vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ15.090vavilov-481Research ArticleОнтологииOntologiesОнтологии в биоинформатике и системной биологииOntologies in bioinformatics and systems biologyПодколодныйН. Л.PodkolodnyyN. L.pnl@bionet.nsc.ruПодколоднаяО. А.PodkolodnayaO. A.Федеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, Россия Федеральное государственное бюджетное учреждение науки Институт вычислительной математики и математической геофизики Сибирского отделения Российской академии наук, Новосибирск, Россия Федеральное государственное автономное образовательное учреждение высшего образования «Новосибирский национальный исследовательский государственный университет», Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Institute of Computational Mathematics and Mathematical Geophysics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaRussian FederationФедеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaRussian Federation201502012016196652660Copyright © Подколодный Н.Л., Подколодная О.А., 20162016Подколодный Н.Л., Подколодная О.А.Podkolodnyy N.L., Podkolodnaya O.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/481

Компьютерное моделирование в настоящее время становится центральной научной парадигмой системной биологии и основным инструментом для теоретического исследования и понимания механизмов функционирования сложных живых систем. Увеличение количества и сложности этих моделей приводит к необходимости их коллективной разработки, повторного использования, верификации, описания вычислительного эксперимента и его результатов. При разработке форматов представления знаний для математического моделирования биологических систем активно применяют онтологическое моделирование предметной области. В этом смысле онтологию, связанную со всей совокупностью форматов, обеспечивающих поддержку исследований в системной биологии, в частности компьютерное моделирование биологических систем и процессов, можно считать первым приближением к онтологии системной биологии. В обзоре кратко представлены особенности предметной области (биоинформатика, системная биология, биомедицина), основные мотивации в развитии онтологий и наиболее важные примеры онтологического моделирования и семантического анализа на разных уровнях иерархии знаний: молекулярно-генетическом, клеточном, тканевом, органов и организма. Биоинформатика и системная биология являются прекрасным полигоном для отработки технологий и эффективного использования онтологического моделирования. Создание нескольких десятков базовых ссылочных онтологий и их верификация позволяют использовать эти онтологии в качестве источников знаний для интеграции и построения более сложных моделей предметной области, ориентированных на решение конкретных задач биомедицины и биотехнологии. Дальнейшая формализация и накопление онтологических знаний, а также использование формальных методов их анализа могут поднять весь цикл научных исследований в области системной биологии на новый технологический уровень.

Computer simulation is now becoming a central scientific paradigm of systems biology and the basic tool for the theoretical study and understanding of the complex mechanisms of living systems. The increase in the number and complexity of these models leads to the need for their collaborative development, reuse of models, and their verification, and the description of the computational experiment and its results. Ontological modeling is used to develop formats for knowledge-oriented mathematical modeling of biological systems. In this sense, ontology associated with the entire set of formats, supporting research in systems biology, in particular, computer modeling of biological systems and processes can be regarded as a first approximation to the ontology of systems biology. This review summarizes the features of the subject area (bioinformatics, systems biology, and biomedicine), the main motivation for the development of ontologies and the most important examples of ontological modeling and semantic analysis at different levels of the hierarchy of knowledge: the molecular genetic level, cellular level, tissue levels of organs and the body. Bioinformatics and systems biology is an excellent ground for testing technologies and efficient use of ontological modeling. Several dozens of verified basic reference ontologies now represent a source of knowledge for the integration and development of more complex domain models aimed at addressing specific issues in biomedicine and biotechnology. Further formalization and ontological accumulation of knowledge and the use of formal methods of analysis can take the entire cycle of research in systems biology to a new technological level.

онтологическое моделированиебиоинформатикасистемная биологияontological modelingbioinformaticssystems biologyReferencesПодколодный Н.Л. Онтологическое моделирование в биоинформатике и системной биологии. Онтологическое моделирование. ИПИ РАН, 2011:233-269.Antezana E., Egaña M., Blondé W., Illarramendi A., Bilbao I., De Baets B., Stevens R., Mironov V., Kuiper M. The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol. 2009;10(5):R58. DOI 10.1186/gb-2009-10-5-r58Подколодный Н.Л., Игнатьева Е.В., Подколодная О.А., Колчанов Н.А. Информационная поддержка исследования механизмов регуляции транскрипции: онтологический подход. Вавиловский журнал генетики и селекции. 2012;16(4/1):742-755.Bada M., Hunter L. Enrichment of OBO ontologies. J. Biomed. Inform. 2007;40:300-315.Antezana E., Egaña M., Blondé W., Illarramendi A., Bilbao I., De Baets B., Stevens R., Mironov V., Kuiper M. The Cell Cycle Ontology: an application ontology for the representation and integratedBeck T., Morgan H., Blake A., Wells S., Hancock J.M., Mallon A.-M. Practical application of ontologies to annotate and analyze large-scale raw mouse phenotype data. BMC Bioinformatics. 2009;10(Suppl5): S2. DOI 10.1186/1471-2105-10-S5-S2analysis of the cell cycle process. Genome Biol. 2009;10(5):R58. DOI 10.1186/gb-2009-10-5-r58Bodenreider O. Biomedical ontologies in action: Role in knowledge management, data integration and decision support. IMIA Yearbook Medical Informatics, 2008.Bada M., Hunter L. Enrichment of OBO ontologies. J. Biomed. Inform. 2007;40:300-315.Bodenreider O., Stevens R. Bio-ontologies: Current trends and future directions. Brief Bioinform. 2006;7(3):256-274.Beck T., Morgan H., Blake A., Wells S., Hancock J.M., Mallon A.-M. Practical application of ontologies to annotate and analyze large-scale raw mouse phenotype data. BMC Bioinformatics. 2009;10(Suppl5):S2. DOI 10.1186/1471-2105-10-S5-S2Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)–toward standards for microarray data. Nat. Genet. 2001;29:365-371.Bodenreider O. Biomedical ontologies in action: Role in knowledge management, data integration and decision support. IMIA Yearbook Medical Informatics, 2008.Carbon S., Ireland A., Mungall C.J., Shu S., Marshall B., Lewis S. Ami-GO: online access to ontology and annotation data. Bioinformatics. 2009;25(2):288-289. DOI 10.1093/bioinformatics/btn615Bodenreider O., Stevens R. Bio-ontologies: Current trends and future directions. Brief Bioinform. 2006;7(3):256-274.Chandrasekaran B., Josephson J.R., Benjamins V.R. What are ontologies and why do we need them? IEEE Intelligent Systems. 1999;14(1): 20-26. DOI 10.1109/5254.747902Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)–toward standards for microarray data. Nat. Genet. 2001;29:365-371.Chapman W.W., Cohen K.B. Current issues in biomedical text mining and natural language processing. J. Biomed. Inform. 2009;42:757- 759. DOI 10.1016/j.jbi.2009.09.001Carbon S., Ireland A., Mungall C.J., Shu S., Marshall B., Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25(2):288-289. DOI 10.1093/bioinformatics/btn615Chelliah V., Endler L., Juty N., Laibe C., Li C., Rodriguez N., Le Novère N. Data integration and semantic enrichment of systems biology models and simulations. Data integration in the life sciences. Lecture Notes in Computer Science. 2009;5647:5-15.Chandrasekaran B., Josephson J.R., Benjamins V.R. What are ontologies and why do we need them? IEEE Intelligent Systems. 1999;14(1): 20-26. DOI 10.1109/5254.747902Chen Q., Chen Y.-P.P., Zhang C. Detecting inconsistency in biological molecular databases using ontologies. Data Min. Knowl. Disc. 2007;15:275-296. DOI 10.1007/s10618-007-0071-0Chapman W.W., Cohen K.B. Current issues in biomedical text mining and natural language processing. J. Biomed. Inform. 2009;42:757-759. DOI 10.1016/j.jbi.2009.09.001Conesa A., Gotz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics. 2008;2008:619832. DOI 10.1155/2008/619832Chelliah V., Endler L., Juty N., Laibe C., Li C., Rodriguez N., Le Novère N. Data integration and semantic enrichment of systems biology models and simulations. Data integration in the life sciences. Lecture Notes in Computer Science. 2009;5647:5-15.Cunningham F., Moore B., Ruiz-Schultz N., Ritchie G.R., Eilbeck K. Improving the Sequence Ontology terminology for genomic variant annotation. J. Biomed Semantics. 2015; 6:32. DOI 10.1186/s13326-015-0030-4Chen Q., Chen Y.-P.P., Zhang C. Detecting inconsistency in biological molecular databases using ontologies. Data Min. Knowl. Disc. 2007;15:275-296. DOI 10.1007/s10618-007-0071-0Dada J.O., Spasić I., Paton N.W., Mendes P. SBRML: a markup language for associating systems biology data with models. Bioinformatics. 2010;26(7):932-938. DOI 10.1093/bioinformatics/btq069Conesa A., Gotz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics. 2008;2008:619832. DOI 10.1155/2008/619832Day-Richter J., Harris M.A., Haendel M. Gene ontology OBO-edit working group, Lewis S. OBO-Edit – an ontology editor for biologists. Bioinformatics. 2007;23(16):2198-2200.Cunningham F., Moore B., Ruiz-Schultz N., Ritchie G.R., Eilbeck K. Improving the Sequence Ontology terminology for genomic variant annota­tion. J. Biomed Semantics. 2015; 6:32. DOI 10.1186/s13326- 015-0030-4Demir E., Cary M.P., Paley S. et al. The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 2010;28:935-942. DOI 10.1038/nbt.1666Dada J.O., Spasić I., Paton N.W., Mendes P. SBRML: a markup language for associating systems biology data with models. Bioinformatics. 2010;26(7):932-938. DOI 10.1093/bioinformatics/btq069Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucl. Acids Res. 2015;43(Database issue):D1049-D1056. DOI 10.1093/nar/gku1179Day-Richter J., Harris M.A., Haendel M. Gene ontology OBO-edit working group, Lewis S. OBO-Edit – an ontology editor for biologists. Bioinformatics. 2007;23(16):2198-2200.Graham E., Moss J., Burton N., Armit C., Richardson L., Baldock R.D. The atlas of mouse development eHistology resource. Development. 2015;142:1909-1911. DOI 10.1242/dev.124917Demir E., Cary M.P., Paley S. et al. The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 2010;28:935-942. DOI 10.1038/nbt.1666Gruber T.R. Toward principles for the design of ontologies used for knowledge sharing. Int. J. Human-Computer Studies.1995;43(5/6): 907-928.Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucl. Acids Res. 2015;43(Database issue):D1049-D1056. DOI 10.1093/nar/gku1179Huaiyu M.I., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J.,Rabkin S., Guo N., Muruganujan A., Doremieux O., Campbell M.J., Kitano H., Thomas P.D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 2005; 33(suppl.1):D284-D288. DOI 10.1093/nar/gki078Graham E., Moss J., Burton N., Armit C., Richardson L., Baldock R.D. The atlas of mouse development eHistology resource. Development. 2015;142:1909-1911. DOI 10.1242/dev.124917Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor V., Goryanin I.I., Hedley W. J., Hodgman T.C., Hofmeyr J.H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novère N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19(4):524-31.Gruber T.R. Toward principles for the design of ontologies used for knowledge sharing. Int. J. Human-Computer Studies.1995;43(5/6):907-928.Huntley R.P., Sawford T., Mutowo-Meullenet P., Shypitsyna A., Bonilla C., Martin M.J., O’Donovan C. The GOA database: Gene Ontology annotation updates for 2015. Nucl. Acids Res. 2015;43(Database issue): D1057-D1063. DOI 10.1093/nar/gku1113Онтологии в биоинформатике и системной биологии Н.Л. Подколодный О.А. Подколодная Huaiyu M.I., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J., Rabkin S., Guo N., Muruganujan A., Doremieux O., Campbell M.J., Kitano H., Thomas P.D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 2005; 33(suppl.1):D284-D288. DOI 10.1093/nar/gki078Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucl. Acids Res. 2004;32 (Database issue):D277-80.Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor V., Goryanin I.I., Hedley W.J., Hodgman T.C., Hofmeyr J.H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novère N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19(4):524-31.Karp P.D., Weaver D., Paley S., Fulcher C., Kubo A., Kothari A., Krummenacker M., Subhraveti P., Weerasinghe D., Gama-Castro S., Huerta A.M., Muñiz-Rascado L., Bonavides-Martinez C., Weiss V., Peralta- Gil M., Santos-Zavaleta A., Schröder I., Mackie A., Gunsalus R., Collado-Vides J., Keseler I.M., Paulsen I. The EcoCyc Database. Ecosal Plus. 2014;2014. DOI 10.1128/ecosalplusHuntley R.P., Sawford T., Mutowo-Meullenet P., Shypitsyna A., Bonilla C., Martin M.J., O.Donovan C. The GOA database: Gene Ontology annotation updates for 2015. Nucl. Acids Res. 2015;43(Database issue):D1057-D1063. DOI 10.1093/nar/gku1113Keet C.M., Roos M., Marshall M.S. A survey of requirements for automated reasoning services for bio-ontologies in owl. Workshop on OWL: Experiences and Directions. Innsbruck, Austria, 2007.Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucl. Acids Res. 2004;32 (Database issue):D277-80.Khatri P., Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 2005; 21(18):3587-3595.Karp P.D., Weaver D., Paley S., Fulcher C., Kubo A., Kothari A., Krummenacker M., Subhraveti P., Weerasinghe D., Gama-Castro S., Huerta A.M., Muñiz-Rascado L., Bonavides-Martinez C., Weiss V., Peralta-Gil M., Santos-Zavaleta A., Schröder I., Mackie A., Gunsalus R., Collado-Vides J., Keseler I.M., Paulsen I. The EcoCyc Database. Ecosal Plus. 2014;2014. DOI 10.1128/ecosalplusKitano H. Systems biology: a brief overview. Science. 2002;295:1662-1664.Keet C.M., Roos M., Marshall M.S. A survey of requirements for automated reasoning services for bio-ontologies in owl. Workshop on OWL: Experiences and Directions. Innsbruck, Austria, 2007.Klein T.E., Chang J.T., Cho M.K., Easton K.L., Fergerson R., Hewett M., Lin Z., Liu Y., Liu S., Oliver D.E., Rubin D.L., Shafa F., Stuart J. M., Altman R.B. Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenomics J. 2001;1: 167-170.Khatri P., Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 2005; 21(18):3587-3595.Le Novère N., Finney A., Hucka M., Bhalla U.S., Campagne F., Collado-Vides J., Crampin E.J., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 2005;23(12):1509-1515.Kitano H. Systems biology: a brief overview. Science. 2002;295:1662-1664.Livingston K.M., Bada M., Baumgartner W.A. Jr, Hunter L.E. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015;16:126. DOI 10.1186/s12859-015-0559-3Klein T.E., Chang J.T., Cho M.K., Easton K.L., Fergerson R., Hewett M., Lin Z., Liu Y., Liu S., Oliver D.E., Rubin D.L., Shafa F., Stuart J.M., Altman R.B. Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenomics J. 2001;1: 167-170.Lloyd C.M., Halstead M.D.B., Nielsen P.F. CellML: its future, present and past. Progr. Biophys. Mol. Biol. 2004;85(2/3):433-450.Le Novère N., Finney A., Hucka M., Bhalla U.S., Campagne F., ColladoVides J., Crampin E.J., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 2005;23(12):1509-1515.Martin D., Brun C., Remy E., Mouren P., Thieffry D., Jacq B. GOTool-Box: functional analysis of gene datasets based on Gene Ontology. Genome Biol. 2004;5(12):R101.Livingston K.M., Bada M., Baumgartner W.A. Jr, Hunter L.E. KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinformatics. 2015;16:126. DOI 10.1186/s12859-015-0559-3Mi H., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J., Rabkin S., Guo N., Muruganujan A., Doremieux O., Campbell M.J., Kitano H., Thomas P.D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 2005;1:33 (Database issue):D284-8.Lloyd C.M., Halstead M.D.B., Nielsen P.F. CellML: its future, present and past. Progr. Biophys. Mol. Biol. 2004;85(2/3):433-450.Noy N.F., Shah N.H., Whetzel P.L., Dai B., Dorf M., Griffith N., Jonquet C., Rubin D.L., Storey M.A., Chute C.G., Musen M.A. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucl. Acids Res. 2009;37:W170-W173. DOI 10.1093/nar/gkp440Martin D., Brun C., Remy E., Mouren P., Thieffry D., Jacq B. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol. 2004;5(12):R101.Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., Salama J.J., Moore S., Wojcik J., Bader G.D., Vidal M., Cusick M.E., Gerstein M., Gavin A.C., Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., Mulder N.,Mi H., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J., Rabkin S., Guo N., Muruganujan A., Doremieux O., Campbell M.J., Kitano H., Thomas P.D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 2005;1:33 (Database issue):D284-8.Gilson M., Niepmann M., Burgoon L., De Las Rivas J., Prieto C., Perreau V.M., Hogue C., Mewes H.W., Apweiler R., Xenarios I., Eisenberg D., Cesareni G., Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 2007;25(8):894-898.Noy N.F., Shah N.H., Whetzel P.L., Dai B., Dorf M., Griffith N., Jonquet C., Rubin D.L., Storey M.A., Chute C.G., Musen M.A. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucl. Acids Res. 2009;37:W170-W173. DOI 10.1093/nar/gkp440Podkolodnyy N.L. Ontological modeling in bioinformatics and systems biology. Trudy Vtorogo simpoziuma “Ontologicheskoe modelirovanie” [Proceedings of the 2nd Symposium “Ontological modeling” ]. Moscow, IPI RAN, 2011:233-269.Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stmpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., Salama J.J., Moore S., Wojcik J., Bader G.D., Vidal M., Cusick M.E., Gerstein M., Gavin A.C., Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., Mulder N., Gilson M., Niepmann M., Burgoon L., De Las Rivas J., Prieto C., Perreau V.M., Hogue C., Mewes H.W., Apweiler R., Xenarios I., Eisenberg D., Cesareni G., Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 2007;25(8):894-898.Podkolodnyy N.L., Ignatieva E.V., Podkolodnaya O.A., Kolchanov N. A. Information suppotr of research on transcriptional regulatory mechanisms: an ontological approach. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2012; 16(4/1):742-755.Rosse C., Mejino J.L.Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36(6): 478-500.Rosse C., Mejino J.L.Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36(6): 478-500.Rosse C., Mejino J.L.V. The Foundational Model of Anatomy Ontology. Anatomy Ontologies for Bioinformatics: Principles and Practice. Eds A. Burger, D. Davidson, R. Baldock. N.Y.: Springer, 2007.Rosse C., Mejino J.L.V. The Foundational Model of Anatomy Ontology. Anatomy Ontologies for Bioinformatics: Principles and Practice. Eds A. Burger, D. Davidson, R. Baldock. N.Y.: Springer, 2007.Schober D., Smith B., Lewis S.E., Kusnierczyk W., Lomax J., Mungall C., Taylor C.F., Rocca-Serra P., Sansone S.A. Survey-based naming conventions for use in OBO foundry ontology development. BMC Bioinformatics. 2009;27;10:125. DOI 10.1186/1471-2105-10-125Schober D., Smith B., Lewis S.E., Kusnierczyk W., Lomax J., Mungall C., Taylor C.F., Rocca-Serra P., Sansone S.A. Survey-based naming conventions for use in OBO foundry ontology development. BMC Bioinformatics. 2009;27;10:125. DOI 10.1186/1471-2105-10-125Shah N.H., Jonquet C., Chiang A.P., Butte A.J., Chen R., Musen M.A. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009;10(Suppl. 2):S1. DOI 10.1186/1471-2105-10-S2-S1Shah N.H., Jonquet C., Chiang A.P., Butte A.J., Chen R., Musen M.A. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009;10(Suppl. 2):S1. DOI 10.1186/1471-2105-10-S2-S1Smith B., Williams J., Schulze-Kremer S. The Ontology of the Gene Ontology. AMIA Annual Symp. Proceedings, 2003.Smith B., Williams J., Schulze-Kremer S. The Ontology of the Gene Ontology. AMIA Annual Symp. Proceedings, 2003.Smith B., Ashburner M., Rosse C., Bard J., Bug W., Ceusters W., Goldberg L.J., Eilbeck K., Ireland A., Mungall C.J., OBI Consortium, Leontis N., Rocca-Serra P., Ruttenberg A., Sansone S.A., Scheuermann R.H., Shah N., Whetzel P.L., Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotech. 2007;25(11):1251-1255.Smith B., Ashburner M., Rosse C., Bard J., Bug W., Ceusters W., Goldberg L.J., Eilbeck K., Ireland A., Mungall C.J., OBI Consortium, Leontis N., Rocca-Serra P., Ruttenberg A., Sansone S.A., Scheuermann R.H., Shah N., Whetzel P.L., Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotech. 2007;25(11):1251-1255.Srinivas K. OWL Reasoning in the Real World: Searching for Godot. Proc. of the 22nd Intern. Workshop on Description Logics (DL 2009), Oxford, UK, July 27–30, 2009.Srinivas K. OWL Reasoning in the Real World: Searching for Godot. Proc. of the 22nd Intern. Workshop on Description Logics (DL 2009), Oxford, UK, July 27–30, 2009.Stevens R., Aranguren M.E., Wolstencroft K., Sattler U., Drummond N., Horridge M., Rector A. Using OWL to model biological knowledge. Int. J. Human-Computer Studies cfm?id=1247774. 2007;65(7):583-594.Stevens R., Aranguren M.E., Wolstencroft K., Sattler U., Drummond N., Horridge M., Rector A. Using OWL to model biological knowledge. Int. J. Human-Computer Studies http://portal.acm.org/citation. cfm?id=1247774. 2007;65(7):583-594.Stevens R., Baker P., Bechhofer S., Ng G., Jacoby A., Paton N.W., Goble C.A., Brass A. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics. 2000;16(2):184-185.Stevens R., Baker P., Bechhofer S., Ng G., Jacoby A., Paton N.W., Goble C.A., Brass A. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics. 2000;16(2):184-185.Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K.Jr., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., Dunn M.J., Heck A.J., Leitner A., Macht M., Mann M., Martens L., Neubert T.A., Patterson S.D., Ping P., Seymour S.L., Souda P., Tsugita A., Vandekerckhove J., Vondriska T.M., Whitelegge J.P., Wilkins M.R., Xenarios I., Yates J.R. 3rd, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 2007;25(8):887-893.Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K.Jr., Jones A. R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., Dunn M.J., Heck A. J., Leitner A., Macht M., Mann M., Martens L., Neubert T.A., Patterson S.D., Ping P., Seymour S.L., Souda P., Tsugita A., Vandekerckhove J., Vondriska T.M., Whitelegge J.P., Wilkins M. R., Xenarios I., Yates J.R. 3rd, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 2007;25(8):887-893.Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., Diemer K., Muruganujan A., Narechania A. PANTHER: a library of protein families and subfamilies indexed by function.Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., Diemer K., Muruganujan A., Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003;13(9):2129-2141. PubMed PMID:12952881; PubMed Central PMCID: PMC403709.Genome Res. 2003;13(9):2129-2141. PubMed PMID:12952881; PubMed Central PMCID: PMC403709.Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A.K., Moraru I.I., Nickerson D., Snoep J.L., Le Novère, N. Reproducible computational biology experiments with SED-ML – the simulation experiment description markup language. BMC Systems Biol. 2011;5:198.Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A.K., Moraru I.I., Nickerson D., Snoep J.L., Le Novère, N. Reproducible computational biology experiments with SED-ML – the simulation experiment description markup language. BMC Systems Biol. 2011;5:198.Whetzel P.L., Parkinson H., Causton H.C., Fan L., Fostel J., Fragoso G., Game L., Heiskanen M., Morrison N., Rocca-Serra P., Sansone S.A., Taylor C., White J., Stoeckert C.J.Jr. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006;22(7):866-73.Whetzel P.L., Parkinson H., Causton H.C., Fan L., Fostel J., Fragoso G., Game L., Heiskanen M., Morrison N., Rocca-Serra P., Sansone S.A., Taylor C., White J., Stoeckert C.J.Jr. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006;22(7):866-73.Winston M.E., Chaffin R., Herrman D. A taxonomy of part-whole relations. Cognitive Sci. 1987;11:417-444.Winston M.E., Chaffin R., Herrman D. A taxonomy of part-whole relations. Cognitive Sci. 1987;11:417-444.Winston M.E., Chaffin R., Herrman D. A taxonomy of part-whole relations. Cognitive Sci. 1987;11:417-444.

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