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A group theoretic approach to model comparison with simplicial representations. J Math Biol 2022; 85:48. [PMID: 36209430 PMCID: PMC9548478 DOI: 10.1007/s00285-022-01807-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/31/2022] [Accepted: 07/25/2022] [Indexed: 10/28/2022]
Abstract
AbstractThe complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we develop mathematical models to further our understanding of these systems. Because biological systems are generally not well understood, most mathematical models of these systems are based on experimental data, resulting in a seemingly heterogeneous collection of models that ostensibly represent the same system. To understand the system we therefore need to understand how the different models are related to each other, with a view to obtaining a unified mathematical description. This goal is complicated by the fact that a number of distinct mathematical formalisms may be employed to represent the same system, making direct comparison of the models very difficult. A methodology for comparing mathematical models based on their underlying conceptual structure is therefore required. In previous work we developed an appropriate framework for model comparison where we represent models, specifically the conceptual structure of the models, as labelled simplicial complexes and compare them with the two general methodologies of comparison by distance and comparison by equivalence. In this article we continue the development of our model comparison methodology in two directions. First, we present a rigorous and automatable methodology for the core process of comparison by equivalence, namely determining the vertices in a simplicial representation, corresponding to model components, that are conceptually related and the identification of these vertices via simplicial operations. Our methodology is based on considerations of vertex symmetry in the simplicial representation, for which we develop the required mathematical theory of group actions on simplicial complexes. This methodology greatly simplifies and expedites the process of determining model equivalence. Second, we provide an alternative mathematical framework for our model-comparison methodology by representing models as groups, which allows for the direct application of group-theoretic techniques within our model-comparison methodology.
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2
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Smirnov P, Smith I, Safikhani Z, Ba-Alawi W, Khodakarami F, Lin E, Yu Y, Martin S, Ortmann J, Aittokallio T, Hafner M, Haibe-Kains B. Evaluation of statistical approaches for association testing in noisy drug screening data. BMC Bioinformatics 2022; 23:188. [PMID: 35585485 PMCID: PMC9118710 DOI: 10.1186/s12859-022-04693-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug sensitivity data has proven to be a particularly challenging field for identifying associations to inform patient treatment. RESULTS To address this, we introduce two semi-parametric variations on the commonly used concordance index: the robust concordance index and the kernelized concordance index (rCI, kCI), which incorporate measurements about the noise distribution from the data. We demonstrate that common statistical tests applied to the concordance index and its variations fail to control for false positives, and introduce efficient implementations to compute p-values using adaptive permutation testing. We then evaluate the statistical power of these coefficients under simulation and compare with Pearson and Spearman correlation coefficients. Finally, we evaluate the various statistics in matching drugs across pharmacogenomic datasets. CONCLUSIONS We observe that the rCI and kCI are better powered than the concordance index in simulation and show some improvement on real data. Surprisingly, we observe that the Pearson correlation was the most robust to measurement noise among the different metrics.
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Affiliation(s)
- Petr Smirnov
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Ian Smith
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Zhaleh Safikhani
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | | | - Eva Lin
- Department of Discovery Oncology, Genentech Inc., South San Francisco, USA
| | - Yihong Yu
- Department of Discovery Oncology, Genentech Inc., South San Francisco, USA
| | - Scott Martin
- Department of Discovery Oncology, Genentech Inc., South San Francisco, USA
| | - Janosch Ortmann
- Département d'analytique, opérations et technologies de l'information, École des sciences de la gestion, Université du Québec à Montréal, Montréal, Canada
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway.,iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marc Hafner
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, Canada. .,Princess Margaret Cancer Center, University Health Network, Toronto, Canada. .,Vector Institute, Toronto, Canada.
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Vittadello ST, Stumpf MPH. Model comparison via simplicial complexes and persistent homology. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211361. [PMID: 34659787 PMCID: PMC8511761 DOI: 10.1098/rsos.211361] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/16/2021] [Indexed: 05/21/2023]
Abstract
In many scientific and technological contexts, we have only a poor understanding of the structure and details of appropriate mathematical models. We often, therefore, need to compare different models. With available data we can use formal statistical model selection to compare and contrast the ability of different mathematical models to describe such data. There is, however, a lack of rigorous methods to compare different models a priori. Here, we develop and illustrate two such approaches that allow us to compare model structures in a systematic way by representing models as simplicial complexes. Using well-developed concepts from simplicial algebraic topology, we define a distance between models based on their simplicial representations. Employing persistent homology with a flat filtration provides for alternative representations of the models as persistence intervals, which represent model structure, from which the model distances are also obtained. We then expand on this measure of model distance to study the concept of model equivalence to determine the conceptual similarity of models. We apply our methodology for model comparison to demonstrate an equivalence between a positional-information model and a Turing-pattern model from developmental biology, constituting a novel observation for two classes of models that were previously regarded as unrelated.
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Affiliation(s)
- Sean T. Vittadello
- School of BioSciences and School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael P. H. Stumpf
- School of BioSciences and School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
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Guo L, Rong L, Xu X. The changes of triacylglycerol and inflammatory factors during dialysis treatment of hypertriglyceridemia during pregnancy and analysis of nursing countermeasure. Am J Transl Res 2021; 13:6745-6751. [PMID: 34306421 PMCID: PMC8290644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 02/09/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To investigate the changes of triacylglycerol and inflammatory factors after hypertriglyceridemia acute pancreatitis (HTG-AP) dialysis during pregnancy and to analyze the nursing strategies. METHODS 50 patients treated with HTG-AP dialysis in our hospital from February 2017 to June 2019 were selected. The patient's vital signs, triglyceride (TG), total cholesterol (TC), TG and TC decline rates before treatment, 1, 3, and 5 days after treatment and inflammatory factors [tumor necrosis factor-α (TNF-α), Interleukin-1β (IL-1β), Interleukin-6 (IL-6), Interleukin-10 (IL-10) level changes] were measured, as well as the acute physiological and chronic health evaluation II (APACHEII), multiple organ dysfunction syndromes (MODS), systemic inflammatory response syndrome (SIRS) and maternal treatment outcomes. RESULTS There was no significant change in body temperature before and after treatment (P>0.05); The heart rate, WBC, CRP before and after treatment were statistically different (P<0.05); Compared with before treatment, serum levels of TG and TC significantly decreased after treatment, and the rate of decrease was significantly increased (P<0.05); Compared with before treatment, the levels of inflammatory factors (TNF-α, IL-1β, IL-6, IL-10) gradually decreased after treatment, and the serum levels of patient's TNF-α, IL-1β, IL-6, IL-10 after 5 days of treatment were more significant (P<0.05); Compared with before treatment, APACHEll, MODS and SIRS scores significantly decreased after treatment, and APACHEll, MODS and SIRS scores were better after 5 days of treatment (P<0.05); The mortality rate during treatment was 2.00%; the complication rate was 32.00%, including 5 cases of acute respiratory distress syndrome, 4 cases of pleural effusion, 4 cases of lung infection, 2 cases of acute renal insufficiency and 1 case of shock. CONCLUSION Dialysis treatment can promote the recovery of HTG-AP patients promptly, improve triglycerides, and reduce inflammation. After the targeted nursing intervention, the treatment efficacy significantly improved.
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Affiliation(s)
- Lin Guo
- Physical Examination Center of Traditional Chinese Medicine Hospital, Penglai Hospital of Traditional Chinese MedicinePenglai, Shandong, China
| | - Lingzhi Rong
- Department of Gynecology and Obstetrics of Dongying Second People’s HospitalDongying, Shandong, China
| | - Xuewei Xu
- Department of Critical Care Medicine, The Third Hospital of Shandong ProvinceJinan, Shandong, China
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Dixit VA, Singh P. A property-response perspective on modern toxicity assessment and drug toxicity index (DTI). In Silico Pharmacol 2021; 9:37. [PMID: 34017677 PMCID: PMC8124026 DOI: 10.1007/s40203-021-00096-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/05/2021] [Indexed: 11/26/2022] Open
Abstract
Toxicity related failures in drug discovery and clinical development have motivated scientists and regulators to develop a wide range of in-vitro, in-silico tools coupled with data science methods. Older drug discovery rules are being constantly modified to churn out any hidden predictive value. Nonetheless, the dose-response concepts remain central to all these methods. Over the last 2 decades medicinal chemists, and pharmacologists have observed that different physicochemical, and pharmacological properties capture trends in toxic responses. We propose that these observations should be viewed in a comprehensive property-response framework where dose is only a factor that modifies the inherent toxicity potential. We then introduce the recently proposed "Drug Toxicity Index (DTI)" and briefly summarize its applications. A webserver is available to calculate DTI values (https://all-tool-kit.github.io/Web-Tool.html).
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Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS Pilani), Vidya Vihar Campus, Street number 41, Pilani, Rajasthan 333031 India
| | - Pragati Singh
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani (BITS Pilani), Vidya Vihar Campus, Street number 41, Pilani, Rajasthan 333031 India
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Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology. Brief Bioinform 2019; 20:540-550. [PMID: 30462164 PMCID: PMC6433895 DOI: 10.1093/bib/bby087] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/08/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.
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Affiliation(s)
- Maxwell Lewis Neal
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, USA
| | - Matthias König
- Department of Biology, Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany
| | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Keele, UK
| | - Reza Kalbasi
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Koray Atalag
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Vijayalakshmi Chelliah
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael T Cooling
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Daniel L Cook
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sharon Crook
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, USA
| | - Miguel de Alba
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Alan Garny
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - John H Gennari
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Michael Hucka
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Chris Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA
| | - Brett G Olivier
- Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Modelling of Biological Processes, BioQUANT/COS, Heidelberg University, Germany
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Martin Scharm
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Vasundra Touré
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anil Wipat
- School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch, South Africa
| | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
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Henze R, Mu C, Puljiz M, Kamaleson N, Huwald J, Haslegrave J, di Fenizio PS, Parker D, Good C, Rowe JE, Ibrahim B, Dittrich P. Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint. Sci Rep 2019; 9:3902. [PMID: 30846816 PMCID: PMC6405958 DOI: 10.1038/s41598-019-40648-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 02/19/2019] [Indexed: 02/05/2023] Open
Abstract
The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. A sequence of manual and automatic coarse-grainings finally leads to the coarsest deterministic and stochastic models containing only four molecular species and four states for each kinetochore, respectively. We are able to relate each more coarse-grained level to a finer one, which allows us to relate model parameters between coarse-grainings and which provides a more precise meaning for the elements of the more abstract models. Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by showing spatial organizations during mitotic checkpoint inactivation. We demonstrate how these models lead to insights if the model has different “meaningful” behaviors that differ in the set of (molecular) species. We conclude that understanding, modeling and analyzing complex bio-molecular systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatically applied and that allow the different levels of abstraction to be related.
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Affiliation(s)
- Richard Henze
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Chunyan Mu
- School of Computing, Teesside University, Teesside, UK
| | - Mate Puljiz
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | | | - Jan Huwald
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | | | | | - David Parker
- School of Computer Science, University of Birmingham, Birmingham, UK
| | | | - Jonathan E Rowe
- School of Computer Science, University of Birmingham, Birmingham, UK
| | - Bashar Ibrahim
- Chair of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University of Jena, Jena, Germany.
| | - Peter Dittrich
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
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8
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Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D. Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC SYSTEMS BIOLOGY 2018; 12:53. [PMID: 29650016 PMCID: PMC5898004 DOI: 10.1186/s12918-018-0553-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/21/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable. METHODS We analysed 13734 models from BioModels Database and the Physiome Model Repository. For each model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database. RESULTS We observed continuous updates in the majority of models. Surprisingly, even the early models are still being modified. We furthermore detected that many updates target annotations, which improves the information one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are available from GitHub https://github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at https://hub.docker.com/r/binfalse/bives-statsgenerator/ . The website https://most.bio.informatik.uni-rostock.de/ provides interactive access to model versions and their evolutionary statistics. CONCLUSION The reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a model's provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the maintainers of model repositories to offer transparent model provenance to their users.
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Affiliation(s)
- Martin Scharm
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
| | - Tom Gebhardt
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
| | - Vasundra Touré
- Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491 Norway
| | - Andrea Bagnacani
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
- Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600 South Africa
| | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051 Germany
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9
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Lambusch F, Waltemath D, Wolkenhauer O, Sandkuhl K, Rosenke C, Henkel R. Identifying frequent patterns in biochemical reaction networks: a workflow. Database (Oxford) 2018; 2018:5048438. [PMID: 29992320 PMCID: PMC6030809 DOI: 10.1093/database/bay051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/27/2018] [Accepted: 04/29/2018] [Indexed: 11/15/2022]
Abstract
Computational models in biology encode molecular and cell biological processes. Many of these models can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical goals of an investigation thus include understanding of model parts, identification of reoccurring patterns and recognition of biologically relevant motifs. The large number and size of available models, however, require automated methods to support researchers in achieving their goals. Specifically for the problem of finding patterns in large networks only partial solutions exist. We propose a workflow that identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language. The workflow utilizes a subgraph mining algorithm to detect the network patterns. Once patterns are identified, the textual pattern description can automatically be converted into a graphical representation. Furthermore, information about the distribution of patterns among a selected set of models can be retrieved. The workflow was validated with 575 models from the curated branch of BioModels. In this paper, we highlight interesting and frequent structural patterns. Furthermore, we provide exemplary patterns that incorporate terms from the Systems Biology Ontology. Our workflow can be applied to a custom set of models or to models already existing in our graph database MaSyMoS. The occurrences of frequent patterns may give insight into the encoding of central biological processes, evaluate postulated biological motifs or serve as a similarity measure for models that share common structures.Database URL: https://github.com/FabienneL/BioNet-Mining.
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Affiliation(s)
- Fabienne Lambusch
- Business Information Systems, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa
| | - Kurt Sandkuhl
- Business Information Systems, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
- ITMO University, 49 Kronverksky Pr., St. Petersburg, Russia
| | - Christian Rosenke
- Visual Computing and Computer Graphics, University of Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Ron Henkel
- Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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