Mapping between the OBO and OWL ontology languages

Syed Hamid Tirmizi, Juan Sequeda, and Daniel P. Miranker are with the Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA -- Stuart Aitken is with the Artificial Intelligence Applications Institute, The University of Edinburgh, Edinburgh EH8 9LE, UK and the Informatics Life-Sciences Institute, The University of Edinburgh, Edinburgh EH8 9LE, UK -- Dilvan A. Moreira is with the Department of Computer Science, Mathematics and Computing Institute, University of São Paulo, São Carlos, São Paulo, Brazil -- Chris Mungall is with the Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA -- NIgam H. Shah is with the Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford, California 94305, USA -- Daniel P. Miranker is with the Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78701, USABackground: Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL. Results: We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Conclusions: Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.Computer SciencesInstitute for Cellular and Molecular [email protected]

An ontological investigation over human relations in linked data

The research presented in this article is motivated by the increasing importance of complex human relations in linked data, either extracted from social networks, or found in existing databases. The FOAF vocabulary, targeted in our research, plays a central role in those data, and is a model for lightweight ontologies largely used in linked data, such as the DBpedia ontology and schema-org. We provide an overview of FOAF and other approaches for describing human relations, followed by a detailed analysis and critique of the FOAF Relationship Vocabulary, the most important FOAF extension. We propose an explicit formal axiomatization of this vocabulary, and an ontological analysis concerning the properties used to describe human relationships. We analyze the distribution of human relations based on their epistemological status, and define an ontoepistemic meta-property as characteristic of some of these predicates. Our analysis is generalizable to semantic modeling of social networks. Additionally, the modeling patterns used in other relevant linked data vocabularies are analyzed for comparison

Functional requirements to shape generation in CAD

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, June 2003.Includes bibliographical references (p. 119-121).An outstanding issue in computer-aided design (CAD) is the creation of geometric shapes from the description of functional requirements (FRs). This thesis presents a method that can generate assembled shapes from the given FRs without human intervention. To achieve this goal, the design process follows a V-model of decomposition and integration based on axiomatic design. The V-model consists of three main sub-processes; (1) a top-down decomposition of FRs and design parameters (DPs), (2) mapping of DPs into geometric entities, and (3) a bottom-up integration of the geometric entities. A shape decomposition technique is used in the V-model to generate solid cells from the geometric entities in the CAD models based on FRs. These cells are stored and reused during the integration process. A set of cells mapped to an FR is called a functional geometric feature (FGF) to differentiate it from geometric features defined by only geometric characteristics. Each FGF has mating faces as its pre-defined interfaces. Links of FR-DP-FGF-INTERFACES and their hierarchies are made and stored in the database as fundamental units for automatic assembled shape generation. The retrieval of proper FGF from the database is performed by matching a query FR with stored FRs by a lexical search based on the frequency of words and the sequence of the words in the FR statements using a synonym checking system. The language-matching rate is calculated as a value of FRmetric between 0 and 1. A computer algorithm automatically combines and assembles the retrieved FGFs. Genetic algorithm (GA) searches for the best combination for matching interface types and generates assembly sequences.(cont.) From the highest-valued chromosome, the computer algorithm automatically assembles FGFs by coordinating, orienting, and positioning with reference to the given mating conditions and calculates geometric interface-ability to a value of INTERFACEmetric between 0 and 1. The higher the values of FRmetric and INTERFACEmetric, the better the generated design solution for the given FRs that must be satisfied. The process of top-down decomposition and bottom-up integration reduces the number of possible combinations of interfacing FGFs. Design matrix visually relates FRs to FGFs. The method presented in this thesis has demonstrated that a "functional CAD" can aid designers in generating conceptual design solutions from functional descriptions, in reusing existing CAD models, and in creating new designs.by Jinpyung Chung.Ph.D

An Approach for Automatic Generation of on-line Information Systems based on the Integration of Natural Language Processing and Adaptive Hypermedia Techniques

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid. Escuela Politécnica Superior, Departamento de ingeniería informática. Fecha de lectura: 29-05-200

Building Concept Representations from Reusable Components

Our goal is to build knowledge-based systems capable of answering a wide variety of questions, including questions that are unanticipated when the knowledge base is built. For systems to achieve this level of competence and generality, they require the ability to dynamically construct new concept representations, and to do so in response to the questions and tasks posed to them. Our approach to meeting this requirement is to build knowledge bases of generalized, representational components, and to develop methods for automatically composing components on demand. This work extends the normal inheritance approach used in frame-based systems, and imports ideas from several different areas of AI, in particular compositional modeling, terminological reasoning, and ontological engineering. The contribution of this work is a novel integration of these methods that improves the efficiency of building knowledge bases and the robustness of using them. Introduction Our goal is the construction o..