CelO - Cell Component Ontology

What is?

CelOWS project aims at using and discussing ontologies and semantic rules for creation, validation, storage and sharing of biological models. CelO ontology captures the structure of a cell model and properties of functional components. It is used to describe, query and compose CellML models, improving reuse and composition of existent components and allowing semantic validation of new models.

Where?

The first version of the project was developed as part of a thesis at Master Program in Computational Modeling, Federal University of Juiz de Fora, Brazil.

Why?

CelO ontology represents biological models of cellular electrophysiology. The use of an expressive logic language to represent models enriches the application of inference mechanisms and definition of semantic rules. The semantic annotation improves CellML models and allows the creation of new models, adding functionality and flexibility to modeling process.

How?

The project used OWL-DL to develop the ontology and SWRL to express the rules. Main tools are XSLT, Protegé-OWL Editor/API, Pellet 1.5 reasoner, Jess Rule Engine.

Who?

Msc. Ely Edison Matos (ely . matos at ufjf . edu . br)
Dr. Fernanda Campos (fernanda . campos at ufjf . edu . br)
Dr. Regina Braga (regina . braga at ufjf . edu .br)
Dr. Rodrigo Weber (rodrigo . weber at ufjf . edu .br)
Daniele Palazzi (daniele . palazzi at ice . ufjf . br)

Publications

E.E. Matos, F. Campos, R. Braga and D. Palazzi, CelOWS: An ontology based framework for the provision of semantic web services related to biological models, Journal of Biomedical Informatics 43 (2010), pp. 125–136. DOI

Matos, E. E, Campos, F., Braga, R., Weber, R., Palazzi, D. (2009). "CelOWS: a service oriented architecture to define query and reuse biological models". In ICCS 2009: Compute. Discover. Innovate. Baton Rouge. USA.

Matos, E. E, Mendes, L. F.; Campos, F., Braga, R. (2009)"ASOW-Science: a service oriented framework to support e-Science Applications" in IRI 2009, Las Vegas, USA.

Matos, E. E., Campos, F., Braga, R., Weber, R. (2008). "Composição de modelos para a fisiologia: uma proposta de infraestrutura de e-Science baseada em ontologias". In: Anais do XXVIII Congresso da SBC, Belém do Pará, Pará, Brasil.

Matos, E. E. "CelOWS: um Framework Baseado em Ontologias com Serviços Web para Modelagem Conceitual em Biologia Sistêmica". Dissertação de Mestrado. Mestrado em Modelagem Computacional. Universidade Federal de Juiz de Fora. Brasil. 2008.

Matos, E. et al. (2007) "MathWS: Broker de Serviços Web para e-Science". 1st Brazilian e-Science WorkShop. in conjunction with 22nd Brazilian Symposium on Data Base, João Pessoa, Brazil.