Controlled vocabularies and semantics in systems biology - Wikidata - wikimedia - TriplyDB

Controlled vocabularies and semantics in systems biology

Controlled vocabularies and semantics in systems biology

http://www.wikidata.org/entity/Q28732715

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Annotation-based feature extraction from sets of SBML models Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language The Reactome pathway knowledgebase BiGG Models: A platform for integrating, standardizing and sharing genome-scale models Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative Data management strategies for multinational large-scale systems biology projects Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools Precise generation of systems biology models from KEGG pathways Structure-based classification and ontology in chemistry The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies Nanoinformatics: a new area of research in nanomedicine The evolution of standards and data management practices in systems biology COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project BioModels: Content, Features, Functionality, and Use Path2Models: large-scale generation of computational models from biochemical pathway maps Combining computational models, semantic annotations and simulation experiments in a graph database Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 Qualitative translation of relations from BioPAX to SBML qual Global open data management in metabolomics JSBML 1.0: providing a smorgasbord of options to encode systems biology models.A dedicated database system for handling multi-level data in systems biology ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.Correlating information contents of gene ontology terms to infer semantic similarity of gene products.Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions CSEO - the Cigarette Smoke Exposure Ontology.The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.Tav4SB: integrating tools for analysis of kinetic models of biological systems HuPSON: the human physiology simulation ontology.Multiscale modeling and data integration in the virtual physiological rat project.LibKiSAO: a Java library for Querying KiSAO.Controlled vocabularies and ontologies in proteomics: overview, principles and practice Improving collaboration by standardization efforts in systems biology.Structure, function, and behaviour of computational models in systems biology The systems biology simulation core algorithm An analysis of a 'community-driven' reconstruction of the human metabolic network Linking gene expression to phenotypes via pathway information.Automatising the analysis of stochastic biochemical time-series.

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Controlled vocabularies and semantics in systems biology

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Molecular Systems Biology

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Controlled vocabularies and semantics in systems biology

@en

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Alice Villeger

http://www.w3.org/2001/XMLSchema#string

Andrew Finney

http://www.w3.org/2001/XMLSchema#string

Anna Zhukova

http://www.w3.org/2001/XMLSchema#string

Christian Knüpfer

http://www.w3.org/2001/XMLSchema#string

Darren J Wilkinson

http://www.w3.org/2001/XMLSchema#string

James Lu

http://www.w3.org/2001/XMLSchema#string

Matthew Pocock

http://www.w3.org/2001/XMLSchema#string

Rainer Machne

http://www.w3.org/2001/XMLSchema#string

P2860

Relations in biomedical ontologies

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail

Gene ontology: tool for the unification of biology

BioModels.net Web Services, a free and integrated toolkit for computational modelling software

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

The BioPAX community standard for pathway data sharing

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

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10.1038/MSB.2011.77

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Nicolas Le Novère

Michel Dumontier

Sarala M. Wimalaratne

Allyson L Lister

Nicolas Rodriguez

Mélanie Courtot

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