman, Matthew ^d   Kersey, Paul ^a   Schedl, Tim ^e   Stein, Lincoln ^b   Sternberg, Paul W ^b,f   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^c California Institute of Technology   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENOMICS; DATA ANALYSIS; DATA MINING; GENE FUNCTION; GENE SEQUENCE; GENETIC DATABASE; GENOME ANALYSIS; GENOMICS; HUMAN; MEDICAL RESEARCH; NONHUMAN; PARASITE IDENTIFICATION; PLATYHELMINTH; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTOZOAL GENETICS; SEQUENCE ANALYSIS; SOFTWARE DESIGN; WORMBASE DATABASE; ANIMAL; CAENORHABDITIS ELEGANS; GENE; GENETICS; GENOME; MOLECULAR GENETICS; NEMATODE; SOFTWARE;

ANIMALS; CAENORHABDITIS ELEGANS; DATABASES, GENETIC; GENES, HELMINTH; GENOME, HELMINTH; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; NEMATODA; PLATYHELMINTHS; SOFTWARE;

EID: 84976875290     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1217     Document Type: Article

References (44)

1. Platt, H. M. (1994) Foreword. In: Lorenezen, S (ed). The Phylogenetic Systematics of Free-living Nematodes. The Ray Society, London, pp. 1-2.
2. Zhang, Z. Q. (2013) Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness (Addenda 2013). Zootaxa, 3703, 1-82.
3. De Ley, P. (2006) A quick tour of nematode diversity and the backbone of nematode phylogeny. WormBook, doi:10.1895/wormbook.1.41.1.
4. Brenner, S. (1974) The genetics of Caenorhabditis elegans. Genetics, 77, 71-94.
5. Riddle, D. L., Blumenthal, T., Meyer, B. J. and Priess, J. R. (1997) C.elegans II. 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
6. Harris, T. W., Baran, J., Bieri, T., Cabunoc, A., Chan, J., Chen, W. J., Davis, P., Done, J., Grove, C., Howe, K. et al. (2014) WormBase 2014: new views of curated biology. Nucleic Acids Res., 42, D789-D793.
7. Schwarz, E. M., Korhonen, P. K., Campbell, B. E., Young, N. D., Jex, A. R., Jabbar, A., Hall, R. S., Mondal, A., Howe, A. C., Pell, J. et al. (2013) The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biol., 14, R89.
8. Laing, R., Kikuchi, T., Martinelli, A., Tsai, I. J., Beech, R. N., Redman, E., Holroyd, N., Bartley, D. J., Beasley, H., Britton, C. et al. (2013) The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol., 14, R88.
9. Jex, A. R., Liu, S., Li, B., Young, N. D., Hall, R. S., Li, Y., Yang, L., Zeng, N., Xu, X., Xiong, Z. et al. (2011) Ascaris suum draft genome. Nature, 479, 529-533.
10. Wang, J., Mitreva, M., Berriman, M., Thorne, A., Magrini, V., Koutsovoulos, G., Kumar, S., Blaxter, M. L. and Davis, R. E. (2012) Silencing of germline-expressed genes by DNA elimination in somatic cells. Dev. Cell, 23, 1072-1080.
11. Holt, C. and Yandell, M. (2011) MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12, 491.
12. Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S. and Morgenstern, B. (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res., 34, W435-W439.
13. Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y. O. and Borodovsky, M. (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res., 18, 1979-1990.
14. Korf, I. (2004) Gene finding in novel genomes. BMC Bioinformatics, 5, 59.
15. She, R., Chu, J. S., Uyar, B., Wang, J., Wang, K. and Chen, N. (2011) genBlastG: using BLAST searches to build homologous gene models. Bioinformatics, 27, 2141-2143.
16. Otto, T. D., Dillon, G. P., Degrave, W. S. and Berriman, M. (2011) RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res., 39, e57.
17. Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E. (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
18. Nguyen, N., Hickey, G., Raney, B. J., Armstrong, J., Clawson, H., Zweig, A., Karolchik, D., Kent, W. J., Haussler, D. and Paten, B. (2014) Comparative assembly hubs: web-accessible browsers for comparative genomics. Bioinformatics, 30, 3293-3301.
19. Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D. and Haussler, D. (2011) Cactus: algorithms for genome multiple sequence alignment. Genome Res., 21, 1512-1528.
20. Hickey, G., Paten, B., Earl, D., Zerbino, D. and Haussler, D. (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics, 29, 1341-1342.
21. Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G. et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236-1240.
22. Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
23. McLaren, W., Pritchard, B., Rios, D., Chen, Y., Flicek, P. and Cunningham, F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics, 26, 2069-2070.
24. Yates, A., Beal, K., Keenan, S., McLaren, W., Pignatelli, M., Ritchie, G. R., Ruffier, M., Taylor, K., Vullo, A. and Flicek, P. (2015) The Ensembl REST API: ensembl data for any language. Bioinformatics, 31, 143-145.
25. Kinsella, R. J., Kahari, A., Haider, S., Zamora, J., Proctor, G., Spudich, G., Almeida-King, J., Staines, D., Derwent, P., Kerhornou, A. et al. (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford), bar030.
26. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
27. dos Santos, G., Schroeder, A. J., Goodman, J. L., Strelets, V. B., Crosby, M. A., Thurmond, J., Emmert, D. B., Gelbart, W. M. and FlyBase, C. (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res., 43, D690-D697.
28. Costanzo, M. C., Engel, S. R., Wong, E. D., Lloyd, P., Karra, K., Chan, E. T., Weng, S., Paskov, K. M., Roe, G. R., Binkley, G. et al. (2014) Saccharomyces genome database provides new regulation data. Nucleic Acids Res., 42, D717-D725.
29. Ruzicka, L., Bradford, Y. M., Frazer, K., Howe, D. G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C. E., Eagle, A. E. et al. (2015) ZFIN, The zebrafish model organism database: Updates and new directions. Genesis, 53, 498-509.
30. Eppig, J. T., Blake, J. A., Bult, C. J., Kadin, J. A., Richardson, J. E. and Mouse Genome Database, G. (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res., 43, D726-D736.
31. Berardini, T. Z., Reiser, L., Li, D., Mezheritsky, Y., Muller, R., Strait, E. and Huala, E. (2015) The arabidopsis information resource: Making and mining the 'gold standard' annotated reference plant genome. Genesis, 53, 474-485.
32. Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J. and Holmes, I. H. (2009) JBrowse: a next-generation genome browser. Genome Res., 19, 1630-1638.
33. Lee, R. Y. and Sternberg, P. W. (2003) Building a cell and anatomy ontology of Caenorhabditis elegans. Comp. Funct. Genomics, 4, 121-126.
34. Kibbe, W. A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C. J., Binder, J. X., Malone, J., Vasant, D. et al. (2015) Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res., 43, D1071-D1078.
35. Schindelman, G., Fernandes, J. S., Bastiani, C. A., Yook, K. and Sternberg, P. W. (2011) Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics, 12, 32.
36. Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res., 43, D1049-D1056.
37. Smith, R. N., Aleksic, J., Butano, D., Carr, A., Contrino, S., Hu, F., Lyne, M., Lyne, R., Kalderimis, A., Rutherford, K. et al. (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics, 28, 3163-3165.
38. Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G. and Kasprzyk, A. (2009) BioMart-biological queries made easy. BMC Genomics, 10, 22.
39. Nakamura, Y., Cochrane, G., Karsch-Mizrachi, I. and International Nucleotide Sequence Database Collaboration. (2013) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res., 41, D21-D24.
40. Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., Humphrey, J., Kerhornou, A., Khobova, J. et al. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res., 42, D546-D552.
41. Rosenbloom, K. R., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M. et al. (2015) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43, D670-D681.
42. Yook, K., Harris, T. W., Bieri, T., Cabunoc, A., Chan, J., Chen, W. J., Davis, P., Cruz, N., Duong, A., Fang, R. et al. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 40, D735-D741.
43. Amberger, J. S., Bocchini, C. A., Schiettecatte, F., Scott, A. F. and Hamosh, A. (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM (R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
44. Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L. and Overington, J. P. (2015) ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Res., 43, W612-W620.