Erick Antezana
Norwegian University of Science and Technology, Department of Biology, Department Member
- Bio-ontologies engineering to enable systems biology.edit
Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life... more
Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research.
The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop'for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins,... more
The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop'for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle?
Abstract The vast amounts of knowledge in the biomedical domain have paved the way for a new paradigm in biological research called Systems Biology, essentially an approach that relies on the integration of all available knowledge of a... more
Abstract The vast amounts of knowledge in the biomedical domain have paved the way for a new paradigm in biological research called Systems Biology, essentially an approach that relies on the integration of all available knowledge of a biological system in a single model. This approach promotes a comprehensive understanding of biological systems, driven by data integration and mathematical modelling.
Abstract Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concepts within the biomedical domain. The ontologies within the OBO Foundry are usually represented in the OBO ontology language. While... more
Abstract Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concepts within the biomedical domain. The ontologies within the OBO Foundry are usually represented in the OBO ontology language. While being human-readable, this language lacks the computational rigour required for the Semantic Web (SW).
Abstract Biomedical ontologies are key to the success of Semantic Web technologies in Life Sciences; therefore, it is important to provide appropriate tools for their development and further exploitation. The Ontology Pre Processor... more
Abstract Biomedical ontologies are key to the success of Semantic Web technologies in Life Sciences; therefore, it is important to provide appropriate tools for their development and further exploitation. The Ontology Pre Processor Language (OPPL) can be used for automating the complex manipulation needed to devise biomedical ontologies with richer axiomatic content, which in turn pave the way towards advanced biological data analyses.
Abstract Over the last decade the biological sciences have been widely embracing Systems Biology and its various data integration approaches to discover new knowledge. Molecular Systems Biology aims to develop hypotheses based on... more
Abstract Over the last decade the biological sciences have been widely embracing Systems Biology and its various data integration approaches to discover new knowledge. Molecular Systems Biology aims to develop hypotheses based on integrated, or modelled data. These hypotheses can be subsequently used to design new experiments for testing, leading to an improved understanding of the biology; a more accurate model of the biological system and therefore an improved ability to develop hypotheses.
Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life... more
Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyberinfrastructure researchers to jointly tackle important challenges in the area of in silico biological research.
Background The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse... more
Background The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected.
Background Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data integration solutions. The Semantic Web is expected to link all the data present on the Internet instead of... more
Background Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data integration solutions. The Semantic Web is expected to link all the data present on the Internet instead of linking just documents. One of the foundations of the Semantic Web technologies is the knowledge representation language Resource Description Framework (RDF).
Abstract Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a... more
Abstract Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as a semi-automated process in three steps:(i) defining a logic-based representation language;(ii) building a consistent ontology using that language; and (iii) exploiting the ontology through querying.
Abstract New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than... more
Abstract New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than an asset. The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especially if they work with approaches that thoroughly depend on knowledge integration, such as systems biology.
Abstract. We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run... more
Abstract. We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query specific.
Background Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching... more
Background Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology.
Genomics technologies generate vast amounts of data of a wide variety of types and complexities, and at a growing pace. The analysis of such data and the mining of the resulting information is insufficient without a contextual... more
Genomics technologies generate vast amounts of data of a wide variety of types and complexities, and at a growing pace. The analysis of such data and the mining of the resulting information is insufficient without a contextual interpretation, that is, biological knowledge deduced from the data. This knowledge states the data's biological meaning in terms of, for instance, molecular function, cellular location, or network interactions. Biological knowledge is diverse, vast, complex, and volatile.
Research Interests:
Research Interests:
Abstract. Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied... more
Abstract. Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the ...