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Ward Blondé

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I have a master degree as a civil engineer physics, after which I did a PhD in Bioinformatics. However, after my post-doc in 2013, I got interested in metaphysics. A central idea is that the combination of evolutionary conservation and cosmological natural selection results in supernaturalism, as explained in my EMAAN argument.
Supervisors: Martin Kuiper, Bernard De Baets, Stefan Schulz, and Ludger Jansen

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Papers by Ward Blondé

EMAAN: An Evolutionary Multiverse Argument against Naturalism

In this paper, an evolutionary multiverse argument against naturalism (EMAAN) is presented: E1. I... more In this paper, an evolutionary multiverse argument against naturalism (EMAAN) is presented: E1. In an evolutionary multiverse, phenomena have variable evolutionary ages. E2. After some time T, the development of the empirical sciences will be evolutionarily conserved. E3. The phenomena with an evolutionary age above T are methodologically supernatural. Entities are classified according to whether they are (1) physical and spatiotemporal, (2) causally efficacious, and (3) either observed by or explanatorily necessary for the empirical sciences. While the conjunction of (1) and (2) is taken to be sufficient for existence in reality, the negation of (3) defines methodological supernaturalness. EMAAN uses a generalization of evolutionary theory, namely cosmological natural selection, to argue that phenomena evolve that fulfill conditions (1) and (2), but not (3). This shows that methodologically supernatural phenomena have a clear epistemology according to a theory that is grounded in the commitments of naturalism. Supernatural phenomena are not observed by the empirical sciences because the empirical sciences themselves are supernaturally guided and predestined to develop according to an evolutionarily conserved plan. In spite of this scientific plan, there is room for afterlives and supernaturality in the everyday experience.

CAN AN ETERNAL LIFE START FROM THE MINIMAL FINE-TUNING FOR INTELLIGENCE

Since modern physicists made more and more advances in precisely measuring the fundamental consta... more Since modern physicists made more and more advances in precisely measuring the fundamental constants in nature, cosmologists have been confronted with this problem: how do we declare that nature's constants are fine-tuned for the emergence of life? Many cosmologists assume nowadays that the big bang universe originates from a multiverse that consists of very many universes. Some of these must be fine-tuned for life. A fascinating question arises: Would there be any chance on a life after our death in this multiverse? In this paper, I show two things about the multiverse. First, universes in the multiverse acquire an unlimited amount of additional fine-tuning for intelligent life over the course of many universe generations. Such additional fine-tuning may consist of travelling between universes and an afterlife on a distant planet. Second, evolutionary conservation in the evolution of universes in the multiverse provides a declaration why we observe a universe that roughly has the minimal fine-tuning to support intelligent life.

An Evolutionary Argument for a Self-Explanatory, Benevolent Metaphysics

In this paper, a metaphysics is proposed that includes everything that can be represented by a we... more In this paper, a metaphysics is proposed that includes everything that can be represented by a well-founded multiset. It is shown that this metaphysics, apart from being self-explanatory, is also benevolent. Paradoxically, it turns out that the probability that we were born in another life than our own is zero. More insights are gained by inducing properties from a metaphysics that is not self-explanatory. In particular, digital metaphysics is analyzed, which claims that only computable things exist. First of all, it is shown that digital metaphysics contradicts itself by leading to the conclusion that the shortest computer program that computes the world is infinitely long. This means that the Church-Turing conjecture must be false. Secondly, the applicability of Occam's razor is explained by evolution: in an evolving physics it can appear at each moment as if the world is caused by only finitely many things. Thirdly and most importantly, this metaphysics is benevolent in the sense that it organizes itself to fulfill the deepest wishes of its observers. Fourthly, universal computers with an infinite memory capacity cannot be built in the world. And finally, all the properties of the world, both good and bad, can be explained by evolutionary conservation.

Using the relation ontology Metarel for modelling Linked Data as multi-digraphs

by Ward Blondé and V. Mironov

The Semantic Web standards OWL and RDF are often used to represent biomedical information as Link... more The Semantic Web standards OWL and RDF are often used to represent biomedical information as Linked Data, however, the OWL/RDF syntax, which combines both, was never optimised for querying. By combining two formal paradigms for modelling Linked Data, namely multi-digraphs and Description Logic, many precise terms for relations have emerged that are defined in the Metarel relation ontology. They are especially useful in Linked Data and RDF knowledge bases that 1) rely on SPARQL querying and 2) require semantic support for chains of relations. Metarel-described multi-digraphs were used for knowledge integration and reasoning in three RDF knowledge bases in the domain of genome biology: BioGateway, Cell Cycle Ontology and Gene Expression Knowledge Base. These knowledge bases integrate both data, like Kegg, and ontologies, like Gene Ontology, in the same RDF graphs. Their libraries with biomedically relevant SPARQL queries show the practical benefits of this semantic paradigm. In addition to the management of RDF stores, this paper describes how Metarel can be used for remodelling Linked Data as SPARQL-friendly and semantically rich multi-digraphs. Metarel can be downloaded from http://www.semantic-systems-biology.org/metarel.

Metarel, an ontology facilitating advanced querying of biomedical knowledge

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts ... more 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: 1) defining a logic-based representation language; 2) building a consistent ontology using that language; and 3) exploiting the ontology through querying. Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological RDF knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases. Availability: SPARUL code, a query endpoint and curated relation types in OBO Format, RDF and OWL 2 DL are freely available at http://www.semantic-systems-biology.org/metarel.

Benchmarking triple stores with biological data

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena... more 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. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer-its response time was better than average for all the 24 queries; it showed a very good scalability and a reasonable run-to-run reproducibility.

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automa... more The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycle Ontology facilitates a detailed analysis of cell cycle-related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building. Rationale Molecular biology has spent the past two decades cataloguing genes, expression levels, proteins, molecular interactions and more. The combination of all these catalogues should enable a biologist to start building a comprehensive picture of a biological system rather than only looking at the individual components. The formation of representations of these components into a network that describes a biological system constitutes the first step in allowing a biologist to develop an understanding of the behavior of a system. If adequate kinetic and other parameters can be obtained or estimated, such models can be used for network simulations in a mathematical framework, making them particularly useful to study the emergent properties of such a system [1-5]. These models provide the basis for much of systems biology that is built on integrative data analysis and mathematical modeling [6-9]. In systems biology, dynamic simulations with a model of a biological process serve as a means to validate the model's architecture and parameters, and to provide hypotheses for new experiments. Complementary to such model-dependent hypothesis generation , the field of computational reasoning promises to provide a powerful additional source of new hypotheses concerning biological network components. The integration of biological knowledge from various sources and the alignment of their representations into one common representation are recognized as critical steps toward hypothesis building [10,11]. Such an integrated information resource is essential for exploration and exploitation by both humans

BioGateway: a semantic systems biology tool for the life sciences

Background: Life scientists need help in coping with the plethora of fast growing and scattered k... more Background: Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance.

Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies

While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge R... more While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org.

Structuring the life sciences resourceome for Semantic Systems Biology: lessons from the BioGateway project

The application of Semantic Web technologies in the life sciences for data integration is still n... more The application of Semantic Web technologies in the life sciences for data integration is still nascent. We have recently built Bio-Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio-Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider acceptance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sou... more 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: 1) defining a logic-based representation language; 2) building a consistent ontology using that language; and 3) exploiting the ontology through querying. Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological RDF knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases. Availability: SPARUL code, a query endpoint and curated relation types in OBO Format, RDF and OWL 2 DL are freely available at http://www.semantic-systems-biology.org/metarel.

The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration

Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concept... more 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 humanreadable, this language lacks the computational rigour required for the Semantic Web (SW). Consequently, the RDF and OWL languages, both fundamental components of the SW technology stack, are being increasingly adopted by the biomedical community to exchange biological knowledge in a computer intelligible form. Some of the OBO-formatted ontologies have been made available in OWL, thus signalling a move towards the SW. OWL provides support for automated reasoning, which is its raison d'être. Unfortunately, automated reasoning on the massive volumes of data that are typical of the biomedical domain is riddled with performance limitations. Due to consistent support for the SPARQL specification in triplestore implementations, as well as the ability to simulate some types of reasoning with precomputed closures, RDF has evolved into a language of choice for knowledge exchange within the framework of the SW. Here, we discuss the need to establish a foundry charged with the task of harmonizing biomedical RDF resources, acting along the same lines as the OBO Foundry. To substantiate the need for an RDF Foundry, we provide the outcome of a small survey we have conducted to highlight the domain coverage, redundancies, and comprehensiveness of results obtained from a few representative distributed resources available today.

Benchmarking triple stores with biological data

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena... more 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. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer -its response time was better than average for all the 24 queries; it showed a very good scalability and a reasonable run-to-run reproducibility.

Drafts by Ward Blondé

Proving God without Dualism: Improving the Swinburne- Moreland Argument from Consciousness

by Ludger Jansen and Ward Blondé

With substance dualism and the existence of God, Swinburne (2004) and Moreland (2010) have argued... more With substance dualism and the existence of God, Swinburne (2004) and Moreland (2010) have argued for a very powerful explanatory mechanism that can readily explain several philosophical problems related to consciousness. However, their positions come with presuppositions and ontological commitments which many are not prepared to share. The aim of this paper is to improve on the Swinburne-Moreland argument from consciousness by developing an argument for the existence of God from consciousness without being committed to substance dualism. The argument proceeds by suggesting a solution to the exceptional-point-of-view problem, i.e., the question how it can be explained that there is a conscious being lucky enough to experience the point of view of a relatively tiny brain amidst a giant universe that is indifferent about which physical entities it brings about according to the laws of physics.

EMAAN: An Evolutionary Multiverse Argument against Naturalism

In this paper, an evolutionary multiverse argument against naturalism (EMAAN) is presented: E1. I... more In this paper, an evolutionary multiverse argument against naturalism (EMAAN) is presented: E1. In an evolutionary multiverse, phenomena have variable evolutionary ages. E2. After some time T, the development of the empirical sciences will be evolutionarily conserved. E3. The phenomena with an evolutionary age above T are methodologically supernatural. Entities are classified according to whether they are (1) physical and spatiotemporal, (2) causally efficacious, and (3) either observed by or explanatorily necessary for the empirical sciences. While the conjunction of (1) and (2) is taken to be sufficient for existence in reality, the negation of (3) defines methodological supernaturalness. EMAAN uses a generalization of evolutionary theory, namely cosmological natural selection, to argue that phenomena evolve that fulfill conditions (1) and (2), but not (3). This shows that methodologically supernatural phenomena have a clear epistemology according to a theory that is grounded in the commitments of naturalism. Supernatural phenomena are not observed by the empirical sciences because the empirical sciences themselves are supernaturally guided and predestined to develop according to an evolutionarily conserved plan. In spite of this scientific plan, there is room for afterlives and supernaturality in the everyday experience.

CAN AN ETERNAL LIFE START FROM THE MINIMAL FINE-TUNING FOR INTELLIGENCE

Since modern physicists made more and more advances in precisely measuring the fundamental consta... more Since modern physicists made more and more advances in precisely measuring the fundamental constants in nature, cosmologists have been confronted with this problem: how do we declare that nature's constants are fine-tuned for the emergence of life? Many cosmologists assume nowadays that the big bang universe originates from a multiverse that consists of very many universes. Some of these must be fine-tuned for life. A fascinating question arises: Would there be any chance on a life after our death in this multiverse? In this paper, I show two things about the multiverse. First, universes in the multiverse acquire an unlimited amount of additional fine-tuning for intelligent life over the course of many universe generations. Such additional fine-tuning may consist of travelling between universes and an afterlife on a distant planet. Second, evolutionary conservation in the evolution of universes in the multiverse provides a declaration why we observe a universe that roughly has the minimal fine-tuning to support intelligent life.

An Evolutionary Argument for a Self-Explanatory, Benevolent Metaphysics

In this paper, a metaphysics is proposed that includes everything that can be represented by a we... more In this paper, a metaphysics is proposed that includes everything that can be represented by a well-founded multiset. It is shown that this metaphysics, apart from being self-explanatory, is also benevolent. Paradoxically, it turns out that the probability that we were born in another life than our own is zero. More insights are gained by inducing properties from a metaphysics that is not self-explanatory. In particular, digital metaphysics is analyzed, which claims that only computable things exist. First of all, it is shown that digital metaphysics contradicts itself by leading to the conclusion that the shortest computer program that computes the world is infinitely long. This means that the Church-Turing conjecture must be false. Secondly, the applicability of Occam's razor is explained by evolution: in an evolving physics it can appear at each moment as if the world is caused by only finitely many things. Thirdly and most importantly, this metaphysics is benevolent in the sense that it organizes itself to fulfill the deepest wishes of its observers. Fourthly, universal computers with an infinite memory capacity cannot be built in the world. And finally, all the properties of the world, both good and bad, can be explained by evolutionary conservation.

Using the relation ontology Metarel for modelling Linked Data as multi-digraphs

by Ward Blondé and V. Mironov

The Semantic Web standards OWL and RDF are often used to represent biomedical information as Link... more The Semantic Web standards OWL and RDF are often used to represent biomedical information as Linked Data, however, the OWL/RDF syntax, which combines both, was never optimised for querying. By combining two formal paradigms for modelling Linked Data, namely multi-digraphs and Description Logic, many precise terms for relations have emerged that are defined in the Metarel relation ontology. They are especially useful in Linked Data and RDF knowledge bases that 1) rely on SPARQL querying and 2) require semantic support for chains of relations. Metarel-described multi-digraphs were used for knowledge integration and reasoning in three RDF knowledge bases in the domain of genome biology: BioGateway, Cell Cycle Ontology and Gene Expression Knowledge Base. These knowledge bases integrate both data, like Kegg, and ontologies, like Gene Ontology, in the same RDF graphs. Their libraries with biomedically relevant SPARQL queries show the practical benefits of this semantic paradigm. In addition to the management of RDF stores, this paper describes how Metarel can be used for remodelling Linked Data as SPARQL-friendly and semantically rich multi-digraphs. Metarel can be downloaded from http://www.semantic-systems-biology.org/metarel.

Metarel, an ontology facilitating advanced querying of biomedical knowledge

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts ... more 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: 1) defining a logic-based representation language; 2) building a consistent ontology using that language; and 3) exploiting the ontology through querying. Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological RDF knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases. Availability: SPARUL code, a query endpoint and curated relation types in OBO Format, RDF and OWL 2 DL are freely available at http://www.semantic-systems-biology.org/metarel.

Benchmarking triple stores with biological data

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena... more 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. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer-its response time was better than average for all the 24 queries; it showed a very good scalability and a reasonable run-to-run reproducibility.

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automa... more The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycle Ontology facilitates a detailed analysis of cell cycle-related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building. Rationale Molecular biology has spent the past two decades cataloguing genes, expression levels, proteins, molecular interactions and more. The combination of all these catalogues should enable a biologist to start building a comprehensive picture of a biological system rather than only looking at the individual components. The formation of representations of these components into a network that describes a biological system constitutes the first step in allowing a biologist to develop an understanding of the behavior of a system. If adequate kinetic and other parameters can be obtained or estimated, such models can be used for network simulations in a mathematical framework, making them particularly useful to study the emergent properties of such a system [1-5]. These models provide the basis for much of systems biology that is built on integrative data analysis and mathematical modeling [6-9]. In systems biology, dynamic simulations with a model of a biological process serve as a means to validate the model's architecture and parameters, and to provide hypotheses for new experiments. Complementary to such model-dependent hypothesis generation , the field of computational reasoning promises to provide a powerful additional source of new hypotheses concerning biological network components. The integration of biological knowledge from various sources and the alignment of their representations into one common representation are recognized as critical steps toward hypothesis building [10,11]. Such an integrated information resource is essential for exploration and exploitation by both humans

BioGateway: a semantic systems biology tool for the life sciences

Background: Life scientists need help in coping with the plethora of fast growing and scattered k... more Background: Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance.

Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies

While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge R... more While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org.

Structuring the life sciences resourceome for Semantic Systems Biology: lessons from the BioGateway project

The application of Semantic Web technologies in the life sciences for data integration is still n... more The application of Semantic Web technologies in the life sciences for data integration is still nascent. We have recently built Bio-Gateway, an RDF store that integrates all the candidate OBO Foundry ontologies with other resources such as SWISS-PROT. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse formats. We present a detailed analysis of the obstacles that had to be solved in creating Bio-Gateway. In doing so, we demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. The time is ripe for launching a community effort aiming at a wider acceptance and application of Semantic Web technologies in the life sciences domain. We make a public call for the creation of a forum that strives to implement a truly semantic life science foundation of a type of Systems Biology that we named Semantic Systems Biology.

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sou... more 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: 1) defining a logic-based representation language; 2) building a consistent ontology using that language; and 3) exploiting the ontology through querying. Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological RDF knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases. Availability: SPARUL code, a query endpoint and curated relation types in OBO Format, RDF and OWL 2 DL are freely available at http://www.semantic-systems-biology.org/metarel.

The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration

Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concept... more 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 humanreadable, this language lacks the computational rigour required for the Semantic Web (SW). Consequently, the RDF and OWL languages, both fundamental components of the SW technology stack, are being increasingly adopted by the biomedical community to exchange biological knowledge in a computer intelligible form. Some of the OBO-formatted ontologies have been made available in OWL, thus signalling a move towards the SW. OWL provides support for automated reasoning, which is its raison d'être. Unfortunately, automated reasoning on the massive volumes of data that are typical of the biomedical domain is riddled with performance limitations. Due to consistent support for the SPARQL specification in triplestore implementations, as well as the ability to simulate some types of reasoning with precomputed closures, RDF has evolved into a language of choice for knowledge exchange within the framework of the SW. Here, we discuss the need to establish a foundry charged with the task of harmonizing biomedical RDF resources, acting along the same lines as the OBO Foundry. To substantiate the need for an RDF Foundry, we provide the outcome of a small survey we have conducted to highlight the domain coverage, redundancies, and comprehensiveness of results obtained from a few representative distributed resources available today.

Benchmarking triple stores with biological data

We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena... more 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. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer -its response time was better than average for all the 24 queries; it showed a very good scalability and a reasonable run-to-run reproducibility.

Proving God without Dualism: Improving the Swinburne- Moreland Argument from Consciousness

by Ludger Jansen and Ward Blondé

With substance dualism and the existence of God, Swinburne (2004) and Moreland (2010) have argued... more With substance dualism and the existence of God, Swinburne (2004) and Moreland (2010) have argued for a very powerful explanatory mechanism that can readily explain several philosophical problems related to consciousness. However, their positions come with presuppositions and ontological commitments which many are not prepared to share. The aim of this paper is to improve on the Swinburne-Moreland argument from consciousness by developing an argument for the existence of God from consciousness without being committed to substance dualism. The argument proceeds by suggesting a solution to the exceptional-point-of-view problem, i.e., the question how it can be explained that there is a conscious being lucky enough to experience the point of view of a relatively tiny brain amidst a giant universe that is indifferent about which physical entities it brings about according to the laws of physics.