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Gröne N, Grüneisen B, Klein K, de Bono B, Czauderna T, Schreiber F. Layout of anatomical structures and blood vessels based on the foundational model of anatomy. J Integr Bioinform 2024; 0:jib-2024-0023. [PMID: 38996084 DOI: 10.1515/jib-2024-0023] [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: 05/07/2024] [Accepted: 05/21/2024] [Indexed: 07/14/2024] Open
Abstract
We present a method for the layout of anatomical structures and blood vessels based on information from the Foundational Model of Anatomy (FMA). Our approach integrates a novel vascular layout into the hierarchical treemap representation of anatomy as used in ApiNATOMY. Our method aims to improve the comprehension of complex anatomical and vascular data by providing readable visual representations. The effectiveness of our method is demonstrated through a prototype developed in VANTED, showing potential for application in research, education, and clinical settings.
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Affiliation(s)
- Niklas Gröne
- Department of Computer and Information Science, 570542 University of Konstanz , Konstanz, Germany
| | | | - Karsten Klein
- Department of Computer and Information Science, 570542 University of Konstanz , Konstanz, Germany
| | - Bernard de Bono
- Whitby et al, LLC, Indianapolis, IN, USA
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, 570542 University of Konstanz , Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Australia
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2
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de Bono B, Gillespie T, Surles-Zeigler MC, Kokash N, Grethe JS, Martone M. Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. Front Physiol 2022; 13:795303. [PMID: 35547570 PMCID: PMC9083405 DOI: 10.3389/fphys.2022.795303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
We present (i) the ApiNATOMY workflow to build knowledge models of biological connectivity, as well as (ii) the ApiNATOMY TOO map, a topological scaffold to organize and visually inspect these connectivity models in the context of a canonical architecture of body compartments. In this work, we outline the implementation of ApiNATOMY's knowledge representation in the context of a large-scale effort, SPARC, to map the autonomic nervous system. Within SPARC, the ApiNATOMY modeling effort has generated the SCKAN knowledge graph that combines connectivity models and TOO map. This knowledge graph models flow routes for a number of normal and disease scenarios in physiology. Calculations over SCKAN to infer routes are being leveraged to classify, navigate and search for semantically-linked metadata of multimodal experimental datasets for a number of cross-scale, cross-disciplinary projects.
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Affiliation(s)
- Bernard de Bono
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Tom Gillespie
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | | | - Natallia Kokash
- Faculty of Humanities, University of Amsterdam, Amsterdam, Netherlands
| | - Jeff S. Grethe
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Maryann Martone
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
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3
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Osanlouy M, Bandrowski A, de Bono B, Brooks D, Cassarà AM, Christie R, Ebrahimi N, Gillespie T, Grethe JS, Guercio LA, Heal M, Lin M, Kuster N, Martone ME, Neufeld E, Nickerson DP, Soltani EG, Tappan S, Wagenaar JB, Zhuang K, Hunter PJ. The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. Front Physiol 2021; 12:693735. [PMID: 34248680 PMCID: PMC8265045 DOI: 10.3389/fphys.2021.693735] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/28/2021] [Indexed: 02/01/2023] Open
Abstract
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.
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Affiliation(s)
- Mahyar Osanlouy
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Anita Bandrowski
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Bernard de Bono
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - David Brooks
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | - Richard Christie
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Nazanin Ebrahimi
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Tom Gillespie
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Jeffrey S. Grethe
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | | | - Maci Heal
- MBF Bioscience, Williston, VT, United States
| | - Mabelle Lin
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Niels Kuster
- IT'IS Foundation, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Swiss Federal Institute of Technology (ETHZ), Zurich, Switzerland
| | - Maryann E. Martone
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Esra Neufeld
- IT'IS Foundation, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Swiss Federal Institute of Technology (ETHZ), Zurich, Switzerland
| | - David P. Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Elias G. Soltani
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | | | | | - Peter J. Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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4
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Kokash N, de Bono B. Knowledge Representation for Multi-Scale Physiology Route Modeling. Front Neuroinform 2021; 15:560050. [PMID: 33664662 PMCID: PMC7921311 DOI: 10.3389/fninf.2021.560050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022] Open
Abstract
We present a framework for the topological and semantic assembly of multiscale physiology route maps. The framework, called ApiNATOMY, consists of a knowledge representation (KR) model and a set of knowledge management (KM) tools. Using examples of ApiNATOMY route maps, we present a KR format that is suitable for the analysis and visualization by KM tools. The conceptual KR model provides a simple method for physiology experts to capture process interactions among anatomical entities. In this paper, we outline the KR model, modeling format, and the KM procedures to translate concise abstraction-based specifications into fully instantiated models of physiology processes.
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Affiliation(s)
- Natallia Kokash
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Bernard de Bono
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia.,Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Luthert PJ, Serrano L, Kiel C. Opportunities and Challenges of Whole-Cell and -Tissue Simulations of the Outer Retina in Health and Disease. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual processing starts in the outer retina, where photoreceptor cells sense photons that trigger electrical responses. Retinal pigment epithelial cells are located external to the photoreceptor layer and have critical functions in supporting cell and tissue homeostasis and thus sustaining a healthy retina. The high level of specialization makes the retina vulnerable to alterations that promote retinal degeneration. In this review, we discuss opportunities and challenges in proposing whole-cell and -tissue simulations of the human outer retina. An implicit position taken throughout this review is that mapping diverse data sets onto integrative computational models is likely to be a pivotal approach to understanding complex disease and developing novel interventions.
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Affiliation(s)
- Philip J. Luthert
- Institute of Ophthalmology and National Institute for Health Research (NIHR) Biomedical Research Centre, University College London, London EC1V 9EL, United Kingdom
| | - Luis Serrano
- European Molecular Biology Laboratory (EMBL)/Centre for Genomic Regulation (CRG) Systems Biology Research Unit, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Christina Kiel
- European Molecular Biology Laboratory (EMBL)/Centre for Genomic Regulation (CRG) Systems Biology Research Unit, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology Ireland, Charles Institute of Dermatology, and School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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6
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de Bono B, Safaei S, Grenon P, Hunter P. Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs. Interface Focus 2017; 8:20170026. [PMID: 29285348 DOI: 10.1098/rsfs.2017.0026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We introduce, and provide examples of, the application of the bond graph formalism to explicitly represent biophysical processes between and within modular biological compartments in ApiNATOMY. In particular, we focus on modelling scenarios from acid-base physiology to link distinct process modalities as bond graphs over an ApiNATOMY circuit of multiscale compartments. The embedding of bond graphs onto ApiNATOMY compartments provides a semantically and mathematically explicit basis for the coherent representation, integration and visualisation of multiscale physiology processes together with the compartmental topology of those biological structures that convey these processes.
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Affiliation(s)
- B de Bono
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - S Safaei
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - P Grenon
- Farr Institute, University College London, London, UK
| | - P Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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7
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Wu H, Oellrich A, Girges C, de Bono B, Hubbard TJ, Dobson RJ. Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease. Database (Oxford) 2017; 2017:3091736. [PMID: 28365743 PMCID: PMC5467557 DOI: 10.1093/database/bax027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/23/2017] [Accepted: 03/08/2017] [Indexed: 12/20/2022]
Abstract
Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator. Using techniques similar to those of summarisation, we developed an algorithm that relies on linguistic, semantic and spatial features. Employing this algorithm on a test set manually corrected for tool imprecision, we achieved a macro F 1 -measure of 0.51, which is an increase of 132% compared to the best bag-of-words baseline model. A user based evaluation was also conducted to assess the usefulness of the methodology on 40 unseen publications, which reveals that in 85% of cases all highlighted sentences are relevant to the curation task and in about 65% of the cases, the highlights are sufficient to support the knowledge curation task without needing to consult the full text. In conclusion, we believe that these are promising results for a step in automating the recognition of curation-relevant sentences. Refining our approach to pre-digest papers will lead to faster processing and cost reduction in the curation process. Database URL https://github.com/KHP-Informatics/NapEasy.
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Affiliation(s)
- Honghan Wu
- Department of Biostatistics and Health Informatics, King's College London, De Crespigny Park, Denmark Hill London SE5 8AF, UK
- School of Computer and Software, Nanjing University of Information Science and Technology, 219 Ningliu Road, Nanjing, China, 210044
| | - Anika Oellrich
- Department of Biostatistics and Health Informatics, King's College London, De Crespigny Park, Denmark Hill London SE5 8AF, UK
| | - Christine Girges
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London Gower Street, WC1E 6BT, UK
| | - Bernard de Bono
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London Gower Street, WC1E 6BT, UK
| | - Tim J.P. Hubbard
- Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Richard J.B. Dobson
- Department of Biostatistics and Health Informatics, King's College London, De Crespigny Park, Denmark Hill London SE5 8AF, UK
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London Gower Street, WC1E 6BT, UK
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8
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Cooling MT, Nickerson DP, Nielsen PMF, Hunter PJ. Modular modelling with Physiome standards. J Physiol 2016; 594:6817-6831. [PMID: 27353233 PMCID: PMC5134412 DOI: 10.1113/jp272633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/26/2016] [Indexed: 01/27/2023] Open
Abstract
KEY POINTS The complexity of computational models is increasing, supported by research in modelling tools and frameworks. But relatively little thought has gone into design principles for complex models. We propose a set of design principles for complex model construction with the Physiome standard modelling protocol CellML. By following the principles, models are generated that are extensible and are themselves suitable for reuse in larger models of increasing complexity. We illustrate these principles with examples including an architectural prototype linking, for the first time, electrophysiology, thermodynamically compliant metabolism, signal transduction, gene regulation and synthetic biology. The design principles complement other Physiome research projects, facilitating the application of virtual experiment protocols and model analysis techniques to assist the modelling community in creating libraries of composable, characterised and simulatable quantitative descriptions of physiology. ABSTRACT The ability to produce and customise complex computational models has great potential to have a positive impact on human health. As the field develops towards whole-cell models and linking such models in multi-scale frameworks to encompass tissue, organ, or organism levels, reuse of previous modelling efforts will become increasingly necessary. Any modelling group wishing to reuse existing computational models as modules for their own work faces many challenges in the context of construction, storage, retrieval, documentation and analysis of such modules. Physiome standards, frameworks and tools seek to address several of these challenges, especially for models expressed in the modular protocol CellML. Aside from providing a general ability to produce modules, there has been relatively little research work on architectural principles of CellML models that will enable reuse at larger scales. To complement and support the existing tools and frameworks, we develop a set of principles to address this consideration. The principles are illustrated with examples that couple electrophysiology, signalling, metabolism, gene regulation and synthetic biology, together forming an architectural prototype for whole-cell modelling (including human intervention) in CellML. Such models illustrate how testable units of quantitative biophysical simulation can be constructed. Finally, future relationships between modular models so constructed and Physiome frameworks and tools are discussed, with particular reference to how such frameworks and tools can in turn be extended to complement and gain more benefit from the results of applying the principles.
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Affiliation(s)
| | | | - Poul M. F. Nielsen
- Auckland Bioengineering Institutethe University of AucklandNew Zealand
- Department of Engineering Sciencethe University of AucklandNew Zealand
| | - Peter J. Hunter
- Auckland Bioengineering Institutethe University of AucklandNew Zealand
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Satagopam V, Gu W, Eifes S, Gawron P, Ostaszewski M, Gebel S, Barbosa-Silva A, Balling R, Schneider R. Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. BIG DATA 2016; 4:97-108. [PMID: 27441714 PMCID: PMC4932659 DOI: 10.1089/big.2015.0057] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Translational medicine is a domain turning results of basic life science research into new tools and methods in a clinical environment, for example, as new diagnostics or therapies. Nowadays, the process of translation is supported by large amounts of heterogeneous data ranging from medical data to a whole range of -omics data. It is not only a great opportunity but also a great challenge, as translational medicine big data is difficult to integrate and analyze, and requires the involvement of biomedical experts for the data processing. We show here that visualization and interoperable workflows, combining multiple complex steps, can address at least parts of the challenge. In this article, we present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health. Three Web services-tranSMART, a Galaxy Server, and a MINERVA platform-are combined into one big data pipeline. Native visualization capabilities enable the biomedical experts to get a comprehensive overview and control over separate steps of the workflow. The capabilities of tranSMART enable a flexible filtering of multidimensional integrated data sets to create subsets suitable for downstream processing. A Galaxy Server offers visually aided construction of analytical pipelines, with the use of existing or custom components. A MINERVA platform supports the exploration of health and disease-related mechanisms in a contextualized analytical visualization system. We demonstrate the utility of our workflow by illustrating its subsequent steps using an existing data set, for which we propose a filtering scheme, an analytical pipeline, and a corresponding visualization of analytical results. The workflow is available as a sandbox environment, where readers can work with the described setup themselves. Overall, our work shows how visualization and interfacing of big data processing services facilitate exploration, analysis, and interpretation of translational medicine data.
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Affiliation(s)
- Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Wei Gu
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Serge Eifes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
- Information Technology for Translational Medicine (ITTM) S.A., Esch-Belval, Luxembourg
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Stephan Gebel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Adriano Barbosa-Silva
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
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Thomas S, Wolstencroft K, de Bono B, Hunter PJ. A physiome interoperability roadmap for personalized drug development. Interface Focus 2016; 6:20150094. [PMID: 27051513 DOI: 10.1098/rsfs.2015.0094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The goal of developing therapies and dosage regimes for characterized subgroups of the general population can be facilitated by the use of simulation models able to incorporate information about inter-individual variability in drug disposition (pharmacokinetics), toxicity and response effect (pharmacodynamics). Such observed variability can have multiple causes at various scales, ranging from gross anatomical differences to differences in genome sequence. Relevant data for many of these aspects, particularly related to molecular assays (known as '-omics'), are available in online resources, but identification and assignment to appropriate model variables and parameters is a significant bottleneck in the model development process. Through its efforts to standardize annotation with consequent increase in data usability, the human physiome project has a vital role in improving productivity in model development and, thus, the development of personalized therapy regimes. Here, we review the current status of personalized medicine in clinical practice, outline some of the challenges that must be overcome in order to expand its applicability, and discuss the relevance of personalized medicine to the more widespread challenges being faced in drug discovery and development. We then review some of (i) the key data resources available for use in model development and (ii) the potential areas where advances made within the physiome modelling community could contribute to physiologically based pharmacokinetic and physiologically based pharmacokinetic/pharmacodynamic modelling in support of personalized drug development. We conclude by proposing a roadmap to further guide the physiome community in its on-going efforts to improve data usability, and integration with modelling efforts in the support of personalized medicine development.
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Affiliation(s)
- Simon Thomas
- Cyprotex Discovery Ltd , 15 Beech Lane, Macclesfield SK10 2DR , UK
| | - Katherine Wolstencroft
- Leiden Institute of Advanced Computer Science , Leiden University , 111 Snellius, Niels Bohrweg 1, 2333 CA Leiden , The Netherlands
| | - Bernard de Bono
- Farr Institute, University College London, London NW1 2DA, UK; Auckland Bioengineering Institute, The University of Auckland, Auckland 1010, New Zealand
| | - Peter J Hunter
- Auckland Bioengineering Institute , The University of Auckland , Auckland 1010 , New Zealand
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Hofmann-Apitius M, Ball G, Gebel S, Bagewadi S, de Bono B, Schneider R, Page M, Kodamullil AT, Younesi E, Ebeling C, Tegnér J, Canard L. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. Int J Mol Sci 2015; 16:29179-206. [PMID: 26690135 PMCID: PMC4691095 DOI: 10.3390/ijms161226148] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 12/22/2022] Open
Abstract
Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies-data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European Commission (EC).
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Affiliation(s)
- Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Institutszentrum Birlinghoven, Sankt Augustin D-53754, Germany.
- Rheinische Friedrich-Wilhelms-Universitaet Bonn, University of Bonn, Bonn 53113, Germany.
| | - Gordon Ball
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, and Unit of Clinical Epidemiology, Karolinska University Hospital, Stockholm SE-171 77, Sweden.
- Science for Life Laboratories, Karolinska Institutet, Stockholm SE-171 77, Sweden.
| | - Stephan Gebel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg.
| | - Shweta Bagewadi
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Institutszentrum Birlinghoven, Sankt Augustin D-53754, Germany.
| | - Bernard de Bono
- Institute of Health Informatics, University College London, London NW1 2DA, UK.
- Auckland Bioengineering Institute, University of Auckland, Symmonds Street, Auckland 1142, New Zealand.
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg.
| | - Matt Page
- Translational Bioinformatics, UCB Pharma, 216 Bath Rd, Slough SL1 3WE, UK.
| | - Alpha Tom Kodamullil
- Rheinische Friedrich-Wilhelms-Universitaet Bonn, University of Bonn, Bonn 53113, Germany.
| | - Erfan Younesi
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Institutszentrum Birlinghoven, Sankt Augustin D-53754, Germany.
| | - Christian Ebeling
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Institutszentrum Birlinghoven, Sankt Augustin D-53754, Germany.
| | - Jesper Tegnér
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, and Unit of Clinical Epidemiology, Karolinska University Hospital, Stockholm SE-171 77, Sweden.
- Science for Life Laboratories, Karolinska Institutet, Stockholm SE-171 77, Sweden.
| | - Luc Canard
- Translational Science Unit, SANOFI Recherche & Développement, 1 Avenue Pierre Brossolette, Chilly-Mazarin Cedex 91385, France.
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12
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Fontecave-Jallon J, Thomas SR. Implementation of a model of bodily fluids regulation. Acta Biotheor 2015; 63:269-82. [PMID: 25935135 PMCID: PMC4531145 DOI: 10.1007/s10441-015-9250-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/27/2015] [Indexed: 01/24/2023]
Abstract
The classic model of blood pressure regulation by Guyton et al. (Annu Rev Physiol 34:13–46, 1972a; Ann Biomed Eng 1:254–281, 1972b) set a new standard for quantitative exploration of physiological function and led to important new insights, some of which still remain the focus of debate, such as whether the kidney plays the primary role in the genesis of hypertension (Montani et al. in Exp Physiol 24:41–54, 2009a; Exp Physiol 94:382–388, 2009b; Osborn et al. in Exp Physiol 94:389–396, 2009a; Exp Physiol 94:388–389, 2009b).
Key to the success of this model was the fact that the authors made the computer code (in FORTRAN) freely available and eventually provided a convivial user interface for exploration of model behavior on early microcomputers (Montani et al. in Int J Bio-med Comput 24:41–54, 1989). Ikeda et al. (Ann Biomed Eng 7:135–166, 1979) developed an offshoot of the Guyton model targeting especially the regulation of body fluids and acid–base balance; their model provides extended renal and respiratory functions and would be a good basis for further extensions.
In the interest of providing a simple, useable version of Ikeda et al.’s model and to facilitate further such extensions, we present a practical implementation of the model of Ikeda et al. (Ann Biomed Eng 7:135–166, 1979), using the ODE solver Berkeley Madonna.
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Affiliation(s)
- Julie Fontecave-Jallon
- />CNRS, TIMC-IMAG Laboratory CNRS UMR 5525, PRETA Team, University Joseph Fourier-Grenoble 1, 38041 Grenoble, France
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13
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McKeever S, Johnson D. The role of markup for enabling interoperability in health informatics. Front Physiol 2015; 6:152. [PMID: 26042043 PMCID: PMC4434901 DOI: 10.3389/fphys.2015.00152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/27/2015] [Indexed: 11/13/2022] Open
Abstract
Interoperability is the faculty of making information systems work together. In this paper we will distinguish a number of different forms that interoperability can take and show how they are realized on a variety of physiological and health care use cases. The last 15 years has seen the rise of very cheap digital storage both on and off site. With the advent of the Internet of Things people's expectations are for greater interconnectivity and seamless interoperability. The potential impact these technologies have on healthcare are dramatic: from improved diagnoses through immediate access to a patient's electronic health record, to in silico modeling of organs and early stage drug trials, to predictive medicine based on top-down modeling of disease progression and treatment. We will begin by looking at the underlying technology, classify the various kinds of interoperability that exist in the field, and discuss how they are realized. We conclude with a discussion on future possibilities that big data and further standardizations will enable.
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Affiliation(s)
- Steve McKeever
- Department of Informatics and Media, Uppsala UniversityUppsala, Sweden
- Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO)Saint Petersburg, Russia
| | - David Johnson
- Data Science Institute, Imperial College LondonLondon, UK
- Department of Computing, Imperial College LondonLondon, UK
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de Bono B, Safaei S, Grenon P, Nickerson DP, Alexander S, Helvensteijn M, Kok JN, Kokash N, Wu A, Yu T, Hunter P, Baldock RA. The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. Front Physiol 2015; 6:24. [PMID: 25759670 PMCID: PMC4338662 DOI: 10.3389/fphys.2015.00024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/14/2015] [Indexed: 01/11/2023] Open
Abstract
A key challenge for the physiology modeling community is to enable the searching, objective comparison and, ultimately, re-use of models and associated data that are interoperable in terms of their physiological meaning. In this work, we outline the development of a workflow to modularize the simulation of tissue-level processes in physiology. In particular, we show how, via this approach, we can systematically extract, parcellate and annotate tissue histology data to represent component units of tissue function. These functional units are semantically interoperable, in terms of their physiological meaning. In particular, they are interoperable with respect to [i] each other and with respect to [ii] a circuitboard representation of long-range advective routes of fluid flow over which to model long-range molecular exchange between these units. We exemplify this approach through the combination of models for physiology-based pharmacokinetics and pharmacodynamics to quantitatively depict biological mechanisms across multiple scales. Links to the data, models and software components that constitute this workflow are found at http://open-physiology.org/.
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Affiliation(s)
- Bernard de Bono
- Centre for Health Informatics and Multiprofessional Education, University College London London, UK ; Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Soroush Safaei
- Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Pierre Grenon
- Centre for Health Informatics and Multiprofessional Education, University College London London, UK
| | - David P Nickerson
- Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Samuel Alexander
- Centre for Health Informatics and Multiprofessional Education, University College London London, UK
| | - Michiel Helvensteijn
- Leiden Institute of Advanced Computer Science, University of Leiden Leiden, Netherlands
| | - Joost N Kok
- Leiden Institute of Advanced Computer Science, University of Leiden Leiden, Netherlands
| | - Natallia Kokash
- Leiden Institute of Advanced Computer Science, University of Leiden Leiden, Netherlands
| | - Alan Wu
- Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Tommy Yu
- Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland Auckland, New Zealand
| | - Richard A Baldock
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh Edinburgh, UK
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15
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de Bono B, Grenon P, Baldock R, Hunter P. Functional tissue units and their primary tissue motifs in multi-scale physiology. J Biomed Semantics 2013; 4:22. [PMID: 24103658 PMCID: PMC4126067 DOI: 10.1186/2041-1480-4-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/24/2013] [Indexed: 01/14/2023] Open
Abstract
Background Histology information management relies on complex knowledge derived from morphological tissue analyses. These approaches have not significantly facilitated the general integration of tissue- and molecular-level knowledge across the board in support of a systematic classification of tissue function, as well as the coherent multi-scale study of physiology. Our work aims to support directly these integrative goals. Results We describe, for the first time, the precise biophysical and topological characteristics of functional units of tissue. Such a unit consists of a three-dimensional block of cells centred around a capillary, such that each cell in this block is within diffusion distance from any other cell in the same block. We refer to this block as a functional tissue unit. As a means of simplifying the knowledge representation of this unit, and rendering this knowledge more amenable to automated reasoning and classification, we developed a simple descriptor of its cellular content and anatomical location, which we refer to as a primary tissue motif. In particular, a primary motif captures the set of cellular participants of diffusion-mediated interactions brokered by secreted products to create a tissue-level molecular network. Conclusions Multi-organ communication, therefore, may be interpreted in terms of interactions between molecular networks housed by interconnected functional tissue units. By extension, a functional picture of an organ, or its tissue components, may be rationally assembled using a collection of these functional tissue units as building blocks. In our work, we outline the biophysical rationale for a rigorous definition of a unit of functional tissue organization, and demonstrate the application of primary motifs in tissue classification. In so doing, we acknowledge (i) the fundamental role of capillaries in directing and radically informing tissue architecture, as well as (ii) the importance of taking into full account the critical influence of neighbouring cellular environments when studying complex developmental and pathological phenomena.
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Affiliation(s)
- Bernard de Bono
- Auckland Bioengineering Institute, University of Auckland, Symonds Street, Auckland 1010, New Zealand.
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16
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Abstract
MOTIVATION A crucial phenomenon of our times is the diminishing marginal returns of investments in pharmaceutical research and development. A potential reason is that research into diseases is becoming increasingly complex, and thus more burdensome, for humans to handle. We sought to investigate whether we could measure research complexity by analyzing the published literature. RESULTS Through the text mining of the publication record of multiple diseases, we have found that the complexity and novelty of disease research has been increasing over the years. Surprisingly, we have also found that research on diseases with higher publication rate does not possess greater complexity or novelty than that on less-studied diseases. We have also shown that the research produced about a disease can be seen as a differentiated area of knowledge within the wider biomedical research. For our analysis, we have conceptualized disease research as a parallel multi-agent search in which each scientific agent (a scientist) follows a search path based on a model of a disease. We have looked at trends in facts published for diseases, measured their diversity and turnover using the entropy measure and found similar patterns across disease areas. CONTACT raul.rodriguez-esteban@roche.com.
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Affiliation(s)
- Raul Rodriguez-Esteban
- Computational Biology, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
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17
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Grenon P, de Bono B. Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology. BMC Bioinformatics 2013; 14:131. [PMID: 23590598 PMCID: PMC3685606 DOI: 10.1186/1471-2105-14-131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 03/18/2013] [Indexed: 12/21/2022] Open
Abstract
Background In this paper, we use: i) formalised anatomical knowledge of connectivity between body structures and ii) a formal theory of physiological transport between fluid compartments in order to define and make explicit the routes followed by proteins to a site of interaction. The underlying processes are the objects of mathematical models of physiology and, therefore, the motivation for the approach can be understood as using knowledge representation and reasoning methods to propose concrete candidate routes corresponding to correlations between variables in mathematical models of physiology. In so doing, the approach projects physiology models onto a representation of the anatomical and physiological reality which underpins them. Results The paper presents a method based on knowledge representation and reasoning for eliciting physiological communication routes. In doing so, the paper presents the core knowledge representation and algorithms using it in the application of the method. These are illustrated through the description of a prototype implementation and the treatment of a simple endocrine scenario whereby a candidate route of communication between ANP and its receptors on the external membrane of smooth muscle cells in renal arterioles is elicited. The potential of further development of the approach is illustrated through the informal discussion of a more complex scenario. Conclusions The work presented in this paper supports research in intercellular communication by enabling knowledge‐based inference on physiologically‐related biomedical data and models.
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Affiliation(s)
- Pierre Grenon
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
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18
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de Bono B, Hunter P. Integrating knowledge representation and quantitative modelling in physiology. Biotechnol J 2013; 7:958-72. [PMID: 22887885 DOI: 10.1002/biot.201100304] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A wealth of potentially shareable resources, such as data and models, is being generated through the study of physiology by computational means. Although in principle the resources generated are reusable, in practice, few can currently be shared. A key reason for this disparity stems from the lack of consistent cataloguing and annotation of these resources in a standardised manner. Here, we outline our vision for applying community-based modelling standards in support of an automated integration of models across physiological systems and scales. Two key initiatives, the Physiome Project and the European contribution - the Virtual Phsysiological Human Project, have emerged to support this multiscale model integration, and we focus on the role played by two key components of these frameworks, model encoding and semantic metadata annotation. We present examples of biomedical modelling scenarios (the endocrine effect of atrial natriuretic peptide, and the implications of alcohol and glucose toxicity) to illustrate the role that encoding standards and knowledge representation approaches, such as ontologies, could play in the management, searching and visualisation of physiology models, and thus in providing a rational basis for healthcare decisions and contributing towards realising the goal of of personalized medicine.
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Affiliation(s)
- Bernard de Bono
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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19
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Baynam G, Walters M, Claes P, Kung S, LeSouef P, Dawkins H, Gillett D, Goldblatt J. The facial evolution: looking backward and moving forward. Hum Mutat 2012; 34:14-22. [PMID: 23033261 DOI: 10.1002/humu.22219] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/30/2012] [Indexed: 01/16/2023]
Abstract
Three-dimensional (3D) facial analysis is ideal for high-resolution, nonionizing, noninvasive objective, high-throughput phenotypic, and phenomic studies. It is a natural complement to (epi)genetic technologies to facilitate advances in the understanding of rare and common diseases. The face is uniquely reflective of the primordial tissues, and there is evidence supporting the application of 3D facial analysis to the investigation of variation and disease including studies showing that the face can reflect systemic health, provides diagnostic clues to disorders, and that facial variation reflects biological pathways. In addition, facial variation has been related to evolutionary factors. The purpose of this review is to look backward to suggest that knowledge of human evolution supports, and may instruct, the application and interpretation of studies of facial morphology for documentation of human variation and investigation of its relationships with health and disease. Furthermore, in the context of advances of deep phenotyping and data integration, to look forward to suggest approaches to scalable implementation of facial analysis, and to suggest avenues for future research and clinical application of this technology.
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Affiliation(s)
- Gareth Baynam
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Australia
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20
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Abstract
In medical contexts, the word "phenotype" is used to refer to some deviation from normal morphology, physiology, or behavior. The analysis of phenotype plays a key role in clinical practice and medical research, and yet phenotypic descriptions in clinical notes and medical publications are often imprecise. Deep phenotyping can be defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The emerging field of precision medicine aims to provide the best available care for each patient based on stratification into disease subclasses with a common biological basis of disease. The comprehensive discovery of such subclasses, as well as the translation of this knowledge into clinical care, will depend critically upon computational resources to capture, store, and exchange phenotypic data, and upon sophisticated algorithms to integrate it with genomic variation, omics profiles, and other clinical information. This special issue of Human Mutation offers a number of articles describing computational solutions for current challenges in deep phenotyping, including semantic and technical standards for phenotype and disease data, digital imaging for facial phenotype analysis, model organism phenotypes, and databases for correlating phenotypes with genomic variation.
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Affiliation(s)
- Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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