Towards a common semantic representation of informed consent for biobank specimens

Biospecimen-based research is rapidly growing in the post genomic era, and includes the need to retrieve specimens from distributed biobanks of various size and complexity in a fashion that ethically preserves the expressed wishes of specimen donors as represented by the informed consent process and its artifacts. This paper briefly describes existing work along these lines, presents some challenges unique to biobanks, and presents our own work on an ontology of informed consent. Keywords— BioBank, Informed consent; ontology; ICO; OBO Foundry, Basic Formal Ontology (BFO), OBI ontology

[1]  ISBER NEWS,et al.  International society for biological and environmental repositories. , 2009, Biopreservation and biobanking.

[2]  B. Knoppers,et al.  Trends in ethical and legal frameworks for the use of human biobanks , 2007, European Respiratory Journal.

[3]  Julie Evans,et al.  Model Formulation: The BRIDG Project: A Technical Report , 2008, J. Am. Medical Informatics Assoc..

[4]  Mor Peleg,et al.  The Ontology of Clinical Research (OCRe): An informatics foundation for the science of clinical research , 2014, J. Biomed. Informatics.

[5]  Alan Ruttenberg,et al.  Ontobee: A Linked Data Server and Browser for Ontology Terms , 2011, ICBO.

[6]  Robert E. Hewitt,et al.  Biobanking: the foundation of personalized medicine , 2011, Current opinion in oncology.

[7]  Barry Smith,et al.  SNAP and SPAN: Towards Dynamic Spatial Ontology , 2004, Spatial Cogn. Comput..

[8]  Yongqun He,et al.  Ontodog: a web-based ontology community view generation tool , 2014, Bioinform..

[9]  Mathias Brochhausen,et al.  Developing a semantically rich ontology for the biobank-administration domain , 2013, Journal of Biomedical Semantics.

[10]  Csongor Nyulas,et al.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications , 2011, Nucleic Acids Res..

[11]  M. Fransson,et al.  A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS. , 2012, Biopreservation and biobanking.

[12]  Anand K. Gramopadhye,et al.  Development of an Electronic Research Permissions Management System to Enhance Informed Consents and Capture Research Authorizations Data , 2013, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

[13]  María Adela Grando,et al.  Building and Evaluating an Ontology-based Tool for Reasoning about Consent Permission , 2013, AMIA.

[14]  Frank J. Manion,et al.  Security and privacy requirements for a multi-institutional cancer research data grid: an interview-based study , 2009, BMC Medical Informatics Decis. Mak..

[15]  Ryan R Brinkman,et al.  OntoFox: web-based support for ontology reuse , 2010, BMC Research Notes.

[16]  G. Henderson,et al.  Characterizing biobank organizations in the U.S.: results from a national survey , 2013, Genome Medicine.