The RICORDO approach to semantic interoperability for biomedical data and models: Strategy, standards and solutions

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  De Bono, Bernard ^a,c   Hoehndorf, Robert ^b   Wimalaratne, Sarala ^a   Gkoutos, George ^b   Grenon, Pierre ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80054074775     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-313     Document Type: Article

References (67)

1. A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. Hrynaszkiewicz I, BMC Res Notes 2010 3 235 10.1186/1756-0500-3-235 20813027
2. Health Technology Assessment Programme, NHS National Institute for Health Research. http://www.hta.ac.uk/funding/troubleshooting/index.html#hta88
3. BBSRC data sharing policy. http://www.bbsrc.ac.uk/funding/news/2007/0704- data-sharing.aspx
4. Cancer Research UK Data Sharing Guidelines. http://science. cancerresearchuk.org/funding/terms-conditions-and-policies/policy-data-sharing/ data-sharing-guidelines/
5. Wellcome Trust Data Sharing Policy. http://www.wellcome.ac.uk/About-us/ Policy/Spotlight-issues/Data-sharing/
6. Medical Research Council Data Sharing Initiative. http://www.mrc.ac.uk/ Ourresearch/Ethicsresearchguidance/Datasharinginitiative/index.htm
7. Geospatial resources for supporting data standards, guidance and best practice in health informatics. Mathys T, Kamel Boulos MN, BMC Res Notes 2011 4 19 10.1186/1756-0500-4-19 21269487
8. VPH EP6: Technical report on the annotation of the Guyton Model. de Bono B, Grenon P, Book VPH EP6: Technical report on the annotation of the Guyton Model 2011 (Editor ed.eds.). City
9. RICORDO FP7 STREP. http://www.ricordo.eu
10. Virtual Physiological Human Network of Excellence. http://www.vph-noe.eu
11. A vision and strategy for the virtual physiological human in 2010 and beyond. Hunter P, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, et al. Philos Transact A Math Phys Eng Sci 2010 368 2595 2614 10.1098/rsta.2010.0048 20439264
12. Innovative Medicines Initiative. http://www.imi.europa.eu/
13. The Innovative Medicines Initiative: a pre-competitive initiative to enhance the biomedical science base of Europe to expedite the development of new medicines for patients. Hunter AJ, Drug discovery today 2008 13 371 373 10.1016/j.drudis.2008.02.009 18468553
14. Drug and Disease Library and Modeling Framework. http://www.ddmore.eu/
15. mEducator. http://www.meducator.net/
16. CDISC standard-based electronic archiving of clinical trials. Kuchinke W, Aerts J, Semler SC, Ohmann C, Methods Inf Med 2009 48 408 413 10.3414/ME9236 19621114
17. Getting started in text mining. Cohen KB, Hunter L, PLoS computational biology 2008 4 20 10.1371/journal.pcbi.0040020 18225946 (Pubitemid 351230849)
18. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. Nature biotechnology 2007 25 1251 1255 10.1038/nbt1346 17989687 (Pubitemid 350076511)
19. An open annotation ontology for science on web 3.0. Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T, J Biomed Semantics 2011 2 Suppl 2 4 10.1186/2041-1480-2-S2-S4 21624159
20. Achieving interoperability for metadata registries using comparative object modeling. Park YR, Kim JH, Stud Health Technol Inform 2010 160 1136 1139 20841861
21. Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, et al. Stand Genomic Sci 2010 3 232 234 10.4056/sigs.1383476 21304724
22. An open repositories network development for medical teaching resources. Soula G, Darmoni S, Le Beux P, Renard JM, Dahamna B, Fieschi M, Stud Health Technol Inform 2010 160 610 614 20841759
23. The BRIDG project: a technical report. Fridsma DB, Evans J, Hastak S, Mead CN, J Am Med Inform Assoc 2008 15 130 137 18096907 (Pubitemid 351288539)
24. The medical dictionary for regulatory activities (MedDRA). Brown EG, Wood L, Wood S, Drug Saf 1999 20 109 117 10.2165/00002018-199920020-00002 10082069 (Pubitemid 29101275)
25. Assessing applicability of ontological principles to different types of biomedical vocabularies. Ingenerf J, Linder R, Methods Inf Med 2009 48 459 467 10.3414/ME0628 19448888
26. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Nature genetics 2000 25 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
27. ChEBI-Chemical Entities of Biological Interest. de Matos P, Ennis M, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M, Degtyarenko K, NAR Molecular Biology Database Collection 2007
28. The Protein Ontology: a structured representation of protein forms and complexes. Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, et al. Nucleic acids research 2011 39 539 545 10.1093/nar/gkq907 20935045
29. The Foundational Model of Anatomy Ontology. Rosse C, Mejino JLV, Anatomy Ontologies for Bioinformatics: Principles and Practice Springer, Burger A, Davidson D, Baldock R, 2007 59 117
30. The human phenotype ontology. Robinson PN, Mundlos S, Clin Genet 2010 77 525 534 10.1111/j.1399-0004.2010.01436.x 20412080
31. Concepts and synonymy in the UMLS Metathesaurus. Merrill GH, J Biomed Discov Collab 2009 4 7 19838995
32. National Center for Biomedical Ontology. http://www.bioontology.org/
33. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions. Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, BMC Microbiol 2009 9 Suppl 1 1 10.1186/1471-2180-9-S1-S1 19278549
34. Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community. Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW, BMC bioinformatics 2011 12 32 10.1186/1471-2105-12-32 21261995
35. Pathbase and the MPATH ontology: community resources for mouse histopathology. Schofield PN, Gruenberger M, Sundberg JP, Vet Pathol 2010 47 1016 1020 10.1177/0300985810374845 20587689
36. The RNA Ontology Consortium: an open invitation to the RNA community. Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, et al. RNA 2006 12 533 541 10.1261/rna.2343206 16484377
37. Ontologies for biologists: a community model for the annotation of genomic data. Ashburner M, Mungall CJ, Lewis SE, Cold Spring Harbor symposia on quantitative biology 2003 68 227 235 10.1101/sqb.2003.68.227 15338622 (Pubitemid 38955571)
38. Minimum information requested in the annotation of biochemical models (MIRIAM). Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, et al. Nature biotechnology 2005 23 1509 1515 10.1038/nbt1156 16333295 (Pubitemid 41752928)
39. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, et al. Nucleic acids research 2006 34 689 691 10.1093/nar/gkj092 16381960
40. The CellML Model Repository. Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF, Bioinformatics (Oxford, England) 2008 24 2122 2123 10.1093/bioinformatics/btn390
41. Lister AL, Pocock M, Wipat A, Integration of constraints documented in SBML, SBO and the SBML manual facilitates validation of biological models Newcastle upon Tyne: University of Newcastle upon Tyne, Computing Science 2007
42. PhysiomeSpace: digital library service for biomedical data. Testi D, Quadrani P, Viceconti M, Philos Transact A Math Phys Eng Sci 2010 368 2853 2861 20478910
43. Toward an Ontological Treatment of Disease and Diagnosis. Scheuermann RH, Ceusters W, Smith B, Proceedings of the 2009 AMIA Summit on Translational Bioinformatics 2009 116 120
44. A translation approach to portable ontologies. Gruber TR, Knowledge Acquisition 1993 5 199 220 10.1006/knac.1993.1008
45. Using ontologies to describe mouse phenotypes. Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D, Genome biology 2005 6 8 10.1186/gb-2005-6-5- p8 15642100
46. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. Laibe C, Le Novere N, BMC Syst Biol 2007 1 58 10.1186/1752-0509-1-58 18078503 (Pubitemid 351338751)
47. Data exchange strategy specification. Formal document specifying the overall VPH data exchange strategy and relevant components like file formats. de Bono B, Gkoutos G, Wimalaratne S, 2010 http://www.ricordo.eu/system/files/ RICORDO-D4.1.pdf
48. VPH Annotation Requirements Report delivered to WP3. Grenon P, Cook D, Gkoutos G, Burger A, Skot Jensen T, Hunter P, de Bono B, 2010 http://www.ricordo.eu/system/files/RICORDO-D2.2.pdf
49. VPH Technical Infrastructure Requirements Report delivered to WP4. Wimalaratne S, Grenon P, Hoehndorf R, Gkoutos G, de Bono B, 2010 http://www.ricordo.eu/system/files/RICORDO-D2.3.pdf
50. Documentation of prototype RICORDO repository and basic web-based query system. Wimalaratne S, Grenon P, Hoehndorf R, Gkoutos G, de Bono B, 2011 http://www.ricordo.eu/system/files/RICORDO-D4.3.pdf
51. ChEBI: a database and ontology for chemical entities of biological interest. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M, Nucleic acids research 2008 36 344 350 17932057
52. Establishing the RICORDO set of dictionaries. de Bono B, Burger A, Gkoutos G, Davidson D, Skot Jensen T, Cook D, 2010 http://www.ricordo.eu/system/ files/RICORDO-D2.1.pdf
53. Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Cook DL, Mejino JL, Neal ML, Gennari JH, Conf Proc IEEE Eng Med Biol Soc 2009 2009 2791 2794 19964601
54. Report on composite annotation architecture. Cook D, Gennari J, Mejino O, Gkoutos G, Hoehndorf R, Grenon P, de Bono B, 2010 http://www.ricordo.eu/system/ files/RICORDO-D5.1.pdf
55. nSPARQL: A navigational language for RDF. Pérez J, Arenas M, Gutierrez C, Web Semantics: Science, Services and Agents on the World Wide Web 2010 8 255 270 10.1016/j.websem.2010.01.002
56. Pellet: A practical OWL-DL reasoner. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y, Web Semantics: Science, Services and Agents on the World Wide Web 2007 5 51 53 10.1016/j.websem.2007.03.004 (Pubitemid 46856283)
57. Relations in biomedical ontologies. Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C, Genome biology 2005 6 46 10.1186/gb-2005-6-5-r46 15892874
58. RICORDO Resources. http://www.ricordo.eu/relevant-resources
59. RICORDO ToolSet. https://sites.google.com/site/ricordotoolset/home
60. DICOM demystified: a review of digital file formats and their use in radiological practice. Graham RN, Perriss RW, Scarsbrook AF, Clinical radiology 2005 60 1133 1140 10.1016/j.crad.2005.07.003 16223609 (Pubitemid 41511606)
61. FieldML: concepts and implementation. Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ, Philos Transact A Math Phys Eng Sci 2009 367 1869 1884 10.1098/rsta.2009.0025 19380316
62. Computational Anatomy Atlas of the Heart. Ordas S, Oubel E, Sebastian R, Frangi AF, 5th International Symposium on Image and Signal Processing and Analysis, 2007 ISPA 2007 2007 338 342
63. EMAP and EMAGE: a framework for understanding spatially organized data. Baldock RA, Bard JB, Burger A, Burton N, Christiansen J, Feng G, Hill B, Houghton D, Kaufman M, Rao J, et al. Neuroinformatics 2003 1 309 325 10.1385/NI:1:4:309 15043218 (Pubitemid 37346048)
64. EMAGE - Edinburgh Mouse Atlas of Gene Expression: 2008 update. Venkataraman S, Stevenson P, Yang Y, Richardson L, Burton N, Perry TP, Smith P, Baldock RA, Davidson DR, Christiansen JH, Nucleic acids research 2008 36 860 865 18077470
65. HumLoc Server. http://www.cbs.dtu.dk/services/HumLoc-1.0/
66. Circulation: overall regulation. Guyton AC, Coleman TG, Granger HJ, Annual review of physiology 1972 34 13 46 10.1146/annurev.ph.34.030172.000305 4334846
67. An ontology for cell types. Bard J, Rhee SY, Ashburner M, Genome biology 2005 6 21 10.1186/gb-2005-6-2-r21 15693950