Developing a kidney and urinary pathway knowledge base

Journal of Biomedical Semantics

Volumn 2, Issue 2, 2011, Pages

  Jupp, Simon ^a   Klein, Julie ^b,c   Schanstra, Joost ^b,c   Stevens, Robert ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b INSERM   (France)

^c UNIVERSITÉ DE TOULOUSE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84055221252     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-2-S2-S7     Document Type: Article

References (78)

1. Nahas AME, Bello AK: Chronic kidney disease: the global challenge. Lancet. 2005, 365 (9456): 331-340. 10.1016/S0140-6736(05)17789-7.
2. e-LICO: [ http://www.e-lico.eu ]
3. Serban F, Kietz JU, Bernstein A: An Overview of Intelligent Data Assistants for Data Analysis. Proc. of the 3rd Planning to Learn Workshop (WS9) at ECAI'10. 2010, 7-14.
4. Decramer S, de Peredo AG, Breuil B, Mischak H, Monsarrat B, Bascands JL, Schanstra JP: Urine in Clinical Proteomics. Molecular and Cellular Proteomics. 2008, 7 (10): 1850-1862. 10.1074/mcp.R800001-MCP200.
5. Davidson SB, Overton C, Buneman P: Challenges in Integrating Biological Data Sources. Journal of Computational Biology. 1995, 2: 557-572. 10.1089/cmb.1995.2.557.
6. Goble C, Stevens R: State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics. 2008, 41 (5): 687-693. 10.1016/j.jbi.2008.01.008. Semantic Mashup of Biomedical Data
7. Galperin MY: The Molecular Biology Database Collection: 2008 update. Nucleic Acids Research. 2008, 36 (suppl 1): D2-D4.
8. Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A: BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 2009, 37 (Web Server issue): W23-W27. 10.1093/nar/gkp265.
9. Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA: BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research. 2010, 38 (suppl 2): W689-W694. 10.1093/nar/gkq394.
10. Zhao J, Goble C, Stevens R: An Identity Crisis in the Life Sciences. Nucleic Acids Research. 2006, 254-269.
11. Shared Names. [ http://sharedname.org ]
12. van Iersel M, Pico A, Kelder T, Gao J, Ho I, Hanspers K, Conklin B, Evelo C: The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics. 2010, 11: 5-10.1186/1471-2105-11-5.
13. Venkatesh T, Harlow H: Integromics: challenges in data integration. Genome Biology. 2002, 3 (8): REPORTS4027-10.1186/gb-2002-3-8-reports4027.
14. Akula SP, Miriyala RN, Thota H, Rao AA, Gedela S: Techniques for integrating omics data. 2009
15. Al-Daihani B, Gray A, Kille P: Bioinformatics Data Source Integration Based on Semantic Relationships Across Species. Data Mining and Bioinformatics, Volume 4316 of Lecture Notes in Computer Science. Edited by: Dalkilic M, Kim S, Yang J. 2006, Springer Berlin / Heidelberg, 78-93.
16. Töpel T, Kormeier B, Klassen A, Hofestädt R: BioDWH: a data warehouse kit for life science data integration. J Integr Bioinform. 2008, 5 (2): [ http://www.biomedsearch.com/nih/BioDWH-Data-Warehouse-Kit-Life/20134070.html ]
17. Achard F, Vaysseix G, Barillot E: XML, bioinformatics and data integration. Bioinformatics. 2001, 17 (2): 115-125. 10.1093/bioinformatics/17.2.115.
18. Hsing M, Cherkasov A: Integration of Biological Data with Semantic Networks. Current Bioinformatics. 2006, 1 (18): 273-290. 10.2174/157489306777827946.
19. Rector AL, Bechhofer S, Goble CA, Horrocks I, Nowlan WA, Solomon WD: The GRAIL concept modelling language for medical terminology. Artificial Intelligence in Medicine. 1997, 9 (2): 139-171. 10.1016/S0933-3657(96)00369-7.
20. Stevens R, Aranguren ME, Wolstencroft K, Sattler U, Drummond N, Horridge M, Rector A: Using OWL to model biological knowledge. International Journal of Human-Computer Studies. 2007, 65 (7): 583-594. 10.1016/j.ijhcs.2007.03.006. Knowledge representation with ontologies: Present challenges - Future possibilities
21. Bechhofer S, van Harmelen F, Hendler J, Horrocks I, McGuinness DL, Patel-Schneider PF, Stein LA: OWL Web Ontology Language Reference. W3C Recommendation. 2004, [ http://www.w3.org/TR/owl-ref/ ]
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 SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 2007, 25 (11): 1251-1255. 10.1038/nbt1346.
23. Berners-Lee T, Hendler J, Lassila O: The Semantic Web. Scientific American. 2001, 284 (5): 34-43. 10.1038/scientificamerican0501-34.
24. W3C Recommendation, World Wide Web Consortium: RDF Primer. Edited by: Manola F, Miller E. 2004, [ http://www.w3.org/TR/rdf-primer/ ]
25. Ruttenberg A, Rees JA, Samwald M, Marshall MS: Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings in Bioinformatics. 2009, 10 (2): 193-204. 10.1093/bib/bbp004.
26. Antezana E, Kuiper M, Mironov V: Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics. 2009, 10 (4): 392-407. 10.1093/bib/bbp024.
27. Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A: A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics. 2009, 10 (Suppl 10): S10-10.1186/1471-2105-10-S10-S10.
28. Dhanapalan L, Chen JY: A case study of integrating protein interaction data using semantic web technology. Int J Bioinform Res Appl. 2007, 3 (3): 286-302. 10.1504/IJBRA.2007.015004.
29. Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP: An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence. J. of Biomedical Informatics. 2008, 41: 752-765. 10.1016/j.jbi.2008.02.006.
30. Lam H, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong G, Liu N, Crasto C, Morse T, Stephens S, Cheung KH: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics. 2007, 8 (Suppl 3): S4-10.1186/1471-2105-8-S3-S4.
31. Antezana E, Blonde W, Egana M, Rutherford A, Stevens R, De Baets B, Mironov V, Kuiper M: BioGateway: a semantic systems biology tool for the life sciences. BMC Bioinformatics. 2009, 10 (Suppl 10): S11-10.1186/1471-2105-10-S10-S11.
32. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics. 2008, 41 (5): 706-716. 10.1016/j.jbi.2008.03.004. Semantic Mashup of Biomedical Data
33. Ruttenberg A, Rees J, Stephens S, Samwald M, Cheung KH: A Prototype Knowledge Base for the Life Sciences. W3C Interest Group Note. [ http://www.w3.org/TR/hcls-kb/ ]
34. Higgins JP, Wang L, Kambham N, Montgomery K, Mason V, Vogelmann SU, Lemley KV, Brown PO, Brooks JD, van de Rijn M: Gene Expression in the Normal Adult Human Kidney Assessed by Complementary DNA Microarray. Mol. Biol. Cell. 2004, 15 (2): 649-656. 10.1091/mbc.E03-06-0432.
35. Chabardés-Garonne D, Méjean A, Aude JC, Cheval L, Di Stefano A, Gaillard MC, Imbert-Teboul M, Wittner M, Balian C, Anthouard V, Robert C, Surens B, Wincker P, Weissenbach J, Doucet A, Elalouf JM: A panoramic view of gene expression in the human kidney. Proceedings of the National Academy of Sciences of the United States of America. 2003, 100 (23): 13710-13715. 10.1073/pnas.2234604100.
36. EuReGene - European Renal genome Project. [ http://www.euregene.org/ ]
37. Mischak H, Schanstra JP, Vlahou A: Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Prot. Clin. Appl. 2010, 4 (4): 464-478. 10.1002/prca.200900189.
38. Adachi J, Kumar C, Zhang Y, Olsen J, Mann M: The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biology. 2006, 7 (9): R80-10.1186/gb-2006-7-9-r80.
39. Bizer C, Heath T, Berners-Lee T: Linked Data - The Story So Far. International Journal on Semantic Web and Information Systems (IJSWIS). 2009
40. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research. 2009, 37 (suppl 2): W170-W173. 10.1093/nar/gkp440.
41. Gene Ontology Annotations. [ http://www.ebi.ac.uk/GOA ]
42. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics. 2003, 36 (6): 478-500. 10.1016/j.jbi.2003.11.007. Unified Medical Language System
43. Hayamizu T, Mangan M, Corradi J, Kadin J, Ringwald M: The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biology. 2005, 6 (3): R29-10.1186/gb-2005-6-3-r29.
44. Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biology. 2010, 11: R2-10.1186/gb-2010-11-1-r2.
45. Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLJ, Mungall CJ, Smith B: CARO - The Common Anatomy Reference Ontology. Anatomy Ontologies for Bioinformatics Principles and Practice Volume. Edited by: Albert Burger, Duncan Davidson and Richard Baldock. 2007, Springer
46. Vertebrate Anatomy Ontology. [ http://www.ebi.ac.uk/ebiwiki/VBO/index.php/Main_Page ]
47. Bard J, Rhee S, Ashburner M: An ontology for cell types. Genome Biology. 2005, 6 (2): R21-10.1186/gb-2005-6-2-r21.
48. Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C: Relations in biomedical ontologies. Genome Biology. 2005, 6 (5): R46-10.1186/gb-2005-6-5-r46.
49. Consortium GO: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research. 2004, 32 (suppl 1): D258-D261.
50. Horridge M, Tsarkov D: Supporting Early Adoption of OWL 1.1 with Protege-OWL and FaCT++. OWL: Experiences and Directions (OWLED 2006). 2006, Athens, GA
51. Peters B, Ruttenberg A, Greenbaum J, Courtot M, Brinkman R, Whetzel P, Schober D, Sansone SA, Scheuerman R, Rocca-Serra P: Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates. International Conference on Biomedical Ontology. 2009
52. O'Connor MJ, Halaschek-Wiener C, Musen MA: Mapping Master: a Spreadsheet to OWL Mapping Language. International Semantic Web Conference (ISWC). 2010
53. EuroKUP. [ http://www.eurokup.org ]
54. Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Stevens R, Wolstencroft K: Populous: A template tool for populating OWL ontologies. Semantic Web Application and Tools for the Life Sciences. 2010
55. Semantic Web Health Care and Life Sciences (HCLS) Interest Group. [ http://www.w3.org/2001/sw/hcls ]
56. Entre Gene. [ http://www.ncbi.nlm.nih.gov/gene ]
57. UniProt Knowledgebase. [ http://www.uniprot.org ]
58. KEGG. [ http://www.genome.jp/kegg ]
59. microCosm. [ http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ ]
60. Homologene. [ http://www.ncbi.nlm.nih.gov/homologene ]
61. Bio2RDF ontology. [ http://bio2rdf.org ]
62. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SAA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium: Modeling biomedical experimental processes with OBI. Journal of biomedical semantics. 2010, 1 Suppl 1 (Suppl 1): S7+-
63. Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010, 26 (8): 1112-1118. 10.1093/bioinformatics/btq099.
64. Gkoutos G, Green E, Mallon AM, Hancock J, Davidson D: Using ontologies to describe mouse phenotypes. Genome Biology. 2004, 6: R8-10.1186/gb-2004-6-1-r8.
65. Rohloff K, Dean M, Emmons I, Ryder D, Sumner J: An Evaluation of Triple-Store Technologies for Large Data Stores. On the Move to Meaningful Internet Systems 2007: OTM 2007 Workshops, Volume4806 of Lecture Notes in Computer Science. Edited by: Meersman R, Tari Z, Herrero P. 2007, Springer Berlin / Heidelberg, 1105-1114. 10.1007/978-3-540-76890-6_38,
66. Comparison of Triple Stores. [ http://www.bioontology.org/wiki/images/6/6a/Triple_Stores.pdf ]
67. Broekstra J, Kampman A, van Harmelen F: Sesame: A Generic Architecture for Storing and Querying RDF and RDF Schema. The Semantic Web - ISWC 2002, Volume 2342 of Lecture Notes in Computer Science. Edited by: Horrocks I, Hendler J. 2002, Springer Berlin / Heidelberg, 54-68.
68. Kiryakov A, Ognyanov D, Manov D: OWLIM - A Pragmatic Semantic Repository for OWL. WISE Workshops, Volume 3807 of Lecture Notes in Computer Science. Edited by: Dean M, Guo Y, Jun W, Kaschek R, Krishnaswamy S, Pan Z, Sheng QZ. 2005, Springer, 182-192. full_text. [ http://dblp.uni-trier.de/db/conf/wise/wise2005w.html#KiryakovOM05 ]
69. Pubby. [ http://www4.wiwiss.fu-berlin.de/pubby/ ]
70. Kidney and Urinary Pathway Knowledge Base (KUP KB). [ http://www.e-lico.eu/kupkb ]
71. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y: Pellet: A practical OWL-DL reasoner. Web Semant. 2007, 5 (2): 51-53. 10.1016/j.websem.2007.03.004. [ http://dx.doi.org/10.1016/j.websem.2007.03.004 ]
72. Tsarkov D, Horrocks I: FaCT++ Description Logic Reasoner: System Description. Proc. of the Int.Joint Conf. on Automated Reasoning (IJCAR 2006), Volume 4130 of Lecture Notes in Artificial Intelligence. 2006, Springer, 292-297.
73. Motik B, Shearer R, Horrocks I: Hypertableau Reasoning for Description Logics. Journal of Artificial Intelligence Research. 2009, 36: 165-228.
74. ON KUP Challenge. [ http://tunedit.org/challenge/ON ]
75. Glimm B, Krötzsch M: SPARQL Beyond Subgraph Matching. Proceedings of the 9th International Semantic Web Conference (ISWC'10), Volume 6496 of LNCS. Edited by: Patel-Schneider PF, Pan Y, Glimm B, Hitzler P, Mika P, Pan J, Horrocks I. 2010, Springer, 241-256.
76. SPARQL 1.1 Entailment Regimes. [ http://www.w3.org/TR/2010/WD-sparql11-entailment-20100126/ ]
77. Sirin E, Parsia B: SPARQL-DL: SPARQL Query for OWL-DL. OWLED 2007: Proceedings of the Third International Workshop on OWL: Experiences and Directions. 2007, Innsbruck, Austria, [ http://ceur-ws.org/Vol-258/paper14.pdf ]
78. The Gene Ontology Consortium: Gene Ontology: Tool for the Unification of Biology. Nature Genetics. 2000, 25: 25-29. 10.1038/75556.