Integrating hierarchical controlled vocabularies with OWL ontology: A case study from the domain of molecular interactions

Many efforts at standardising terminologies within the biological domain have resulted in the construction of hierarchical controlled vocabularies that capture domain knowledge. Vocabularies, such as the PSI-MI vocabulary, capture both deep and extensive domain knowledge, in the OBO (Open Biomedical Ontologies) format. However hierarchical vocabularies, such as PSI-MI which are represented in OBO, only represent simple parent-child relationships between terms. By contrast, ontologies constructed using the Web Ontology Language (OWL), such as BioPax, define many richer types of relationships between terms. OWL provides a semantically rich structured language for expressing classes and sub-classes of entities and properties, relationships between them and domain-specific rules or axioms that can be applied to extract new information through semantic inferencing. In order to fully exploit the domain knowledge inherent in domain-specific controlled vocabularies, they need to be represented as OWL-DL ontologies, rather than in formats such as OBO. In this paper, we describe a method for converting OBO vocabularies into OWL and class instances represented as OWL-RDF triples. This approach preserves the hierarchical arrangement of the domain knowledge whilst also making the underlying parent-child relationships available to inferencing engines. This approach also has clear advantages over existing methods which incorporate terms from external controlled vocabularies as literals stripped of the context associated with their place in the hierarchy. By preserving this context, we enable machine inferencing over the ordered domain knowledge captured in OBO controlled vocabularie

Methodology for integration of fisher's ecological knowledge in fisheries biology and management using knowledge representation (artificial intelligence)

Presentado na International Conference "Putting Fisher's Knowledge to Work", Vancouver, Canadá, 27-30 agosto de 2001[abstract] The fisheries crisis of the last decades and the overexploitation of a great number of stocks (FAO 1995) have been due mainly to the inadequacy of scientific knowledge, uncertainties in assessments and/or failures of the management systems. These problems are critical when the management of coastal ecosystems and artisanal fisheries is involved. These systems possess great complexity due to the high number of human factors that influence their functioning and the fishing activity. Small-scale coastal fisheries have a much greater social significance than offshore industrial fisheries, despite the larger economical importance of the latter (only in macro-economic terms). The artisanal coastal fisheries in Galicia (NW Spain) are in a general state of overexploitation derived from the mismatch between management (derived implicitly from models designed for industrial finfisheries) and the biological and socioeconomic context. Freire and García-Allut (2000) proposed a new management policy (based on the establishment of territorial users’ rights, the involvement of fishers in the assessment and management process in collaboration with the government agencies, and the use of protected areas and minimum landing sizes as key regulations) to solve the above problems. As well as a new management system, research should pay special attention to the design and use of inexpensive and rapid methodologies to get relevant scientific data, and introduce local or traditional ecological knowledge of the fishers to the assessment and management process. In this paper, we analyze the values and characteristics of fishers’ ecological knowledge (FEK). Using the artisanal coastal fisheries of Galicia as a case study, we present the objectives of the integration of FEK in fisheries biology and management and propose a methodology for that goal. The use of Artificial Intelligence (AI) as a tool for the analysis and integration of FEK is discussed, and the role of Knowledge Representation, a branch of AI, is described to show the epistemological and technological adequacy of the chosen languages and tools in a non-computer science foru

Terminological representation, natural language & relation algebra

In this paper I establish a link between {\sc kl-one}-based knowledge representation concerned with {\em terminological representation} and the work of P. Suppes (1976,1979,1981) and M. B\"ottner (1985,1989) in computational linguistics. I show how this link can be utilised for the problem of finding adequate terminological representations for given information formulated in ordinary English

Axiomatizations of arithmetic and the first-order/second-order divide

It is often remarked that first-order Peano Arithmetic is non-categorical but deductively well-behaved, while second-order Peano Arithmetic is categorical but deductively ill-behaved. This suggests that, when it comes to axiomatizations of mathematical theories, expressive power and deductive power may be orthogonal, mutually exclusive desiderata. In this paper, I turn to Hintikka’s (Philos Top 17(2):69–90, 1989) distinction between descriptive and deductive approaches in the foundations of mathematics to discuss the implications of this observation for the first-order logic versus second-order logic divide. The descriptive approach is illustrated by Dedekind’s ‘discovery’ of the need for second-order concepts to ensure categoricity in his axiomatization of arithmetic; the deductive approach is illustrated by Frege’s Begriffsschrift project. I argue that, rather than suggesting that any use of logic in the foundations of mathematics is doomed to failure given the impossibility of combining the descriptive approach with the deductive approach, what this apparent predicament in fact indicates is that the first-order versus second-order divide may be too crude to investigate what an adequate axiomatization of arithmetic should look like. I also conclude that, insofar as there are different, equally legitimate projects one may engage in when working on the foundations of mathematics, there is no such thing as the One True Logic for this purpose; different logical systems may be adequate for different projects

El razonamiento defectible y sus fronteras epistémico-metodológicas.

Sin resume

Reasoning about temporal relations : a maximal tractable subclass of Allen\u27s interval algebra

We introduce a new subclass of Allen\u27s interval algebra we call "ORD-Horn subclass", which is a strict superset of the "pointisable subclass". We prove that reasoning in the ORD-Horn subclass is a polynomial-time problem and show that the path-consistency method is sufficient for deciding satisfiability. Further, using an extensive machine-generated case analysis, we show that the ORD-Horn subclass is a maximal tractable subclass of the full algebra (assuming P neq NP). In fact, it is the unique greatest tractable subclass amongst the subclasses that contain all basic relations