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CellML metadata standards, associated tools and repositories.

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website.

Pubmed ID: 19380315 RIS Download

Mesh terms: Biophysics | Computer Simulation | Database Management Systems | Programming Languages

Research resources used in this publication

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Data used in this publication

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Associated grants

  • Agency: Wellcome Trust, Id:

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This is a list of tools and resources that we have found mentioned in this publication.


Biological Pathways Exchange

BioPAX (Biological Pathway Exchange) aims to facilitate the integration and exchange of data maintained in biological pathway databases. BioPAX Level 3 covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions. BioPAX Level 2 covers metabolic pathways, molecular interactions and protein post-translational modifications and is backwards compatible with Level 1. Future levels will expand support for signaling pathways, gene regulatory networks and genetic interactions. And lastly, BioPAX Level 1 represents metabolic pathway information. Sponsors: The BioPAX project is funded in part by U.S. Department of Energy Workshop Grant #DE-FG02-04ER63931 and by Award Number P41HG004118 from the National Human Genome Research Institute.

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System for the Analysis of Biochemical Pathways - Reaction Kinetics Database

A database based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modelers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases are provided for users to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file. The reaction kinetics data are obtained by manual extraction from literature sources and curated.

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GO

A community-based bioinformatics resource consisting of three structured controlled vocabularies (ontologies) for the annotation of gene products with respect to their molecular function, cellular component, and biological role in a species-independent manner. This initiative to standardize the representation of gene and gene product attributes across species and databases is an effort to address the need for consistent descriptions of gene products in different databases. The Gene Ontology project encourages input from the community into both the content of the GO and annotation using GO. There are three separate aspects to this effort: first, they write and maintain the ontologies themselves; second, they make cross-links between the ontologies and the genes and gene products in the collaborating databases; and third, they develop tools that facilitate the creation, maintenance and use of ontologies. The controlled vocabularies are structured so that users can query them at different levels: for example, uers can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or users can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.

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Virtual Physiological Human Network of Excellence

The VPH NoE is a project which aims to help support and progress European research in biomedical modeling and simulation of the human body. This project will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries. The VPH Network of Excellence (VPH NoE) is designed to foster, harmonize and integrate pan-European research in the field of i) patient-specific computer models for personalised and predictive healthcare and ii) ICT-based tools for modeling and simulation of human physiology and disease-related processes. The main objectives of the VPH Network of Excellence are to support the: :- Coordination of research portfolios of VPH NoE partners through initiation of Exemplar integrative research projects that encourage inter-institution and interdisciplinary VPH research; :- Integration of research infrastructures of VPH NoE partners through development of the VPH ToolKit: a shared and mutually accessible source of research equipment, managerial and research infrastructures, facilities and services; :- Development of a portfolio of interdisciplinary training activities including a formal consultation on, and assessment of, VPH careers; :- Establishment of a core set of VPH-related dissemination and networking activities which will engage everyone from partners within the VPH NoE/other VPH projects, to national policy makers, to the public at large; :- Creation of Industrial, Clinical and Scientific Advisory Boards that will jointly guide the direction of the VPH NoE and, through consultation, explore the practical and legal options for real and durable integration within the VPH research community; :- Implementation of key working groups that will pursue specific issues relating to VPH, notably integrating VPH research worldwide through international physiome initiatives. Finally, by involving clinical and industrial stakeholders, VPH NoE also plans to lay a reliable ground to support sustainable interactions and collaboration between research and healthcare communities. Virtual Physiological Human lists, as its main target outcome, patient-specific computer models for personalized and predictive healthcare and ICT-based tools for modeling and simulation of human physiology and disease-related processes. Collaborative projects (IPs and STREPs) within the call will meet specific objectives, addressing: patient-specific computational modeling and simulation of organs or systems data integration and new knowledge extraction and clinical applications and demonstration of tangible benefits of patient-specific computational models. The networking action outlined within the call - the VPH NoE - should serve to connect these efforts, and lay the foundations for the methodological and technical framework to support such research. It should also build on previous EC investment in this field, including the outcomes of VPH type' projects funded within the EU Sixth Framework Programme, and through other National and International initiatives. The Virtual Physiological Human Network of Excellence (VPH NoE) has been designed with "service to the community" of VPH researchers as its primary purpose. Its aims range from the development of a VPH ToolKit and associated infrastructural resources, through integration of models and data across the various relevant levels of physiological structure and functional organization, to VPH community building and support. The VPH NoE aims to foster the development of new and sustainable educational, training and career structures for those involved in VPH related science, technology and medicine. The VPH NoE constitutes a leading group of universities, institutes and organizations who will, by integrating their experience and ongoing activities in VPH research, promote the creation of an environment that actively supports and nurtures interdisciplinary research, education, training and strategic development. The VPH NoE will lead the coordination of diverse activities within the VPH Initiative to help deliver: new environments for predictive, patient-specific, evidence-based, more effective and safer healthcare; improved semantic interoperability of biomedical information and contribution to a common health information infrastructure; facile, on-demand access to distributed European computational infrastructure to support clinical decision making; and increased European multidisciplinary research excellence in biomedical informatics and molecular medicine by fostering closer cooperation between ICT, medical device, medical imaging, pharmaceutical and biotech companies. The VPH NoE will connect the diverse VPH Initiative projects, including not only those funded as part of the VPH initiative but also those of previous EC frameworks and national funding schemes, together with industry, healthcare providers, and international organizations, thereby ensuring that these impacts will be realized. VPH NoE work packages and project structure The VPH NoE activities are divided between five main work packages (follow the links at the top of the page for more information on each). In brief, the focus of each work package is as follows: -Work package 1: Network Management -Work package 2: VPH NoE Exemplar Projects -Work package 3: VPH NoE ToolKit development -Work package 4: VPH NoE Training and Career Development -Work package 5: Spreading Excellence within the VPH NoE and VPH-I In view of its role as the networking action for the VPH Initiative, all VPH NoE activities have been designed to serve and interconnect not only the VPH NoE core members, but also the projects funded within the VPH call (VPH-I) and the wider research community. Key activities which the VPH NoE will pursue, in support of the development of a research environment which facilitates integrative, interdisciplinary and multilevel VPH research, are: -Support for integrative research -Training and dissemination activities -Networking activities Sponsors: VPH NoE is supported by The Directorate-General Research (DG RTD) and The Directorate-General Information Society and Media (DG INFSO).

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European Bioinformatics Institute

A non-profit academic organization for research and services in bioinformatics that provides freely available data from life science experiments, performs basic research in computational biology, and offers an extensive user training programme, supporting researchers in academia and industry. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures.

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BioCarta Pathways

BioCarta Pathways allows users to observe how genes interact in dynamic graphical models. Online maps available within this resource depict molecular relationships from areas of active research. In an open source approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.

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SBML

A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.

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CellML

The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.

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CellML Model Repository

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

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Dublin Core

An open organization engaged in the development of interoperable online metadata standards that support a broad range of purposes and business models. DCMI''s activities include work on architecture and modeling, discussions and collaborative work in DCMI Communities and DCMI Task Groups, annual conferences and workshops, standards liaison, and educational efforts to promote widespread acceptance of metadata standards and practices. The Dublin Core Metadata Initiative provides simple standards to facilitate the finding, sharing and management of information. DCMI does this by: * Developing and maintaining international standards for describing resources * Supporting a worldwide community of users and developers * Promoting widespread use of Dublin Core solutions The major characteristics of DCMI as an organization are (the three Is): * Independent: DCMI is not controlled by specific commercial or other interests and is not biased towards specific domains nor does it mandate specific technical solutions * International: DCMI encourages participation from organizations anywhere in the world, respecting linguistic and cultural differences * Influenceable: DCMI is an open organization aiming at building consensus among the participating organizations; there are no prerequisites for participation The development and maintenance of a core set of metadata terms (the DCMI Metadata Terms) continues to be one of the main activities of DCMI. In addition, DCMI is developing guidelines and procedures to help implementers define and describe their usage of Dublin Core metadata in the form of Application Profiles. This work is done in a work structure that provides discussion and cooperation platforms for specific communities (e.g. education, government information, corporate knowledge management) or specific interests (e.g. technical architecture, accessibility). Anyone wishing to participate may do so by simply joining the appropriate mailing list for the activity of interest. The DC-General mailing list is the general forum for community participation and announcements.

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