ssmuБюллетень сибирской медициныBulletin of Siberian Medicine1682-03631819-3684Siberian State Medical University, the Ministry of Healthcare of the Russian Federation10.20538/1682-0363-2012-1-111-121ssmu-417Research ArticleНАУЧНЫЙ И УЧЕБНЫЙ ПРОЦЕСС: МЕТОДИЧЕСКИЙ СЕМИНАРSCIENTIFIC AND STUDYING PROCESS: METHODIC SEMINARБазы данных коллекций биологического материала: организация сопроводительной информацииDatabases of biological collection: organization of associated informationБуйкинС. В.BuikinS. V.stepan_buikin@mail.ruБрагинаЕ. Ю.BraginaYe. Yu.stepan_buikin@mail.ruКоневаЛ. А.KonevaL. A.stepan_buikin@mail.ruПузырёвВ. П.PuzyryovV. P.stepan_buikin@mail.ruНИИ медицинской генетики СО РАМН, г. ТомскRussian FederationНИИ медицинской генетики СО РАМН, Сибирский государственный медицинский университет, г. ТомскRussian Federation201228022012111111121Copyright © Буйкин С.В., Брагина Е.Ю., Конева Л.А., Пузырёв В.П., 20122012Буйкин С.В., Брагина Е.Ю., Конева Л.А., Пузырёв В.П.Buikin S.V., Bragina Y.Y., Koneva L.A., Puzyryov V.P.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://bulletin.ssmu.ru/jour/article/view/417

Данный обзор посвящен проблеме организации и хранения сопроводительной информации для биологических коллекций. Рассмотрены основные принципы разработки структуры баз данных для этих целей. Проведен обзор баз данных биологических коллекций и биобанков в России и мире. Представлена структура базы данных биобанка НИИ медицинской генетики СО РАМН (г. Томск).

The review discusses problem of organization and storage of associated information for biological collection. Basic principles of database structure development are presented. Databases for biological collections and biobanks in Russiaand other countries are reviewed. Structure of database of Biobank of Institute of Medical Genetics SB RAMS is described.

биобанкбаза данныхмногофакторные заболеванияbiobankdatabasecomplex diseasesReferencesБрагина Е.Ю., Буйкин С.В. Влияние численности контрольной выборки на значимость ассоциаций генетических маркеров с развитием мультифакториальных заболеваний // Якут. мед. журн. 2009. № 2 (26). С. 142—144.Брагина Е.Ю., Буйкин С.В. Влияние численности контрольной выборки на значимость ассоциаций генетических маркеров с развитием мультифакториальных заболеваний // Якут. мед. журн. 2009. № 2 (26). С. 142—144.Брагина Е.Ю., Буйкин С.В., Пузырев В.П. Биологические банки: проблемы и перспективы их использования в исследованиях генетических аспектов комплексных заболеваний человека // Мед. генетика. 2009. № 3. С. 20—27.Брагина Е.Ю., Буйкин С.В., Пузырев В.П. Биологические банки: проблемы и перспективы их использования в исследованиях генетических аспектов комплексных заболеваний человека // Мед. генетика. 2009. № 3. С. 20—27.Буйкин С.В., Брагина Е.Ю., Конева Л.А. Разработка структуры базы данных для биобанков // Якут. мед. журн. 2011 № 1. С. 70—73.Буйкин С.В., Брагина Е.Ю., Конева Л.А. Разработка структуры базы данных для биобанков // Якут. мед. журн. 2011 № 1. С. 70—73.Игнасимуту С. Основы биоинформатики. М.; Ижевск: НИЦ «Регулярная и хаотическая динамика»; Институт компьютерных исследований, 2007. 320 с.Игнасимуту С. Основы биоинформатики. М.; Ижевск: НИЦ «Регулярная и хаотическая динамика»; Институт компьютерных исследований, 2007. 320 с.Кычкина О.И., Кононова С.К., Фёдорова С.А. и др. О деятельности банка ДНК наследственных патологий и популяций народов Республики Саха (Якутия) // Тез. докл. III Междунар. науч.-практ. конф. 2006. 73 с.Кычкина О.И., Кононова С.К., Фёдорова С.А. и др. О деятельности банка ДНК наследственных патологий и популяций народов Республики Саха (Якутия) // Тез. докл. III Междунар. науч.-практ. конф. 2006. 73 с.Русинова Г.Г., Адамова Г.В., Осовец С.В. и др. Банк ДНК людей, подвергшихся профессиональному облучению. Цели и перспективы // Генетика. 2001. Т. 37, № 9. С. 1307—1310.Русинова Г.Г., Адамова Г.В., Осовец С.В. и др. Банк ДНК людей, подвергшихся профессиональному облучению. Цели и перспективы // Генетика. 2001. Т. 37, № 9. С. 1307—1310.Сабанов А. Безопасность баз данных // Connect. 2006. № 4. С. 25—37.Сабанов А. Безопасность баз данных // Connect. 2006. № 4. С. 25—37.Соколов А. Средства защиты персональных данных: проблемы оценки соответствия // Connect. 2008. № 12. С. 25—37.Соколов А. Средства защиты персональных данных: проблемы оценки соответствия // Connect. 2008. № 12. С. 25—37.Asslaber M., Zatloukal K. Biobanks: transnational, European and global networks // Brief. Funct. Genomics Proteomic. 2007. V. 6 (3). P. 193—201.Asslaber M., Zatloukal K. Biobanks: transnational, European and global networks // Brief. Funct. Genomics Proteomic. 2007. V. 6 (3). P. 193—201.Austin M.A., Harding S., McElroy C. Genebanks: a comparison of eight proposed international genetic databases // Community Genet. 2003. V. 6 (1). P. 37—45.Austin M.A., Harding S., McElroy C. Genebanks: a comparison of eight proposed international genetic databases // Community Genet. 2003. V. 6 (1). P. 37—45.Beale T. Archetypes: Constraint-based Domain Models for Future-proof Information Systems // http://www.openehr.org. 2008.Beale T. Archetypes: Constraint-based Domain Models for Future-proof Information Systems // http://www.openehr.org. 2008.Bingham S., Riboli E. Diet and cancer — the European pro-spective investigation into cancer and nutrition // Nat. Rev. Cancer. 2004. V. 4. P. 206—215.Bingham S., Riboli E. Diet and cancer — the European pro-spective investigation into cancer and nutrition // Nat. Rev. Cancer. 2004. V. 4. P. 206—215.Dangl A. The IT-infrastructure of a biobank for an academic medical center // Stud. Health. Technol. Inform. 2010. V. 160. P. 1334—1338.Dangl A. The IT-infrastructure of a biobank for an academic medical center // Stud. Health. Technol. Inform. 2010. V. 160. P. 1334—1338.Early W. Database management systems for process safety // J. of Hazardous Materials. 2006. V. 130. P. 53—57.Early W. Database management systems for process safety // J. of Hazardous Materials. 2006. V. 130. P. 53—57.Feero W.G., Guttmacher A.E. Genome wide Association Studies and assessment of the risk of disease // N. Engl. J. Med. 2010. V. 363. P. 166 —176.Feero W.G., Guttmacher A.E. Genome wide Association Studies and assessment of the risk of disease // N. Engl. J. Med. 2010. V. 363. P. 166 —176.Galloux J.C. An empirical survey on biobanking of human genetic material and data in six EU countries // Eur. J. Hum. Genet. 2003. V. 11. P. 475—488.Galloux J.C. An empirical survey on biobanking of human genetic material and data in six EU countries // Eur. J. Hum. Genet. 2003. V. 11. P. 475—488.GeneLink: A data management system designed to facilitate genetic studies of complex traits. URL: http://research. nhgri.nih.gov/genelink.GeneLink: A data management system designed to facilitate genetic studies of complex traits. URL: http://research. nhgri.nih.gov/genelink.Gillanders E.M., Masiello A., Gildea D. et al. GeneLink: a database to facilitate genetic studies of complex traits // BMC Genomics. 2004. V. 5, № 81. P. 1—14.Gillanders E.M., Masiello A., Gildea D. et al. GeneLink: a database to facilitate genetic studies of complex traits // BMC Genomics. 2004. V. 5, № 81. P. 1—14.Godard B., Schmidtke J., Cassiman J.J., Aymé S. Data stor-age and DNA banking for biomedical research: informed consent, confidentiality, quality issues, ownership, return of benefits. A professional perspective // Eur. J. Hum. Genet. 2003. V. 11. P. 88—122.Godard B., Schmidtke J., Cassiman J.J., Aymé S. Data stor-age and DNA banking for biomedical research: informed consent, confidentiality, quality issues, ownership, return of benefits. A professional perspective // Eur. J. Hum. Genet. 2003. V. 11. P. 88—122.Grimson J. Delivering the electronic healthcare record for the 21 century // Int. J. Med. Inform. 2001. V. 64. P. 111—127.Grimson J. Delivering the electronic healthcare record for the 21 century // Int. J. Med. Inform. 2001. V. 64. P. 111—127.Gurwitz D., Fortier I., Lunshof J.E., Knoppers B.M. Chil-dren and Population Biobanks // Science. 2009. V. 325. № 5942. P. 818—819.Gurwitz D., Fortier I., Lunshof J.E., Knoppers B.M. Chil-dren and Population Biobanks // Science. 2009. V. 325. № 5942. P. 818—819.Hagberg B., Hanefeld F., Percy A., Skjeldal O. An update on clinically applicable diagnostic criteria in Rett syndrome // Eur. J. Paediatr. Neurol. 2002. V. 6. P. 293—297.Hagberg B., Hanefeld F., Percy A., Skjeldal O. An update on clinically applicable diagnostic criteria in Rett syndrome // Eur. J. Paediatr. Neurol. 2002. V. 6. P. 293—297.Hansson M.G. Combining efficiency and concerns about in-tegrity when using human biobanks // Stud. Hist. Philos. Biol. Biomed. Sci. 2006. V. 37 (3). P. 520—532.Hansson M.G. Combining efficiency and concerns about in-tegrity when using human biobanks // Stud. Hist. Philos. Biol. Biomed. Sci. 2006. V. 37 (3). P. 520—532.Illig T., Gieger C., Zhai G. et al. A genome-wide perspec-tive of genetic variation in human metabolism // Nat. Genet. 2010. V. 42, № 2. P. 137—141.Illig T., Gieger C., Zhai G. et al. A genome-wide perspec-tive of genetic variation in human metabolism // Nat. Genet. 2010. V. 42, № 2. P. 137—141.Kaiser J. Biobanks: Population Databases Boom, From Ice-land to the U.S. Science. 2002. V. 298. P. 1158—1161.Kaiser J. Biobanks: Population Databases Boom, From Ice-land to the U.S. Science. 2002. V. 298. P. 1158—1161.Kristianson K.J., Ljunggren H., Gustafsson L.L. Data extraction from a semi-structured electronic medical record system for outpatients: A model to facilitate the access and use of data for quality control and research // Health Informatics Journal. 2009. V. 15, № 4. P. 305—319.Kristianson K.J., Ljunggren H., Gustafsson L.L. Data extraction from a semi-structured electronic medical record system for outpatients: A model to facilitate the access and use of data for quality control and research // Health Informatics Journal. 2009. V. 15, № 4. P. 305—319.Laurvick C.L., de Klerk N., Bower C. Rett syndrome in Australia: a review of the epidemiology // J. Pediatr. 2006. V. 48. P. 347—352.Laurvick C.L., de Klerk N., Bower C. Rett syndrome in Australia: a review of the epidemiology // J. Pediatr. 2006. V. 48. P. 347—352.Leslie Н. International developments in openEHR archetypes and templates // Health information management journal. 2008. V. 37, № 1. P. 38—39.Leslie Н. International developments in openEHR archetypes and templates // Health information management journal. 2008. V. 37, № 1. P. 38—39.Little J., Higgins J.P., Ioannidis J.P. et al. Strengthening the reporting of genetic association studies (STREGA): an ex-tension of the STROBE Statement // Hum. Genet. 2009. V. 125. P. 131—151.Little J., Higgins J.P., Ioannidis J.P. et al. Strengthening the reporting of genetic association studies (STREGA): an ex-tension of the STROBE Statement // Hum. Genet. 2009. V. 125. P. 131—151.Litton J.E. Biobank informatics: connecting genotypes and phenotypes. Methods Mol. Biol. 2011. V. 675. Р. 343—3461.Litton J.E. Biobank informatics: connecting genotypes and phenotypes. Methods Mol. Biol. 2011. V. 675. Р. 343—3461.Marrugat J., Lopez-Lopez J.R., Heras M. et al. The HERACLES cardiovascular Network // Rev. Esp. Cardiol. 2008. V. 61, № 1. P. 66—75.Marrugat J., Lopez-Lopez J.R., Heras M. et al. The HERACLES cardiovascular Network // Rev. Esp. Cardiol. 2008. V. 61, № 1. P. 66—75.Martin N., Krol P., Smith S. et al. A national registry for ju-venile dermatomyositis and other paediatric idiopathic in-flammatory myopathies: 10 years' experience; the Juvenile Dermatomyositis National (UK and Ireland) Cohort Biomarker Study and Repository for Idiopathic Inflammatory Myopathies // Rheumatology. 2011. V. 50, № 1. P. 137—145.Martin N., Krol P., Smith S. et al. A national registry for ju-venile dermatomyositis and other paediatric idiopathic in-flammatory myopathies: 10 years' experience; the Juvenile Dermatomyositis National (UK and Ireland) Cohort Biomarker Study and Repository for Idiopathic Inflammatory Myopathies // Rheumatology. 2011. V. 50, № 1. P. 137—145.Matimba A., Oluka M.N., Ebeshi B.U. et al. Establishment of a biobank and pharmacogenetics database of African populations // Eur. J. of Human Genetics. 2008. V. 16. P. 780—785.Matimba A., Oluka M.N., Ebeshi B.U. et al. Establishment of a biobank and pharmacogenetics database of African populations // Eur. J. of Human Genetics. 2008. V. 16. P. 780—785.Muilu J., Peltonen L., Litton J.-E. The federated database — a basis for biobanking-baesd post-genome studies, inte-grating phenome and genome date from 600000 twin pairs in Europe // Eur. J.l of Human Genetics. 2007. V. 15. P. 718—723.Muilu J., Peltonen L., Litton J.-E. The federated database — a basis for biobanking-baesd post-genome studies, inte-grating phenome and genome date from 600000 twin pairs in Europe // Eur. J.l of Human Genetics. 2007. V. 15. P. 718—723.Narod S., Rosenblatt D., Lamothe E. The banking of DNA for the prevention of genetic disease // Clin. Invest. Med. 1991. V. 14. P. 359—362.Narod S., Rosenblatt D., Lamothe E. The banking of DNA for the prevention of genetic disease // Clin. Invest. Med. 1991. V. 14. P. 359—362.Pukkala E., Andersen A., Berglund G. et al. Nordic biologi-cal specimen banks as basis for studies of and control more than 2 million sample donors, 25 million years and 100 000 prospective cancers // Acta Oncologica. 2007. V. 46. P. 286—307.Pukkala E., Andersen A., Berglund G. et al. Nordic biologi-cal specimen banks as basis for studies of and control more than 2 million sample donors, 25 million years and 100 000 prospective cancers // Acta Oncologica. 2007. V. 46. P. 286—307.Riegman P.H., Morente M.M., Betsou F. et al. Biobanking for better healthcare // Mol. Oncol. 2008. V. 2. P. 213—222.Riegman P.H., Morente M.M., Betsou F. et al. Biobanking for better healthcare // Mol. Oncol. 2008. V. 2. P. 213—222.Riegman P.H., Dinjens W.N., Oomen M.H. et al. TuBaFrost 1: uniting local frozen tumour banks into a European network: an overview // Eur. J. Cancer. 2006. V. 42. P. 2678—2683.Riegman P.H., Dinjens W.N., Oomen M.H. et al. TuBaFrost 1: uniting local frozen tumour banks into a European network: an overview // Eur. J. Cancer. 2006. V. 42. P. 2678—2683.Robertson L., Hall S.E., Jacoby P. The association between behavior and genotype in Rett syndrome using the Australian Rett Syndrome Database // Am. J. Med. Genet. 2006. V. 5, № 41. P. 177—183.Robertson L., Hall S.E., Jacoby P. The association between behavior and genotype in Rett syndrome using the Australian Rett Syndrome Database // Am. J. Med. Genet. 2006. V. 5, № 41. P. 177—183.Sampieri K., Meloni I., Scala E. et al. Italian Rett database and biobank // Hum. Mutat. 2007. V. 4. P. 329—335.Sampieri K., Meloni I., Scala E. et al. Italian Rett database and biobank // Hum. Mutat. 2007. V. 4. P. 329—335.Sampogna C. Creation and governance of human genetic re-search databases Organization for Economic Co-operation and Development, OECD Publishing, 2006. 159 p.Sampogna C. Creation and governance of human genetic re-search databases Organization for Economic Co-operation and Development, OECD Publishing, 2006. 159 p.Savova G.K., Masanz J.J., Ogren P.V. et al. Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications // J. Am. Med. Inform. Assoc. 2010. V. 17, № 5. P. 507—513Savova G.K., Masanz J.J., Ogren P.V. et al. Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications // J. Am. Med. Inform. Assoc. 2010. V. 17, № 5. P. 507—513Schena F.P. Cerullo G., Torres D.D. et al. The IgA nephropathy Biobank. An important starting point for the genetic dissection of a complex trait // BMC Nephrol. 2005. V. 6. P. 14.Schena F.P. Cerullo G., Torres D.D. et al. The IgA nephropathy Biobank. An important starting point for the genetic dissection of a complex trait // BMC Nephrol. 2005. V. 6. P. 14.Sherman J.K. Synopsis of the use of frozen human semen since 1964: state of the art of human semen banking // Fertil. Steril. 1973. V. 24. P. 397—412.Sherman J.K. Synopsis of the use of frozen human semen since 1964: state of the art of human semen banking // Fertil. Steril. 1973. V. 24. P. 397—412.Sirugo G., Schim L., Sam O. et al. A national DNA bank in the Gambia, West Africa, and genomic research in developing countries // Nat. Genet. 2004. V. 36. P. 785—786.Sirugo G., Schim L., Sam O. et al. A national DNA bank in the Gambia, West Africa, and genomic research in developing countries // Nat. Genet. 2004. V. 36. P. 785—786.Späth M.B., Grimson J. Applying the archetype approach to the database of a biobank information management system // Int. J. Med. Inform. 2011. V. 80, № 3. P. 205—26.Späth M.B., Grimson J. Applying the archetype approach to the database of a biobank information management system // Int. J. Med. Inform. 2011. V. 80, № 3. P. 205—26.Tassé A.M., Budin-Ljøsne I., Knoppers B.M., Harris J.R. Retrospective access to data: the ENGAGE consent experi-ence // Eur. J. Hum. Genet. 2010. V. 18, № 7. P. 741—745.Tassé A.M., Budin-Ljøsne I., Knoppers B.M., Harris J.R. Retrospective access to data: the ENGAGE consent experi-ence // Eur. J. Hum. Genet. 2010. V. 18, № 7. P. 741—745.The openEHR Foundation // http://www.openehr.org.The openEHR Foundation // http://www.openehr.org.Troyer D. Biorepository standards and protocols for collecting, processing, and storing human tissues // Methods Mol. Biol. 2008. V. 441. P. 193—220.Troyer D. Biorepository standards and protocols for collecting, processing, and storing human tissues // Methods Mol. Biol. 2008. V. 441. P. 193—220.Watson P.H., Wilson-McManus J.E., Barnes R.O. et al. Evolutionary concepts in biobanking—the BC BioLibrary // J. Trans. Med. 2009. V. 7. P. 95.Watson P.H., Wilson-McManus J.E., Barnes R.O. et al. Evolutionary concepts in biobanking—the BC BioLibrary // J. Trans. Med. 2009. V. 7. P. 95.Yuille M., Dixon K., Platt A. et al. The UK DNA banking network: a «fair access» biobank // Cell Tissue Bank. 2010. V. 11. P. 241—251.Yuille M., Dixon K., Platt A. et al. The UK DNA banking network: a «fair access» biobank // Cell Tissue Bank. 2010. V. 11. P. 241—251.

The authors declare that there are no conflicts of interest present.