The semantic web in translational medicine: Current applications and future directions

Briefings in Bioinformatics

Volumn 16, Issue 1, 2013, Pages 89-103

  Machado, Catia M ^a   Rebholz Schuhmann, Dietrich ^b   Freitas, Ana T ^c   Couto, Francisco M ^a  

^a UNIVERSITY OF LISBON   (Portugal)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF LISBON   (Portugal)

Author keywords

Data integration; Data interoperability; Data sharing; Knowledge discovery; Semantic web; Translational medicine

Indexed keywords

ALGORITHM; BIOLOGY; HUMAN; INFORMATION DISSEMINATION; INTERNET; PROCEDURES; TRANSLATIONAL RESEARCH;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HUMANS; INFORMATION DISSEMINATION; INTERNET; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84895439085     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt079     Document Type: Article

References (73)

1. Hey T, Tansley S, Tolle K. The Fourth Paradigm: Data-Intensive Scientific Discovery. Washington: Microsoft Research, 2009.
2. Webb CP, Pass HI. Translation research: from accurate diagnosis to appropriate treatment. J Transl Med 2004;2:35.
3. Albani S, Prakken B. The advancement of translational medicine-from regional challenges to global solutions. NatMed 2009;15:1006-9.
4. Woolf SH. The meaning of translational research and why it matters. JAMA 2008;299:211-3.
5. Wang W. Global health and translational medicine new drivers for medicine and medical sciences. J Med Med Sci 2012;3:126-7.
6. Louie B, Mork P, Martin-Sanchez F, et al. Data integration and genomic medicine. J Biomed Inform 2007;40:5-16.
7. Committee on Models for Biomedical Reasearch. Models for Biomedical Research: A New Perspective. Washington, D.C.:National Academy Press, 1985.
8. Davidson SB, Overton C, Buneman P. Challenges in integrating biological data sources. JComputBiol 1995;2:557-72.
9. Sagotsky JA, Zhang L, Wang Z, et al. Life sciences and the web: a new era for collaboration. Mol Syst Biol 2008;4:201.
10. Berners-Lee T, Hendler J, Lassila O. The Semantic Web. Sci Am 2001;284:34-43.
11. Rebholz-Schuhmann D, Oellrich A, Hoehndorf R. Textmining solutions for biomedical research: enabling integrative biology. Nat Rev Genet 2012;13:829-39.
12. World Wide Web Consortium. http://www.w3.org/(9 July 2013, date last accessed).
13. Semantic Web Standards. http://www.w3.org/standards/semanticweb/(9 July 2013, date last accessed).
14. RDF PrimerçW3C Recommendation. http://www.w3.org/TR/2004/REC-rdf-primer-20040210/(9 July 2013, date last accessed).
15. Universal Resource Identifier (URI) current status. http://www.w3.org/standards/techs/uri#w3c_all (9 July 2013, date last accessed).
16. R2RML:RDB to RDF Mapping Language. http://www.w3. org/TR/2012/REC-r2rml-20120927/(9 July 2013, date last accessed).
17. RDFVocabularyDescription Language1.0:RDFSchema. http://www.w3.org/TR/rdf-schema/(9 July 2013, date last accessed).
18. OWL Web Ontology Language Current Status. http://www.w3.org/standards/techs/owl#w3c all (9 July 2013, date last accessed).
19. Baader F, Calvanese D, McGuinness D, et al. (eds). The Description Logic Handbook: Theory, Implementation, and Applications. New York: Cambridge University Press, 2003.
20. SPARQL Current Status. http://www.w3.org/standards/techs/sparql#w3c all (9 July 2013, date last accessed).
21. SPARQL 1.1 Entailment Regimes. http://www.w3.org/TR/2013/REC-sparql11-entailment-20130321/(31 August 2013, date last accessed).
22. RDQLçA Query Language for RDF. http://www.w3.org/Submission/RDQL/(9 July 2013, date last accessed).
23. Gruber TR. A translation approach to portable ontology specifications. Knowl Acquis 1993;5:199-220.
24. Ashburner M, Ball CA, Blake JA, et al. Gene Ontology:tool for the unification of biology. NatGenet 2000;25:25-9.
25. Systematized Nomenclature of Medicine-Clinical Terms (SNOMED). http://www.ihtsdo.org/snomed-ct/(9 July 2013, date last accessed).
26. Stein LD. Integrating biological databases. Nat Rev Genet 2003;4:337-45.
27. Couto F, Pinto H. The next generation of similarity measures that fully explore the semantics in biomedical ontologies. J Bioinform Comput Biol 2013;11:1-12.
28. The OBO Flat File Format Specification, version 1.2. http://www.geneontology.org/GO.format.obo-1_2.shtml (9 July 2013, date last accessed).
29. OBO Flat File Format Syntax and Semantics and Mapping to OWL Web Ontology Language. http://www.cs.man.ac.uk/~horrocks/obo/(6 October 2013, date last accessed).
30. OboInOwl -Mapping OBO to OWL. http://www.bioontology. org/wiki/index.php/OboInOwl:Main_Page (6 October 2013, date last accessed).
31. Tirmizi SH, Aitken S, Moreira DA, et al. Mapping between the OBO and OWL ontology languages. J Biomed Semantics 2011;2: S3.
32. Linked Data - Design Issues. http://www.w3.org/DesignIssues/LinkedData.html (9 July 2013, date last accessed).
33. Best Practices for Publishing Linked Data. https://dvcs.w3.org/hg/gld/raw-file/default/bp/index.html (9 July 2013, date last accessed).
34. Linked Data Glossary. http://www.w3.org/TR/2013/NOTE-ld-glossary-20130627/(9 July 2013, date last accessed).
35. Dodds L, Davis I. Linked Data Patterns: A pattern catalogue for modelling, publishing, and consuming Linked Data. 2012. http://patterns.dataincubator.org/book/(31 August 2013, date last accessed).
36. Heath T, Bizer C. Linked Data: Evolving theWeb into a Global Data Space (1st edition). Synthesis Lectures on the Semantic Web: Theory and Technology; 1:1,1-136. Morgan & Claypool, 2011.
37. Cheung K, Frost H, Marshall M, et al. A journey to semantic web query federation in the life sciences. BMCBioinformatics 2009;10:S10.
38. Harrow I, Filsell W, Woollard P, et al. Towards virtual knowledge broker services for semantic integration of life science literature and data sources. Drug DiscovToday 2013;18:428-34.
39. Linking Open Data by the W3C Semantic Web Education and Outreach Interest Group. http://www.w3.org/wiki/SweoIG/TaskForces/CommunityProjects/LinkingOpen Data (9 July 2013, date last accessed).
40. Linking Open Data Cloud. http://datahub.io/group/lodcloud (19 August 2013, date last accessed).
41. State of the LOD Cloud. http://www4.wiwiss.fu-berlin. de/lodcloud/state/(19 August 2013, date last accessed).
42. PubMed. http://www.ncbi.nlm.nih.gov/pubmed/(9 July 2013, date last accessed).
43. The UniProt Consortium. The Universal Protein Resource (UniProt). Nucleic Acids Res 2007;35:D193-7.
44. Gudivada RC, Qu XA, Chen J, et al. Identifying diseasecausal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge. J Biomed Inform 2008;41:717-29.
45. Coulet A, Smail-Tabbone M, Benlian P, et al. Ontologyguided data preparation for discovering genotype-phenotype relationships. BMC Bioinformatics 2008;9:S3.
46. Colombo G, Merico D, Boncoraglio G, et al. An ontological modeling approach to cerebrovascular disease studies: the NEUROWEB case. J Biomed Inform 2010;43:469-84.
47. Agorastos T, Koutkias V, Falelakis M, et al. Semantic integration of cervical cancer data repositories to facilitate multicenter association studies: the ASSIST approach. Cancer Inform 2009;8:31-44.
48. Siddiqi J, Akhgar B, Gruzdz A, et al. Automated Diagnosis System to Support Colon Cancer Treatment: MATCH. In:Fifth International Conference on Information Technology: New Generations. IEEE Press, 2008. p. 201-5.
49. Rebholz-Schuhmann D, Grabmuller C, Kavaliauskas S, et al. Semantic integration of gene-disease associations for Type 2 Diabetes mellitus from literature and 2 biomedical data resources. DrugDiscovToday 2013.
50. Pathak J, Kiefer RC, Bielinski SJ, et al. Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank. J Biomed Semant 2012;3:10.
51. Qu X, Gudivada R, Jegga A, et al. Semantic Web-based data representation and reasoning applied to disease mechanism and pharmacology. In: Bioinformatics and Biomedicine Workshops. IEEE International Conference, 2007;131-43.
52. Chen H, Mao Y, Zheng X, et al. Towards semantic e-science for traditional Chinese medicine. BMC Bioinformatics 2007;8:S6.
53. Sahoo SS, Zeng K, Bodenreider O, et al. From "glycosyltransferase" to "congenital muscular dystrophy":integrating knowledge from NCBI Entrez Gene and the Gene Ontology. In: Studies in Health Technology and Informatics, Vol. 129. MEDINFO 2007. Amsterdam, Netherlands: IOS Press, 2007, p.1260-4.
54. Ruttenberg A, Rees JA, Samwald M, et al. Life sciences on the Semantic Web: the Neurocommons and beyond. Brief Bioinform 2009;10:193-204.
55. Semantic web Health Care and Life Sciences Interest Group/Linking Open Drug Data. http://www.w3.org/wiki/HCLSIG/LODD (6 September 2013, date last accessed).
56. The Open Biological and Biomedical Ontologies. http://www.obofoundry.org/(6 September 2013, date last accessed).
57. SenseLab Neurobiology databases. http://senselab.med. yale.edu/(6 September 2013, date last accessed).
58. DBpedia. http://dbpedia.org/About (6 September 2013, date last accessed).
59. Belleau F, Nolin M, Tourigny N, et al. Bio2RDF: towards a mashup to build bioinformatics knowledge systems. JBiomed Inf 2008;41:706-16.
60. Linked Clinical Trials (LinkedCT) project. http://linkedct. org/about/(6 September 2013, date last accessed).
61. Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34:D668-72.
62. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 2004;32:D267-70.
63. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.
64. Maglott D, Ostell J, Pruitt KD, et al. Entrez Gene: genecentered information at NCBI. Nucleic Acids Res 2005;33:D54-8.
65. Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:D514-7.
66. Sioutos N, Coronado S, Haber MW, et al. NCI Thesaurus:a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 2007;40:30-43.
67. Committee on A Framework for Developing a New Taxonomy of Disease. Toward a PrecisionMedicine: Building a Knowledge Network for Biomedical Research and a NewTaxonomy of Disease. Washington, D.C.: National Academy Press, 2011.
68. Sahoo SS, Nguyen V, Bodenreider O, et al. A unified framework for managing provenance information in translational research. BMC Bioinformatics 2011;12:461.
69. PROV-DM: The PROV Data Model. http://www.w3. org/TR/2012/CR-prov-dm-20121211/(9 July 2013, date last accessed).
70. Almeida JS, Deus HF, Maass W. S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics 2010;11:387.
71. Deus HF, Correa MC, Stanislaus R, et al. S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. BMCBioinformatics 2011;12:285.
72. Williams AJ, Harland L, Groth P, et al. Open PHACTS:semantic interoperability for drug discovery. Drug Discov Today 2012;17:1188-98.
73. The Innovative Medicines Initiative. http://www.imi. europa.eu/(9 July 2013, date last accessed).