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2008 Genome Informatics Series  
A system-dynamics-centered ontology, called the Cell System Ontology (CSO), has been developed for representation of diverse biological pathways.  ...  This paper discusses three criteria for validating the pathway data based on CSO as follows: (1) structurally correct models in terms of Petri nets, (2) biologically correct models to capture biological  ...  CSO defines classes for modeling, visualizing, and simulating biological pathways and relationships between classes in the Web Ontology Language (OWL) [12] .  ... 
doi:10.11234/gi1990.20.25 fatcat:wenwbbixtvfhtkh5fpjhdcbkia

Rule-based reasoning for system dynamics in cell systems

Euna Jeong, Masao Nagasaki, Satoru Miyano
2008 Genome Informatics Series  
A system-dynamics-centered ontology, called the Cell System Ontology (CSO), has been developed for representation of diverse biological pathways.  ...  This paper discusses three criteria for validating the pathway data based on CSO as follows: (1) structurally correct models in terms of Petri nets, (2) biologically correct models to capture biological  ...  CSO defines classes for modeling, visualizing, and simulating biological pathways and relationships between classes in the Web Ontology Language (OWL) [12] .  ... 
pmid:19425120 fatcat:ak57cwqh2rfh3d5h4a2fudal3q

Kinetic Modeling Using BioPAX Ontology

Oliver Ruebenacker, Ion I. Moraru, James C. Schaff, Michael L. Blinov
2007 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)  
However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation.  ...  We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell  ...  Ontologies provide a great deal of flexibility in data representation, analysis and visualization.  ... 
doi:10.1109/bibm.2007.55 pmid:20862270 pmcid:PMC2941992 fatcat:m7zbzfdnfrbmvobxcbpjh6g3ey


2006 Biocomputing 2007  
We introduce Chalkboard, a prototype tool for representing and displaying cell-signaling pathway knowledge, for carrying out simple qualitative reasoning over these pathways, and for generating quantitative  ...  The design of Chalkboard has been driven by the need to quickly model and visualize alternative hypotheses about uncertain pathway knowledge.  ...  Even the limited set of primitive Action and Entities in Chalkboard's current ontology provides a rich and flexible vocabulary for creating models of complex cell biological systems.  ... 
doi:10.1142/9789812772435_0003 fatcat:iclxjztns5ah7jz5asya56mnsa

Toxicology ontology perspectives

Barry Hardy
2012 ALTEX: Alternatives to Animal Experimentation  
Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated  ...  OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources.  ...  implementation of QSARs (Quantitative Structure-Activity Relationships) for toxicology, Project Reference Number Health- F5-2008-200787 (2008-2011). the research leading to these results has received  ... 
doi:10.14573/altex.2012.2.139 pmid:22562487 fatcat:ixzxgpvnbvd2peamgwe2loy5ge

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano
2008 BMC Systems Biology  
As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons.  ...  The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models.  ...  We would also thank researchers and developers of the TRANSPATH database for giving useful information of the database, especially, Holger Karas, Edgar Wingender, Nico Voss, Ines Liebich, Ruy Jauregui,  ... 
doi:10.1186/1752-0509-2-53 pmid:18570683 pmcid:PMC2474843 fatcat:ghhtegtj2za3tiy7rxdupqeqqu

Standards and ontologies in computational systems biology

Herbert M. Sauro, Frank T. Bergmann
2008 Essays in Biochemistry  
In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed.  ...  Software tools such as developer libraries and basic editing tools are also introduced together with a discussion on the future of modeling languages and visualization tools in systems biology.  ...  We would also like to thank Anastasia Deckard for critically reading the manuscript.  ... 
doi:10.1042/bse0450211 pmid:18793134 pmcid:PMC2728449 fatcat:e4o7fvlubjdndnm3af2f5savai

An ontology for collaborative construction and analysis of cellular pathways

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. Cetin-Atalay
2004 Bioinformatics  
Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data.  ...  Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events.  ...  The ultimate goal is to build a model for a cell as a whole with mechanistic details and to be able to perform functional computations and simulations over this model.  ... 
doi:10.1093/bioinformatics/btg416 pmid:14960461 fatcat:qz57tj6xaja37emtpykzj62vn4

Integrating systems biology models and biomedical ontologies

Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook, Georgios V Gkoutos
2011 BMC Systems Biology  
We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish  ...  Results: We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems  ...  Acknowledgements We thank Maxwell Neal for his input and critical discussions, and two anonymous reviewers for valuable comments on our manuscript.  ... 
doi:10.1186/1752-0509-5-124 pmid:21835028 pmcid:PMC3170340 fatcat:qn4f6b6535fltgovu3dmllokam

An ontology for biological function based on molecular interactions

P. D. Karp
2000 Bioinformatics  
Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function.  ...  The functional ontology developed for the EcoCyc database is presented.  ...  Julio Collado contributed to the design of the ontology for regulatory events. Milton Saier and Ian Paulsen contributed to the design of the ontology for transport.  ... 
doi:10.1093/bioinformatics/16.3.269 pmid:10869020 fatcat:u2u6rpzq4jg7biswqqhpuhorla

Ontology-based instance data validation for high-quality curated biological pathways

Euna Jeong, Masao Nagasaki, Kazuko Ueno, Satoru Miyano
2011 BMC Bioinformatics  
This approach is applied to data in Cell System Ontology which is a comprehensive ontology that represents complex biological pathways with dynamics and visualization.  ...  Rules are defined to correct models against biological semantics and improve models for dynamic simulation.  ...  Authors' contributions EJ and MN conceived the basic idea. KU and MN created the macrophage models to be evaluated. EJ defined the rules for the validation and implemented the rule-based system.  ... 
doi:10.1186/1471-2105-12-s1-s8 pmid:21342591 pmcid:PMC3044316 fatcat:2yumy256rrfg7ba3bczxwafzx4

Ontological foundations for biology knowledge models

C D Hafner, N Fridman
1996 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
This paper analyzes the ontological requirements for representing biology knowledge, and identifies several areas where current knowledge representation (KR) paradigms need to be extended.  ...  We focus on the representation of experimental materials and methods, and the reasoning task of intelligent information retrieval; however, the ontological issues we raise apply to biology (and experimental  ...  Miller and the anonymous reviewers for helpful comments on an earlier draft of this paper.  ... 
pmid:8877507 fatcat:rwfu2oys2vbjzkzha75lhxrczm

Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models

Belén Juanes Cortés, José Antonio Vera-Ramos, Ruth C. Lovering, Pascale Gaudet, Astrid Laegreid, Colin Logie, Stefan Schulz, María del Mar Roldán-García, Martin Kuiper, Jesualdo Tomás Fernández-Breis
2021 Biochimica et Biophysica Acta. Gene Regulatory Mechanisms  
The Gene Ontology has demonstrated that ontologies play a fundamental role in biological data interoperability and integration.  ...  The models have been implemented using Protégé, a general ontology editor, and Noctua, the tool developed by the Gene Ontology Consortium for the development of causal activity models to capture more comprehensive  ...  Acknowledgements We thank the support of the Noctua development team, and the scientific exchange with the members of the GO, SO and GREEKC consortia.  ... 
doi:10.1016/j.bbagrm.2021.194766 pmid:34710644 fatcat:4lc2w2otgfhfrjyjxqaxtiv6zm

Integrating evolving brain–gene ontology and connectionist-based system for modeling and knowledge discovery

Nikola Kasabov, Vishal Jain, Lubica Benuskova
2008 Neural Networks  
We would like to thank Scott Heappey for creating all the animations, Simei Gomes Wysoski for programming the neurogenetic simulator, and Paulo C. M. Gottgtroy for initial work on BGO development.  ...  Acknowledgments This work is supported by a NERF grant AUTX0201 and by KEDRI.  ...  Results obtained by simulating the neurogenetic models will become new facts to be integrated within the BGO, which will close the loop of new knowledge discovery and representation in the ontology knowledge  ... 
doi:10.1016/j.neunet.2007.12.041 pmid:18343308 fatcat:nycrcrvnq5chpkiuwsuskoopmu

Integration of the Gene Ontology into an object-oriented architecture

Daniel Shegogue, W Jim Zheng
2005 BMC Bioinformatics  
Gene Ontology into an object-oriented model.  ...  However, there is no single representation that integrates all the terms into one cohesive model.  ...  Furthermore, UML models can be translated into code, facilitating the creation of simulations. 16 The standardization of biological system modeling and integration is growing rapidly.  ... 
doi:10.1186/1471-2105-6-113 pmid:15885145 pmcid:PMC1156866 fatcat:c5r7ajbttbboxctazrouw2ddzq
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