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Biomedical Repositories for Simulation Studies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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2
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Frainay C, Aros S, Chazalviel M, Garcia T, Vinson F, Weiss N, Colsch B, Sedel F, Thabut D, Junot C, Jourdan F. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. Bioinformatics 2019; 35:274-283. [PMID: 29982278 PMCID: PMC6330003 DOI: 10.1093/bioinformatics/bty577] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Motivation Metabolomics has shown great potential to improve the understanding of complex diseases, potentially leading to therapeutic target identification. However, no single analytical method allows monitoring all metabolites in a sample, resulting in incomplete metabolic fingerprints. This incompleteness constitutes a stumbling block to interpretation, raising the need for methods that can enrich those fingerprints. We propose MetaboRank, a new solution inspired by social network recommendation systems for the identification of metabolites potentially related to a metabolic fingerprint. Results MetaboRank method had been used to enrich metabolomics data obtained on cerebrospinal fluid samples from patients suffering from hepatic encephalopathy (HE). MetaboRank successfully recommended metabolites not present in the original fingerprint. The quality of recommendations was evaluated by using literature automatic search, in order to check that recommended metabolites could be related to the disease. Complementary mass spectrometry experiments and raw data analysis were performed to confirm these suggestions. In particular, MetaboRank recommended the overlooked α-ketoglutaramate as a metabolite which should be added to the metabolic fingerprint of HE, thus suggesting that metabolic fingerprints enhancement can provide new insight on complex diseases. Availability and implementation Method is implemented in the MetExplore server and is available at www.metexplore.fr. A tutorial is available at https://metexplore.toulouse.inra.fr/com/tutorials/MetaboRank/2017-MetaboRank.pdf. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Clément Frainay
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | | | | | - Thomas Garcia
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Florence Vinson
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Nicolas Weiss
- Unité de Réanimation Neurologique, Département de Neurologie, Pôle des Maladies du Système Nerveux Central, Groupement Hospitalier Pitié-Salpêtrière Charles Foix, Assistance Publique - Hôpitaux de Paris, Paris, France.,Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies Métaboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiométabolisme et Nutrition, ICAN, Paris, France
| | - Benoit Colsch
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and
| | | | - Dominique Thabut
- Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris & INSERM UMR_S 938, CDR Saint-Antoine Maladies Métaboliques, Biliaires et Fibro-inflammatoire du Foie & Institut de Cardiométabolisme et Nutrition, ICAN, Paris, France.,Unité de Soins Intensifs d'Hépato-gastroentérologie, Groupement Hospitalier Pitié-Salpêtrière-Charles Foix, Assistance Publique - Hôpitaux de Paris et Université Pierre et Marie Curie Paris 6, Paris, France
| | - Christophe Junot
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Université Paris-Saclay, MetaboHUB, Gif-sur-Yvette, France and
| | - Fabien Jourdan
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, Toulouse, France
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3
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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4
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Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D. Notions of similarity for systems biology models. Brief Bioinform 2018; 19:77-88. [PMID: 27742665 PMCID: PMC5862271 DOI: 10.1093/bib/bbw090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/28/2016] [Indexed: 01/23/2023] Open
Abstract
Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases.
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Affiliation(s)
| | | | | | | | | | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany
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5
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Merlet B, Paulhe N, Vinson F, Frainay C, Chazalviel M, Poupin N, Gloaguen Y, Giacomoni F, Jourdan F. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. Front Mol Biosci 2016; 3:2. [PMID: 26909353 PMCID: PMC4754433 DOI: 10.3389/fmolb.2016.00002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.
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Affiliation(s)
- Benjamin Merlet
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
| | - Nils Paulhe
- Nutrition Humaine, Plateforme d'Exploration du Métabolisme, Institut National de la Recherche Agronomique, Centre Clermont-Ferrand–Theix, UMR 1019Saint-Genès-Champanelle, France
| | - Florence Vinson
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
| | - Clément Frainay
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
| | - Maxime Chazalviel
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
| | - Nathalie Poupin
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
| | - Yoann Gloaguen
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, UK
| | - Franck Giacomoni
- Nutrition Humaine, Plateforme d'Exploration du Métabolisme, Institut National de la Recherche Agronomique, Centre Clermont-Ferrand–Theix, UMR 1019Saint-Genès-Champanelle, France
| | - Fabien Jourdan
- TOXALIM (Research Centre in Food Toxicology), Institut National de la Recherche Agronomique, UMR1331, Université de ToulouseToulouse, France
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6
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Frainay C, Jourdan F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Brief Bioinform 2016; 18:43-56. [PMID: 26822099 DOI: 10.1093/bib/bbv115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/16/2015] [Indexed: 11/13/2022] Open
Abstract
Untargeted metabolomics makes it possible to identify compounds that undergo significant changes in concentration in different experimental conditions. The resulting metabolomic profile characterizes the perturbation concerned, but does not explain the underlying biochemical mechanisms. Bioinformatics methods make it possible to interpret results in light of the whole metabolism. This knowledge is modelled into a network, which can be mined using algorithms that originate in graph theory. These algorithms can extract sub-networks related to the compounds identified. Several attempts have been made to adapt them to obtain more biologically meaningful results. However, there is still no consensus on this kind of analysis of metabolic networks. This review presents the main graph approaches used to interpret metabolomic data using metabolic networks. Their advantages and drawbacks are discussed, and the impacts of their parameters are emphasized. We also provide some guidelines for relevant sub-network extraction and also suggest a range of applications for most methods.
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Olivier BG, Swat MJ, Moné MJ. Modeling and Simulation Tools: From Systems Biology to Systems Medicine. Methods Mol Biol 2016; 1386:441-63. [PMID: 26677194 DOI: 10.1007/978-1-4939-3283-2_19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Modeling is an integral component of modern biology. In this chapter we look into the role of the model, as it pertains to Systems Medicine, and the software that is required to instantiate and run it. We do this by comparing the development, implementation, and characteristics of tools that have been developed to work with two divergent methodologies: Systems Biology and Pharmacometrics. From the Systems Biology perspective we consider the concept of "Software as a Medical Device" and what this may imply for the migration of research-oriented, simulation software into the domain of human health.In our second perspective, we see how in practice hundreds of computational tools already accompany drug discovery and development at every stage of the process. Standardized exchange formats are required to streamline the model exchange between tools, which would minimize translation errors and reduce the required time. With the emergence, almost 15 years ago, of the SBML standard, a large part of the domain of interest is already covered and models can be shared and passed from software to software without recoding them. Until recently the last stage of the process, the pharmacometric analysis used in clinical studies carried out on subject populations, lacked such an exchange medium. We describe a new emerging exchange format in Pharmacometrics which covers the non-linear mixed effects models, the standard statistical model type used in this area. By interfacing these two formats the entire domain can be covered by complementary standards and subsequently the according tools.
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Affiliation(s)
- Brett G Olivier
- Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands.
| | - Maciej J Swat
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Martijn J Moné
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands.,Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
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Henkel R, Wolkenhauer O, Waltemath D. Combining computational models, semantic annotations and simulation experiments in a graph database. Database (Oxford) 2015; 2015:bau130. [PMID: 25754863 PMCID: PMC4352687 DOI: 10.1093/database/bau130] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 12/28/2022]
Abstract
Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models' structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/
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Affiliation(s)
- Ron Henkel
- University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
| | - Olaf Wolkenhauer
- University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
| | - Dagmar Waltemath
- University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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9
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Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics 2015; 31:1875-7. [PMID: 25638809 PMCID: PMC4443684 DOI: 10.1093/bioinformatics/btv064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/27/2015] [Indexed: 11/12/2022] Open
Abstract
Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact:sarala@ebi.ac.uk
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Affiliation(s)
- Sarala M Wimalaratne
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Jerven Bolleman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Toshiaki Katayama
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Michel Dumontier
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nicole Redaschi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Camille Laibe
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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10
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Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C. BioModels: ten-year anniversary. Nucleic Acids Res 2014; 43:D542-8. [PMID: 25414348 PMCID: PMC4383975 DOI: 10.1093/nar/gku1181] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140 000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels’ first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.
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Affiliation(s)
- Vijayalakshmi Chelliah
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ishan Ajmera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Raza Ali
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marine Dumousseau
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mihai Glont
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gaël Jalowicki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vincent Knight-Schrijver
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Audald Lloret-Villas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jean-Baptiste Pettit
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicolas Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael Schubert
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarala M Wimalaratne
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yangyang Zhao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Camille Laibe
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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