A collaborative methodology for developing a semantic model for interlinking Cancer Chemoprevention linked-data sources

Semantic Web

Volumn 5, Issue 2, 2014, Pages 127-142

  Zeginis, Dimitris ^a,b   Hasnain, Ali ^c   Loutas, Nikolaos ^a,b,c   Deus, Helena Futscher ^c   Fox, Ronan ^c   Tarabanis, Konstantinos ^a,b  

^a INFORMATION TECHNOLOGIES INSTITUTE   (Greece)

^b UNIVERSITY OF MACEDONIA   (Greece)

^c NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Cancer Chemoprevention; Collaborative model development; common data model; HCLS; linked data

Indexed keywords

EID: 84918592304     PISSN: 15700844     EISSN: 22104968     Source Type: Journal    
DOI: 10.3233/SW-130112     Document Type: Article

References (103)

1. Aggregated computational toxicology resource (ACToR), http://actor.epa.gov/actor/faces/ACToRHome.jsp.
2. M.B. Almeida, A proposal to evaluate ontology content, Applied Ontology 4 (2009), 245-265.
3. ArrayExpress, http://www.ebi.ac.uk/arrayexpress/.
4. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight and J.T. Eppig, Gene ontology: Tool for the unification of biology, The Gene Ontology Consortium. Nature Genet. 25 (2000), 25-29.
5. G.D. Bader and M.P. Cary, BioPAX - Biological pathways exchange language, Level 2, Version 1.0 Documentation, doi: http://www.biopax.org/release/biopax- level2-documentation. pdf, 2005.
6. C.A. Ball and A. Brazma, MGED standards: Work in progress, Omics 2006 10 (2006), 138-144.
7. F. Belleau, M.-A. Nolin, N. Tourigny, P. Rigault and J. Morissette, Bio2RDF: Towards a mashup to build bioinformatics knowledge systems, J. Biomed. Inform. 41 (2008), 706-716.
8. Bibliographic reference ontology (BiRO), http://purl.org/ spar/biro.
9. BioGRID, http://thebiogrid.org/.
10. E. Blanco, G. Parra and R. Guigó, Using geneid to identify genes, in: Current Protocols in Bioinformatics, Vol. 18: 4.3.1-4.3.28, D. Baxevanis and B. Davison, eds, John Wiley & Sons Inc., New York, 2007.
11. U. Bojars, J.G. Breslin, V. Peristeras, G. Tummarello and S. Decker, Interlinking the social web with semantics, IEEE Intelligent Systems 23 (2008), 29-40.
12. C. Brewster, H. Alani, S. Dasmahapatra and Y. Wilk, Data driven ontology evaluation, in: International Conference on Language Resources and Evaluation, European Language Resources Association, Lisbon, Portugal, 2004.
13. M. Brochhausen, A. Spear, C. Cocos, G. Weiler, L. Martìn, A. Anguita, H. Stenzhorn, E. Daskalaki, F. Schera, U. Schwarz, S. Sfakianakis, S. Kiefer, M. Dörr, N. Graf and M. Tsiknakis, The ACGT master ontology and its applications - Towards an ontology-driven cancer research and management system, Journal of Biomedical Informatics 44 (2011), 8-25.
14. J. Brooke, SUS: A "quick and dirty" usability scale, in: Usability Evaluation in Industry, P.W. Jordan, B. Thomas, B.A. Weerdmeester and I.L. McClelland, eds, Taylor & Francis, London, 1996, pp. 189-194.
15. Cancer gene expression database (CGED), http:// lifesciencedb.jp/cged/.
16. Cancer prevetion network, http://www.cancerpreventionnetwork. org/.
17. R. Caspi, H. Foerster, C.A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S.Y. Rhee, A.G. Shearer, C. Tissier, T.C. Walk, P. Zhang and P.D. Karp, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Res. 36(Database issue) (2008), 623-D631.
18. A. Ceol, A.A. Chatr, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli and G. Cesareni, MINT, the molecular interaction database, Nucleic Acids Res. 38(Database issue) (2010), 532-539.
19. E.G. Cerami, G.D. Bader, B. Gross and C. Sander, cPath: Open source software for collecting, storing, and querying biological pathways, BMC Bioinformatics 7 (2006), 497.
20. ChemDB, http://cdb.ics.uci.edu/.
21. Chemical compounds database (Chembase), http://www. chembase.com/.
22. Chemical entities of biological interest (ChEBI), http:// www.ebi.ac.uk/chebi/.
23. ChemSpider, http://www.chemspider.com/.
24. P. Ciccarese, E. Wu, G. Wong, M. Ocana, J. Kinoshita, A. Ruttenberg and T. Clark, The SWAN biomedical discourse ontology, Journal of Biomedical Informatics 41 (2008), 739-751.
25. ClinicalTrials, http://clinicaltrials.gov/.
26. O. Corcho, M. Fernández-lópez, A. Gómez-pérez and A. López, Building legal ontologies with METHONTOLOGY and WebODE, in: Law and the Semantic Web, V.R. Benjamins, P. Casanovas, J. Breuker and A. Gangemi, eds, LNCS, Vol. 3369, Springer-Verlag, Heidelberg, 2005, pp. 142-157.
27. D. Corpet and S. Tache, Most effective colon cancer chemopreventive agents in rats: A systematic review of aberrant crypt foci and tumor data, ranked by potency, Nutrition and Cancer 43 (2002), 1-21.
28. M. Courtot, W. Bug, F. Gibson, A. Lister, J. Malone, D. Schober, R. Brinkman and A. Ruttenberg, The OWL of biomedical investigations, in: OWLED Workshop on OWL: Experiences and Directions, Collocated with the 7th International Semantic Web Conference (ISWC-2008), CEURWS. org, C. Dolbear, A. Ruttenberg and U. Sattler, eds, Karlsruhe, Germany, 2008.
29. C. Crichton, J. Davies, J. Gibbons, S. Harris, A. Tsui and J. Brenton, Metadata-driven software for clinical trials, in: ICSE Workshop on Software Engineering in Health Care (SEHC'09), IEEE Computer Society Washington, DC, USA, 2009.
30. Dailymed, http://dailymed.nlm.nih.gov.
31. Dietary supplements labels database, http:// dietarysupplements.nlm.nih. gov/dietary/.
32. Diseasome, http://diseasome.eu/.
33. E. Beißwanger, S. Schulz, H. Stenzhorn and U. Hahn, BioTop: An upper domain ontology for the life sciences - A description of its current structure, contents, and interfaces to OBO ontologies, Applied Ontology 3 (2008), 205-212.
34. FRBR-aligned bibliographic ontology (FaBiO), http://purl. org/spar/fabio.
35. GenBank, http://www.ncbi.nlm.nih.gov/genbank/.
36. Gene expression omnibus (GEO), http://www.ncbi.nlm. nih.gov/geo/.
37. C. Gerhäuser, K. Klimo, E. Heiss, I. Neumann, A. Gamal-Eldeen, J. Knauft, G.-Y. Liu, S. Sitthimonchai and N. Frank, Mechanism-based in vitro screening of potential cancer chemopreventive agents, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 523-524 (2003), 163-172.
38. A. Gómez-Pérez, Ontology evaluation, in: Handbook on Ontologies, S. Staab and R. Studer, eds, Springer-Verlag, Berlin, 2004, pp. 251-274.
39. GRANATUM project consortium, Deliverable D1.1 - Requirements Analysis, available at: http://www.granatum.org/ pub/bscw.cgi/d7070/Granatum-D1.1- Requirements-Analys is.pdf, 2011.
40. GRANATUM: A social collaborative working space semantically interlinking biomedical researchers, knowledge and data for the design and execution of in-silico models and experimments in cancer chemoprevention, http://granatum. org/.
41. P. Grenon, BFO in a nutshell: A bicategorial axiomatization of BFO and comparison with DOLCE, IFOMIS report, University of Leipzig, 2003, available at: http://www.ifomis.org/ Research/IFOMISReports/IFOMIS%20Report%2006-2003. pdf.
42. M. Grüninger and M. Fox, Methodology for the design and evaluation of ontologies, in: IJCAI Workshop on Basic Ontological Issues in Knowledge Sharing, Montreal, Canada 1995.
43. HapMap, http://hapmap.ncbi.nlm.nih.gov/.
44. A. Hasnain, R. Fox, S. Decker and H.F. Deus, Cataloguing and linking life sciences LOD cloud, in: 1st International Workshop on Ontology Engineering in a Data-driven World (OEDW 2012) collocated with 8th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2012), Galway, Ireland, 2012.
45. HUGO gene nomenclature committee (HGNC), http://www.genenames.org/.
46. INOX: Pathway database, http://www.inoh.org/.
47. iRefIndex: A reference index for protein interaction data, http://irefindex.uio.no.
48. G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu and L. Matthews, et al., Reactome: A knowledgebase of biological pathways, Nucleic Acids Research (2005), D428- D432.
49. Y. Kalfoglou and B. Hu, Issues with evaluating and using publicly available ontologies, in: Handbook of Software Engineering and Knowledge Engineering, C. Chen, ed., 2006.
50. S. Kerrien, B. Aranda, L. Breuza, A. Bridge, F. Broackes- Carter, C. Chen, M. Duesbury, M. Dumousseau, M. Feuermann, U. Hinz, C. Jandrasits, R. Jimenez, J. Khadake, U. Mahadevan, P. Masson, I. Pedruzzi, E. Pfeiffenberger, P. Porras, A. Raghunath, B. Roechert, S. Orchard and H. Hermjakob, The IntAct molecular interaction database in 2012, Nucleic Acids Research 40(Database issue) (2012), D841-D846.
51. Kyoto encyclopedia of genes and genomes (KEGG), http:// www.genome.jp/kegg/.
52. Z. Li, M. Yang and K. Ramani, A methodology for engineering ontology acquisition and validation, Artif. Intell. Eng. Des. Anal. Manuf. 23 (2009), 37-51.
53. D. Lindberg, B. Humphreys and A. McCray, The unified medical language system, Methods of Information and Medicine 32 (1993), 281-291.
54. Linked clinical trials (LinkedCT), http://linkedct.org/.
55. S. Liu, M. Wei, R. Moore, V. Ganesan and S. Nelson, RxNorm: Prescription for electronic drug information exchange, IT Professional 7 (2005), 17-23.
56. H.J. Lowe and G.O. Barnett, Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches, Journal of the American Medical Assocation (JAMA) 271 (1994), 1103-1108.
57. A. Maedche and S. Staab, Measuring similarity between ontologies, in: Knowledge Engineering and Knowledge Management. Ontologies and the Semantic Web, 13th International Conference, EKAW 2002, A. Gómez-Pérez, R. Benjamins, eds, Lecture Notes in Computer Science, Vol. 2473, Springer, 2002, pp. 251-263.
58. G. Maiga and D. Williams, A flexible approach for user evaluation of biomedical ontologies, International Journal of Computing and ICT Research 2 (2008), 62-74.
59. J. Malone, E. Holloway, T. Adamusiak, M. Kapushesky, J. Zheng, N. Kolesnikov, A. Zhukova, A. Brazma and H. Parkinson, Modeling Sample variables with an experimental factor ontology, Bioinformatics 26 (2010), 1112- 1118.
60. R.G. Mehta, R. Naithani, L. Huma, M. Hawthorne, R.M. Moriarty, D.L. McCormick, V.E. Steele and L. Kopelovich, Efficacy of Chemopreventive agents in mouse mammary gland organ culture (MMOC) model: A comprehensive review, Current Medicinal Chemistry 15 (2008), 2785-2825.
61. Mouse genome informatics (MGI), http://www.informatics. jax.org/.
62. National cancer institute (NCI) thesaurus, http://ncit.nci.nih. gov/.
63. Nature publishing group: Linked data platform, http://data. nature.com.
64. NCBI, HomoloGene, http://www.ncbi.nlm.nih.gov/ homologene.
65. NCBI, Online mendelian inheritance in man (OMIM), http:// www.ncbi.nlm.nih.gov/omim.
66. NCBI, Reference sequence (RefSeq), http://www.ncbi.nlm. nih.gov/RefSeq/.
67. NeuroCommons, http://neurocommons.org.
68. D. Nishimura, BioCarta, Biotech Software & Internet Report 2 (2001), 117-120.
69. N. Noy and D. McGuinness, Ontology development 101: A guide to creating your first ontology, Tech. Rep. KSL-01-05 and SMI-2001-0800, Stanford University, Stanford, CA, Knowledge Systems Laboratory and Stanford Medical Informatics, 2001.
70. C. Nuria, Ontology evaluation through usability measures, in: Proc. of OTM Workshops'2009, R. Meersman, P. Herrero and T. Dillon, eds, LNCS, Vol. 5872, 2009, pp. 594-603.
71. A. Öhgren and K. Sandkuhl, Towards a methodology for ontology development in small and medium-sized enterprises, in: International Conference on Applied Computing, IADIS, N. Guimarães and P. Isaias, eds, Algarve, Portugal, 2005, pp. 369-376.
72. Ontotext, Linked life data, http://linkedlifedata.com/.
73. open-BioMed.org.uk, http://www.open-biomed.org.uk/.
74. Pharmacogenomics knowledge base (PharmGKB), http:// www.pharmgkb.org/.
75. A. Pico, T. Kelder, M.v. Iersel, K. Hanspers, B. Conklin and C. Evelo, WikiPathways: Pathway editing for the people, PLoS Biol 6 (2008), e184.
76. S. Pinto, S. Staab and C. Tempich, DILIGENT: Towards a fine-grained methodology for distributed loosely-controllled and evolving engineering of ontologies, in: Proc. of the 16th Eureopean Conference on Artificial Intelligence, R.L. de Mántaras and L. Saitta, eds, IOS Press, 2004, pp. 393- 397.
77. M. Poveda-Villalón, M.C. Suárez-Figueroa and A. Gómez-Pérez, Validating ontologies with OOPS!, in: Knowledge Engineering and Knowledge Management, A. Teije, J. Völker, S. Handschuh, H. Stuckenschmidt, M. d'Acquin, A. Nikolov, N. Aussenac-Gilles and N. Hernandez, eds, Vol. 7603, Springer Berlin, Heidelberg, 2012, pp. 267-281.
78. K. Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, L. Balakrishnan, A. Marimuthu, S. Banerjee, D. Somanathan, A. Sebastian, S. Rani, S.R.S, K. Harrys, S. Kanth, M. Ahmed, M. Kashyap, R. Mohmood, Y. Ramachandra, V. Krishna, B. Rahiman, S. Mohan, P. Ranganathan, S. Ramabadran, R. Chaerkady and A. Pandey, Human Protein Reference Database, Nucleic Acids Research 37 (2009), 767-72.
79. V. Presutti, E. Blomqvist, E. Daga and A. Gangemi, Patternbased ontology design, in: Ontology Engineering in a Networked World, M.C. Suárez- Figueroa, A. Gómez-Pérez, E. Motta and A. Gangemi, eds, Springer Berlin, Heidelberg, 2012, pp. 35-64, ISBN: 978-3-642-24794-1.
80. Protein database, http://www.hprd.org/.
81. Protein information Resource:iProClass, http://pir. georgetown.edu/ iproclass/.
82. PubChem, http://pubchem.ncbi.nlm.nih.gov/.
83. PubMed dietary supplement subset, http://ods.od.nih.gov/ research/PubMed-Dietary-Supplement-Subset.aspx.
84. PubMed, http://www.ncbi.nlm.nih.gov/pubmed.
85. Repartoire database, http://repairtoire.genesilico.pl/.
86. P. Romero, J. Wagg, M.L. Green, D. Kaiser, M. Krummenacker and P.D. Karp, Computational prediction of human metabolic pathways from the complete human genome, Genome Biology 6 (2004), 1-17.
87. M. Sabou and M. Fernandez, Ontology (network) evaluation, in: Ontology Engineering in a Networked World, M.C. Suárez-Figueroa, A. Gómez-Pérez, E. Motta and A. Gangemi, eds, Springer Berlin, Heidelberg, 2012, pp. 193-212.
88. Saccharomyces Genome Database (SGD), http://www.yeastgenome.org/.
89. S.-A. Sansone, P. Rocca-Serra, D. Field, E. Maguire, C. Taylor, O. Hofmann, H. Fang, S. Neumann, W. Tong, L. Amaral-Zettler, K. Begley, T. Booth, L. Bougueleret, G. Burns, B. Chapman, T. Clark, L.-A. Coleman, J. Copeland, S. Das, A.d. Daruvar, P.d. Matos, I. Dix, S. Edmunds, C.T. Evelo, M.J. Forster, P. Gaudet, J. Gilbert, C. Goble, J.L. Griffin, D. Jacob, J. Kleinjans, L. Harland, K. Haug, H. Hermjakob, S.J.H. Sui, A. Laederach, S. Liang, S. Marshall, A. McGrath, E. Merrill, D. Reilly, M. Roux, C.E. Shamu, C.A. Shang, C. Steinbeck, A. Trefethen, B. Williams-Jones, K. Wolstencroft, I. Xenarios and W. Hide, Toward interoperable bioscience data, Nature Genetics 44 (2012), 121-126.
90. D. Shotton, CiTO, the Citation Typing Ontology, Journal of Bio-medical Semantics 1(Suppl. 1) (2010), S6.
91. Sider, http://sideeffects.embl.de/.
92. Sigma-Aldrich, https://www.sigmaaldrich.com/catalog/.
93. B. Smith, M. Ashburner, C. Rosse, C. Bard, W. Bug, W. Ceusters, L.J. Goldberg, K. Eilbeck, A. Ireland, C.J. Mungall, N. Leontis, P. Rocca-Serra, A. Ruttenberg, S.A. Sansone, R.H. Scheuermann, N. Shah, P.L. Whetzel and S. Lewis, The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 25 (2007), 1251-1255.
94. M.C. Suárez-Figueroa, A. Gómez-Pérez, E. Motta, A. Gangemi, eds, Ontology Engineering in a Networked World, Springer, 2012, ISBN: 978-3-642-24794-1.
95. M.C. Suárez-Figueroa, NeOn methodology for building ontology networks: Specification, scheduling and reuse, Dissertations in Artificial Intelligence 338 (2012), ISBN: 978-3- 89838-338-7, IOS Press.
96. Y. Sure, S. Staab and R. Studer, On-to-knowledge methodology, in: Handbook on Ontologies, S. Staab and R. Studer, eds, Springer, 2003, pp. 117-132.
97. TOXicology data NETwork (TOXNET), http://toxnet.nlm.nih.gov/.
98. A. Tsao, E. Kim and W.K. Hong, Chemoprevention of cancer, A Cancer Journal for Clinicians 54 (2004), 150-180, John Wiley & Sons, Ltd.
99. Universal protein resource (UniProt), http://www.uniprot. org/.
100. M. Uschold and M. Gruninger, Ontologies: Principles, methods and applications, Knowledge Engineering Review 11 (1996), 93-136.
101. B. Villazón-Terrazas, L.M. Vilches-Blázquez, O. Corcho and A. Gómez-Pérez, Methodological guidelines for publishing government linked data, in: Linking Government Data, D. Wood, ed, Springer, New York, 2011, pp. 27-49.
102. D.S. Wishart, C. Knox, A.C. Guo, D. Cheng, S. Shrivastava, D. Tzur, B. Gautam and M. Hassanali, DrugBank: A knowledgebase for drugs, drug actions and drug targets, Nucleic Acids Research 36 (2008), D901-D906.
103. R.C. Young and C.M. Wilson, Cancer prevention past, present, and future, Clinical Cancer Research 8 (2002), 11-16.