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BMC Medical Informatics and Decision Making
Published in: BMC Medical Informatics and Decision Making 1/2017

Open Access 01-12-2017 | Technical advance

Orchestrating differential data access for translational research: a pilot implementation

Authors: Marco Brandizi, Olga Melnichuk, Raffael Bild, Florian Kohlmayer, Benedicto Rodriguez-Castro, Helmut Spengler, Klaus A. Kuhn, Wolfgang Kuchinke, Christian Ohmann, Timo Mustonen, Mikael Linden, Tommi Nyrönen, Ilkka Lappalainen, Alvis Brazma, Ugis Sarkans

Published in: BMC Medical Informatics and Decision Making | Issue 1/2017

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Abstract

Background

Translational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consider issues of data confidentiality, identifiability, extent of consent, and data usage agreements. All these ethical, social and legal aspects must be incorporated into a differential management of restricted access to sensitive data.

Methods

In this paper we present a pilot system that uses several common open source software components in a novel combination to coordinate access to heterogeneous biomedical data repositories containing open data (open access) as well as sensitive data (restricted access) in the domain of biobanking and biosample research. Our approach is based on a digital identity federation and software to manage resource access entitlements.

Results

Open source software components were assembled and configured in such a way that they allow for different ways of restricted access according to the protection needs of the data. We have tested the resulting pilot infrastructure and assessed its performance, feasibility and reproducibility.

Conclusions

Common open source software components are sufficient to allow for the creation of a secure system for differential access to sensitive data. The implementation of this system is exemplary for researchers facing similar requirements for restricted access data. Here we report experience and lessons learnt of our pilot implementation, which may be useful for similar use cases. Furthermore, we discuss possible extensions for more complex scenarios.
Footnotes
1
http://​www.​ebi.​ac.​uk/​biosamples/​group/​SAMEG299071. The list of all the data set records uploaded for the pilot are available at https://​goo.​gl/​SVXZ3A.
 
2
Ibid.
 
3
This can be computed by means of the RDF/SPARQL endpoint, e.g., https://​goo.​gl/​ti4S34
 
Literature
1.
Woolf SH. The meaning of translational research and why it matters. JAMA. 2008;299:211–3.PubMed
2.
Cohrs RJ, Tyler M, Parviz G, Luc B, Higgins PJ, Aamir S. Translational medicine definition by the european society for translational medicine. New Horizons Transl Med. 2015;2:86–8.CrossRef
3.
Chute CG, Ullman-Cullere M, Wood GM, Lin SM, He M, Pathak J. Some experiences and opportunities for big data in translational research. Genet Med. 2013;15:802–9.CrossRefPubMedPubMedCentral
4.
5.
Beck T, Tim B, Sirisha G, Søren B, Norbert G, Lemke HU, et al. Knowledge engineering for health: a new discipline required to bridge the ‘ICT gap’ between research and healthcare. Hum Mutat. 2012;33:797–802.CrossRefPubMed
6.
7.
Mello MM, Francer JK, Wilenzick M, Teden P, Bierer BE, Barnes M. Preparing for responsible sharing of clinical trial data. N Engl J Med. 2013;369:1651–8.CrossRefPubMed
8.
Melander H, Ahlqvist-Rastad J, Meijer G, Beermann B. Evidence b (i) ased medicine—selective reporting from studies sponsored by pharmaceutical industry: review of studies in new drug applications. BMJ Br Medical J Publ Group. 2003;326:1171–3.CrossRef
9.
10.
Safran C, Bloomrosen M, Hammond WE, Labkoff S, Markel-Fox S, Tang PC, et al. Toward a national framework for the secondary use of health data: an american medical informatics association white paper. J Am Med Inform Assoc. 2007;14:1–9.CrossRefPubMedPubMedCentral
11.
McGuire AL, Basford M, Dressler LG, Fullerton SM, Koenig BA, Li R, et al. Ethical and practical challenges of sharing data from genome-wide association studies: the eMERGE consortium experience. Genome Res. 2011;21:1001–7.CrossRefPubMedPubMedCentral
12.
13.
14.
Chadwick R, Levitt M, Shickle D. The Right to Know and the Right Not to Know: Genetic Privacy and Responsibility. Cambridge: Cambridge University Press; 2014.
15.
Appari A, Ajit A, Johnson ME. Information security and privacy in healthcare: current state of research. Int J Internet Enterp Manag. 2010;6:279.CrossRef
16.
Fernández-Alemán JL, Señor IC, Lozoya PÁO, Ambrosio T. Security and privacy in electronic health records: a systematic literature review. J Biomed Inform. 2013;46:541–62.CrossRefPubMed
17.
Moolchan ET, Mermelstein R. Research on tobacco use among teenagers: ethical challenges. J Adolesc Health. 2002;30:409–17.CrossRefPubMed
18.
Harding A, Harper B, Stone D, O’Neill C, Berger P, Harris S, et al. Conducting research with tribal communities: sovereignty, ethics, and data-sharing issues. Environ Health Perspect. 2012;120:6–10.CrossRefPubMed
19.
Weiss MG, Ramakrishna J, Somma D. Health-related stigma: rethinking concepts and interventions. Psychol Health Med. 2006;11:277–87.CrossRefPubMed
20.
Cook JE, Purdie-Vaughns V, Meyer IH, Busch JTA. Intervening within and across levels: a multilevel approach to stigma and public health. Soc Sci Med. 2014;103:101–9.CrossRefPubMed
21.
Clayton EW. Ethical, legal, and social implications of genomic medicine. N Engl J Med. 2003;349:562–9.CrossRefPubMed
22.
23.
Doshi P, Jefferson T, Del Mar C. The imperative to share clinical study reports: recommendations from the tamiflu experience. PLoS Med. 2012;9:e1001201.CrossRefPubMedPubMedCentral
24.
25.
Hoffman S, Podgurski A. Balancing privacy, autonomy, and scientific needs in electronic health records research. 2011.
26.
27.
Bertino E, Takahashi K. Identity Management: Concepts, Technologies, and Systems. Boston: Artech House; 2011.
28.
29.
Kalloniatis C, Christos K, Haralambos M, Manousakis V, Shareeful I, Stefanos G, et al. Towards the design of secure and privacy-oriented information systems in the cloud: identifying the major concepts. Comput Stand Interfaces. 2014;36:759–75.CrossRef
30.
Fabian B, Benjamin F, Tatiana E, Philipp J. Collaborative and secure sharing of healthcare data in multi-clouds. Inf Syst. 2015;48:132–50.CrossRef
31.
Falcão-Reis F, Costa-Pereira A, Correia ME. Access and privacy rights using web security standards to increase patient empowerment. Stud Health Technol Inform. 2008;137:275–85.PubMed
32.
33.
Field L, Stephanie S, Jon I, Wittenburg P, Los W, Broeder D, Hardisty A, Repo S, Jenkinson A. Realising the full potential of research data: common challenges in data management, sharing and integration across scientific disciplines. 2013. http://​dx.​doi.​org/​10.​5281/​zenodo.​7636. Accessed 16 Mar 2017.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, et al. The BioSample database (BioSD) at the european bioinformatics institute. Nucleic Acids Res. 2012;40:D64–70.CrossRefPubMed
44.
Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, et al. Updates to BioSamples database at european bioinformatics institute. Nucleic Acids Res. 2014;42:D50–2.CrossRefPubMed
45.
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, et al. ArrayExpress update--simplifying data submissions. Nucleic Acids Res. 2015;43:D1113–6.CrossRefPubMed
46.
Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44:D447–56.CrossRefPubMed
47.
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2014;43:D805–11.CrossRefPubMedPubMedCentral
48.
49.
50.
51.
Norlin L, Fransson MN, Eriksson M, Merino-Martinez R, Anderberg M, Kurtovic S, et al. A minimum data Set for sharing biobank samples, information, and data: MIABIS. Biopreserv Biobank. 2012;10:343–8.CrossRefPubMed
52.
53.
54.
55.
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, et al. The european genome-phenome archive of human data consented for biomedical research. Nat Genet. 2015;47:692–5.CrossRefPubMed
56.
57.
58.
59.
60.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C. Bioinformatics meets user-centred design: a perspective. PLoS Comput Biol. 2012;8:e1002554.CrossRefPubMedPubMedCentral
61.
62.
63.
Kuhn KA, Bild R, Anton G, Schuffenhauer S, Wichmann H-E. Connecting biobanks of large european cohorts (EU project BBMRI-LPC). Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2016;59:385–9.CrossRefPubMed
64.
65.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, et al. Making sense of big data in health research: towards an EU action plan. Genome Med. 2016;8:71.CrossRefPubMedPubMedCentral
66.
67.
Crosswell LC, Thornton JM. ELIXIR: a distributed infrastructure for european biological data. Trends Biotechnol. 2012;30:241–2.CrossRefPubMed
68.
69.
70.
71.
Deng M, Mina D, Kim W, Riccardo S, Bart P, Wouter J. A privacy threat analysis framework: supporting the elicitation and fulfillment of privacy requirements. Requir Eng. 2010;16:3–32.CrossRef
72.
Gross T. Security analysis of the SAML single sign-on browser/artifact profile. Computer security applications conference, 2003. Proceedings. 19th annual. 2003. p. 298–307.
73.
74.
75.
Chang RKC. Defending against flooding-based distributed denial-of-service attacks: a tutorial. IEEE Commun Mag. 2002;40:42–51.CrossRef
76.
77.
Potter B, McGraw G. Software security testing. IEEE Secur Privacy Mag. 2004;2:81–5.CrossRef
78.
Myers GJ, Sandler C, Badgett T. The Art of Software Testing. Hoboken: Wiley; 2011.
79.
80.
81.
82.
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2:401–4.CrossRefPubMed
83.
Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, et al. The COSMIC (catalogue of somatic mutations in cancer) database and website. Br J Cancer. 2004;91:355–8.PubMedPubMedCentral
84.
Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, et al. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 2012;40:D57–63.CrossRefPubMed
85.
Splendiani A, Gündel M, Austyn JM, Cavalieri D, Scognamiglio C, Brandizi M. Knowledge sharing and collaboration in translational research, and the DC-THERA directory. Brief Bioinform. 2011;12:562–75.CrossRefPubMedPubMedCentral
86.
Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, et al. Research resources: curating the new eagle-i discovery system. Database. 2012;2012:bar067.CrossRefPubMedPubMedCentral
87.
Canuel V, Rance B, Avillach P, Degoulet P, Burgun A. Translational research platforms integrating clinical and omics data: a review of publicly available solutions. Brief Bioinform. 2015;16:280–90.CrossRefPubMed
88.
89.
Recordon D, Reed D. OpenID 2.0: a platform for user-centric identity management. Proceedings of the second ACM workshop on digital identity management. New York: ACM; 2006. p. 11–6.
90.
Kwon J, Johnson ME. Security practices and regulatory compliance in the healthcare industry. J Am Med Inform Assoc. 2013;20:44–51.CrossRefPubMed
91.
Barkley J. Comparing simple role based access control models and access control lists. Proceedings of the second ACM workshop on Role-based access control. Fairfax: ACM; 1997. p. 127–32.
92.
Røstad L. Access control in healthcare information systems. Trondheim: Norwegian University of Science and Technology; 2008.
93.
Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, et al. caGrid 1.0: an enterprise Grid infrastructure for biomedical research. J Am Med Inform Assoc. 2008;15:138–49.CrossRefPubMedPubMedCentral
94.
Kho AN, Hynes DM, Goel S, Solomonides AE, Price R, Hota B, et al. CAPriCORN: Chicago area patient-centered outcomes research network. J Am Med Inform Assoc. 2014;21:607–11.CrossRefPubMedPubMedCentral
95.
Razick S, Močnik R, Thomas LF, Ryeng E, Drabløs F, Sætrom P. The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences. Database. 2014;2014:bau027.CrossRefPubMedPubMedCentral
96.
Murtagh MJ, Demir I, Jenkings KN, Wallace SE, Murtagh B, Boniol M, et al. Securing the data economy: translating privacy and enacting security in the development of DataSHIELD. Public Health Genomics. 2012;15:243–53.CrossRefPubMed
97.
98.
Murphy SN, Gainer V, Mendis M, Churchill S, Kohane I. Strategies for maintaining patient privacy in i2b2. J Am Med Inform Assoc. 2011;18 Suppl 1:103–8.CrossRef
99.
McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, et al. SHRINE: enabling nationally scalable multi-site disease studies. PLoS One. 2013;8:e55811.CrossRefPubMedPubMedCentral
100.
Boyd AD, Saxman PR, Hunscher DA, Smith KA, Morris TD, Kaston M, et al. The university of Michigan honest broker: a Web-based service for clinical and translational research and practice. J Am Med Inform Assoc. 2009;16:784–91.CrossRefPubMedPubMedCentral
101.
van Panhuis WG, Paul P, Emerson C, Grefenstette J, Wilder R, Herbst AJ, et al. A systematic review of barriers to data sharing in public health. BMC Public Health. 2014;14:1144.CrossRefPubMedPubMedCentral
102.
Lee LM, Gostin LO. Ethical collection, storage, and use of public health data: a proposal for a national privacy protection. JAMA. 2009;302:82–4.CrossRefPubMed
103.
104.
Goodman KW, Adams S, Berner ES, Embi PJ, Hsiung R, Hurdle J, et al. AMIA’s code of professional and ethical conduct. J Am Med Inform Assoc. 2013;20:141–3.CrossRefPubMedPubMedCentral
105.
Knoppers BM, Harris JR, Budin-Ljøsne I, Dove ES. A human rights approach to an international code of conduct for genomic and clinical data sharing. Hum Genet. 2014;133:895–903.CrossRefPubMedPubMedCentral
106.
Malin B, Karp D, Scheuermann RH. Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research. J Investig Med. 2010;58:11–8.CrossRefPubMedPubMedCentral
107.
Yu F, Ji Z. Scalable privacy-preserving data sharing methodology for genome-wide association studies: an application to iDASH healthcare privacy protection challenge. BMC Med Inform Decis Mak. 2014;14 Suppl 1:S3.CrossRefPubMed
108.
Jiang X, Zhao Y, Wang X, Malin B, Wang S, Ohno-Machado L, et al. A community assessment of privacy preserving techniques for human genomes. BMC Med Inform Decis Mak. 2014;14 Suppl 1:S1.CrossRefPubMed
109.
Lin Z, Owen AB, Altman RB. Genetics. Genomic research and human subject privacy. Science. 2004;305:183.CrossRefPubMed
110.
111.
112.
113.
114.
Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, et al. The electronic medical records and genomics (eMERGE) network: past, present, and future. Genet Med. 2013;15:761–71.CrossRefPubMedPubMedCentral
115.
116.
Kuchinke W, Krauth C, Bergmann R, Karakoyun T, Woollard A, Schluender I, et al. Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing. BMC Med Inform Decis Mak. 2016;16:1144.CrossRef
117.
118.
119.
120.
121.
122.
Berners-Lee T, Tim B-L, James H, Ora L. The semantic Web. Sci Am. 2001;284:34–43.CrossRef
123.
Bizer C. The emerging Web of linked data. IEEE Intell Syst. 2009;24:87–92.CrossRef
124.
Bizer C, Christian B, Tom H, Tim B-L. Linked data - the story So Far. Int J Semant Web Inf Syst. 2009;5:1–22.
125.
126.
Villata S, Serena V, Nicolas D, Fabien G, Amelie G. An Access Control Model for Linked Data. Lect Notes Comput Sci. 2011. p. 454–63.
127.
128.
Schwarte A, Haase P, Hose K, Schenkel R, Schmidt M, et al. FedX: optimization techniques for federated query processing on linked data. In: Aroyo L, Welty C, Alani H, Taylor J, Bernstein A, Kagal L, editors. The semantic Web – ISWC 2011. Berlin: Springer Berlin Heidelberg; 2011. p. 601–16.CrossRef
129.
Biancini A, Florio L, Haase M, Hardt M, Jankowski M, Jensen J, et al. AARC: first draft of the blueprint architecture for authentication and authorisation infrastructures. ArXiv [cs.CR]. 2016. http://​arxiv.​org/​abs/​1611.​07832. Accessed 16 Mar 2017.
Metadata
Title
Orchestrating differential data access for translational research: a pilot implementation
Authors
Marco Brandizi
Olga Melnichuk
Raffael Bild
Florian Kohlmayer
Benedicto Rodriguez-Castro
Helmut Spengler
Klaus A. Kuhn
Wolfgang Kuchinke
Christian Ohmann
Timo Mustonen
Mikael Linden
Tommi Nyrönen
Ilkka Lappalainen
Alvis Brazma
Ugis Sarkans
Publication date
01-12-2017
Publisher
BioMed Central
Published in
BMC Medical Informatics and Decision Making / Issue 1/2017
Electronic ISSN: 1472-6947
DOI
https://doi.org/10.1186/s12911-017-0424-6

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