Rehm, H.L., Page, A.J.H., Smith, L., Adams, J.B., Alterovitz, G., Babb, L.J., Barkley, M.P., Baudis, M., Beauvais, M.J.S., Beck, T., et al. GA4GH: international policies and standards for data sharing across genomic research and healthcare. Cell Genomics, 1, 2021 100029-1–100029-33.
Thorogood, A., Rehm, H.L., Goodhand, P., Page, A.J.H., Joly, Y., Baudis, M., Rambla, J., Navarro, A., Nyronen, T.H., Linden, M., et al. International Federation of Genomic Medicine Databases Using GA4GH Standards. Cell Genomics, 1, 2021 100032-1–100032-5.
Woolley, J.P., Kirby, E., Leslie, J., Jeanson, F., Cabili, M.N., Rushton, G., Hazard, J.G., Ladas, V., Veal, C.D., Gibson, S.J., et al. Responsible sharing of biomedical data and biospecimens via the “Automatable Discovery and Access Matrix” (ADA-M). npj Genomic Med. 3 (2018), 1–6.
GA4GH Data Use and Researcher ID work stream. https://ga4gh-duri.github.io/.
Voisin, C., Linden, M., Dyke, S.O.M., Bowers, S.R., Reinold, K., Lawson, J., Li, S., Ota Wang, V., Barkley, M.P., Bernick, D., et al. GA4GH Passport standard for digital identity and access permissions. Cell Genomics, 1, 2021 100030-1–100030-12.
Cabili, M.N., Lawson, J., Saltzman, A., Rushton, G., O'Rourke, P., Wilbanks, J., Rodriguez, L.L., Nyronen, T., Courtot, M., Donnelly, S., Philippakis, A.A., Empirical validation of an automated approach to data use oversight. Cell Genomics, 1, 2021 100031-1–100031-6.
Tryka, K.A., Hao, L., Sturcke, A., Jin, Y., Wang, Z.Y., Ziyabari, L., Lee, M., Popova, N., Sharopova, N., Kimura, M., Feolo, M., NCBI's Database of Genotypes and Phenotypes: dbGaP. Nucleic Acids Res. 42 (2014), D975–D979.
Lappalainen, I., Almeida-King, J., Kumanduri, V., Senf, A., Spalding, J.D., Ur-Rehman, S., Saunders, G., Kandasamy, J., Caccamo, M., Leinonen, R., et al. The European Genome-phenome Archive of human data consented for biomedical research. Nat. Genet. 47 (2015), 692–695.
Dyke, S.O.M., Philippakis, A.A., Rambla De Argila, J., Paltoo, D.N., Luetkemeier, E.S., Knoppers, B.M., Brookes, A.J., Spalding, J.D., Thompson, M., Roos, M., et al. Consent Codes: Upholding Standard Data Use Conditions. PLoS Genet., 12, 2016, e1005772.
Lin, Y., Harris, M.R., Manion, F.J., Eisenhauer, E., Zhao, B., Shi, W., Karnovsky, A, He, Y, Development of a BFO-Based Informed Consent Ontology (ICO). Proceedings of the 5th International Conference on Biomedical Ontologies (ICBO), 2014 Houston, Texas, USA.
DUO tracker. https://github.com/EBISPOT/DUO/issues.
DUO governance policy. https://github.com/EBISPOT/DUO/blob/master/Governance2021.md.
Web Ontology Language Reference. https://www.w3.org/TR/owl-ref/.
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., et al., OBI Consortium. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25 (2007), 1251–1255.
Shefchek, K.A., Harris, N.L., Gargano, M., Matentzoglu, N., Unni, D., Brush, M., Keith, D., Conlin, T., Vasilevsky, N., Zhang, X.A., et al. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48:D1 (2020), D704–D715.
Grenon, P., Smith, B., Goldberg, L., Biodynamic ontology: applying BFO in the biomedical domain. Stud. Health Technol. Inform. 102 (2004), 20–38.
Jupp, S., Burdett, T., Malone, J., Leroy, C., Pearce, M., McMurry, J., et al. A new Ontology Lookup Service at EMBL-EBI. Proceedings of the 8th International Conference on Semantic Web Applications and Tools for Life Sciences, Cambridge, UK., 2015, 118–119.
DUO Github repository. https://github.com/EBISPOT/DUO.
Overton, J.A., Cuffaro, M., The OBO Foundry Operations Committee Technical Working Group. Mungall, C.J., String of PURLs – frugal migration and maintenance of persistent identifiers. Data Science. 3 (2020), 3–13.
DUO releases. http://purl.obolibrary.org/obo/duo/releases/.
DUO October 2017 release. http://purl.obolibrary.org/obo/duo/releases/2017-10-16/duo.owl.
Matentzoglu, N., Leo, J., Hudhra, V., Parsia, B., Sattler, U., et al. A survey of current, stand-alone OWL Reasoners. Proceedings of the 4th International Workshop on OWL Reasoner Evaluation (ORE-2015). Athens, Greece, 2015 June 6, 2015.
Hancock, J.M., SPARQL (SPARQL Protocol and RDF Query Language). Dictionary of Bioinformatics and Computational Biology, 2004, Wiley.
Courtot, M., Gibson, F., Lister, A., Malone, J., Schober, D., Brinkman, R.R., Ruttenberg, A., et al. MIREOT: The minimum information to reference an external ontology term. Applied Ontology 6 (2011), 23–33.
Kazakov, Y., Krötzsch, M., Simančík, F., The Incredible ELK. J. Autom. Reason. 53 (2014), 1–61.
Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.W., da Silva Santos, L.B., Bourne, P.E., et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data, 3, 2016, 160018.
Powell, K., The broken promise that undermines human genome research. Nature 590 (2021), 198–201.
NIH Releases New Policy for Data Management and Sharing. https://osp.od.nih.gov/2020/10/29/nih-releases-new-policy-data-management-and-sharing/.
Vasilevsky, N.A., Foster, E.D., Engelstad, M.E., Carmody, L., Might, M., Chambers, C., Dawkins, H.J.S., Lewis, J., Della Rocca, M.G., Snyder, M., et al. Plain-language medical vocabulary for precision diagnosis. Nat. Genet. 50 (2018), 474–476.
GA4GH releases three new deliverables to support responsible genomic data sharing. https://www.ga4gh.org/news/ga4gh-releases-three-new-deliverables-to-support-responsible-genomic-data-sharing/.
Finnish institute for health and welfare. https://thl.fi/en/web/thl-biobank.
Bender, D., Sartipi, K., HL7 FHIR: An Agile and RESTful approach to healthcare information exchange. Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems. 2013 326–331.
Thorogood, A., Policy-aware data lakes: a flexible approach to achieve legal interoperability for global research collaborations. J. Law Biosci., 7, 2020, a065.
