The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Journal of Biomedical Semantics

Volumn 1, Issue , 2010, Pages

  Katayama, Toshiaki ^a   Arakawa, Kazuharu ^a   Nakao, Mitsuteru ^a   Ono, Keiichiro ^a   Aoki Kinoshita, Kiyoko F ^a   Yamamoto, Yasunori ^a   Yamaguchi, Atsuko ^a   Kawashima, Shuichi ^a   Chun, Hong Woo ^a   Aerts, Jan ^a   Aranda, Bruno ^a   Barboza, Lord H ^a   Bonnal, Raoul J P ^a   Bruskiewich, Richard ^a   Bryne, Jan C ^a   Fernández, José M ^a   Funahashi, Akira ^a   Gordon, Paul M K ^a   Goto, Naohisa ^a   Groscurth, Andreas ^a   Gutteridge, Alex ^a   Holland, Richard ^a   Kano, Yoshinobu ^a   Kawas, Edward A ^a   Kerhornou, Arnaud ^a   Kibukawa, Eri ^a   Kinjo, Akira R ^a   Kuhn, Michael ^a   Lapp, Hilmar ^a   Lehvaslaiho, Heikki ^a   Nakamura, Hiroyuki ^a   Nakamura, Yasukazu ^a   Nishizawa, Tatsuya ^a   Nobata, Chikashi ^a   Noguchi, Tamotsu ^a   Oinn, Thomas M ^a   Okamoto, Shinobu ^a   Owen, Stuart ^a   Pafilis, Evangelos ^a   Pocock, Matthew ^a   Prins, Pjotr ^a   Ranzinger, René ^a   Reisinger, Florian ^a   Salwinski, Lukasz ^a   Schreiber, Mark ^a   Senger, Martin ^a   Shigemoto, Yasumasa ^a   Standley, Daron M ^a   Sugawara, Hideaki ^a   Tashiro, Toshiyuki ^a   Trelles, Oswaldo ^a   Vos, Rutger A ^a   Wilkinson, Mark D ^a   York, William ^a   Zmasek, Christian M ^a   Asai, Kiyoshi ^a   Takagi, Toshihisa ^a   more..

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84859350703     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-1-8     Document Type: Review

References (88)

1. Stockinger H, Attwood T, Chohan SN, Cote R, Cudre-Mauroux P, Falquet L, Fernandes P, Finn RD, Hupponen T, Korpelainen E, et al. Experience using web services for biological sequence analysis. Brief Bioinform 2008, 9:493-505. 10.1093/bib/bbn029, 2989672, 18621748.
2. Sayers E, Barrett T, Benson D, Bryant S, Canese K, Chetvernin V, Church D, Dicuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 2008, 37:D5-D15. 10.1093/nar/gkn741, 2686545, 18940862.
3. Labarga A, Valentin F, Anderson M, Lopez R. Web services at the European bioinformatics institute. Nucleic Acids Res 2007, 35:W6-W11. 10.1093/nar/gkm291, 1933145, 17576686.
4. Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Research 2008, 37:D16-D18. 10.1093/nar/gkn724, 2686496, 18927114.
5. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucl Acids Res 2007, D480-D484. 10.1093/nar/gkm882, 2238879, 18077471.
6. Standley DM, Kinjo AR, Kinoshita K, Nakamura H. Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform 2008, 9:276-285. 10.1093/bib/bbn015, 18430752.
7. Stein L. Creating a bioinformatics nation. Nature 2002, 417:119-120. 10.1038/417119a, 12000935.
8. Navas-Delgado I, Rojano-Munoz M, Ramirez S, Perez A, Aldana-Montes J, Trelles O. Intelligent client for integrating bioinformatics services. Bioinformatics 2006, 22:106-111. 10.1093/bioinformatics/bti740, 16257987.
9. Wilkinson MD, Links M. BioMOBY: an open source biological web services proposal. Brief Bioinform 2002, 3:331-341. 10.1093/bib/3.4.331, 12511062.
10. Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform 2008, 9:220-231. 10.1093/bib/bbn003, 18238804.
11. Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C, Fuellen G, Gilbert J, Korf I, Lapp H, et al. The Bioperl Toolkit: Perl Modules for the Life Sciences. Genome Res 2002, 12:1611-1618. 10.1101/gr.361602, 187536, 12368254.
12. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25:1422-1423. 10.1093/bioinformatics/btp163, 2682512, 19304878.
13. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: Bioinformatics software for the Ruby programming language. Bioinformatics 2951089, 20739307.
14. Holland RCG, Down T, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ. BioJava: an Open-Source Framework for Bioinformatics. Bioinformatics (Oxford, England) 2008, 24:2096-2097. 10.1093/bioinformatics/btn397, 2530884, 18689808.
15. Stajich JE, Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we?. Brief Bioinform 2006, 7:287-296. 10.1093/bib/bbl026, 16899494.
16. BioHackathon 2008. , http://hackathon.dbcls.jp/
17. DBCLS: Database Center for Life Science. , http://dbcls.rois.ac.jp/
18. CBRC: Computational Biology Research Center. , http://www.cbrc.jp/
19. Zdobnov EM, Lopez R, Apweiler R, Etzold T. The EBI SRS server--recent developments. Bioinformatics 2002, 18:368-373. 10.1093/bioinformatics/18.2.368, 11847095.
20. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The distributed annotation system. BMC Bioinformatics 2001, 2:7. 10.1186/1471-2105-2-7, 58584, 11667947.
21. Sugawara H, Ogasawara O, Okubo K, Gojobori T, Tateno Y. DDBJ with new system and face. Nucleic Acids Research 2007, 36:D22-D24. 10.1093/nar/gkm889, 2238829, 17962300.
22. Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M. DBGET/LinkDB: an integrated database retrieval system. Pacific Symposium on Biocomputing 1998, 683-694.
23. Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 2000, 16:276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
24. Web Services @ W3C. , http://www.w3.org/2002/ws/
25. WSDL. , http://www.w3.org/TR/wsdl
26. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T. Taverna: a tool for building and running workflows of services. Nucleic Acids Res 2006, 34:W729-W732. 10.1093/nar/gkl320, 1538887, 16845108.
27. Gordon P, Sensen C. Seahawk: moving beyond HTML in Web-based bioinformatics analysis. BMC Bioinformatics 2007, 8:208. 10.1186/1471-2105-8-208, 1906838, 17577405.
28. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 2003, 19:305-306. 10.1093/bioinformatics/19.2.305, 12538262.
29. myGrid. , http://www.mygrid.org.uk/
30. MOWserv. , http://www.inab.org/MOWServ/
31. G-language GAE. , http://www.g-language.org/
32. Gordon PMK, Sensen CW. Creating Bioinformatics Semantic Web Services from Existing Web Services: A real-world application of SAWSDL. Proceedings of the IEEE International Conference on Web Services 2008, 608-614.
33. Open Bio Foundation. , http://open-bio.org/
34. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32:D449-451. 10.1093/nar/gkh086, 308820, 14681454.
35. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 2007, 35:D358-D362. 10.1093/nar/gkl825, 1669762, 17098935.
36. Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 2008, 36:D684-D688. 10.1093/nar/gkm795, 2238848, 18084021.
37. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010, 38:D525-531. 10.1093/nar/gkp878, 2808934, 19850723.
38. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, et al. IntAct--open source resource for molecular interaction data. Nucleic Acids Res 2007, 35:D561-D565. 10.1093/nar/gkl958, 1751531, 17145710.
39. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2:2366-2382. 10.1038/nprot.2007.324, 17947979.
40. Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE 2008, 96:1254-1265.
41. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
42. BioPAX. , http://www.biopax.org/
43. Stromback L, Lambrix P. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 2005, 21:4401-4407. 10.1093/bioinformatics/bti718, 16234320.
44. Stromback L, Jakoniene V, Tan H, Lambrix P. Representing, storing and accessing molecular interaction data: a review of models and tools. Brief Bioinform 2006, 7:331-338. 10.1093/bib/bbl039, 17132622.
45. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol 2004, 22:177-183. 10.1038/nbt926, 14755292.
46. IntAct PSIQUIC Web Service. , http://www.ebi.ac.uk/intact/psicquic/webservices
47. iRefIndex. , http://irefindex.uio.no/
48. IMEx. , http://imex.sourceforge.net/
49. Marchal I, Golfier G, Dugas O, Majed M. Bioinformatics in glycobiology. Biochimie 2003, 85:75-81. 10.1016/S0300-9084(03)00068-3, 12765777.
50. Bohne-Lang A, Lang E, Förster T, von der Lieth CW. LINUCS: linear notation for unique description of carbohydrate sequences. Carbohydr Res 2001, 336:1-11. 10.1016/S0008-6215(01)00230-0, 11675023.
51. Aoki K, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa M. KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucl Acids Res 2004, 32:W267-272. 10.1093/nar/gkh473, 441611, 15215393.
52. GLYDE-II. , http://glycomics.ccrc.uga.edu/GLYDE-II/
53. CIPRES. , http://www.phylo.org/
54. Kepler Project. , http://www.kepler-project.org/
55. Han MV, Zmasek CM. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 2009, 10:356. 10.1186/1471-2105-10-356, 2774328, 19860910.
56. nexml - phylogenetic data as xml. , http://www.nexml.org/
57. Maddison DR, Swofford DL, Maddison WP. NEXUS: an extensible file format for systematic information. Syst Biol 1997, 46:590-621. 10.1093/sysbio/46.4.590, 11975335.
58. Clark T, Martin S, Liefeld T. Globally distributed object identification for biological knowledgebases. Brief Bioinform 2004, 5:59-70. 10.1093/bib/5.1.59, 15153306.
59. phyloXML Web Service API. , http://evoinfo.nescent.org/PhyloWS
60. Database Interop Hackathon. , https://www.nescent.org/wg/evoinfo/index.php?title=Database_Interop_Hackathon
61. Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 2006, 22:2971-2972. 10.1093/bioinformatics/btl505, 17021158.
62. Maddison DR, Schulz K-S, Maddison WP. The Tree of Life Web Project. Zootaxa 2007, 1668:19-40.
63. CQL: Contextual Query Language. , http://www.loc.gov/standards/sru/specs/cql.html
64. TreeBase. , http://www.treebase.org/
65. Apache UIMA. , http://incubator.apache.org/uima/
66. Baumgartner WA, Cohen KB, Hunter L. An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab 2008, 3:1. 10.1186/1747-5333-3-1, 2276192, 18230184.
67. BioNLP UIMA Component Respository. , http://bionlp-uima.sourceforge.net/
68. U-Compare. , http://u-compare.org/
69. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through Web services: Calling Whatizit. Bioinformatics 2007, 24:296-298. 10.1093/bioinformatics/btm557, 18006544.
70. Termine. , http://www.nactem.ac.uk/software/termine/
71. Fernandez JM, Hoffmann R, Valencia A. iHOP web services. Nucleic Acids Res 2007, 35:W21-26. 10.1093/nar/gkm298, 1933131, 17485473.
72. Leitner FKM, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing meta-services for biomedical information extraction. Genome Biology 2008, 9:S6.
73. Allie. , http://allie.dbcls.jp/
74. The DDBJ/EMBL/GenBank Feature Table Definition. , http://www.insdc.org/documents/feature_table.html
75. BioSQL. , http://biosql.org/
76. MTOM. , http://www.w3.org/TR/soap12-mtom/
77. BitTorrent. , http://www.bittorrent.com/
78. Foster I, Czajkowski K, Ferguson DE, Frey J, Graham S, Maguire T, Snelling D, Tuecke S. Modeling and managing State in distributed systems: the role of OGSI and WSRF. Proceedings of the IEEE 2005, 93:604-612.
79. OASIS standards. , http://www.oasis-open.org/
80. WS-I Organization. , http://www.ws-i.org/
81. Miyazaki S, Sugawara H, Ikeo K, Gojobori T, Tateno Y. DDBJ in the stream of various biological data. Nucleic Acids Res 2004, 32:D31-D34. 10.1093/nar/gkh127, 308861, 14681352.
82. Embrace Network of Excellence. , http://www.embracegrid.info/
83. InstantSOAP. , http://instantsoap.sourceforge.net/
84. SoapLab. , http://www.ebi.ac.uk/Tools/webservices/soaplab/overview
85. Life Sciences Analysis Engine Specification. , http://www.omg.org/technology/documents/formal/lsae.htm
86. MyProxy Credential Management Service. , http://grid.ncsa.uiuc.edu/myproxy/
87. Katayama T, Nakao M, Takagi T. TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. Nucleic Acids Research 2010, 38:W706-W711. 10.1093/nar/gkq386, 2896079, 20472643.
88. Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, et al. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics 2007, 3:287-296.