The Ontology for Biomedical Investigations.

Science.gov (United States)

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

Turning to Ontology in STS? Turning to STS through ‘Ontology’

NARCIS (Netherlands)

van Heur, B.; Leydesdorff, L.; Wyatt, S.

2012-01-01

We examine the evidence for the claim of an ‘ontological turn’ in science and technology studies (STS). Despite an increase in references to ‘ontology’ in STS since 1989, we show that there has not so much been an ontological turn as multiple discussions deploying the language of ontology,

Ontology and medical diagnosis.

Science.gov (United States)

Bertaud-Gounot, Valérie; Duvauferrier, Régis; Burgun, Anita

2012-03-01

Ontology and associated generic tools are appropriate for knowledge modeling and reasoning, but most of the time, disease definitions in existing description logic (DL) ontology are not sufficient to classify patient's characteristics under a particular disease because they do not formalize operational definitions of diseases (association of signs and symptoms=diagnostic criteria). The main objective of this study is to propose an ontological representation which takes into account the diagnostic criteria on which specific patient conditions may be classified under a specific disease. This method needs as a prerequisite a clear list of necessary and sufficient diagnostic criteria as defined for lots of diseases by learned societies. It does not include probability/uncertainty which Web Ontology Language (OWL 2.0) cannot handle. We illustrate it with spondyloarthritis (SpA). Ontology has been designed in Protégé 4.1 OWL-DL2.0. Several kinds of criteria were formalized: (1) mandatory criteria, (2) picking two criteria among several diagnostic criteria, (3) numeric criteria. Thirty real patient cases were successfully classified with the reasoner. This study shows that it is possible to represent operational definitions of diseases with OWL and successfully classify real patient cases. Representing diagnostic criteria as descriptive knowledge (instead of rules in Semantic Web Rule Language or Prolog) allows us to take advantage of tools already available for OWL. While we focused on Assessment of SpondyloArthritis international Society SpA criteria, we believe that many of the representation issues addressed here are relevant to using OWL-DL for operational definition of other diseases in ontology.

Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes

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Ontology engineering and knowledge modeling for the plant sciences is expected to contribute to the understanding of the basis of plant traits that determine phenotypic expression in a given environment. Several crop- or clade-specific plant trait ontologies have been developed to describe plant tr...

OpenKnowledge Deliverable 3.3.: A methodology for ontology matching quality evaluation

OpenAIRE

Yatskevich, Mikalai; Giunchiglia, Fausto; McNeill, Fiona; Shvaiko, Pavel

2007-01-01

This document presents an evaluation methodology for the assessment of quality results produced by ontology matchers. In particular, it discusses: (i) several standard quality measures used in the ontology matching evaluation, (ii) a methodology of how to build semiautomatically an incomplete reference alignment allowing for the assessment of quality results produced by ontology matchers and (iii) a preliminary empirical evaluation of the OpenKnowledge ontology matching component.

Protein Annotation from Protein Interaction Networks and Gene Ontology

OpenAIRE

Nguyen, Cao D.; Gardiner, Katheleen J.; Cios, Krzysztof J.

2011-01-01

We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precis...

Physical properties of biological entities: an introduction to the ontology of physics for biology.

Directory of Open Access Journals (Sweden)

Daniel L Cook

Full Text Available As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB, a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.

Physical properties of biological entities: an introduction to the ontology of physics for biology.

Science.gov (United States)

Cook, Daniel L; Bookstein, Fred L; Gennari, John H

2011-01-01

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. © 2011 Cook et al.

Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

International Nuclear Information System (INIS)

Gyurjyan, Vardan; Abbott, D.; Heyes, G.; Jastrzembski, E.; Moffit, B.; Timmer, C.; Wolin, E.

2009-01-01

In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

A UML profile for the OBO relation ontology

Science.gov (United States)

2012-01-01

intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology. PMID:23095840

Ontology Update in the Cognitive Model of Ontology Learning

Directory of Open Access Journals (Sweden)

Zhang De-Hai

2016-01-01

Full Text Available Ontology has been used in many hot-spot fields, but most ontology construction methods are semiautomatic, and the construction process of ontology is still a tedious and painstaking task. In this paper, a kind of cognitive models is presented for ontology learning which can simulate human being’s learning from world. In this model, the cognitive strategies are applied with the constrained axioms. Ontology update is a key step when the new knowledge adds into the existing ontology and conflict with old knowledge in the process of ontology learning. This proposal designs and validates the method of ontology update based on the axiomatic cognitive model, which include the ontology update postulates, axioms and operations of the learning model. It is proved that these operators subject to the established axiom system.

Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Directory of Open Access Journals (Sweden)

Nicola Mulder

2016-06-01

The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.

Unintended consequences of existential quantifications in biomedical ontologies

Directory of Open Access Journals (Sweden)

Boeker Martin

2011-11-01

Full Text Available Abstract Background The Open Biomedical Ontologies (OBO Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL, which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors. Results We analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom, from which we examined a random sample of 2,836 clauses. According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78. We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07. We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations. Conclusions The current OWL releases of OBO Foundry (and Foundry candidate ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.

Model Driven Engineering with Ontology Technologies

Science.gov (United States)

Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

Formal Ontologies and Uncertainty. In Geographical Knowledge

Directory of Open Access Journals (Sweden)

Matteo Caglioni

2014-05-01

Full Text Available Formal ontologies have proved to be a very useful tool to manage interoperability among data, systems and knowledge. In this paper we will show how formal ontologies can evolve from a crisp, deterministic framework (ontologies of hard knowledge to new probabilistic, fuzzy or possibilistic frameworks (ontologies of soft knowledge. This can considerably enlarge the application potential of formal ontologies in geographic analysis and planning, where soft knowledge is intrinsically linked to the complexity of the phenomena under study.  The paper briefly presents these new uncertainty-based formal ontologies. It then highlights how ontologies are formal tools to define both concepts and relations among concepts. An example from the domain of urban geography finally shows how the cause-to-effect relation between household preferences and urban sprawl can be encoded within a crisp, a probabilistic and a possibilistic ontology, respectively. The ontology formalism will also determine the kind of reasoning that can be developed from available knowledge. Uncertain ontologies can be seen as the preliminary phase of more complex uncertainty-based models. The advantages of moving to uncertainty-based models is evident: whether it is in the analysis of geographic space or in decision support for planning, reasoning on geographic space is almost always reasoning with uncertain knowledge of geographic phenomena.

VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

Science.gov (United States)

Khazai, Bijan; Kunz-Plapp, Tina; Büscher, Christian; Wegner, Antje

2014-05-01

The concept of vulnerability, as well as its implementation in vulnerability assessments, is used in various disciplines and contexts ranging from disaster management and reduction to ecology, public health or climate change and adaptation, and a corresponding multitude of ideas about how to conceptualize and measure vulnerability exists. Three decades of research in vulnerability have generated a complex and growing body of knowledge that challenges newcomers, practitioners and even experienced researchers. To provide a structured representation of the knowledge field "vulnerability assessment", we have set up an ontology-based semantic wiki for reviewing and representing vulnerability assessments: VuWiki, www.vuwiki.org. Based on a survey of 55 vulnerability assessment studies, we first developed an ontology as an explicit reference system for describing vulnerability assessments. We developed the ontology in a theoretically controlled manner based on general systems theory and guided by principles for ontology development in the field of earth and environment (Raskin and Pan 2005). Four key questions form the first level "branches" or categories of the developed ontology: (1) Vulnerability of what? (2) Vulnerability to what? (3) What reference framework was used in the vulnerability assessment?, and (4) What methodological approach was used in the vulnerability assessment? These questions correspond to the basic, abstract structure of the knowledge domain of vulnerability assessments and have been deduced from theories and concepts of various disciplines. The ontology was then implemented in a semantic wiki which allows for the classification and annotation of vulnerability assessments. As a semantic wiki, VuWiki does not aim at "synthesizing" a holistic and overarching model of vulnerability. Instead, it provides both scientists and practitioners with a uniform ontology as a reference system and offers easy and structured access to the knowledge field of

Ontological foundations for evolutionary economics: A Darwinian social ontology

NARCIS (Netherlands)

Stoelhorst, J.W.

2008-01-01

The purpose of this paper is to further the project of generalized Darwinism by developing a social ontology on the basis of a combined commitment to ontological continuity and ontological commonality. Three issues that are central to the development of a social ontology are addressed: (1) the

Best behaviour? Ontologies and the formal description of animal behaviour.

Science.gov (United States)

Gkoutos, Georgios V; Hoehndorf, Robert; Tsaprouni, Loukia; Schofield, Paul N

2015-10-01

The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain.

NanoParticle Ontology for Cancer Nanotechnology Research

Science.gov (United States)

Thomas, Dennis G.; Pappu, Rohit V.; Baker, Nathan A.

2010-01-01

Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO. PMID:20211274

The Cognitive Paradigm Ontology: Design and Application

Science.gov (United States)

Laird, Angela R.

2013-01-01

We present the basic structure of the Cognitive Paradigm Ontology (CogPO) for human behavioral experiments. While the experimental psychology and cognitive neuroscience literature may refer to certain behavioral tasks by name (e.g., the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. Drawing from the taxonomy developed and used by the BrainMap project (www.brainmap.org) for almost two decades to describe key components of published functional imaging results, we have developed an ontology capable of representing certain characteristics of the cognitive paradigms used in the fMRI and PET literature. The Cognitive Paradigm Ontology is being developed to be compliant with the Basic Formal Ontology (BFO), and to harmonize where possible with larger ontologies such as RadLex, NeuroLex, or the Ontology of Biomedical Investigations (OBI). The key components of CogPO include the representation of experimental conditions focused on the stimuli presented, the instructions given, and the responses requested. The use of alternate and even competitive terminologies can often impede scientific discoveries. Categorization of paradigms according to stimulus, response, and instruction has been shown to allow advanced data retrieval techniques by searching for similarities and contrasts across multiple paradigm levels. The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community. PMID:21643732

A unified anatomy ontology of the vertebrate skeletal system.

Directory of Open Access Journals (Sweden)

Wasila M Dahdul

Full Text Available The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO, to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish and multispecies (teleost, amphibian vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages, and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO, Gene Ontology (GO, Uberon, and Cell Ontology (CL, and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A unified anatomy ontology of the vertebrate skeletal system.

Science.gov (United States)

Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Science.gov (United States)

Dahdul, Wasila M.; Balhoff, James P.; Blackburn, David C.; Diehl, Alexander D.; Haendel, Melissa A.; Hall, Brian K.; Lapp, Hilmar; Lundberg, John G.; Mungall, Christopher J.; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E.; Vickaryous, Matthew K.; Westerfield, Monte; Mabee, Paula M.

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

Where to Publish and Find Ontologies? A Survey of Ontology Libraries

Science.gov (United States)

d'Aquin, Mathieu; Noy, Natalya F.

2011-01-01

One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to “talk” to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing—and surprisingly diverse—landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries a ects their features, content, and potential exploitation in applications. From reviewing eleven ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address. PMID:22408576

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

Science.gov (United States)

Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

2017-06-07

Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

The MMI Device Ontology: Enabling Sensor Integration

Science.gov (United States)

Rueda, C.; Galbraith, N.; Morris, R. A.; Bermudez, L. E.; Graybeal, J.; Arko, R. A.; Mmi Device Ontology Working Group

2010-12-01

The Marine Metadata Interoperability (MMI) project has developed an ontology for devices to describe sensors and sensor networks. This ontology is implemented in the W3C Web Ontology Language (OWL) and provides an extensible conceptual model and controlled vocabularies for describing heterogeneous instrument types, with different data characteristics, and their attributes. It can help users populate metadata records for sensors; associate devices with their platforms, deployments, measurement capabilities and restrictions; aid in discovery of sensor data, both historic and real-time; and improve the interoperability of observational oceanographic data sets. We developed the MMI Device Ontology following a community-based approach. By building on and integrating other models and ontologies from related disciplines, we sought to facilitate semantic interoperability while avoiding duplication. Key concepts and insights from various communities, including the Open Geospatial Consortium (eg., SensorML and Observations and Measurements specifications), Semantic Web for Earth and Environmental Terminology (SWEET), and W3C Semantic Sensor Network Incubator Group, have significantly enriched the development of the ontology. Individuals ranging from instrument designers, science data producers and consumers to ontology specialists and other technologists contributed to the work. Applications of the MMI Device Ontology are underway for several community use cases. These include vessel-mounted multibeam mapping sonars for the Rolling Deck to Repository (R2R) program and description of diverse instruments on deepwater Ocean Reference Stations for the OceanSITES program. These trials involve creation of records completely describing instruments, either by individual instances or by manufacturer and model. Individual terms in the MMI Device Ontology can be referenced with their corresponding Uniform Resource Identifiers (URIs) in sensor-related metadata specifications (e

Best behaviour? Ontologies and the formal description of animal behaviour

KAUST Repository

Gkoutos, Georgios V.

2015-07-28

The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain. © 2015 Springer Science+Business Media New York

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Science.gov (United States)

Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

2011-07-01

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

Semi-automated ontology generation and evolution

Science.gov (United States)

Stirtzinger, Anthony P.; Anken, Craig S.

2009-05-01

Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural

Quantum ontologies

International Nuclear Information System (INIS)

Stapp, H.P.

1988-12-01

Quantum ontologies are conceptions of the constitution of the universe that are compatible with quantum theory. The ontological orientation is contrasted to the pragmatic orientation of science, and reasons are given for considering quantum ontologies both within science, and in broader contexts. The principal quantum ontologies are described and evaluated. Invited paper at conference: Bell's Theorem, Quantum Theory, and Conceptions of the Universe, George Mason University, October 20-21, 1988. 16 refs

Use artificial neural network to align biological ontologies.

Science.gov (United States)

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

The Proteasix Ontology.

Science.gov (United States)

Arguello Casteleiro, Mercedes; Klein, Julie; Stevens, Robert

2016-06-04

The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone.

Integrating phenotype ontologies with PhenomeNET

KAUST Repository

Rodriguez-Garcia, Miguel Angel

2017-12-19

Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

Process attributes in bio-ontologies

Directory of Open Access Journals (Sweden)

Andrade André Q

2012-08-01

Full Text Available Abstract Background Biomedical processes can provide essential information about the (mal- functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency. Results We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity. Conclusions We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity.

Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

NARCIS (Netherlands)

Breukers, J.A.P.J.; Hoekstra, R.J.

2004-01-01

For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

Protein annotation from protein interaction networks and Gene Ontology.

Science.gov (United States)

Nguyen, Cao D; Gardiner, Katheleen J; Cios, Krzysztof J

2011-10-01

We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precision and 60% recall versus 45% and 26% for Majority and 24% and 61% for χ²-statistics, respectively. Copyright © 2011 Elsevier Inc. All rights reserved.

SPONGY (SPam ONtoloGY): email classification using two-level dynamic ontology.

Science.gov (United States)

Youn, Seongwook

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

SPONGY (SPam ONtoloGY: Email Classification Using Two-Level Dynamic Ontology

Directory of Open Access Journals (Sweden)

Seongwook Youn

2014-01-01

Full Text Available Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user’s background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1 to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2 to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

SPONGY (SPam ONtoloGY): Email Classification Using Two-Level Dynamic Ontology

Science.gov (United States)

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance. PMID:25254240

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Science.gov (United States)

Diehl, Alexander D; Meehan, Terrence F; Bradford, Yvonne M; Brush, Matthew H; Dahdul, Wasila M; Dougall, David S; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E; Vasilevsky, Nicole A; Haendel, Melissa A; Blake, Judith A; Mungall, Christopher J

2016-07-04

The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the

Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.

Science.gov (United States)

Seddig-Raufie, Djamila; Jansen, Ludger; Schober, Daniel; Boeker, Martin; Grewe, Niels; Schulz, Stefan

2012-09-21

Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as

Ontology Extraction Tools: An Empirical Study with Educators

Science.gov (United States)

Hatala, M.; Gasevic, D.; Siadaty, M.; Jovanovic, J.; Torniai, C.

2012-01-01

Recent research in Technology-Enhanced Learning (TEL) demonstrated several important benefits that semantic technologies can bring to the TEL domain. An underlying assumption for most of these research efforts is the existence of a domain ontology. The second unspoken assumption follows that educators will build domain ontologies for their…

TrhOnt: building an ontology to assist rehabilitation processes.

Science.gov (United States)

Berges, Idoia; Antón, David; Bermúdez, Jesús; Goñi, Alfredo; Illarramendi, Arantza

2016-10-04

One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TRHONT, an application ontology that can assist physiotherapists in the management of the patients' evolution via reasoning supported by semantic technology. The ontology was developed following the NeOn Methodology. It integrates knowledge from ontological (e.g. FMA ontology) and non-ontological resources (e.g. a database of movements, exercises and treatment protocols) as well as additional physiotherapy-related knowledge. We demonstrate how the ontology fulfills the purpose of providing a reference model for the representation of the physiotherapy-related information that is needed for the whole physiotherapy treatment of patients, since they step for the first time into the physiotherapist's office, until they are discharged. More specifically, we present the results for each of the intended uses of the ontology listed in the document that specifies its requirements, and show how TRHONT can answer the competency questions defined within that document. Moreover, we detail the main steps of the process followed to build the TRHONT ontology in order to facilitate its reproducibility in a similar context. Finally, we show an evaluation of the ontology from different perspectives. TRHONT has achieved the purpose of allowing for a reasoning process that changes over time according to the patient's state and performance.

Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

Science.gov (United States)

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

2014-01-01

to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

Using concept similarity in cross ontology for adaptive e-Learning systems

Directory of Open Access Journals (Sweden)

B. Saleena

2015-01-01

Full Text Available e-Learning is one of the most preferred media of learning by the learners. The learners search the web to gather knowledge about a particular topic from the information in the repositories. Retrieval of relevant materials from a domain can be easily implemented if the information is organized and related in some way. Ontologies are a key concept that helps us to relate information for providing the more relevant lessons to the learner. This paper proposes an adaptive e-Learning system, which generates a user specific e-Learning content by comparing the concepts with more than one system using similarity measures. A cross ontology measure is defined, which consists of fuzzy domain ontology as the primary ontology and the domain expert’s ontology as the secondary ontology, for the comparison process. A personalized document is provided to the user with a user profile, which includes the data obtained from the processing of the proposed method under a User score, which is obtained through the user evaluation. The results of the proposed e-Learning system under the designed cross ontology similarity measure show a significant increase in performance and accuracy under different conditions. The assessment of the comparative analysis, showed the difference in performance of our proposed method over other methods. Based on the assessment results it is proved that the proposed approach is effective over other methods.

SSDOnt: An Ontology for Representing Single-Subject Design Studies.

Science.gov (United States)

Berges, Idoia; Bermúdez, Jesus; Illarramendi, Arantza

2018-02-01

Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate granularity for looking for information about them. Therefore, the search for those study designs relies heavily on a syntactical search on the abstract, keywords or full text of the publications about the study, which entails some limitations. To present SSDOnt, a specific purpose ontology for describing and annotating single-subject design studies, so that complex questions can be asked about them afterwards. The ontology was developed following the NeOn methodology. Once the requirements of the ontology were defined, a formal model was described in a Description Logic and later implemented in the ontology language OWL 2 DL. We show how the ontology provides a reference model with a suitable terminology for the annotation and searching of single-subject design studies and their main components, such as the phases, the intervention types, the outcomes and the results. Some mappings with terms of related ontologies have been established. We show as proof-of-concept that classes in the ontology can be easily extended to annotate more precise information about specific interventions and outcomes such as those related to autism. Moreover, we provide examples of some types of queries that can be posed to the ontology. SSDOnt has achieved the purpose of covering the descriptions of the domain of single-subject research studies. Schattauer GmbH.

Using a Foundational Ontology for Reengineering a Software Enterprise Ontology

Science.gov (United States)

Perini Barcellos, Monalessa; de Almeida Falbo, Ricardo

The knowledge about software organizations is considerably relevant to software engineers. The use of a common vocabulary for representing the useful knowledge about software organizations involved in software projects is important for several reasons, such as to support knowledge reuse and to allow communication and interoperability between tools. Domain ontologies can be used to define a common vocabulary for sharing and reuse of knowledge about some domain. Foundational ontologies can be used for evaluating and re-designing domain ontologies, giving to these real-world semantics. This paper presents an evaluating of a Software Enterprise Ontology that was reengineered using the Unified Foundation Ontology (UFO) as basis.

Interoperability between phenotype and anatomy ontologies.

Science.gov (United States)

Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

2010-12-15

Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

Invariance as a Tool for Ontology of Information

Directory of Open Access Journals (Sweden)

Marcin J. Schroeder

2016-03-01

Full Text Available Attempts to answer questions regarding the ontological status of information are frequently based on the assumption that information should be placed within an already existing framework of concepts of established ontological statuses related to science, in particular to physics. However, many concepts of physics have undetermined or questionable ontological foundations. We can look for a solution in the recognition of the fundamental role of invariance with respect to a change of reference frame and to other transformations as a criterion for objective existence. The importance of invariance (symmetry as a criterion for a primary ontological status can be identified in the methodology of physics from its beginnings in the work of Galileo, to modern classifications of elementary particles. Thus, the study of the invariance of the theoretical description of information is proposed as the first step towards ontology of information. With the exception of only a few works among publications which set the paradigm of information studies, the issues of invariance were neglected. Orthodox analysis of information lacks conceptual framework for the study of invariance. The present paper shows how invariance can be formalized for the definition of information and, accompanying it, mathematical formalism proposed by the author in his earlier publications.

Building a Chemical Ontology using Methontology and the Ontology Design Environment

OpenAIRE

Fernández López, Mariano; Gómez-Pérez, A.; Pazos Sierra, Alejandro; Pazos Sierra, Juan

1999-01-01

METHONTOLOGY PROVIDES GUIDELINES FOR SPECIFYING ONTOLOGIES AT THE KNOWLEDGE LEVEL, AS A SPECIFICATION OF A CONCEPTUALIZATION. ODE ENABLES ONTOLOGY CONSTRUCTION, COVERING THE ENTIRE LIFE CYCLE AND AUTOMATICALLY IMPLEMENTING ONTOLOGIES

Automatic Tamil lyric generation based on ontological interpretation ...

Indian Academy of Sciences (India)

In this work, we use an ontology to determine the semantic information from ... Hence, to study the context-based lyric generation process, we referred to ...... Mann C W and Moore A J 1981 Computer Generation of Multiparagraph English text.

Development of Ontology and 3D Software for the Diseases of Spine

Directory of Open Access Journals (Sweden)

Seungbock Lee

2015-01-01

Full Text Available KISTI is carrying out an e-Spine project for spinal diseases to prepare for the aged society, so-called NAP. The purpose of the study is to build a spine ontology that represents the anatomical structure and disease information which is compatible with simulation model of KISTI. The final use of the ontology includes diagnosis of diseases and setting treatment directions by the clinicians. The ontology was represented using 3D software. Twenty diseases were selected to be represented after discussions with a spine specialist. Several ontology studies were reviewed, reference books were selected for each disease and were organized in MS Excel. All the contents were then reviewed by the specialists. Altova SemanticWorks and Protégé were used to code spine ontology with OWL Full model. Links to the images from KISTI and sample images of diseases were included in the ontology. The OWL ontology was also reviewed by the specialists again with Protégé. We represented unidirectional ontology from anatomical structure to disease, images, and treatment. The ontology was human understandable. It would be useful for the education of medical students or residents studying diseases of spine. But in order for the computer to understand the ontology, a new model with OWL DL or Lite is needed.

Towards Process-Ontology: A Critical Study of Substance-Ontological Premises

DEFF Research Database (Denmark)

Seibt, Johanna

The thesis proposes therapeutic revision of fundamental assumptions in contemporary ontological thought. I show that non of the prevalent theories of objects, by virtue of certain implicit substance-ontological assumptions provides a viable account of the numerical, qualitative, and trans-tempora......-ontological presuppositions, I finally explore the result of rejecting all of them and sketch a scheme basic on dynamic masses which promises to yield coherent explanation of the ontological features of those complex processes that we commonly call objects....

COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

Science.gov (United States)

Cui, Licong

Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance

SUGOI: automated ontology interchangeability

CSIR Research Space (South Africa)

Khan, ZC

2015-04-01

Full Text Available A foundational ontology can solve interoperability issues among the domain ontologies aligned to it. However, several foundational ontologies have been developed, hence such interoperability issues exist among domain ontologies. The novel SUGOI tool...

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Science.gov (United States)

He, Yongqun; Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; Overton, James A; Ong, Edison

2018-01-12

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

The ontology of science teaching in the neoliberal era

Science.gov (United States)

Sharma, Ajay

2017-12-01

Because of ever stricter standards of accountability, science teachers are under an increasing and unrelenting pressure to demonstrate the effects of their teaching on student learning. Econometric perspectives of teacher quality have become normative in assessment of teachers' work for accountability purposes. These perspectives seek to normalize some key ontological assumptions about teachers and teaching, and thus play an important role in shaping our understanding of the work science teachers do as teachers in their classrooms. In this conceptual paper I examine the ontology of science teaching as embedded in econometric perspectives of teacher quality. Based on Foucault's articulation of neoliberalism as a discourse of governmentality in his `The Birth of Biopolitics' lectures, I suggest that this ontology corresponds well with the strong and substantivist ontology of work under neoliberalism, and thus could potentially be seen as reflection of the influence of neoliberal ideas in education. Implications of the mainstreaming of an ontology of teaching that is compatible with neoliberalism can be seen in increasing marketization of teaching, `teaching evangelism', and impoverished notions of learning and teaching. A shift of focus from teacher quality to quality of teaching and building conceptual models of teaching based on relational ontologies deserve to be explored as important steps in preserving critical and socially just conceptions of science teaching in neoliberal times.

Mining rare associations between biological ontologies.

Science.gov (United States)

Benites, Fernando; Simon, Svenja; Sapozhnikova, Elena

2014-01-01

The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

Mining rare associations between biological ontologies.

Directory of Open Access Journals (Sweden)

Fernando Benites

Full Text Available The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

Science.gov (United States)

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Practical ontologies for information professionals

CERN Document Server

AUTHOR|(CDS)2071712

2016-01-01

Practical Ontologies for Information Professionals provides an introduction to ontologies and their development, an essential tool for fighting back against information overload. The development of robust and widely used ontologies is an increasingly important tool in the fight against information overload. The publishing and sharing of explicit explanations for a wide variety of conceptualizations, in a machine readable format, has the power to both improve information retrieval and identify new knowledge. This new book provides an accessible introduction to the following: * What is an ontology? Defining the concept and why it is increasingly important to the information professional * Ontologies and the semantic web * Existing ontologies, such as SKOS, OWL, FOAF, schema.org, and the DBpedia Ontology * Adopting and building ontologies, showing how to avoid repetition of work and how to build a simple ontology with Protege * Interrogating semantic web ontologies * The future of ontologies and the role of the ...

Expert2OWL: A Methodology for Pattern-Based Ontology Development.

Science.gov (United States)

Tahar, Kais; Xu, Jie; Herre, Heinrich

2017-01-01

The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology. This method allows a close and effective collaboration between ontologists and domain experts. Essentially, this tool integrates Excel spreadsheets as part of a pattern-based ontology development and refinement process. Expert2OWL enables us to expedite the development process and modularize the resulting ontologies. We applied this method in the field of Chinese Herbal Medicine (CHM) and used Expert2OWL to automatically generate an accurate Chinese Herbology ontology (CHO). The expressivity of CHO was tested and evaluated using ontology query languages SPARQL and DL. CHO shows promising results and can generate answers to important scientific questions such as which Chinese herbal formulas contain which substances, which substances treat which diseases, and which ones are the most frequently used in CHM.

Product line based ontology reuse in context-aware e-business environment

DEFF Research Database (Denmark)

Zhang, Weishan; Kunz, Thomas

2006-01-01

Improving the reusability of ontology is recognized as increasingly important due to the prevalence of OWL research and applications. But there exists no convincing methodology and tool support in this direction yet. In this paper, we apply ideas from the research and practice with software product...... lines in order to explore this issue. The ontology is developed and managed according to the commonalities and variabilities underlying a specific problem domain. Meta-ontology is used in order to improve the reusability, evolve-ability and customizability of ontology. Another advantage is being able...... to generate needed ontology with the created meta-ontology implemented with XVCL (XML based Variant Configuration Language) technology. We demonstrate our product line based reuse approach with an example B2C application....

Ontology evolution in physics

OpenAIRE

Chan, Michael

2013-01-01

With the advent of reasoning problems in dynamic environments, there is an increasing need for automated reasoning systems to automatically adapt to unexpected changes in representations. In particular, the automation of the evolution of their ontologies needs to be enhanced without substantially sacrificing expressivity in the underlying representation. Revision of beliefs is not enough, as adding to or removing from beliefs does not change the underlying formal language. Gene...

Alignment of ICNP? 2.0 Ontology and a proposed INCP? Brazilian Ontology1

OpenAIRE

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; da N?brega, Maria Miriam Lima

2014-01-01

OBJECTIVE: to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology.METHOD: document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence...

Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Science.gov (United States)

Ochs, Christopher; He, Zhe; Zheng, Ling; Geller, James; Perl, Yehoshua; Hripcsak, George; Musen, Mark A

2016-06-01

An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology. Copyright © 2016 Elsevier Inc. All rights reserved.

Ontology-based Information Retrieval

DEFF Research Database (Denmark)

Styltsvig, Henrik Bulskov

In this thesis, we will present methods for introducing ontologies in information retrieval. The main hypothesis is that the inclusion of conceptual knowledge such as ontologies in the information retrieval process can contribute to the solution of major problems currently found in information...... retrieval. This utilization of ontologies has a number of challenges. Our focus is on the use of similarity measures derived from the knowledge about relations between concepts in ontologies, the recognition of semantic information in texts and the mapping of this knowledge into the ontologies in use......, as well as how to fuse together the ideas of ontological similarity and ontological indexing into a realistic information retrieval scenario. To achieve the recognition of semantic knowledge in a text, shallow natural language processing is used during indexing that reveals knowledge to the level of noun...

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

Science.gov (United States)

2013-01-01

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

An ontological analysis of the electrocardiogram - DOI: 10.3395/reciis.v3i1.242en

Directory of Open Access Journals (Sweden)

Bernardo Gonçalves

2009-04-01

Full Text Available Bioinformatics has been a fertile field for the application of the discipline of formal ontology. The principled representation of biomedical entities has increasingly supported biological research, with direct benefits ranging from the reformulation of medical terminologies to the introduction of new perspectives for enhanced models of Electronic Health Records (EHR. This paper introduces an application-independent ontological analysis of the electrocardiogram (ECG grounded in the Unified Foundational Ontology. With the objective of investigating the phenomena underlying this cardiological exam, we deal with the sub-domains of human heart electrophysiology and anatomy. We then outline an ECG Ontology built upon the OBO Relation Ontology. In addition, the domain ontology sketched here takes inspiration both in the Foundational Model of Anatomy and in the Ontology of Functions proposed under the auspices of the General Formal Ontology (GFO research program.

How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.

Science.gov (United States)

Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A; Noy, Natalya F

2013-05-01

Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product . In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches.

How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects

Science.gov (United States)

Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A.; Noy, Natalya F.

2013-01-01

Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches. PMID:24311994

Biomedical ontologies: toward scientific debate.

Science.gov (United States)

Maojo, V; Crespo, J; García-Remesal, M; de la Iglesia, D; Perez-Rey, D; Kulikowski, C

2011-01-01

Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective. We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies. We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies. Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

Exponential complexity and ontological theories of quantum mechanics

International Nuclear Information System (INIS)

Montina, A.

2008-01-01

Ontological theories of quantum mechanics describe a single system by means of well-defined classical variables and attribute the quantum uncertainties to our ignorance about the underlying reality represented by these variables. We consider the general class of ontological theories describing a quantum system by a set of variables with Markovian (either deterministic or stochastic) evolution. We provide proof that the number of continuous variables cannot be smaller than 2N-2, N being the Hilbert-space dimension. Thus, any ontological Markovian theory of quantum mechanics requires a number of variables which grows exponentially with the physical size. This result is relevant also in the framework of quantum Monte Carlo methods

For reflexivity as an epistemic criterion of ontological coherence and virtuous social theorizing.

Science.gov (United States)

Bouzanis, Christoforos

2017-12-01

This article offers an approach that combines, on the one hand, the philosophical notion of reflexivity, which is related to the ideas of self-reference and paradox, and, on the other hand, the sociological discussion of epistemic reflexivity as a problem of coherence, which was mainly initiated by certain branches of ethnomethodology and social constructionism. This combinatory approach argues for reflexivity as an epistemic criterion of ontological coherence , which suggests that social ontologies should account for the possibility of self-reflective subjectivity - for otherwise they result in a paradoxical conclusion according to which a social scientist reflects on her or his ontological commitments even though these commitments deny her or him the capacity for self-reflection . This analysis presupposes that all human sciences are categorically premised on social ontologies; and it argues for an analytical distinction between self-reflection, which refers to the agential capacity for reflecting on one's own commitments, and the epistemic criterion of reflexivity hereby proposed. These two analytically distinct though interdependent socio-theoretical concepts are frequently conflated in the literature; thus, this article also aims at a 'clearing of the ground' that can be of categorical use to the human sciences.

Data mining for ontology development.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.; Strasburg, Jana (Pacific Northwest National Laboratory, Richland, WA); Stampf, David (Brookhaven National Laboratory, Upton, NY); Neymotin,Lev (Brookhaven National Laboratory, Upton, NY); Czajkowski, Carl (Brookhaven National Laboratory, Upton, NY); Shine, Eugene (Savannah River National Laboratory, Aiken, SC); Bollinger, James (Savannah River National Laboratory, Aiken, SC); Ghosh, Vinita (Brookhaven National Laboratory, Upton, NY); Sorokine, Alexandre (Oak Ridge National Laboratory, Oak Ridge, TN); Ferrell, Regina (Oak Ridge National Laboratory, Oak Ridge, TN); Ward, Richard (Oak Ridge National Laboratory, Oak Ridge, TN); Schoenwald, David Alan

2010-06-01

A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

Feasibility of automated foundational ontology interchangeability

CSIR Research Space (South Africa)

Khan, ZC

2014-11-01

Full Text Available the Source Domain Ontology (sOd), with the domain knowledge com- ponent of the source ontology, the Source Foundational Ontology (sOf ) that is the foundational ontology component of the source ontology that is to be interchanged, and any equivalence... or subsumption mappings between enti- ties in sOd and sOf . – The Target Ontology (tO) which has been interchanged, which comprises the Target Domain Ontology (tOd), with the domain knowledge component of the target ontology, and the Target Foundational Ontology...

Extrametodical truth and ontology of the praxis: The mediator rationality of the phronesis

Directory of Open Access Journals (Sweden)

Gaetano Chiurazzi

2016-05-01

Full Text Available Gadamer’s vindication of the extra-methodical feature of truth in the human sciences put forward in Truth and Method does not mean a mere refusal of method: rather, it arises from the awareness that there are truths which are not reducible to the conditions of repeatability and commensurability set up by methodical thinking. In fact, the truths of the human sciences refer to the ontological dimension of the contingent and the accidental, i.e. to the dimension of the historical. In this essay I aim at highlighting this ontological dimension, which for Aristotle is eminently that of the praxis and of human action. I will show that such an ontology is a consequence of the logical and ontological discussions which crisscrossed Greek thought after the discovery of the incommensurable magnitudes. The ontology of praxis is an ontology which takes into account the “irrationality” represented by the contingent, the accidental, to which a new form of rationality corresponds: that of phrónesis. Phrónesis is in fact not a commensurative but a mediative rationality

DMTO: a realistic ontology for standard diabetes mellitus treatment.

Science.gov (United States)

El-Sappagh, Shaker; Kwak, Daehan; Ali, Farman; Kwak, Kyung-Sup

2018-02-06

Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accuracy. The most important component of any CDSS is its knowledge base. This knowledge base can be formulated using ontologies. The formal description logic of ontology supports the inference of hidden knowledge. Building a complete, coherent, consistent, interoperable, and sharable ontology is a challenge. This paper introduces the first version of the newly constructed Diabetes Mellitus Treatment Ontology (DMTO) as a basis for shared-semantics, domain-specific, standard, machine-readable, and interoperable knowledge relevant to T2DM treatment. It is a comprehensive ontology and provides the highest coverage and the most complete picture of coded knowledge about T2DM patients' current conditions, previous profiles, and T2DM-related aspects, including complications, symptoms, lab tests, interactions, treatment plan (TP) frameworks, and glucose-related diseases and medications. It adheres to the design principles recommended by the Open Biomedical Ontologies Foundry and is based on ontological realism that follows the principles of the Basic Formal Ontology and the Ontology for General Medical Science. DMTO is implemented under Protégé 5.0 in Web Ontology Language (OWL) 2 format and is publicly available through the National Center for Biomedical Ontology's BioPortal at http://bioportal.bioontology.org/ontologies/DMTO . The current version of DMTO includes more than 10,700 classes, 277 relations, 39,425 annotations, 214 semantic rules, and 62,974 axioms. We provide proof of concept for this approach to modeling TPs. The ontology is able to collect and analyze most features of T2DM as well as customize chronic TPs with the most appropriate drugs, foods, and physical exercises. DMTO is ready to be used as a knowledge base for

Modeling issues & choices in the data mining optimization ontology

CSIR Research Space (South Africa)

Keet, CM

2013-05-01

Full Text Available We describe the Data Mining Optimization Ontology (DMOP), which was developed to support informed decision-making at various choice points of the knowledge discovery (KD) process. It can be used as a reference by data miners, but its primary purpose...

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

OpenAIRE

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

2007-01-01

Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to r...

Ontology authoring with Forza

CSIR Research Space (South Africa)

Keet, CM

2014-11-01

Full Text Available Generic, reusable ontology elements, such as a foundational ontology's categories and part-whole relations, are essential for good and interoperable knowledge representation. Ontology developers, which include domain experts and novices, face...

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

Science.gov (United States)

Harrow, Ian; Jiménez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James; Waaler, Arild

2017-12-02

The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

Semantator: annotating clinical narratives with semantic web ontologies.

Science.gov (United States)

Song, Dezhao; Chute, Christopher G; Tao, Cui

2012-01-01

To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator.

A broken symmetry ontology: Quantum mechanics as a broken symmetry

International Nuclear Information System (INIS)

Buschmann, J.E.

1988-01-01

The author proposes a new broken symmetry ontology to be used to analyze the quantum domain. This ontology is motivated and grounded in a critical epistemological analysis, and an analysis of the basic role of symmetry in physics. Concurrently, he is led to consider nonheterogeneous systems, whose logical state space contains equivalence relations not associated with the causal relation. This allows him to find a generalized principle of symmetry and a generalized symmetry-conservation formalisms. In particular, he clarifies the role of Noether's theorem in field theory. He shows how a broken symmetry ontology already operates in a description of the weak interactions. Finally, by showing how a broken symmetry ontology operates in the quantum domain, he accounts for the interpretational problem and the essential incompleteness of quantum mechanics. He proposes that the broken symmetry underlying this ontological domain is broken dilation invariance

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-04

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Science.gov (United States)

Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; He, Yongqun

2015-01-01

It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development. With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following

Evolving BioAssay Ontology (BAO): modularization, integration and applications.

Science.gov (United States)

Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

2014-01-01

The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

Ontologies vs. Classification Systems

DEFF Research Database (Denmark)

Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

2009-01-01

What is an ontology compared to a classification system? Is a taxonomy a kind of classification system or a kind of ontology? These are questions that we meet when working with people from industry and public authorities, who need methods and tools for concept clarification, for developing meta...... data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...... classification systems and meta data taxonomies, should be based on ontologies....

Ontology-based semantic information technology for safeguards: opportunities and challenges

International Nuclear Information System (INIS)

McDaniel, Michael

2014-01-01

The challenge of efficiently handling large volumes of heterogeneous information is a barrier to more effective safeguards implementation. With the emergence of new technologies for generating and collecting information this is an issue common to many industries and problem domains. Several diverse information‑intensive fields are developing and adopting ontology‑based semantic information technology solutions to address issues of information integration, federation and interoperability. Ontology, in this context, refers to the formal specification of the content, structure, and logic of knowledge within a domain of interest. Ontology‑based semantic information technologies have the potential to impact nearly every level of safeguards implementation, from information collection and integration, to personnel training and knowledge retention, to planning and analysis. However, substantial challenges remain before the full benefits of semantic technology can be realized. Perhaps the most significant challenge is the development of a nuclear fuel cycle ontology. For safeguards, existing knowledge resources such as the IAEA’s Physical Model and established upper level ontologies can be used as starting points for ontology development, but a concerted effort must be taken by the safeguards community for such an activity to be successful. This paper provides a brief background of ontologies and semantic information technology, demonstrates how these technologies are used in other areas, offers examples of how ontologies can be applied to safeguards, and discusses the challenges of developing and implementing this technology as well as a possible path forward.

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

Science.gov (United States)

Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

2017-10-01

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

An open annotation ontology for science on web 3.0.

Science.gov (United States)

Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

2011-05-17

There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for

Merged ontology for engineering design: Contrasting empirical and theoretical approaches to develop engineering ontologies

DEFF Research Database (Denmark)

Ahmed, Saeema; Storga, M

2009-01-01

to developing the ontology engineering design integrated taxonomies (EDIT) with a theoretical approach in which concepts and relations are elicited from engineering design theories ontology (DO) The limitations and advantages of each approach are discussed. The research methodology adopted is to map......This paper presents a comparison of two previous and separate efforts to develop an ontology in the engineering design domain, together with an ontology proposal from which ontologies for a specific application may be derived. The research contrasts an empirical, user-centered approach...

Ontological Planning

Directory of Open Access Journals (Sweden)

Ahmet Alkan

2017-12-01

• Is it possible to redefine ontology within the hierarchical structure of planning? We are going to seek answers to some of these questions within the limited scope of this paper and we are going to offer the rest for discussion by just asking them. In light of these assessments, drawing attention, based on ontological knowledge relying on the wholeness of universe, to the question, on macro level planning, of whether or not the ontological realities of man, energy and movements of thinking can provide macro data for planning on a universal level as important factors affecting mankind will be one of the limited objectives of the paper.

Ontological Analysis of Integrated Process Models: testing hypotheses

Directory of Open Access Journals (Sweden)

Michael Rosemann

2001-11-01

Full Text Available Integrated process modeling is achieving prominence in helping to document and manage business administration and IT processes in organizations. The ARIS framework is a popular example for a framework of integrated process modeling not least because it underlies the 800 or more reference models embedded in the world's most popular ERP package, SAP R/3. This paper demonstrates the usefulness of the Bunge-Wand-Weber (BWW representation model for evaluating modeling grammars such as those constituting ARIS. It reports some initial insights gained from pilot testing Green and Rosemann's (2000 evaluative propositions. Even when considering all five views of ARIS, modelers have problems representing business rules, the scope and boundary of systems, and decomposing models. However, even though it is completely ontologically redundant, users still find the function view useful in modeling.

Towards Agile Ontology Maintenance

Science.gov (United States)

Luczak-Rösch, Markus

Ontologies are an appropriate means to represent knowledge on the Web. Research on ontology engineering reached practices for an integrative lifecycle support. However, a broader success of ontologies in Web-based information systems remains unreached while the more lightweight semantic approaches are rather successful. We assume, paired with the emerging trend of services and microservices on the Web, new dynamic scenarios gain momentum in which a shared knowledge base is made available to several dynamically changing services with disparate requirements. Our work envisions a step towards such a dynamic scenario in which an ontology adapts to the requirements of the accessing services and applications as well as the user's needs in an agile way and reduces the experts' involvement in ontology maintenance processes.

Ontology-based indirect interaction of mobile robots for joint task solving: a scenario for obstacle overcoming

Directory of Open Access Journals (Sweden)

Petrov Mikhail

2017-01-01

Full Text Available This paper describes an ontology-based approach to interaction of users and mobile robots for joint task solving. The use of ontologies allows supporting semantic interoperability between robots. The ontologies store knowledge about the tasks to be performed, knowledge about the functionality of robots and the current situation factors like a robot location or busyness. Ontologies are published in a smart space which allows indirect interaction between participants. On the basis of the knowledge, a robot can define a task that is to be performed and get the current status of other robots. The paper presents a reference model of the approach to indirect interaction between mobile robots for joint task solving, an ontology model for the knowledge organization, and application of the presented approach for the scenario for obstacle overcoming.

Benchmarking ontologies: bigger or better?

Directory of Open Access Journals (Sweden)

Lixia Yao

2011-01-01

Full Text Available A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1 four of the most common medical ontologies with respect to a corpus of medical documents and (2 seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.

ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.

Science.gov (United States)

Malhotra, Ashutosh; Younesi, Erfan; Gündel, Michaela; Müller, Bernd; Heneka, Michael T; Hofmann-Apitius, Martin

2014-03-01

Biomedical ontologies offer the capability to structure and represent domain-specific knowledge semantically. Disease-specific ontologies can facilitate knowledge exchange across multiple disciplines, and ontology-driven mining approaches can generate great value for modeling disease mechanisms. However, in the case of neurodegenerative diseases such as Alzheimer's disease, there is a lack of formal representation of the relevant knowledge domain. Alzheimer's disease ontology (ADO) is constructed in accordance to the ontology building life cycle. The Protégé OWL editor was used as a tool for building ADO in Ontology Web Language format. ADO was developed with the purpose of containing information relevant to four main biological views-preclinical, clinical, etiological, and molecular/cellular mechanisms-and was enriched by adding synonyms and references. Validation of the lexicalized ontology by means of named entity recognition-based methods showed a satisfactory performance (F score = 72%). In addition to structural and functional evaluation, a clinical expert in the field performed a manual evaluation and curation of ADO. Through integration of ADO into an information retrieval environment, we show that the ontology supports semantic search in scientific text. The usefulness of ADO is authenticated by dedicated use case scenarios. Development of ADO as an open ADO is a first attempt to organize information related to Alzheimer's disease in a formalized, structured manner. We demonstrate that ADO is able to capture both established and scattered knowledge existing in scientific text. Copyright © 2014 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Assessment Applications of Ontologies.

Science.gov (United States)

Chung, Gregory K. W. K.; Niemi, David; Bewley, William L.

This paper discusses the use of ontologies and their applications to assessment. An ontology provides a shared and common understanding of a domain that can be communicated among people and computational systems. The ontology captures one or more experts' conceptual representation of a domain expressed in terms of concepts and the relationships…

Using Assertion Capabilities of an OWL-Based Ontology for Query Formulation

CERN Document Server

Munir, Kamran; Bloodsworth, Peter; McClatchey, Richard

2008-01-01

This paper reports on the development of a framework to assist users in formulating relational queries without requiring a complete knowledge of the information structure and access mechanisms to underlying data sources. The emphasis here is on exploiting the semantic relationships and assertion capabilities of OWL ontologies to assist clinicians in writing complex queries. This has been achieved using both a bottom-up and top-down approaches to build an ontology model to be the repository for complex end user queries. Relational database schemas are mapped into the newly generated ontology schema to reinforce the current domain ontology being developed. One of the key merits of this approach is that it does not require storing data interpretation, with the added advantage of even not storing database instances as part of the domain ontology, especially for systems with huge volume of data.

Survey on Ontology Mapping

Science.gov (United States)

Zhu, Junwu

To create a sharable semantic space in which the terms from different domain ontology or knowledge system, Ontology mapping become a hot research point in Semantic Web Community. In this paper, motivated factors of ontology mapping research are given firstly, and then 5 dominating theories and methods, such as information accessing technology, machine learning, linguistics, structure graph and similarity, are illustrated according their technology class. Before we analyses the new requirements and takes a long view, the contributions of these theories and methods are summarized in details. At last, this paper suggest to design a group of semantic connector with the ability of migration learning for OWL-2 extended with constrains and the ontology mapping theory of axiom, so as to provide a new methodology for ontology mapping.

A Method for Evaluating and Standardizing Ontologies

Science.gov (United States)

Seyed, Ali Patrice

2012-01-01

The Open Biomedical Ontology (OBO) Foundry initiative is a collaborative effort for developing interoperable, science-based ontologies. The Basic Formal Ontology (BFO) serves as the upper ontology for the domain-level ontologies of OBO. BFO is an upper ontology of types as conceived by defenders of realism. Among the ontologies developed for OBO…

A Method for Building Personalized Ontology Summaries

OpenAIRE

Queiroz-Sousa, Paulo Orlando; Salgado, Ana Carolina; Pires, Carlos Eduardo

2013-01-01

In the context of ontology engineering, the ontology understanding is the basis for its further developmentand reuse. One intuitive eective approach to support ontology understanding is the process of ontology summarizationwhich highlights the most important concepts of an ontology. Ontology summarization identies an excerpt from anontology that contains the most relevant concepts and produces an abridged ontology. In this article, we present amethod for summarizing ontologies that represent ...

The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

Science.gov (United States)

Dönitz, Jürgen; Wingender, Edgar

2012-01-01

The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.

Surreptitious, Evolving and Participative Ontology Development: An End-User Oriented Ontology Development Methodology

Science.gov (United States)

Bachore, Zelalem

2012-01-01

Ontology not only is considered to be the backbone of the semantic web but also plays a significant role in distributed and heterogeneous information systems. However, ontology still faces limited application and adoption to date. One of the major problems is that prevailing engineering-oriented methodologies for building ontologies do not…

Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

Science.gov (United States)

Lieberman, J. E.; Cheatham, M.; Varanka, D.

2015-12-01

Ontologies are playing an increasing role in facilitating mediation and translation between datasets representing diverse schemas, vocabularies, or knowledge communities. This role is relatively straightforward when there is one ontology comprising all relevant common concepts that can be mapped to entities in each dataset. Frequently, one common ontology has not been agreed to. Either each dataset is represented by a distinct ontology, or there are multiple candidates for commonality. Either the one most appropriate (expressive, relevant, correct) ontology must be chosen, or else concepts and relationships matched across multiple ontologies through an alignment process so that they may be used in concert to carry out mediation or other semantic operations. A resulting alignment can be effective to the extent that entities in in the ontologies represent differing terminology for comparable conceptual knowledge. In cases such as spatial ontologies, though, ontological entities may also represent disparate conceptualizations of space according to the discernment methods and application domains on which they are based. One ontology's wetland concept may overlap in space with another ontology's recharge zone or wildlife range or water feature. In order to evaluate alignment with respect to spatial ontologies, alignment has been applied to a series of ontologies pertaining to surface water that are used variously in hydrography (characterization of water features), hydrology (study of water cycling), and water quality (nutrient and contaminant transport) application domains. There is frequently a need to mediate between datasets in each domain in order to develop broader understanding of surface water systems, so there is a practical as well theoretical value in the alignment. From a domain expertise standpoint, the ontologies under consideration clearly contain some concepts that are spatially as well as conceptually identical and then others with less clear

An Ontology for Software Engineering Education

Science.gov (United States)

Ling, Thong Chee; Jusoh, Yusmadi Yah; Adbullah, Rusli; Alwi, Nor Hayati

2013-01-01

Software agents communicate using ontology. It is important to build an ontology for specific domain such as Software Engineering Education. Building an ontology from scratch is not only hard, but also incur much time and cost. This study aims to propose an ontology through adaptation of the existing ontology which is originally built based on a…

Students' flexible use of ontologies and the value of tentative reasoning: Examples of conceptual understanding in three canonical topics of quantum mechanics

Science.gov (United States)

Hoehn, Jessica R.; Finkelstein, Noah D.

2018-06-01

As part of a research study on student reasoning in quantum mechanics, we examine students' use of ontologies, or the way students' categorically organize entities they are reasoning about. In analyzing three episodes of focus group discussions with modern physics students, we present evidence of the dynamic nature of ontologies, and refine prior theoretical frameworks for thinking about dynamic ontologies. We find that in a given reasoning episode ontologies can be dynamic in construction (referring to when the reasoner constructs the ontologies) or application (referring to which ontologies are applied in a given reasoning episode). In our data, we see instances of students flexibly switching back and forth between parallel stable structures as well as constructing and negotiating new ontologies in the moment. Methodologically, we use a collective conceptual blending framework as an analytic tool for capturing student reasoning in groups. In this research, we value the messiness of student reasoning and argue that reasoning in a tentative manner can be productive for students learning quantum mechanics. As such, we shift away from a binary view of student learning which sees students as either having the correct answer or not.

OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories

OpenAIRE

Paschke, Adrian

2013-01-01

In collaborative agile ontology development projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The Apache Maven approach has proven its success in distributed collaborative Software Engineering by its widespread adoption. The contribution of this paper is a new design artifact called OntoMaven. OntoMaven adopts the Maven-based development methodology and ada...

Conceptual querying through ontologies

DEFF Research Database (Denmark)

Andreasen, Troels; Bulskov, Henrik

2009-01-01

is motivated by an obvious need for users to survey huge volumes of objects in query answers. An ontology formalism and a special notion of-instantiated ontology" are introduced. The latter is a structure reflecting the content in the document collection in that; it is a restriction of a general world......We present here ail approach to conceptual querying where the aim is, given a collection of textual database objects or documents, to target an abstraction of the entire database content in terms of the concepts appearing in documents, rather than the documents in the collection. The approach...... knowledge ontology to the concepts instantiated in the collection. The notion of ontology-based similarity is briefly described, language constructs for direct navigation and retrieval of concepts in the ontology are discussed and approaches to conceptual summarization are presented....

Ontology for assessment studies of human-computer-interaction in surgery.

Science.gov (United States)

Machno, Andrej; Jannin, Pierre; Dameron, Olivier; Korb, Werner; Scheuermann, Gerik; Meixensberger, Jürgen

2015-02-01

New technologies improve modern medicine, but may result in unwanted consequences. Some occur due to inadequate human-computer-interactions (HCI). To assess these consequences, an investigation model was developed to facilitate the planning, implementation and documentation of studies for HCI in surgery. The investigation model was formalized in Unified Modeling Language and implemented as an ontology. Four different top-level ontologies were compared: Object-Centered High-level Reference, Basic Formal Ontology, General Formal Ontology (GFO) and Descriptive Ontology for Linguistic and Cognitive Engineering, according to the three major requirements of the investigation model: the domain-specific view, the experimental scenario and the representation of fundamental relations. Furthermore, this article emphasizes the distinction of "information model" and "model of meaning" and shows the advantages of implementing the model in an ontology rather than in a database. The results of the comparison show that GFO fits the defined requirements adequately: the domain-specific view and the fundamental relations can be implemented directly, only the representation of the experimental scenario requires minor extensions. The other candidates require wide-ranging extensions, concerning at least one of the major implementation requirements. Therefore, the GFO was selected to realize an appropriate implementation of the developed investigation model. The ensuing development considered the concrete implementation of further model aspects and entities: sub-domains, space and time, processes, properties, relations and functions. The investigation model and its ontological implementation provide a modular guideline for study planning, implementation and documentation within the area of HCI research in surgery. This guideline helps to navigate through the whole study process in the form of a kind of standard or good clinical practice, based on the involved foundational frameworks

An ontology approach to comparative phenomics in plants

KAUST Repository

Oellrich, Anika

2015-02-25

Background: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. Results: We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. Conclusions: The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics

An ontology approach to comparative phenomics in plants

KAUST Repository

Oellrich, Anika; Walls, Ramona L; Cannon, Ethalinda KS; Cannon, Steven B; Cooper, Laurel; Gardiner, Jack; Gkoutos, Georgios V; Harper, Lisa; He, Mingze; Hoehndorf, Robert; Jaiswal, Pankaj; Kalberer, Scott R; Lloyd, John P; Meinke, David; Menda, Naama; Moore, Laura; Nelson, Rex T; Pujar, Anuradha; Lawrence, Carolyn J; Huala, Eva

2015-01-01

Background: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework. Results: We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes. Conclusions: The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics

A New role of ontologies and advanced scientific visualization in big data analytics

OpenAIRE

Chuprina, Svetlana

2016-01-01

Accessing and contextual semantic searching structured, semi-structured and unstructured information resources and their ontology based analysis in a uniform way across text-free Big Data query implementation is a main feature of approach under discussion. To increase the semantic power of query results’ analysis the ontology based implementation of multiplatform adaptive tools of scientific visualization are demonstrated. The ontologies are used not for integration of heterogeneous resources...

A Uniform Ontology for Software Interfaces

Science.gov (United States)

Feyock, Stefan

2002-01-01

It is universally the case that computer users who are not also computer specialists prefer to deal with computers' in terms of a familiar ontology, namely that of their application domains. For example, the well-known Windows ontology assumes that the user is an office worker, and therefore should be presented with a "desktop environment" featuring entities such as (virtual) file folders, documents, appointment calendars, and the like, rather than a world of machine registers and machine language instructions, or even the DOS command level. The central theme of this research has been the proposition that the user interacting with a software system should have at his disposal both the ontology underlying the system, as well as a model of the system. This information is necessary for the understanding of the system in use, as well as for the automatic generation of assistance for the user, both in solving the problem for which the application is designed, and for providing guidance in the capabilities and use of the system.

Development of FuGO: An Ontology for Functional Genomics Investigations

Science.gov (United States)

Whetzel, Patricia L.; Brinkman, Ryan R.; Causton, Helen C.; Fan, Liju; Field, Dawn; Fostel, Jennifer; Fragoso, Gilberto; Gray, Tanya; Heiskanen, Mervi; Hernandez-Boussard, Tina; Morrison, Norman; Parkinson, Helen; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Schober, Daniel; Smith, Barry; Stevens, Robert; Stoeckert, Christian J.; Taylor, Chris; White, Joe; Wood, Andrew

2009-01-01

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. PMID:16901226

Ontology and anthropology of interanimality: Merleau-Ponty from Tim ingold's perspective

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Ana Cristina Ramírez Barreto

2010-01-01

Full Text Available This essay explores Tim Ingold’s anthropological theory following his references to Merleau-Ponty and the concept of interanimality/interagentivity. It poses some ideas of Ingold’s “poetics of dwelling”, which he highlights from ethnographies of hunter-gatherer peoples, and how these ideas are linked to an ontological consideration which does not dissociate body and person, body and mind, nature and culture, animality and humanity. The paper reviews animal literature in Merleau-Ponty’s philosophy, and Ingold’s critique of “Anthropology of the senses”. It also gives critical clues for the ethical and political implications of this ontology.

Inferring ontology graph structures using OWL reasoning

KAUST Repository

Rodriguez-Garcia, Miguel Angel

2018-01-05

Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies\\' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies\\' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph .Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Inferring ontology graph structures using OWL reasoning.

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Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

2018-01-05

Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

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Lamy, Jean-Baptiste

2017-07-01

Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

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Apweiler Rolf

2006-02-01

Full Text Available Abstract Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. Results The Ontology Lookup Service (OLS was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. Conclusion The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

The Quest to Solve Problems That Don’t Exist: Thought Artifacts in Contemporary Ontology

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Kastrup Bernardo

2017-10-01

Full Text Available Questions about the nature of reality and consciousness remain unresolved in philosophy today, but not for lack of hypotheses. Ontologies as varied as physicalism, microexperientialism and cosmopsychism enrich the philosophical menu. Each of these ontologies faces a seemingly fundamental problem: under physicalism, for instance, we have the ‘hard problem of consciousness,’ whereas under microexperientialism we have the ‘subject combination problem.’ I argue that these problems are thought artifacts, having no grounding in empirical reality. In a manner akin to semantic paradoxes, they exist only in the internal logico-conceptual structure of their respective ontologies.

Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

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Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

2014-10-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

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Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

2014-01-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

Ontology-aided Data Fusion (Invited)

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Raskin, R.

2009-12-01

An ontology provides semantic descriptions that are analogous to those in a dictionary, but are readable by both computers and humans. A data or service is semantically annotated when it is formally associated with elements of an ontology. The ESIP Federation Semantic Web Cluster has developed a set of ontologies to describe datatypes and data services that can be used to support automated data fusion. The service ontology includes descriptors of the service function, its inputs/outputs, and its invocation method. The datatype descriptors resemble typical metadata fields (data format, data model, data structure, originator, etc.) augmented with descriptions of the meaning of the data. These ontologies, in combination with the SWEET science ontology, enable a registered data fusion service to be chained together and implemented that is scientifically meaningful based on machine understanding of the associated data and services. This presentation describes initial results and experiences in automated data fusion.

Ontology of fractures

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Zhong, Jian; Aydina, Atilla; McGuinness, Deborah L.

2009-03-01

Fractures are fundamental structures in the Earth's crust and they can impact many societal and industrial activities including oil and gas exploration and production, aquifer management, CO 2 sequestration, waste isolation, the stabilization of engineering structures, and assessing natural hazards (earthquakes, volcanoes, and landslides). Therefore, an ontology which organizes the concepts of fractures could help facilitate a sound education within, and communication among, the highly diverse professional and academic community interested in the problems cited above. We developed a process-based ontology that makes explicit specifications about fractures, their properties, and the deformation mechanisms which lead to their formation and evolution. Our ontology emphasizes the relationships among concepts such as the factors that influence the mechanism(s) responsible for the formation and evolution of specific fracture types. Our ontology is a valuable resource with a potential to applications in a number of fields utilizing recent advances in Information Technology, specifically for digital data and information in computers, grids, and Web services.

Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web.

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Budovec, Joseph J; Lam, Cesar A; Kahn, Charles E

2014-01-01

The Semantic Web is an effort to add semantics, or "meaning," to empower automated searching and processing of Web-based information. The overarching goal of the Semantic Web is to enable users to more easily find, share, and combine information. Critical to this vision are knowledge models called ontologies, which define a set of concepts and formalize the relations between them. Ontologies have been developed to manage and exploit the large and rapidly growing volume of information in biomedical domains. In diagnostic radiology, lists of differential diagnoses of imaging observations, called gamuts, provide an important source of knowledge. The Radiology Gamuts Ontology (RGO) is a formal knowledge model of differential diagnoses in radiology that includes 1674 differential diagnoses, 19,017 terms, and 52,976 links between terms. Its knowledge is used to provide an interactive, freely available online reference of radiology gamuts ( www.gamuts.net ). A Web service allows its content to be discovered and consumed by other information systems. The RGO integrates radiologic knowledge with other biomedical ontologies as part of the Semantic Web. © RSNA, 2014.

Constructive Ontology Engineering

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Sousan, William L.

2010-01-01

The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in…

Summarization by domain ontology navigation

DEFF Research Database (Denmark)

Andreasen, Troels; Bulskov, Henrik

2013-01-01

of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

THE CIDOC CRM GAME: A Serious Game Approach to Ontology Learning

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Guillem, A.; Bruseker, G.

2017-08-01

Formal ontologies such as CIDOC CRM (Conceptual Reference Model) form part of the central strategy for the medium and longterm integration of cultural heritage data to allow for its greater valorization and dissemination. Despite this, uptake of CIDOC CRM at the ground level of Cultural Heriage (CH) practice is limited. Part of the reason behind this lack of uptake lies in the fact that ontologies are considered too complicated and abstract for application in real life scenarios. This paper presents the rationale behind and the design of a CIDOC CRM game, the intent of which is to provide a learning mechanism to allow learners of wide backgrounds and interests to approach CIDOC CRM in a hands-on and interactive fashion. The CIDOC CRM game consist of decks of cards and game boards that allow players to engage with the concepts of a formal ontology in relation to real data in an entertaining and informative way. It is argued that the CIDOC CRM Game can form an important part of introducing the basic elements of formal ontology and this standard to a wider audience in order to aid wider understanding and adoption of the same.

Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development.

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Elayavilli, Ravikumar Komandur; Liu, Hongfang

2016-01-01

Computational modeling of biological cascades is of great interest to quantitative biologists. Biomedical text has been a rich source for quantitative information. Gathering quantitative parameters and values from biomedical text is one significant challenge in the early steps of computational modeling as it involves huge manual effort. While automatically extracting such quantitative information from bio-medical text may offer some relief, lack of ontological representation for a subdomain serves as impedance in normalizing textual extractions to a standard representation. This may render textual extractions less meaningful to the domain experts. In this work, we propose a rule-based approach to automatically extract relations involving quantitative data from biomedical text describing ion channel electrophysiology. We further translated the quantitative assertions extracted through text mining to a formal representation that may help in constructing ontology for ion channel events using a rule based approach. We have developed Ion Channel ElectroPhysiology Ontology (ICEPO) by integrating the information represented in closely related ontologies such as, Cell Physiology Ontology (CPO), and Cardiac Electro Physiology Ontology (CPEO) and the knowledge provided by domain experts. The rule-based system achieved an overall F-measure of 68.93% in extracting the quantitative data assertions system on an independently annotated blind data set. We further made an initial attempt in formalizing the quantitative data assertions extracted from the biomedical text into a formal representation that offers potential to facilitate the integration of text mining into ontological workflow, a novel aspect of this study. This work is a case study where we created a platform that provides formal interaction between ontology development and text mining. We have achieved partial success in extracting quantitative assertions from the biomedical text and formalizing them in ontological

Defining functional distances over Gene Ontology

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del Pozo Angela

2008-01-01

Full Text Available Abstract Background A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-. However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms. Results We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model Df which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'. Conclusion The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.

Ontological Annotation with WordNet

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Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

2006-06-06

Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

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Whetzel, Patricia L; Parkinson, Helen; Causton, Helen C; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Game, Laurence; Heiskanen, Mervi; Morrison, Norman; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; White, Joseph; Stoeckert, Christian J

2006-04-01

The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online.

Gene Ontology Consortium: going forward.

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2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Building a developmental toxicity ontology.

Science.gov (United States)

Baker, Nancy; Boobis, Alan; Burgoon, Lyle; Carney, Edward; Currie, Richard; Fritsche, Ellen; Knudsen, Thomas; Laffont, Madeleine; Piersma, Aldert H; Poole, Alan; Schneider, Steffen; Daston, George

2018-04-03

As more information is generated about modes of action for developmental toxicity and more data are generated using high-throughput and high-content technologies, it is becoming necessary to organize that information. This report discussed the need for a systematic representation of knowledge about developmental toxicity (i.e., an ontology) and proposes a method to build one based on knowledge of developmental biology and mode of action/ adverse outcome pathways in developmental toxicity. This report is the result of a consensus working group developing a plan to create an ontology for developmental toxicity that spans multiple levels of biological organization. This report provide a description of some of the challenges in building a developmental toxicity ontology and outlines a proposed methodology to meet those challenges. As the ontology is built on currently available web-based resources, a review of these resources is provided. Case studies on one of the most well-understood morphogens and developmental toxicants, retinoic acid, are presented as examples of how such an ontology might be developed. This report outlines an approach to construct a developmental toxicity ontology. Such an ontology will facilitate computer-based prediction of substances likely to induce human developmental toxicity. © 2018 Wiley Periodicals, Inc.

Building a biomedical ontology recommender web service

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Jonquet Clement

2010-06-01

Full Text Available Abstract Background Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use. Methods We present the Biomedical Ontology Recommender web service. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is coverage, or the ontologies that provide most terms covering the input text. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. The final criterion is size, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO Annotator web service. We used all the ontologies from the UMLS Metathesaurus and the NCBO BioPortal. Results We compare and contrast our Recommender by an exhaustive functional comparison to previously published efforts. We evaluate and discuss the results of several recommendation heuristics in the context of three real world use cases. The best recommendations heuristics, rated ‘very relevant’ by expert evaluators, are the ones based on coverage and connectivity criteria. The Recommender service (alpha version is available to the community and is embedded into BioPortal.

A Hydrological Sensor Web Ontology Based on the SSN Ontology: A Case Study for a Flood

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Chao Wang

2017-12-01

Full Text Available Accompanying the continuous development of sensor network technology, sensors worldwide are constantly producing observation data. However, the sensors and their data from different observation platforms are sometimes difficult to use collaboratively in response to natural disasters such as floods for the lack of semantics. In this paper, a hydrological sensor web ontology based on SSN ontology is proposed to describe the heterogeneous hydrological sensor web resources by importing the time and space ontology, instantiating the hydrological classes, and establishing reasoning rules. This work has been validated by semantic querying and knowledge acquiring experiments. The results demonstrate the feasibility and effectiveness of the proposed ontology and its potential to grow into a more comprehensive ontology for hydrological monitoring collaboratively. In addition, this method of ontology modeling is generally applicable to other applications and domains.

APPLICATION OF COMPUTER SYSTEMS ONTOLOGY IN THE PROCESS OF FUTURE ENGINEER AND EDUCATOR’S PRACTICAL ACTIVITY

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Сергій Козіброда

2014-04-01

Full Text Available This article develops the problem of the use of computer systems ontology in the professional activity of future engineers and teachers in the sphere of computer technology. The tasks of automated exchange of formal model descriptions as a main factor of a research performing in the sphere of ontology use have been grounded. The expediency of use of the ontology of computer systems in the following fields of intending engineers and teachers’ training: artificial intelligence, interface, natural language processing, question-answer systems, classification of goods and services semantic mark-up of text, modelling organizational structure of enterprises, systems of reference information (NSI.

Gradient Learning Algorithms for Ontology Computing

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Gao, Wei; Zhu, Linli

2014-01-01

The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting. PMID:25530752

Gradient Learning Algorithms for Ontology Computing

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Wei Gao

2014-01-01

Full Text Available The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting.

Perspectives on ontology learning

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Lehmann, J

2014-01-01

Perspectives on Ontology Learning brings together researchers and practitioners from different communities − natural language processing, machine learning, and the semantic web − in order to give an interdisciplinary overview of recent advances in ontology learning.Starting with a comprehensive introduction to the theoretical foundations of ontology learning methods, the edited volume presents the state-of-the-start in automated knowledge acquisition and maintenance. It outlines future challenges in this area with a special focus on technologies suitable for pushing the boundaries beyond the c

Towards Ontology-Driven Information Systems: Guidelines to the Creation of New Methodologies to Build Ontologies

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Soares, Andrey

2009-01-01

This research targeted the area of Ontology-Driven Information Systems, where ontology plays a central role both at development time and at run time of Information Systems (IS). In particular, the research focused on the process of building domain ontologies for IS modeling. The motivation behind the research was the fact that researchers have…

Database Concepts in a Domain Ontology

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Gorskis Henrihs

2017-12-01

Full Text Available There are multiple approaches for mapping from a domain ontology to a database in the task of ontology-based data access. For that purpose, external mapping documents are most commonly used. These documents describe how the data necessary for the description of ontology individuals and other values, are to be obtained from the database. The present paper investigates the use of special database concepts. These concepts are not separated from the domain ontology; they are mixed with domain concepts to form a combined application ontology. By creating natural relationships between database concepts and domain concepts, mapping can be implemented more easily and with a specific purpose. The paper also investigates how the use of such database concepts in addition to domain concepts impacts ontology building and data retrieval.

Computer support for physiological cell modelling using an ontology on cell physiology.

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Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

2006-01-01

The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

On Algebraic Spectrum of Ontology Evaluation

OpenAIRE

Adekoya Adebayo Felix; kinwale Adio Taofiki; Sofoluwe Adetokunbo

2011-01-01

Ontology evaluation remains an important open problem in the area of its application. The ontology structure evaluation framework for benchmarking the internal graph structures was proposed. The framework was used in transport and biochemical ontology. The corresponding adjacency, incidence matrices and other structural properties due to the class hierarchical structure of the transport and biochemical ontology were computed using MATLAB. The results showed that the choice of suitable choice ...

Crosswalking near-Earth and space physics ontologies in SPASE and ESPAS

Science.gov (United States)

Galkin, I. A.; Fung, S. F.; Benson, R. F.; Heynderickx, D.; Ritschel, B.; King, T. A.; Roberts, D. A.; Hapgood, M. A.; Belehaki, A.

2015-12-01

In order to support scientific discoveries in Heliophysics (HP), with modern data systems, the HP Data Centers actively pursue harmonization of available metadata that allows crossing boundaries between existing data models, conventions, and resource interfaces. The discoverability of HP observations is improved when associated metadata describes their physical content in agreed terms as a part of the resource registration. One of the great challenges of enabling such content-targeted data search capability is the harmonization of domain ontology across data providers. Ontologies are the cornerstones of the content-aware data systems: they define an agreed vocabulary of keywords that capture the essence of domain-specific concepts and their relationships. With the introduction of the Virtual Wave Observatory (VWO), as part of NASA's Virtual System Observatory in 2008, the task of formulating the HP ontology became yet more complicated. Definitions of the wave domain concepts required several layers of specifications that described the generation, propagation, and interaction of the waves with the underlying medium in addition to the observation itself. Simple keyword lists could not provide a sufficiently information-rich description, given the complexity of the wave domain, and the development of a more powerful schema was required. The ontology research at the VWO eventually resulted in a suitable multi-hierarchical design that found its first implementation in 2015 at one of the European space physics data repositories, the near-Earth Space Data Infrastructure for e-Science (ESPAS). Similar to many other European geoscience projects, ESPAS is based on the ISO 19156 Observation and Measurements standard. In cooperation with the NASA VWO, the ESPAS project has deployed a space physics ontology design for all data registration purposes. The VWO science team is now uniquely positioned to establish a crosswalk between the ESPAS ontology based on ISO 19156 and the VWO

Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.

Directory of Open Access Journals (Sweden)

Lucia Manni

Full Text Available Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

DEFF Research Database (Denmark)

Nilsson, Jørgen Fischer; Szymczak, Bartlomiej Antoni; Jensen, P.A.

2009-01-01

We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules...... for producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

A meta-ontological framework for multi-agent systems design

OpenAIRE

Sokolova, Marina; Fernández Caballero, Antonio

2007-01-01

The paper introduces an approach to using a meta-ontology framework for complex multi-agent systems design, and illustrates it in an application related to ecological-medical issues. The described shared ontology is pooled from private sub-ontologies, which represent a problem area ontology, an agent ontology, a task ontology, an ontology of interactions, and the multi-agent system architecture ontology.

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

Science.gov (United States)

Mortensen, Jonathan M; Telis, Natalie; Hughey, Jacob J; Fan-Minogue, Hua; Van Auken, Kimberly; Dumontier, Michel; Musen, Mark A

2016-04-01

Biomedical ontologies contain errors. Crowdsourcing, defined as taking a job traditionally performed by a designated agent and outsourcing it to an undefined large group of people, provides scalable access to humans. Therefore, the crowd has the potential to overcome the limited accuracy and scalability found in current ontology quality assurance approaches. Crowd-based methods have identified errors in SNOMED CT, a large, clinical ontology, with an accuracy similar to that of experts, suggesting that crowdsourcing is indeed a feasible approach for identifying ontology errors. This work uses that same crowd-based methodology, as well as a panel of experts, to verify a subset of the Gene Ontology (200 relationships). Experts identified 16 errors, generally in relationships referencing acids and metals. The crowd performed poorly in identifying those errors, with an area under the receiver operating characteristic curve ranging from 0.44 to 0.73, depending on the methods configuration. However, when the crowd verified what experts considered to be easy relationships with useful definitions, they performed reasonably well. Notably, there are significantly fewer Google search results for Gene Ontology concepts than SNOMED CT concepts. This disparity may account for the difference in performance - fewer search results indicate a more difficult task for the worker. The number of Internet search results could serve as a method to assess which tasks are appropriate for the crowd. These results suggest that the crowd fits better as an expert assistant, helping experts with their verification by completing the easy tasks and allowing experts to focus on the difficult tasks, rather than an expert replacement. Copyright © 2016 Elsevier Inc. All rights reserved.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

Science.gov (United States)

Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

Science.gov (United States)

Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM....biosciencedbc.jp/archive/fantom5/datafiles/LATEST/extra/Ontology/ File size: 1.8 MB Simple search URL - Dat...t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

An ontological approach to domain engineering

NARCIS (Netherlands)

Falbo, R.A.; Guizzardi, G.; Duarte, K.

2002-01-01

Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain

Ontological Order in Scientific Explanation | Park | Philosophical ...

African Journals Online (AJOL)

A conceptually sound explanation, I claim, respects the ontological order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate between scientific realists and antirealists.

OIntEd: online ontology instance editor enabling a new approach to ontology development

NARCIS (Netherlands)

Wibisono, A.; Koning, R.; Grosso, P.; Belloum, A.; Bubak, M.; de Laat, C.

2013-01-01

Ontology development involves people with different background knowledge and expertise. It is an elaborate process, where sophisticated tools for experienced knowledge engineers are available. However, domain experts need simple tools that they can use to focus on ontology instantiation. In this

Interpretations of Ontologies for Breast Cancer

Directory of Open Access Journals (Sweden)

Srinandan Dasmahapatra

2008-07-01

ontology building as guarantors of fidelity to reality. We find that ontologies intended to support medical practice can only be understood within the context of their intended use. The declarative framework within which they are encoded generates the hope that their meaning transcends the specific application context. We show, however, that these declarative statements are to be understood as end products of chains of procedural engagements between humans, materials and communitarian norms. It is only when this scaffolding that brings this representation into existence becomes routine and consensual (within the community that exchanges information indexed against it that the concepts stand in for physiological states with independent dynamics. However, as the state of biomedical knowledge is always in a state of flux, and different institutions and practitioners may be out of sync with respect to such modifications, the concepts embedded in the ontologies are constantly subject to reinterpretation within the context of specific institutional practices. Given the fragmentation of the patient’s body when viewed through various specialised lenses, ontologies can provide placeholders for co-ordinating disparate viewpoints to provide suitable medical interventions. The extent to which such interventions reflect any underlying reality, as manifest in measures of their efficacy, is closely wrapped up in the regulatory apparatus of protocol-guided consensus making. The value of ontologies lies in their reflection of, and support for, the sense-making activities that constitute expertise, not in their transparent access to a metaphysical reality.

Australia’s National Health Programs: An Ontological Mapping

Directory of Open Access Journals (Sweden)

Arkalgud Ramaprasad

2016-11-01

Full Text Available Australia has a large number of health program initiatives whose comprehensive assessment will help refine and redefine priorities by highlighting areas of emphasis, under-emphasis, and non-emphasis. The objectives of our research are to: (a systematically map all the programs onto an ontological framework, and (b systemically analyse their relative emphases at different levels of granularity. We mapped all the health program initiatives onto an ontology with five dimensions, namely: (a Policy-scope, (b Policy-focus, (c Outcomes, (d Type of care, and (e Population served. Each dimension is expanded into a taxonomy of its constituent elements. Each combination of elements from the five dimensions is a possible policy initiative component. There are 30,030 possible components encapsulated in the ontology. It includes, for example: (a National financial policies on accessibility of preventive care for family, and (b Local-urban regulatory policies on cost of palliative care for individual-aged. Four of the authors mapped all of Australia’s health programs and initiatives on to the ontology. Visualizations of the data are used to highlight the relative emphases in the program initiatives. The dominant emphasis of the program initiatives is: [National] [educational, personnel-physician, information] policies on [accessibility, quality] of [preventive, wellness] care for the [community]. However, although (a information is emphasized technology is not; and (b accessibility and quality are emphasized cost, satisfaction, and quality are not. The ontology and the results of the mapping can help systematically reassess and redirect the relative emphases of the programs and initiatives from a systemic perspective.

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

Science.gov (United States)

Cheng, Liang; Jiang, Yue; Ju, Hong; Sun, Jie; Peng, Jiajie; Zhou, Meng; Hu, Yang

2018-01-19

Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and Human Phenotype Ontology (HPO). Because of the advantage of identifying novel relationships between terms, calculating similarity between ontology terms is one of the major tasks in this research area. Though similarities between terms within each ontology have been studied with in silico methods, term similarities across different ontologies were not investigated as deeply. The latest method took advantage of gene functional interaction network (GFIN) to explore such inter-ontology similarities of terms. However, it only used gene interactions and failed to make full use of the connectivity among gene nodes of the network. In addition, all existent methods are particularly designed for GO and their performances on the extended ontology community remain unknown. We proposed a method InfAcrOnt to infer similarities between terms across ontologies utilizing the entire GFIN. InfAcrOnt builds a term-gene-gene network which comprised ontology annotations and GFIN, and acquires similarities between terms across ontologies through modeling the information flow within the network by random walk. In our benchmark experiments on sub-ontologies of GO, InfAcrOnt achieves a high average area under the receiver operating characteristic curve (AUC) (0.9322 and 0.9309) and low standard deviations (1.8746e-6 and 3.0977e-6) in both human and yeast benchmark datasets exhibiting superior performance. Meanwhile, comparisons of InfAcrOnt results and prior knowledge on pair-wise DO-HPO terms and pair-wise DO-GO terms show high correlations. The experiment results show that InfAcrOnt significantly improves the performance of inferring similarities between terms across ontologies in benchmark set.

Aspects of ontology visualization and integration

NARCIS (Netherlands)

Dmitrieva, Joelia Borisovna

2011-01-01

In this thesis we will describe and discuss methodologies for ontology visualization and integration. Two visualization methods will be elaborated. In one method the ontology is visualized with the node-link technique, and with the other method the ontology is visualized with the containment

The Semantic Mapping of Archival Metadata to the CIDOC CRM Ontology

Science.gov (United States)

Bountouri, Lina; Gergatsoulis, Manolis

2011-01-01

In this article we analyze the main semantics of archival description, expressed through Encoded Archival Description (EAD). Our main target is to map the semantics of EAD to the CIDOC Conceptual Reference Model (CIDOC CRM) ontology as part of a wider integration architecture of cultural heritage metadata. Through this analysis, it is concluded…

Length bias correction in gene ontology enrichment analysis using logistic regression.

Science.gov (United States)

Mi, Gu; Di, Yanming; Emerson, Sarah; Cumbie, Jason S; Chang, Jeff H

2012-01-01

When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer genes are more likely to be identified as enriched. These categories, however, are not necessarily biologically more relevant. We show that one can effectively adjust for length bias in Gene Ontology analysis by including transcript length as a covariate in a logistic regression model. The logistic regression model makes the statistical issue underlying length bias more transparent: transcript length becomes a confounding factor when it correlates with both the Gene Ontology membership and the significance of the differential expression test. The inclusion of the transcript length as a covariate allows one to investigate the direct correlation between the Gene Ontology membership and the significance of testing differential expression, conditional on the transcript length. We present both real and simulated data examples to show that the logistic regression approach is simple, effective, and flexible.

Ontology-based specification, identification and analysis of perioperative risks.

Science.gov (United States)

Uciteli, Alexandr; Neumann, Juliane; Tahar, Kais; Saleh, Kutaiba; Stucke, Stephan; Faulbrück-Röhr, Sebastian; Kaeding, André; Specht, Martin; Schmidt, Tobias; Neumuth, Thomas; Besting, Andreas; Stegemann, Dominik; Portheine, Frank; Herre, Heinrich

2017-09-06

Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of adverse events could have been avoided through better organization, more attention or more effective security procedures. Critical situations especially arise during interdisciplinary collaboration and the use of complex medical technology, for example during surgical interventions and in perioperative settings (the period of time before, during and after surgical intervention). In this paper, we present an ontology and an ontology-based software system, which can identify risks across medical processes and supports the avoidance of errors in particular in the perioperative setting. We developed a practicable definition of the risk notion, which is easily understandable by the medical staff and is usable for the software tools. Based on this definition, we developed a Risk Identification Ontology (RIO) and used it for the specification and the identification of perioperative risks. An agent system was developed, which gathers risk-relevant data during the whole perioperative treatment process from various sources and provides it for risk identification and analysis in a centralized fashion. The results of such an analysis are provided to the medical personnel in form of context-sensitive hints and alerts. For the identification of the ontologically specified risks, we developed an ontology-based software module, called Ontology-based Risk Detector (OntoRiDe). About 20 risks relating to cochlear implantation (CI) have already been implemented. Comprehensive testing has indicated the correctness of the data acquisition, risk identification and analysis components, as well as the web-based visualization of results.

Mapping between the OBO and OWL ontology languages.

Science.gov (United States)

Tirmizi, Syed Hamid; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P

2011-03-07

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. 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. 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.

Vaccine and Drug Ontology Studies (VDOS 2014).

Science.gov (United States)

Tao, Cui; He, Yongqun; Arabandi, Sivaram

2016-01-01

The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies.

Ontological Engineering for the Cadastral Domain

DEFF Research Database (Denmark)

Stubkjær, Erik; Stuckenschmidt, Heiner

2000-01-01

conceptualization of the world is that much information remains implicit. Ontologies have set out to overcome the problem of implicit and hidden knowledge by making the conceptualization of a domain (e.g. mathematics) explicit. Ontological engineering is thus an approach to achieve a conceptual rigor...... that characterizes established academic disciplines, like geodesy. Many university courses address more application oriented fields, like cadastral law, and spatial planning, and they may benefit from the ontological engineering approach. The paper provides an introduction to the field of ontological engineering...

Learning Resources Organization Using Ontological Framework

Science.gov (United States)

Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

The paper describes the ontological approach to the knowledge structuring for the e-learning portal design as it turns out to be efficient and relevant to current domain conditions. It is primarily based on the visual ontology-based description of the content of the learning materials and this helps to provide productive and personalized access to these materials. The experience of ontology developing for Knowledge Engineering coursetersburg State University is discussed and “OntolingeWiki” tool for creating ontology-based e-learning portals is described.

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

Science.gov (United States)

Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

2015-07-28

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

Automating Ontological Annotation with WordNet

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

2006-01-22

Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

Leave-two-out stability of ontology learning algorithm

International Nuclear Information System (INIS)

Wu, Jianzhang; Yu, Xiao; Zhu, Linli; Gao, Wei

2016-01-01

Ontology is a semantic analysis and calculation model, which has been applied to many subjects. Ontology similarity calculation and ontology mapping are employed as machine learning approaches. The purpose of this paper is to study the leave-two-out stability of ontology learning algorithm. Several leave-two-out stabilities are defined in ontology learning setting and the relationship among these stabilities are presented. Furthermore, the results manifested reveal that leave-two-out stability is a sufficient and necessary condition for ontology learning algorithm.

Semantic similarity between ontologies at different scales

Energy Technology Data Exchange (ETDEWEB)

Zhang, Qingpeng; Haglin, David J.

2016-04-01

In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

Use of the CIM Ontology

Energy Technology Data Exchange (ETDEWEB)

Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

2006-02-08

There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

Dosimetric verification for radiotherapy quality audit under reference and non-reference conditions in Jiangsu province

International Nuclear Information System (INIS)

Wang Jin; Yu Ningle; Yang Chunyong; Du Xiang; Chen Wei; Luo Suming

2014-01-01

Objective: To verify the methodology for auditing dosimetric parameters in reference and non-reference conditions with thermoluminescent dosimeters (TLDs). Methods: Under reference and non-reference conditions, the established TLD methods were used to observe the absorbed dose variations with depth, SSD, field size and 45 wedges for 10 photon beams at 5 hospitals. Dosimetric parameters, including doses at D_m_a_x points in axis, on 5 electron beams of 9 MeV were measured. The measurement results were compared between the TLDs and plane parallel ionization chambers. Results: For 6 MV photon beams, the relative deviation of between finger ionization chamber method and TLD chips was in the range of -1.7% to 5.4% under on-axis non-reference conditions, and -6.3% to -0.6% under off-axis non-reference conditions, respectively, all within the range of ≤ ±7% as required by the IAEA. The relative deviation between plane parallel chamber and TLD method was -2.3% to 3.7%, within ±5% as required by the IAEA. Conclusions: It is convenient and feasible to use TLD method for quality audits of dosimetric parameters in radiotherapy. (authors)

DEPONTO: A Reusable Dependability Domain Ontology

Directory of Open Access Journals (Sweden)

Teodora Sanislav

2015-08-01

Full Text Available This paper proposes a dependability reusable ontology for knowledge representation. The fundamental knowledge related to dependability follows its taxonomy. Thus, this paper gives an analysis of what is the dependability domain ontology andof its components.The dependability domain ontology plays an important role in ensuring the dependability of information systems by providing support for their diagnosis in case of faults, errors and failures.The proposed ontology is used as a dependability framework in two case study Cyber-Physical Systemswhich demonstrate its reusability within this category of systems.

Anatomy Ontology Matching Using Markov Logic Networks

Directory of Open Access Journals (Sweden)

Chunhua Li

2016-01-01

Full Text Available The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

Core Semantics for Public Ontologies

National Research Council Canada - National Science Library

Suni, Niranjan

2005-01-01

... (schemas or ontologies) with respect to objects. The DARPA Agent Markup Language (DAML) through the use of ontologies provides a very powerful way to describe objects and their relationships to other objects...

Study on distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database

Science.gov (United States)

WANG, Qingrong; ZHU, Changfeng

2017-06-01

Integration of distributed heterogeneous data sources is the key issues under the big data applications. In this paper the strategy of variable precision is introduced to the concept lattice, and the one-to-one mapping mode of variable precision concept lattice and ontology concept lattice is constructed to produce the local ontology by constructing the variable precision concept lattice for each subsystem, and the distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database is proposed to draw support from the special relationship between concept lattice and ontology construction. Finally, based on the standard of main concept lattice of the existing heterogeneous database generated, a case study has been carried out in order to testify the feasibility and validity of this algorithm, and the differences between the main concept lattice and the standard concept lattice are compared. Analysis results show that this algorithm above-mentioned can automatically process the construction process of distributed concept lattice under the heterogeneous data sources.

Methodology for Automatic Ontology Generation Using Database Schema Information

Directory of Open Access Journals (Sweden)

JungHyen An

2018-01-01

Full Text Available An ontology is a model language that supports the functions to integrate conceptually distributed domain knowledge and infer relationships among the concepts. Ontologies are developed based on the target domain knowledge. As a result, methodologies to automatically generate an ontology from metadata that characterize the domain knowledge are becoming important. However, existing methodologies to automatically generate an ontology using metadata are required to generate the domain metadata in a predetermined template, and it is difficult to manage data that are increased on the ontology itself when the domain OWL (Ontology Web Language individuals are continuously increased. The database schema has a feature of domain knowledge and provides structural functions to efficiently process the knowledge-based data. In this paper, we propose a methodology to automatically generate ontologies and manage the OWL individual through an interaction of the database and the ontology. We describe the automatic ontology generation process with example schema and demonstrate the effectiveness of the automatically generated ontology by comparing it with existing ontologies using the ontology quality score.

An ontology for major histocompatibility restriction.

Science.gov (United States)

Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

2016-01-01

MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences among Ontologies

Science.gov (United States)

Peng, Yefei

2010-01-01

An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'s ability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the…

Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships.

Science.gov (United States)

Manda, Prashanti; McCarthy, Fiona; Bridges, Susan M

2013-10-01

The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular bio-ontologies used for describing gene product characteristics. GO annotation data containing terms from multiple sub-ontologies and at different levels in the ontologies is an important source of implicit relationships between terms from the three sub-ontologies. Data mining techniques such as association rule mining that are tailored to mine from multiple ontologies at multiple levels of abstraction are required for effective knowledge discovery from GO annotation data. We present a data mining approach, Multi-ontology data mining at All Levels (MOAL) that uses the structure and relationships of the GO to mine multi-ontology multi-level association rules. We introduce two interestingness measures: Multi-ontology Support (MOSupport) and Multi-ontology Confidence (MOConfidence) customized to evaluate multi-ontology multi-level association rules. We also describe a variety of post-processing strategies for pruning uninteresting rules. We use publicly available GO annotation data to demonstrate our methods with respect to two applications (1) the discovery of co-annotation suggestions and (2) the discovery of new cross-ontology relationships. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Ontology-based multi-agent systems

Energy Technology Data Exchange (ETDEWEB)

Hadzic, Maja; Wongthongtham, Pornpit; Dillon, Tharam; Chang, Elizabeth [Digital Ecosystems and Business Intelligence Institute, Perth, WA (Australia)

2009-07-01

The Semantic web has given a great deal of impetus to the development of ontologies and multi-agent systems. Several books have appeared which discuss the development of ontologies or of multi-agent systems separately on their own. The growing interaction between agents and ontologies has highlighted the need for integrated development of these. This book is unique in being the first to provide an integrated treatment of the modeling, design and implementation of such combined ontology/multi-agent systems. It provides clear exposition of this integrated modeling and design methodology. It further illustrates this with two detailed case studies in (a) the biomedical area and (b) the software engineering area. The book is, therefore, of interest to researchers, graduate students and practitioners in the semantic web and web science area. (orig.)

Theory of the Whole and the Part – Ontological Perspective (E. Husserl, R. Ingarden

Directory of Open Access Journals (Sweden)

Barska Katarzyna

2015-02-01

Full Text Available The purpose of the paper is demonstrate the thesis that Ingarden's ontological system allows a better understanding of the “part-whole” problem then previous theories. Especially, if we take into account the existential ontology of Ingarden, which refers to Husserl “part-whole” theory, we can see that development of terms made by Ingarden sheds new light on old problems. In this context, particularly important is to distinguish between two existential moments: contingancy/inseparatness, because thanks to them we can talk about many different types of relationships and hence many types of objects.

Scientific Digital Libraries, Interoperability, and Ontologies

Science.gov (United States)

Hughes, J. Steven; Crichton, Daniel J.; Mattmann, Chris A.

2009-01-01

Scientific digital libraries serve complex and evolving research communities. Justifications for the development of scientific digital libraries include the desire to preserve science data and the promises of information interconnectedness, correlative science, and system interoperability. Shared ontologies are fundamental to fulfilling these promises. We present a tool framework, some informal principles, and several case studies where shared ontologies are used to guide the implementation of scientific digital libraries. The tool framework, based on an ontology modeling tool, was configured to develop, manage, and keep shared ontologies relevant within changing domains and to promote the interoperability, interconnectedness, and correlation desired by scientists.

Audit Validation Using Ontologies

Directory of Open Access Journals (Sweden)

Ion IVAN

2015-01-01

Full Text Available Requirements to increase quality audit processes in enterprises are defined. It substantiates the need for assessment and management audit processes using ontologies. Sets of rules, ways to assess the consistency of rules and behavior within the organization are defined. Using ontologies are obtained qualifications that assess the organization's audit. Elaboration of the audit reports is a perfect algorithm-based activity characterized by generality, determinism, reproducibility, accuracy and a well-established. The auditors obtain effective levels. Through ontologies obtain the audit calculated level. Because the audit report is qualitative structure of information and knowledge it is very hard to analyze and interpret by different groups of users (shareholders, managers or stakeholders. Developing ontology for audit reports validation will be a useful instrument for both auditors and report users. In this paper we propose an instrument for validation of audit reports contain a lot of keywords that calculates indicators, a lot of indicators for each key word there is an indicator, qualitative levels; interpreter who builds a table of indicators, levels of actual and calculated levels.

An Ontology for Knowledge Representation and Applications

OpenAIRE

Nhon Do

2008-01-01

Ontology is a terminology which is used in artificial intelligence with different meanings. Ontology researching has an important role in computer science and practical applications, especially distributed knowledge systems. In this paper we present an ontology which is called Computational Object Knowledge Base Ontology. It has been used in designing some knowledge base systems for solving problems such as the system that supports studying knowledge and solving analytic ...

A priorean approach to time ontologies

DEFF Research Database (Denmark)

Øhrstrøm, Peter; Schärfe, Henrik

2004-01-01

Any non-trivial top-level ontology should take temporal notions into account. The details of how this should be done, however, are frequently debated. In this paper it is argued that "the four grades of tense-logical involvement" suggested by A.N. Prior form a useful framework for discussing how...... various temporal notions are related in a top-level ontology. Furthermore, a number of modern ontologies are analysed with respect to their incorporation of temporal notions. It is argued that all of them correspond to Prior's first and second grade, and that none of them reflect the views which Prior......'s third and fourth grade represent. Finally, the paper deals with Prior's ideas on a tensed ontology and it is argued that a logic based on the third grade and will be useful in the further development of tensed ontology....

A methodology for creating ontologies for engineering design

DEFF Research Database (Denmark)

Ahmed, Saeema; Kim, S.; Wallace, K.M.

2007-01-01

This paper describes a six-stage methodology for developing ontologies for engineering design, together with the research methods and evaluation of each stage. The methodology focuses upon understanding a user's domain models through empirical research. A case study of an ontology for searching......, indexing, and retrieving engineering knowledge is described. The root concepts of the ontology were elicited from engineering designers. Relationships between concepts are extracted as the ontology is populated. The contribution of this research is a methodology to allow researchers. and industry to create...... ontologies for their particular purpose and a thesaurus for the terms within the ontology....

BiOSS: A system for biomedical ontology selection.

Science.gov (United States)

Martínez-Romero, Marcos; Vázquez-Naya, José M; Pereira, Javier; Pazos, Alejandro

2014-04-01

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

An ontological case base engineering methodology for diabetes management.

Science.gov (United States)

El-Sappagh, Shaker H; El-Masri, Samir; Elmogy, Mohammed; Riad, A M; Saddik, Basema

2014-08-01

Ontology engineering covers issues related to ontology development and use. In Case Based Reasoning (CBR) system, ontology plays two main roles; the first as case base and the second as domain ontology. However, the ontology engineering literature does not provide adequate guidance on how to build, evaluate, and maintain ontologies. This paper proposes an ontology engineering methodology to generate case bases in the medical domain. It mainly focuses on the research of case representation in the form of ontology to support the case semantic retrieval and enhance all knowledge intensive CBR processes. A case study on diabetes diagnosis case base will be provided to evaluate the proposed methodology.

ONSET: Automated foundational ontology selection and explanation

CSIR Research Space (South Africa)

Khan, Z

2012-10-01

Full Text Available It has been shown that using a foundational ontology for domain ontology development is beneficial in theory and practice. However, developers have difficulty with choosing the appropriate foundational ontology, and why. In order to solve...

The mouse-human anatomy ontology mapping project.

Science.gov (United States)

Hayamizu, Terry F; de Coronado, Sherri; Fragoso, Gilberto; Sioutos, Nicholas; Kadin, James A; Ringwald, Martin

2012-01-01

The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

CONCEPTION OF ONTOLOGY-BASED SECTOR EDUCATIONAL SPACE

Directory of Open Access Journals (Sweden)

V. I. Khabarov

2014-09-01

Full Text Available PurposeThe aim of the research is to demonstrate the need for the Conception of Ontology-based Sector Educational Space. This Conception could become the basis for the integration of transport sector university information resources into the open virtual network information resource and global educational space. Its content will be presented by standardized ontology-based knowledge packages for educational programs in Russian and English languages.MethodologyComplex-based, ontological, content-based approaches and scientific principles of interdisciplinarity and standardization of knowledge are suggested as the methodological basis of the research. ResultsThe Conception of Ontology-based Sector Educational Space (railway transport, the method of the development of knowledge packages as ontologies in Russian and English languages, the Russian-English Transport Glossary as a separate ontology are among the expected results of the project implementation.Practical implicationsThe Conception could become the basis for the open project to establish the common resource center for transport universities (railway transport. The Conception of ontology-based sector educational space (railway transport could be adapted to the activity of universities of other economic sectors.

History Matters: Incremental Ontology Reasoning Using Modules

Science.gov (United States)

Cuenca Grau, Bernardo; Halaschek-Wiener, Christian; Kazakov, Yevgeny

The development of ontologies involves continuous but relatively small modifications. Existing ontology reasoners, however, do not take advantage of the similarities between different versions of an ontology. In this paper, we propose a technique for incremental reasoning—that is, reasoning that reuses information obtained from previous versions of an ontology—based on the notion of a module. Our technique does not depend on a particular reasoning calculus and thus can be used in combination with any reasoner. We have applied our results to incremental classification of OWL DL ontologies and found significant improvement over regular classification time on a set of real-world ontologies.

What is nature capable of? Evidence, ontology and speculative medical humanities.

Science.gov (United States)

Savransky, Martin; Rosengarten, Marsha

2016-09-01

Expanding on the recent call for a 'critical medical humanities' to intervene in questions of the ontology of health, this article develops a what we call a 'speculative' orientation to such interventions in relation to some of the ontological commitments on which contemporary biomedical cultures rest. We argue that crucial to this task is an approach to ontology that treats it not as a question of first principles, but as a matter of the consequences of the images of nature that contemporary biomedical research practices espouse when they make claims to evidence, as well as the possible consequences of imagining different worlds in which health and disease processes partake. By attending to the implicit ontological assumptions involved in the method par excellence of biomedical research, namely the randomised controlled trial (RCT), we argue that the mechanistic ontology that tacitly informs evidence-based biomedical research simultaneously authorises a series of problematic consequences for understanding and intervening practically in the concrete realities of health. As a response, we develop an alternative ontological proposition that regards processes of health and disease as always situated achievements. We show that, without disqualifying RCT-based evidence, such a situated ontology enables one to resist the reduction of the realities of health and disease to biomedicine's current forms of explanation. In so doing, we call for medical humanities scholars to actively engage in the speculative question of what nature may be capable of. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

An empirical analysis of ontology reuse in BioPortal.

Science.gov (United States)

Ochs, Christopher; Perl, Yehoshua; Geller, James; Arabandi, Sivaram; Tudorache, Tania; Musen, Mark A

2017-07-01

Biomedical ontologies often reuse content (i.e., classes and properties) from other ontologies. Content reuse enables a consistent representation of a domain and reusing content can save an ontology author significant time and effort. Prior studies have investigated the existence of reused terms among the ontologies in the NCBO BioPortal, but as of yet there has not been a study investigating how the ontologies in BioPortal utilize reused content in the modeling of their own content. In this study we investigate how 355 ontologies hosted in the NCBO BioPortal reuse content from other ontologies for the purposes of creating new ontology content. We identified 197 ontologies that reuse content. Among these ontologies, 108 utilize reused classes in the modeling of their own classes and 116 utilize reused properties in class restrictions. Current utilization of reuse and quality issues related to reuse are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

A Mobile Army of Ontologies

DEFF Research Database (Denmark)

Juul, Jesper

2015-01-01

Presentation at the Ludo-ontologies panel. Do we need ludo-ontologies, and what are they? In this event several scholars of games and videogames discuss these questions from a variety of perspectives. What different game and videogame ontologies exist and could exist, and why they are important...... for game and videogame research? The round table is designed to promote ludo-ontological dialogue in order to make these questions visible and debated. A series of short presentations (approximately 10 minutes each) will be followed by an intense debate through freeform dialogue. After the industrial...... commercialization of games and videogames their study has shifted between approaches focused on players (ludic processes) and artifacts (ludic objects). Some attempts to analyze the relationship between the process and the object have occasionally been done in terms of ‘ontology’ (Zagal 2005; Leino 2010; Gualeni...

Ontology Versioning and Change Detection on the Web

NARCIS (Netherlands)

Klein, Michel; Fensel, Dieter; Kiryakov, Atanas; Ognyanov, Damyan

2002-01-01

To effectively use ontologies on the Web, it is essential that changes in ontologies are managed well. This paper analyzes the topic of ontology versioning in the context of the Web by looking at the characteristics of the version relation between ontologies and at the identification of online

Toward a general ontology for digital forensic disciplines.

Science.gov (United States)

Karie, Nickson M; Venter, Hein S

2014-09-01

Ontologies are widely used in different disciplines as a technique for representing and reasoning about domain knowledge. However, despite the widespread ontology-related research activities and applications in different disciplines, the development of ontologies and ontology research activities is still wanting in digital forensics. This paper therefore presents the case for establishing an ontology for digital forensic disciplines. Such an ontology would enable better categorization of the digital forensic disciplines, as well as assist in the development of methodologies and specifications that can offer direction in different areas of digital forensics. This includes such areas as professional specialization, certifications, development of digital forensic tools, curricula, and educational materials. In addition, the ontology presented in this paper can be used, for example, to better organize the digital forensic domain knowledge and explicitly describe the discipline's semantics in a common way. Finally, this paper is meant to spark discussions and further research on an internationally agreed ontological distinction of the digital forensic disciplines. Digital forensic disciplines ontology is a novel approach toward organizing the digital forensic domain knowledge and constitutes the main contribution of this paper. © 2014 American Academy of Forensic Sciences.

Matching biomedical ontologies based on formal concept analysis.

Science.gov (United States)

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign

The foundational ontology library ROMULUS

CSIR Research Space (South Africa)

Khan, ZC

2013-09-01

Full Text Available . We present here a basic step in that direction with the Repository of Ontologies for MULtiple USes, ROMULUS, which is the first online library of machine-processable, modularised, aligned, and logic-based merged foundational ontologies. In addition...

Tracking Changes during Ontology Evolution

NARCIS (Netherlands)

Noy, Natalya F.; Kunnatur, Sandhya; Klein, Michel; Musen, Mark A.

2004-01-01

As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of documents in large projects. Traditional versioning systems enable users to compare versions, examine changes, and

Ontological engineering versus metaphysics

Science.gov (United States)

Tataj, Emanuel; Tomanek, Roman; Mulawka, Jan

2011-10-01

It has been recognized that ontologies are a semantic version of world wide web and can be found in knowledge-based systems. A recent time survey of this field also suggest that practical artificial intelligence systems may be motivated by this research. Especially strong artificial intelligence as well as concept of homo computer can also benefit from their use. The main objective of this contribution is to present and review already created ontologies and identify the main advantages which derive such approach for knowledge management systems. We would like to present what ontological engineering borrows from metaphysics and what a feedback it can provide to natural language processing, simulations and modelling. The potential topics of further development from philosophical point of view is also underlined.

Nuclear Nonproliferation Ontology Assessment Team Final Report

Energy Technology Data Exchange (ETDEWEB)

Strasburg, Jana D.; Hohimer, Ryan E.

2012-01-01

Final Report for the NA22 Simulations, Algorithm and Modeling (SAM) Ontology Assessment Team's efforts from FY09-FY11. The Ontology Assessment Team began in May 2009 and concluded in September 2011. During this two-year time frame, the Ontology Assessment team had two objectives: (1) Assessing the utility of knowledge representation and semantic technologies for addressing nuclear nonproliferation challenges; and (2) Developing ontological support tools that would provide a framework for integrating across the Simulation, Algorithm and Modeling (SAM) program. The SAM Program was going through a large assessment and strategic planning effort during this time and as a result, the relative importance of these two objectives changed, altering the focus of the Ontology Assessment Team. In the end, the team conducted an assessment of the state of art, created an annotated bibliography, and developed a series of ontological support tools, demonstrations and presentations. A total of more than 35 individuals from 12 different research institutions participated in the Ontology Assessment Team. These included subject matter experts in several nuclear nonproliferation-related domains as well as experts in semantic technologies. Despite the diverse backgrounds and perspectives, the Ontology Assessment team functioned very well together and aspects could serve as a model for future inter-laboratory collaborations and working groups. While the team encountered several challenges and learned many lessons along the way, the Ontology Assessment effort was ultimately a success that led to several multi-lab research projects and opened up a new area of scientific exploration within the Office of Nuclear Nonproliferation and Verification.

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Science.gov (United States)

Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

2015-02-21

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

A Knowledge Engineering Approach to Develop Domain Ontology

Science.gov (United States)

Yun, Hongyan; Xu, Jianliang; Xiong, Jing; Wei, Moji

2011-01-01

Ontologies are one of the most popular and widespread means of knowledge representation and reuse. A few research groups have proposed a series of methodologies for developing their own standard ontologies. However, because this ontological construction concerns special fields, there is no standard method to build domain ontology. In this paper,…

Initial implementation of a comparative data analysis ontology.

Science.gov (United States)

Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

2009-07-03

Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

Using an ontology pattern stack to engineer a core ontology of Accounting Information Systems

NARCIS (Netherlands)

Blums, Ivar; Weigand, Hans

Although the field of Accounting Information Systems (AIS) has a long tradition, there is still a lack of a widely adopted conceptualization. In this paper, The UFO ontology patterns are regarded for application by analogy and extension in the engineering of a core ontology for AIS. The new IASB

Concerning the Importance of Ontological Issues for Cultural Psychology: a Reply to Comments.

Science.gov (United States)

Mironenko, Irina A

2017-09-01

The paper continues the "ontological" discussion in IBPS, addressing the question of the importance of ontological issues for contemporary development of cultural psychology. The language psychological science speaks is considered as an ontological issue and a most topical one for cultural psychology, aiming at "constructing a psychology that is universal while being culture-inclusive" (Valsiner 2009, p.2). Ontological issues could stay implicit and neglected, as long as the 'etant, "the mode of being", "the particularities" were discussed within the circle of adherents of one and the same school, who implicitly had in mind the same 'entre. However, as soon as the discussion involves representatives of different schools, ontological issues become crucial for mutual understanding and meanings of the words have to be explicated. Same words like "psyche", "subjectivity", "social", "culture", etc., - often mean different things when they are pronounces or written by representatives of different theoretical trends. The discussion of the 'etant without clear indicating of the 'entre under consideration is likely to turn into a Babel. Global modernity requires constant efforts and insistent desire for mutual understanding across the diversified global scientific community. Thus, creative collaboration in epistemological developments has to ground on clear comprehension of the ontological stances of the debaters.

Ontological, Epistemological and Methodological Assumptions: Qualitative versus Quantitative

Science.gov (United States)

Ahmed, Abdelhamid

2008-01-01

The review to follow is a comparative analysis of two studies conducted in the field of TESOL in Education published in "TESOL QUARTERLY." The aspects to be compared are as follows. First, a brief description of each study will be presented. Second, the ontological, epistemological and methodological assumptions underlying each study…

XML, Ontologies, and Their Clinical Applications.

Science.gov (United States)

Yu, Chunjiang; Shen, Bairong

2016-01-01

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

A methodology to migrate the gene ontology to a description logic environment using DAML+OIL.

Science.gov (United States)

Wroe, C J; Stevens, R; Goble, C A; Ashburner, M

2003-01-01

The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal expressiveness and the reasoning capabilities of the underlying description logic. Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology. The paper introduces DAML+OIL and demonstrates the activity within each stage of the methodology and the functionality gained.

Versioning System for Distributed Ontology Development

Science.gov (United States)

2016-03-15

Framework for Grid Computing and Semantic Web Services,” Trust Management, Springer Berlin Heidelberg (2004), pp. 16−26. [TIME] W3C, “Time Ontology in...Distributed Ontology Development S.K. Damodaran 15 March 2016 This material is based on work supported by the Assistant Secretary of Defense for...Distributed Ontology Development S.K. Damodaran Formerly Group 59 15 March 2016 Massachusetts Institute of Technology Lincoln Laboratory

The Development of Ontology from Multiple Databases

Science.gov (United States)

Kasim, Shahreen; Aswa Omar, Nurul; Fudzee, Mohd Farhan Md; Azhar Ramli, Azizul; Aizi Salamat, Mohamad; Mahdin, Hairulnizam

2017-08-01

The area of halal industry is the fastest growing global business across the world. The halal food industry is thus crucial for Muslims all over the world as it serves to ensure them that the food items they consume daily are syariah compliant. Currently, ontology has been widely used in computer sciences area such as web on the heterogeneous information processing, semantic web, and information retrieval. However, ontology has still not been used widely in the halal industry. Today, Muslim community still have problem to verify halal status for products in the market especially foods consisting of E number. This research tried to solve problem in validating the halal status from various halal sources. There are various chemical ontology from multilple databases found to help this ontology development. The E numbers in this chemical ontology are codes for chemicals that can be used as food additives. With this E numbers ontology, Muslim community could identify and verify the halal status effectively for halal products in the market.

FOCIH: Form-Based Ontology Creation and Information Harvesting

Science.gov (United States)

Tao, Cui; Embley, David W.; Liddle, Stephen W.

Creating an ontology and populating it with data are both labor-intensive tasks requiring a high degree of expertise. Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data—which some see as Web 3.0—is prohibitive. Can we find ways to streamline these tasks and lower the barrier enough to enable Web 3.0? Toward this end we offer a form-based approach to ontology creation that provides a way to create Web 3.0 ontologies without the need for specialized training. And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology. In addition to harvesting information with respect to an ontology, the approach also annotates web pages and links facts in web pages to ontological concepts, resulting in a web of data superimposed over the web of pages. Experience with our prototype system shows that mappings between conceptual-model-based ontologies and forms are sufficient for creating the kind of ontologies needed for Web 3.0, and experiments with our prototype system show that automatic harvesting, automatic annotation, and automatic superimposition of a web of data over a web of pages work well.

Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.

Science.gov (United States)

Malhotra, Ashutosh; Gündel, Michaela; Rajput, Abdul Mateen; Mevissen, Heinz-Theodor; Saiz, Albert; Pastor, Xavier; Lozano-Rubi, Raimundo; Martinez-Lapiscina, Elena H; Martinez-Lapsicina, Elena H; Zubizarreta, Irati; Mueller, Bernd; Kotelnikova, Ekaterina; Toldo, Luca; Hofmann-Apitius, Martin; Villoslada, Pablo

2015-01-01

In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS). The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology. Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports. The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information.

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

Science.gov (United States)

Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

2018-04-01

With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

Ontology Based Model Transformation Infrastructure

NARCIS (Netherlands)

Göknil, Arda; Topaloglu, N.Y.

2005-01-01

Using MDA in ontology development has been investigated in several works recently. The mappings and transformations between the UML constructs and the OWL elements to develop ontologies are the main concern of these research projects. We propose another approach in order to achieve the collaboration

One Song, Many Works: A Pluralist Ontology of Rock

Directory of Open Access Journals (Sweden)

Dan Burkett

2016-01-01

Full Text Available A number of attempts have been made to construct a plausible ontology of rock music. Each of these ontologies identifies a single type of ontological entity as the “work” in rock music. Yet, all the suggestions advanced to date fail to capture some important considerations about how we engage with music of this tradition. This prompted Lee Brown to advocate a healthy skepticism of higher-order musical ontologies. I argue here that we should instead embrace a pluralist ontology of rock, an ontology that recognizes more than one kind of entity as “the work” in rock music. I contend that this approach has a number of advantages over other ontologies of rock, including that of allowing us to make some comparisons across ontological kinds.

Learning expressive ontologies

CERN Document Server

Völker, J

2009-01-01

This publication advances the state-of-the-art in ontology learning by presenting a set of novel approaches to the semi-automatic acquisition, refinement and evaluation of logically complex axiomatizations. It has been motivated by the fact that the realization of the semantic web envisioned by Tim Berners-Lee is still hampered by the lack of ontological resources, while at the same time more and more applications of semantic technologies emerge from fast-growing areas such as e-business or life sciences. Such knowledge-intensive applications, requiring large scale reasoning over complex domai

The current landscape of pitfalls in Ontologies

CSIR Research Space (South Africa)

Keet, CM

2013-09-01

Full Text Available 2Ontology Engineering Group, Departamento de Inteligencia Artificial, Universidad Polite´cnica de Madrid, Madrid, Spain keet@ukzn.ac.za, {mcsuarez,mpoveda}@fi.upm.es Keywords: Ontology Development : Ontology Quality : Pitfall Abstract: A growing... in Ontologies C. Maria Keet1, Mari Carmen Sua´rez-Figueroa2 and Marı´a Poveda-Villalo´n2 1School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, and UKZN/CSIR-Meraka Centre for Artificial Intelligence Research, Durban, South Africa...

Toward semantic interoperability with linked foundational ontologies in ROMULUS

CSIR Research Space (South Africa)

Khan, ZC

2013-06-01

Full Text Available A purpose of a foundational ontology is to solve interoperability issues among ontologies. Many foundational ontologies have been developed, reintroducing the ontology interoperability problem. We address this with the new online foundational...

Logic and Ontology

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Newton C. A. da Costa

2002-12-01

Full Text Available In view of the present state of development of non classical logic, especially of paraconsistent logic, a new stand regarding the relations between logic and ontology is defended In a parody of a dictum of Quine, my stand May be summarized as follows. To be is to be the value of a variable a specific language with a given underlying logic Yet my stand differs from Quine’s, because, among other reasons, I accept some first order heterodox logics as genuine alternatives to classical logic I also discuss some questions of non classical logic to substantiate my argument, and suggest that may position complements and extends some ideas advanced by L Apostel.

ONTOLOGY-DRIVEN TOOL FOR UTILIZING PROGRAMMING STYLES

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Nikolay Sidorov

2017-07-01

Full Text Available Activities of a programmer will be more effective and the software will be more understandable when within the process of software development, programming styles (standards are used, providing clarity of software texts. Purpose: In this research, we present the tool for the realization of new ontology-based methodology automated reasoning techniques for utilizing programming styles. In particular, we focus on representing programming styles in the form of formal ontologies, and study how description logic reasoner can assist programmers in utilizing programming standards. Our research hypothesis is as follows: ontological representation of programming styles can provide additional benefits over existing approaches in utilizing programmer of programming standards. Our research goal is to develop a tool to support the ontology-based utilizing programming styles. Methods: ontological representation of programming styles; object-oriented programming; ontology-driven utilizing of programming styles. Results: the architecture was obtained and the tool was developed in the Java language, which provide tool support of ontology-driven programming styles application method. On the example of naming of the Java programming language standard, features of implementation and application of the tool are provided. Discussion: application of programming styles in coding of program; lack of automated tools for the processes of programming standards application; tool based on new method of ontology-driven application of programming styles; an example of the implementation of tool architecture for naming rules of the Java language standard.

Crowdsourcing the verification of relationships in biomedical ontologies.

Science.gov (United States)

Mortensen, Jonathan M; Musen, Mark A; Noy, Natalya F

2013-01-01

Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply.

Ontology Enabled Generation of Embedded Web Services

DEFF Research Database (Denmark)

Hansen, Klaus Marius; Zhang, Weishan; Soares, Goncalo Teofilo Afonso Pinheiro

2008-01-01

and software platforms, and of devices state and context changes. To address these challenges, we developed a Web service compiler, Limbo, in which Web Ontology Language (OWL) ontologies are used to make the Limbo compiler aware of its compilation context, such as targeted hardware and software. At the same...... time, knowledge on device details, platform dependencies, and resource/power consumption is built into the supporting ontologies, which are used to configure Limbo for generating resource efficient web service code. A state machine ontology is used to generate stub code to facilitate handling of state...

Product line based ontology development for semantic web service

DEFF Research Database (Denmark)

Zhang, Weishan; Kunz, Thomas

2006-01-01

Ontology is recognized as a key technology for the success of the Semantic Web. Building reusable and evolve-able ontologies in order to cope with ontology evolution and requirement changes is increasingly important. But the existing methodologies and tools fail to support effective ontology reuse...... will lead to the initial implementation of the meta-onotologies using design by reuse and with the objective of design for reuse. After that step new ontologies could be generated by reusing these meta-ontologies. We demonstrate our approach with a Semantic Web Service application to show how to build...

IfcOWL: A case of transforming EXPRESS schemas into ontologies

NARCIS (Netherlands)

Beetz, J.; Leeuwen, van J.P.; Vries, de B.

2009-01-01

Ontologies have been successfully applied as a semantic enabler of communication between both users and applications in fragmented, heterogeneous multinational business environments. In this paper we discuss the underlying principles, their current implementation status, and most importantly, their

Learning Ontology from Object-Relational Database

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Kaulins Andrejs

2015-12-01

Full Text Available This article describes a method of transformation of object-relational model into ontology. The offered method uses learning rules for such complex data types as object tables and collections – arrays of a variable size, as well as nested tables. Object types and their transformation into ontologies are insufficiently considered in scientific literature. This fact served as motivation for the authors to investigate this issue and to write the article on this matter. In the beginning, we acquaint the reader with complex data types and object-oriented databases. Then we describe an algorithm of transformation of complex data types into ontologies. At the end of the article, some examples of ontologies described in the OWL language are given.

Comparing Relational and Ontological Triple Stores in Healthcare Domain

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Ozgu Can

2017-01-01

Full Text Available Today’s technological improvements have made ubiquitous healthcare systems that converge into smart healthcare applications in order to solve patients’ problems, to communicate effectively with patients, and to improve healthcare service quality. The first step of building a smart healthcare information system is representing the healthcare data as connected, reachable, and sharable. In order to achieve this representation, ontologies are used to describe the healthcare data. Combining ontological healthcare data with the used and obtained data can be maintained by storing the entire health domain data inside big data stores that support both relational and graph-based ontological data. There are several big data stores and different types of big data sets in the healthcare domain. The goal of this paper is to determine the most applicable ontology data store for storing the big healthcare data. For this purpose, AllegroGraph and Oracle 12c data stores are compared based on their infrastructural capacity, loading time, and query response times. Hence, healthcare ontologies (GENE Ontology, Gene Expression Ontology (GEXO, Regulation of Transcription Ontology (RETO, Regulation of Gene Expression Ontology (REXO are used to measure the ontology loading time. Thereafter, various queries are constructed and executed for GENE ontology in order to measure the capacity and query response times for the performance comparison between AllegroGraph and Oracle 12c triple stores.

Ontologies, Knowledge Bases and Knowledge Management

National Research Council Canada - National Science Library

Chalupsky, Hans

2002-01-01

...) an application called Strategy Development Assistant (SDA) that uses that ontology. The JFACC ontology served as a basis for knowledge sharing among several applications in the domain of air campaign planning...

A histological ontology of the human cardiovascular system.

Science.gov (United States)

Mazo, Claudia; Salazar, Liliana; Corcho, Oscar; Trujillo, Maria; Alegre, Enrique

2017-10-02

In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology.org/ontologies/HO and https://w3id.org/def/System . The histological ontology is developed to support complex tasks, such as supporting teaching activities, medical practices, and bio-medical research or having natural language interactions.

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

Science.gov (United States)

Bibault, Jean-Emmanuel; Zapletal, Eric; Rance, Bastien; Giraud, Philippe; Burgun, Anita

2018-01-01

Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our "record-and-verify" system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique-Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).

Structure-based classification and ontology in chemistry

Directory of Open Access Journals (Sweden)

Hastings Janna

2012-04-01

Full Text Available Abstract Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures, while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational

Best behaviour? Ontologies and the formal description of animal behaviour

KAUST Repository

Gkoutos, Georgios V.; Hoehndorf, Robert; Tsaprouni, Loukia; Schofield, Paul N.

2015-01-01

underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain. © 2015 Springer Science

An Iterative and Incremental Approach for E-Learning Ontology Engineering

Directory of Open Access Journals (Sweden)

Sudath Rohitha Heiyanthuduwage

2009-03-01

Full Text Available Abstract - There is a boost in the interest on ontology with the developments in Semantic Web technologies. Ontologies play a vital role in semantic web. Even though there is lot of work done on ontology, still a standard framework for ontology engineering has not been defined. Even though current ontology engineering methodologies are available they need improvements. The effort of our work is to integrate various methods, techniques, tools and etc to different stages of proposed ontology engineering life cycle to create a comprehensive framework for ontology engineering. Current methodologies discuss ontology engineering stages and collaborative environments with user collaboration. However, discussion on increasing effectiveness and correct inference has been given less attention. More over, these methodologies provide little discussion on usability of domain ontologies. We consider these aspects as more important in our work. Also, ontology engineering has been done for various domains and for various purposes. Our effort is to propose an iterative and incremental approach for ontology engineering especially for e-learning domain with the intention of achieving a higher usability and effectiveness of e-learning systems. This paper introduces different aspects of the proposed ontology engineering framework and evaluation of it.

Biomedicine: an ontological dissection.

Science.gov (United States)

Baronov, David

2008-01-01

Though ubiquitous across the medical social sciences literature, the term "biomedicine" as an analytical concept remains remarkably slippery. It is argued here that this imprecision is due in part to the fact that biomedicine is comprised of three interrelated ontological spheres, each of which frames biomedicine as a distinct subject of investigation. This suggests that, depending upon one's ontological commitment, the meaning of biomedicine will shift. From an empirical perspective, biomedicine takes on the appearance of a scientific enterprise and is defined as a derivative category of Western science more generally. From an interpretive perspective, biomedicine represents a symbolic-cultural expression whose adherence to the principles of scientific objectivity conceals an ideological agenda. From a conceptual perspective, biomedicine represents an expression of social power that reflects structures of power and privilege within capitalist society. No one perspective exists in isolation and so the image of biomedicine from any one presents an incomplete understanding. It is the mutually-conditioning interrelations between these ontological spheres that account for biomedicine's ongoing development. Thus, the ontological dissection of biomedicine that follows, with particular emphasis on the period of its formal crystallization in the latter nineteenth and early twentieth century, is intended to deepen our understanding of biomedicine as an analytical concept across the medical social sciences literature.

Coupling ontology driven semantic representation with multilingual natural language generation for tuning international terminologies.

Science.gov (United States)

Rassinoux, Anne-Marie; Baud, Robert H; Rodrigues, Jean-Marie; Lovis, Christian; Geissbühler, Antoine

2007-01-01

The importance of clinical communication between providers, consumers and others, as well as the requisite for computer interoperability, strengthens the need for sharing common accepted terminologies. Under the directives of the World Health Organization (WHO), an approach is currently being conducted in Australia to adopt a standardized terminology for medical procedures that is intended to become an international reference. In order to achieve such a standard, a collaborative approach is adopted, in line with the successful experiment conducted for the development of the new French coding system CCAM. Different coding centres are involved in setting up a semantic representation of each term using a formal ontological structure expressed through a logic-based representation language. From this language-independent representation, multilingual natural language generation (NLG) is performed to produce noun phrases in various languages that are further compared for consistency with the original terms. Outcomes are presented for the assessment of the International Classification of Health Interventions (ICHI) and its translation into Portuguese. The initial results clearly emphasize the feasibility and cost-effectiveness of the proposed method for handling both a different classification and an additional language. NLG tools, based on ontology driven semantic representation, facilitate the discovery of ambiguous and inconsistent terms, and, as such, should be promoted for establishing coherent international terminologies.

Construction of ontology augmented networks for protein complex prediction.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

ONTOLOGY IN PHARMACY

Directory of Open Access Journals (Sweden)

L. Yu. Babintseva

2015-05-01

Full Text Available It’s considered ontological models for formalization of knowledge in pharmacy. There is emphasized the view that the possibility of rapid exchange of information in the pharmaceutical industry, it is necessary to create a single information space. This means not only the establishment of uniform standards for the presentation of information on pharmaceutical groups pharmacotherapeutic classifications, but also the creation of a unified and standardized system for the transfer and renewal of knowledge. It is the organization of information in the ontology helps quickly in the future to build expert systems and applications to work with data.

Finding the best visualization of an ontology

DEFF Research Database (Denmark)

Fabritius, Christina; Madsen, Nadia; Clausen, Jens

2006-01-01

An ontology is a classification model for a given domain.In information retrieval ontologies are used to perform broad searches.An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

Finding the best visualization of an ontology

DEFF Research Database (Denmark)

Fabritius, Christina Valentin; Madsen, Nadia Lyngaa; Clausen, Jens

2004-01-01

An ontology is a classification model for a given domain. In information retrieval ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

Manufacturing ontology through templates

Directory of Open Access Journals (Sweden)

Diciuc Vlad

2017-01-01

Full Text Available The manufacturing industry contains a high volume of knowhow and of high value, much of it being held by key persons in the company. The passing of this know-how is the basis of manufacturing ontology. Among other methods like advanced filtering and algorithm based decision making, one way of handling the manufacturing ontology is via templates. The current paper tackles this approach and highlights the advantages concluding with some recommendations.

Initial Implementation of a comparative Data Analysis Ontology

Directory of Open Access Journals (Sweden)

Francisco Prosdocimi

2009-01-01

Full Text Available Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs, representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL, we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO. CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc. that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

Initial Implementation of a Comparative Data Analysis Ontology

Directory of Open Access Journals (Sweden)

Francisco Prosdocimi

2009-07-01

Full Text Available Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: “Operational Taxonomic Units” (OTUs, representing the entities to be compared; “character-state data” representing the observations compared among OTUs; “phylogenetic tree”, representing the historical path of evolution among the entities; and “transitions”, the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL, we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO. CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc. that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

Technique for designing a domain ontology

OpenAIRE

Palagin, A. V.; Petrenko, N. G.; Malakhov, K. S.

2018-01-01

The article describes the technique for designing a domain ontology, shows the flowchart of algorithm design and example of constructing a fragment of the ontology of the subject area of Computer Science is considered.

Decision-Making under Criteria Uncertainty

Science.gov (United States)

Kureychik, V. M.; Safronenkova, I. B.

2018-05-01

Uncertainty is an essential part of a decision-making procedure. The paper deals with the problem of decision-making under criteria uncertainty. In this context, decision-making under uncertainty, types and conditions of uncertainty were examined. The decision-making problem under uncertainty was formalized. A modification of the mathematical decision support method under uncertainty via ontologies was proposed. A critical distinction of the developed method is ontology usage as its base elements. The goal of this work is a development of a decision-making method under criteria uncertainty with the use of ontologies in the area of multilayer board designing. This method is oriented to improvement of technical-economic values of the examined domain.

Ontology modeling in physical asset integrity management

CERN Document Server

Yacout, Soumaya

2015-01-01

This book presents cutting-edge applications of, and up-to-date research on, ontology engineering techniques in the physical asset integrity domain. Though a survey of state-of-the-art theory and methods on ontology engineering, the authors emphasize essential topics including data integration modeling, knowledge representation, and semantic interpretation. The book also reflects novel topics dealing with the advanced problems of physical asset integrity applications such as heterogeneity, data inconsistency, and interoperability existing in design and utilization. With a distinctive focus on applications relevant in heavy industry, Ontology Modeling in Physical Asset Integrity Management is ideal for practicing industrial and mechanical engineers working in the field, as well as researchers and graduate concerned with ontology engineering in physical systems life cycles. This book also: Introduces practicing engineers, research scientists, and graduate students to ontology engineering as a modeling techniqu...

Methodology to build medical ontology from textual resources.

Science.gov (United States)

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2006-01-01

In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.

Markov Chain Ontology Analysis (MCOA).

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Frost, H Robert; McCray, Alexa T

2012-02-03

Biomedical ontologies have become an increasingly critical lens through which researchers analyze the genomic, clinical and bibliographic data that fuels scientific research. Of particular relevance are methods, such as enrichment analysis, that quantify the importance of ontology classes relative to a collection of domain data. Current analytical techniques, however, remain limited in their ability to handle many important types of structural complexity encountered in real biological systems including class overlaps, continuously valued data, inter-instance relationships, non-hierarchical relationships between classes, semantic distance and sparse data. In this paper, we describe a methodology called Markov Chain Ontology Analysis (MCOA) and illustrate its use through a MCOA-based enrichment analysis application based on a generative model of gene activation. MCOA models the classes in an ontology, the instances from an associated dataset and all directional inter-class, class-to-instance and inter-instance relationships as a single finite ergodic Markov chain. The adjusted transition probability matrix for this Markov chain enables the calculation of eigenvector values that quantify the importance of each ontology class relative to other classes and the associated data set members. On both controlled Gene Ontology (GO) data sets created with Escherichia coli, Drosophila melanogaster and Homo sapiens annotations and real gene expression data extracted from the Gene Expression Omnibus (GEO), the MCOA enrichment analysis approach provides the best performance of comparable state-of-the-art methods. A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing state-of-the-art approaches.

Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules.

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Lezcano, Leonardo; Sicilia, Miguel-Angel; Rodríguez-Solano, Carlos

2011-04-01

Semantic interoperability is essential to facilitate the computerized support for alerts, workflow management and evidence-based healthcare across heterogeneous electronic health record (EHR) systems. Clinical archetypes, which are formal definitions of specific clinical concepts defined as specializations of a generic reference (information) model, provide a mechanism to express data structures in a shared and interoperable way. However, currently available archetype languages do not provide direct support for mapping to formal ontologies and then exploiting reasoning on clinical knowledge, which are key ingredients of full semantic interoperability, as stated in the SemanticHEALTH report [1]. This paper reports on an approach to translate definitions expressed in the openEHR Archetype Definition Language (ADL) to a formal representation expressed using the Ontology Web Language (OWL). The formal representations are then integrated with rules expressed with Semantic Web Rule Language (SWRL) expressions, providing an approach to apply the SWRL rules to concrete instances of clinical data. Sharing the knowledge expressed in the form of rules is consistent with the philosophy of open sharing, encouraged by archetypes. Our approach also allows the reuse of formal knowledge, expressed through ontologies, and extends reuse to propositions of declarative knowledge, such as those encoded in clinical guidelines. This paper describes the ADL-to-OWL translation approach, describes the techniques to map archetypes to formal ontologies, and demonstrates how rules can be applied to the resulting representation. We provide examples taken from a patient safety alerting system to illustrate our approach. Copyright © 2010 Elsevier Inc. All rights reserved.

Building an ontology of pulmonary diseases with natural language processing tools using textual corpora.

Science.gov (United States)

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2007-01-01

Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri are not suitable for computer processing. We think the automation of the coding task requires a conceptual modeling of medical items: an ontology. Our task is to help lung specialists code acts and diagnoses with software that represents medical knowledge of this concerned specialty by an ontology. The objective of the reported work was to build an ontology of pulmonary diseases dedicated to the coding process. To carry out this objective, we develop a precise methodological process for the knowledge engineer in order to build various types of medical ontologies. This process is based on the need to express precisely in natural language the meaning of each concept using differential semantics principles. A differential ontology is a hierarchy of concepts and relationships organized according to their similarities and differences. Our main research hypothesis is to apply natural language processing tools to corpora to develop the resources needed to build the ontology. We consider two corpora, one composed of patient discharge summaries and the other being a teaching book. We propose to combine two approaches to enrich the ontology building: (i) a method which consists of building terminological resources through distributional analysis and (ii) a method based on the observation of corpus sequences in order to reveal semantic relationships. Our ontology currently includes 1550 concepts and the software implementing the coding process is still under development. Results show that the proposed approach is operational and indicates that the combination of these methods and the comparison of the resulting terminological structures give interesting clues to a knowledge engineer for the building of an ontology.

Addressing issues in foundational ontology mediation

CSIR Research Space (South Africa)

Khan, ZC

2013-09-01

Full Text Available An approach in achieving semantic interoperability among heterogeneous systems is to offer infrastructure to assist with linking and integration using a foundational ontology. Due to the creation of multiple foundational ontologies, this also means...

Player-Specific Conflict Handling Ontology

Directory of Open Access Journals (Sweden)

Charline Hondrou

2014-09-01

Full Text Available This paper presents an ontology that leads the player of a serious game - regarding conflict handling - to the educative experience from which they will benefit the most. It provides a clearly defined tree of axioms that maps the player’s visually manifested affective cues and emotional stimuli from the serious game to conflict handling styles and proposes interventions. The importance of this ontology lies in the fact that it promotes natural interaction (non-invasive methods and at the same time makes the game as player-specific as it can be for its educational goal. It is an ontology that can be adapted to different educational theories and serve various educational purposes.

Ontology Matching with Semantic Verification.

Science.gov (United States)

Jean-Mary, Yves R; Shironoshita, E Patrick; Kabuka, Mansur R

2009-09-01

ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

The Electronic Notebook Ontology

OpenAIRE

Chalk, Stuart

2016-01-01

Science is rapidly being brought into the electronic realm and electronic laboratory notebooks (ELN) are a big part of this activity. The representation of the scientific process in the context of an ELN is an important component to making the data recorded in ELNs semantically integrated. This presentation will outline initial developments of an Electronic Notebook Ontology (ENO) that will help tie together the ExptML ontology, HCLS Community Profile data descriptions, and the VIVO-ISF ontol...

DeMO: An Ontology for Discrete-event Modeling and Simulation

Science.gov (United States)

Silver, Gregory A; Miller, John A; Hybinette, Maria; Baramidze, Gregory; York, William S

2011-01-01

Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community. PMID:22919114

ContoExam: an ontology on context-aware examinations

NARCIS (Netherlands)

Brandt, P.; Basten, A.A.; Stuijk, S.

2014-01-01

Patient observations in health care, subjective surveys in social research or dyke sensor data in water management are all examples of measurements. Several ontologies already exist to express measurements, W3C's SSN ontology being a prominent example. However, these ontologies address quantities

On the ontological emergence from quantum regime

Energy Technology Data Exchange (ETDEWEB)

Luty, Damian [Adam Mickiewicz University, Poznan (Poland)

2014-07-01

There are several views on the relation between quantum physics and theory of relativity (especially General Relativity, GR). A popular perspective is this: GR with its macroscopic gravitational effects will turn out to be a limit of a more fundamental theory which should consider discrete physics and not deal with continuity (like theory of relativity). Thus, GR will emerge from a more basic theory, which should be quantum-like. One could call this an epistemic emergence view towards fundamental theories. The question is, given that scientific realism is valid: should emergence be a fundamental notion in our ontological view about the evolving, physical Universe? Is there an ontological emergence fully compatible with the notion of fundamentality? I argue that if we want to defend ontological emergence (from quantum to macroscopic regime) as something fundamental, we will arrive at the position of metaphysics of dispositions (and I argue, why this is undesirable), or conclude, that we cannot square fully fundamental ontology with the notion of emergence, and that we have to accept an ontological pluralism relativised to a certain scale. I defend the latter proposition, showing, that epistemic emergence doesn't entail (logically) ontological emergence.

Applications of the ACGT Master Ontology on Cancer

OpenAIRE

Brochhausen, Mathias; Weiler, Gabriele; Martín Martín, Luis; Cocos, Cristian; Stenzhorn, Holger; Graf, Norbert; Dörr, Martin; Tsiknakis, Manolis; Smith, Barry

2008-01-01

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the...

Improving the interoperability of biomedical ontologies with compound alignments.

Science.gov (United States)

Oliveira, Daniela; Pesquita, Catia

2018-01-09

Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ontologies, bridging this gap can be challenging. In the last decade, ontology matching systems have been evolving and are now capable of producing high-quality mappings for life sciences ontologies, usually limited to the equivalence between two ontologies. However, life sciences research is becoming increasingly transdisciplinary and integrative, fostering the need to develop matching strategies that are able to handle multiple ontologies and more complex relations between their concepts. We have developed ontology matching algorithms that are able to find compound mappings between multiple biomedical ontologies, in the form of ternary mappings, finding for instance that "aortic valve stenosis"(HP:0001650) is equivalent to the intersection between "aortic valve"(FMA:7236) and "constricted" (PATO:0001847). The algorithms take advantage of search space filtering based on partial mappings between ontology pairs, to be able to handle the increased computational demands. The evaluation of the algorithms has shown that they are able to produce meaningful results, with precision in the range of 60-92% for new mappings. The algorithms were also applied to the potential extension of logical definitions of the OBO and the matching of several plant-related ontologies. This work is a first step towards finding more complex relations between multiple ontologies. The evaluation shows that the results produced are significant and that the algorithms could satisfy specific integration needs.

Ontology through a Mindfulness Process

Science.gov (United States)

Bearance, Deborah; Holmes, Kimberley

2015-01-01

Traditionally, when ontology is taught in a graduate studies course on social research, there is a tendency for this concept to be examined through the process of lectures and readings. Such an approach often leaves graduate students to grapple with a personal embodiment of this concept and to comprehend how ontology can ground their research.…

Development and Evaluation of an Ontology for Guiding Appropriate Antibiotic Prescribing

Science.gov (United States)

Furuya, E. Yoko; Kuperman, Gilad J.; Cimino, James J.; Bakken, Suzanne

2011-01-01

Objectives To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. Methods We extended existing ontology development methods to create the ontology and implemented the ontology using Protégé-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. Results The ontology includes 199 classes, 10 properties, and 1,636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: 1) antibiotic-microorganism mismatch alert; 2) medication-allergy alert; and 3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. Conclusions This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component—a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks. PMID:22019377

An Ontology for Description of Drug Discovery Investigations

Directory of Open Access Journals (Sweden)

Qi Da

2010-12-01

Full Text Available The paper presents an ontology for the description of Drug Discovery Investigation (DDI. This has been developed through the use of a Robot Scientist “Eve”, and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home

Menthor Editor: An Ontology-Driven Conceptual Modeling Platform

NARCIS (Netherlands)

Moreira, João Luiz; Sales, Tiago Prince; Guerson, John; Braga, Bernardo F.B; Brasileiro, Freddy; Sobral, Vinicius

2016-01-01

The lack of well-founded constructs in ontology tools can lead to the construction of non-intended models. In this demonstration we present the Menthor Editor, an ontology-driven conceptual modelling platform which incorporates the theories of the Unified Foundational Ontology (UFO). We illustrate

Ontology-based intelligent fuzzy agent for diabetes application

NARCIS (Netherlands)

Acampora, G.; Lee, C.-S.; Wang, M.-H.; Hsu, C.-Y.; Loia, V.

2009-01-01

It is widely pointed out that classical ontologies are not sufficient to deal with imprecise and vague knowledge for some real world applications, but the fuzzy ontology can effectively solve data and knowledge with uncertainty. In this paper, an ontology-based intelligent fuzzy agent (OIFA),

War of ontology worlds: mathematics, computer code, or Esperanto?

Science.gov (United States)

Rzhetsky, Andrey; Evans, James A

2011-09-01

The use of structured knowledge representations-ontologies and terminologies-has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

St. Thomas and the hilemorfic ontology

Directory of Open Access Journals (Sweden)

Lawrence Dewan, O.P.

2009-06-01

Full Text Available This article presents the relevancy of Aristotle’s hylemorphic ontology.Aristotle himself highlighted the importance and astonishing complexityof the problem of prime matter’s ontological status and he presenting thesolution in his doctrine of hylemorphism. As Saint Thomas Aquinasnoted, it is a crucial issue for philosophy because all four, hilemorfism,logic, physics and metaphysics, stand or fall depending on a correctunderstanding of the ontology of prime matter and of the kind of causalrelationship which exist between prime matter and substantial form ingenerable and corruptible substance.

Hierarchical Analysis of the Omega Ontology

Energy Technology Data Exchange (ETDEWEB)

Joslyn, Cliff A.; Paulson, Patrick R.

2009-12-01

Initial delivery for mathematical analysis of the Omega Ontology. We provide an analysis of the hierarchical structure of a version of the Omega Ontology currently in use within the US Government. After providing an initial statistical analysis of the distribution of all link types in the ontology, we then provide a detailed order theoretical analysis of each of the four main hierarchical links present. This order theoretical analysis includes the distribution of components and their properties, their parent/child and multiple inheritance structure, and the distribution of their vertical ranks.

Conflict Resolution in Partially Ordered OWL DL Ontologies

NARCIS (Netherlands)

Ji, Q.; Gao, Z.; Huang, Z.

2014-01-01

Inconsistency handling in OWL DL ontologies is an important problem because an ontology can easily be inconsistent when it is generated or modified. Current approaches to dealing with inconsistent ontologies often assume that there exists a total order over axioms and use such an order to select

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

Science.gov (United States)

Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

2015-01-01

Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using INO-based literature mining results, a modified Fisher's exact test was established to analyze significantly over- and under-represented enriched gene-gene interaction types within a specific area. Such a strategy was applied to study the vaccine-mediated gene-gene interactions using all PubMed abstracts. The Vaccine Ontology (VO) and INO were used to support the retrieval of vaccine terms and interaction keywords from the literature. INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies. Current INO includes 540 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms with 'INO_' prefix. A new annotation property, 'has literature mining keywords', was generated to allow the listing of different keywords mapping to the interaction types in INO. Using all PubMed documents published as of 12/31/2013, approximately 266,000 vaccine-associated documents were identified, and a total of 6,116 gene-pairs were associated with at least one INO term. Out of 78 INO interaction terms associated with at least five gene-pairs of the vaccine-associated sub-network, 14 terms were significantly over-represented (i.e., more frequently used) and 17 under-represented based on our modified Fisher's exact test. These over-represented and under-represented terms share some common top-level terms but are distinct at the bottom levels of the INO hierarchy. The analysis of these

An Ontology for Modeling Complex Inter-relational Organizations

Science.gov (United States)

Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.

Science.gov (United States)

Wirkner, Christian S; Göpel, Torben; Runge, Jens; Keiler, Jonas; Klussmann-Fricke, Bastian-Jesper; Huckstorf, Katarina; Scholz, Stephan; Mikó, István; J Yoder, Matthew; Richter, Stefan

2017-09-01

Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the

Aber-OWL: a framework for ontology-based data access in biology

KAUST Repository

Hoehndorf, Robert

2015-01-28

Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net. Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

An Ontological Architecture for Orbital Debris Data

OpenAIRE

Rovetto, Robert J.

2017-01-01

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to ...

Integrating Ontology Debugging and Matching into the eXtreme Design Methodology

OpenAIRE

Dragisic, Zlatan; Lambrix, Patrick; Blomqvist, Eva

2015-01-01

Ontology design patterns (ODPs) and related ontology development methodologies were designed as ways of sharing and reusing best practices in ontology engineering. However, while the use of these reduces the number of issues in the resulting ontologies defects can still be introduced into the ontology due to improper use or misinterpretation of the patterns. Thus, the quality of the developed ontologies is still a major concern. In this paper we address this issue by describing how ontology d...

MultiFarm: A Benchmark for Multilingual Ontology Matching

NARCIS (Netherlands)

Meilicke, C.; García-Castro, R.; Freitas, F.; van Hage, W.R.; Montiel-Ponsoda, E.; Ribeiro de Azevedo, R.; Stuckenschmidt, H.; Svab-Zamazal, O.; Svatek, V.; Tamalin, A.; Wang, S.

2012-01-01

In this paper we present the MultiFarm dataset, which has been designed as a benchmark for multilingual ontology matching. The MultiFarm dataset is composed of a set of ontologies translated in different languages and the corresponding alignments between these ontologies. It is based on the OntoFarm

Integrity and change in modular ontologies

NARCIS (Netherlands)

Stuckenschmidt, Heiner; Klein, Michel

2003-01-01

The benefits of modular representations arc well known from many areas of computer science. In this paper, we concentrate on the benefits of modular ontologies with respect to local containment of terminological reasoning. We define an architecture for modular ontologies that supports local

Collaborative ontology development for the geosciences

NARCIS (Netherlands)

Kalbasi Khoramdashti, R.; Janowicz, K.; Reitsma, F.; Boerboom, L.G.J.; Alasheikh, A.

2014-01-01

Ontology-based information publishing, retrieval, reuse, and integration have become popular research topics to address the challenges involved in exchanging data between heterogeneous sources. However, in most cases ontologies are still developed in a centralized top-down manner by a few knowledge

Building an Ontology of Tablewares using 'Legacy Data'

Directory of Open Access Journals (Sweden)

Daniël van Helden

2018-05-01

Full Text Available This article aims to demonstrate how an ontology can be constructed to encompass many of the criteria needed for more consumption-orientated approaches to Roman tablewares. For this it demonstrates how a dataset in a relational database can be organised for the format and capabilities of an ontology, and then how these data are input into the ontology model. Finally it includes some sample analyses to show the effectiveness of such an ontology for types of analyses that are relevant to this network.

Ontology: ambiguity and accuracy

Directory of Open Access Journals (Sweden)

Marcelo Schiessl

2012-08-01

Full Text Available Ambiguity is a major obstacle to information retrieval. It is source of several researches in Information Science. Ontologies have been studied in order to solve problems related to ambiguities. Paradoxically, “ontology” term is also ambiguous and it is understood according to the use by the community. Philosophy and Computer Science seems to have the most accentuated difference related to the term sense. The former holds undisputed tradition and authority. The latter, in despite of being quite recent, holds an informal sense, but pragmatic. Information Science acts ranging from philosophical to computational approaches so as to get organized collections based on balance between users’ necessities and available information. The semantic web requires informational cycle automation and demands studies related to ontologies. Consequently, revisiting relevant approaches for the study of ontologies plays a relevant role as a way to provide useful ideas to researchers maintaining philosophical rigor, and convenience provided by computers.

Ontology-Based Device Descriptions and Device Repository for Building Automation Devices

Directory of Open Access Journals (Sweden)

Dibowski Henrik

2011-01-01

Full Text Available Device descriptions play an important role in the design and commissioning of modern building automation systems and help reducing the design time and costs. However, all established device descriptions are specialized for certain purposes and suffer from several weaknesses. This hinders a further design automation, which is strongly needed for the more and more complex building automation systems. To overcome these problems, this paper presents novel Ontology-based Device Descriptions (ODDs along with a layered ontology architecture, a specific ontology view approach with virtual properties, a generic access interface, a triple store-based database backend, and a generic search mask GUI with underlying query generation algorithm. It enables a formal, unified, and extensible specification of building automation devices, ensures their comparability, and facilitates a computer-enabled retrieval, selection, and interoperability evaluation, which is essential for an automated design. The scalability of the approach to several ten thousand devices is demonstrated.

Application of neuroanatomical ontologies for neuroimaging data annotation

Directory of Open Access Journals (Sweden)

Jessica A Turner

2010-06-01

Full Text Available The annotation of functional neuroimaging results for data sharing and reuse is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus. This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural and morphological labeling schemas. We annotated a large functional neuroimaging dataset with terms from the ontology and applied a reasoning engine to analyze this dataset in conjunction with the ontology, and achieved successful inferences from the most specific level (e.g., how many subjects showed activation in a sub-part of the middle frontal gyrus to more general (how many activations were found in areas connected via a known white matter tract?. In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes. This neuranatomical ontology is publicly available as a view of FMA at the Bioportal website at http://rest.bioontology.org/bioportal/ontologies/download/10005. The ontological encoding of anatomic knowledge can be exploited by computer reasoning engines to make inferences about neuroanatomical relationships described in imaging datasets using different terminologies. This approach could ultimately enable knowledge discovery from large, distributed fMRI studies or medical record mining.

HuPSON: the human physiology simulation ontology.

Science.gov (United States)

Gündel, Michaela; Younesi, Erfan; Malhotra, Ashutosh; Wang, Jiali; Li, Hui; Zhang, Bijun; de Bono, Bernard; Mevissen, Heinz-Theodor; Hofmann-Apitius, Martin

2013-11-22

Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios.The ontology is freely available at: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html (owl files) and http://bishop.scai.fraunhofer.de/scaiview/ (browser). HuPSON provides a framework for a) annotating simulation experiments, b) retrieving relevant information that are required for modelling, c) enabling interoperability of algorithmic approaches used in biomedical simulation, d) comparing simulation results and e) linking knowledge-based approaches to simulation-based approaches. It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.

Ontology alignment architecture for semantic sensor Web integration.

Science.gov (United States)

Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R; Alarcos, Bernardo

2013-09-18

Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

Ontology Alignment Architecture for Semantic Sensor Web Integration

Directory of Open Access Journals (Sweden)

Bernardo Alarcos

2013-09-01

Full Text Available Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity. Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity’s names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

Development and Evaluation of an Adolescents' Depression Ontology for Analyzing Social Data.

Science.gov (United States)

Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

2016-01-01

This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure.

Ontology-based Metadata Portal for Unified Semantics

Data.gov (United States)

National Aeronautics and Space Administration — The Ontology-based Metadata Portal for Unified Semantics (OlyMPUS) will extend the prototype Ontology-Driven Interactive Search Environment for Earth Sciences...

Quantum physics and relational ontology

Energy Technology Data Exchange (ETDEWEB)

Cordovil, Joao [Center of Philosophy of Sciences of University of Lisbon (Portugal)

2013-07-01

The discovery of the quantum domain of reality put a serious ontological challenge, a challenge that is still well present in the recent developments of Quantum Physics. Physics was conceived from an atomistic conception of the world, reducing it, in all its diversity, to two types of entities: simple, individual and immutable entities (atoms, in metaphysical sense) and composite entities, resulting solely from combinations. Linear combinations, additive, indifferent to the structure or to the context. However, the discovery of wave-particle dualism and the developments in Quantum Field Theories and in Quantum Nonlinear Physical, showed that quantum entities are not, in metaphysical sense, neither simple, nor merely the result of linear (or additive) combinations. In other words, the ontological foundations of Physics revealed as inadequate to account for the nature of quantum entities. Then a fundamental challenge arises: How to think the ontic nature of these entities? In my view, this challenge appeals to a relational and dynamist ontology of physical entities. This is the central hypothesis of this communication. In this sense, this communication has two main intentions: 1) positively characterize this relational and dynamist ontology; 2) show some elements of its metaphysical suitability to contemporary Quantum Physics.

Knowledge Representation in Patient Safety Reporting: An Ontological Approach

Directory of Open Access Journals (Sweden)

Liang Chen

2016-10-01

Full Text Available Purpose: The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. Design/methodology/approach: We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our design, implementation, and evaluation of the ontology at its initial stage. Findings: We describe the design and initial outcomes of the ontology implementation. The evaluation results demonstrate the clinical validity of the ontology by a self-developed survey measurement. Research limitations: The proposed ontology was developed and evaluated using a small number of information sources. Presently, US data are used, but they are not essential for the ultimate structure of the ontology. Practical implications: The goal of improving patient safety can be aided through investigating patient safety reports and providing actionable knowledge to clinical practitioners. As such, constructing a domain specific ontology for patient safety reports serves as a cornerstone in information collection and text mining methods. Originality/value: The use of ontologies provides abstracted representation of semantic information and enables a wealth of applications in a reporting system. Therefore, constructing such a knowledge base is recognized as a high priority in health care.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

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Emanuel Santos

Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Science.gov (United States)

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

Ontologies and Formation Spaces for Conceptual ReDesign of Systems

Directory of Open Access Journals (Sweden)

J. Bíla

2005-01-01

Full Text Available This paper discusses ontologies, methods for developing them and languages for representing them. A special ontology for computational support of the Conceptual ReDesign Process (CRDP is introduced with a simple illustrative example of an application. The ontology denoted as Global context (GLB combines features of general semantic networks and features of UML language. The ontology is task-oriented and domain-oriented, and contains three basic strata – GLBExpl(stratum of Explanation, GLBFAct (stratum of Fields of Activities and GLBEnv (stratum of Environment, with their sub-strata. The ontology has been developed to represent functions of systems and their components in CRDP. The main difference between this ontology and ontologies which have been developed to identify functions (the semantic details in those ontologies must be as deep as possible is in the style of the description of the functions. In the proposed ontology, Formation Spaces were used as lower semantic categories the semantic deepness of which is variable and depends on the actual solution approach of a specialised Conceptual Designer.

Ontology Design of Influential People Identification Using Centrality

Science.gov (United States)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

Self-supervised Chinese ontology learning from online encyclopedias.

Science.gov (United States)

Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

2014-01-01

Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form. In order to avoid the errors in encyclopedias and enrich the learnt ontology, we also apply some machine learning based methods. First, we proof that the self-supervised machine learning method is practicable in Chinese relation extraction (at least for synonymy and hyponymy) statistically and experimentally and train some self-supervised models (SVMs and CRFs) for synonymy extraction, concept-subconcept relation extraction, and concept-instance relation extraction; the advantages of our methods are that all training examples are automatically generated from the structural information of encyclopedias and a few general heuristic rules. Finally, we evaluate SSCO in two aspects, scale and precision; manual evaluation results show that the ontology has excellent precision, and high coverage is concluded by comparing SSCO with other famous ontologies and knowledge bases; the experiment results also indicate that the self-supervised models obviously enrich SSCO.

BioPortal: An Open-Source Community-Based Ontology Repository

Science.gov (United States)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its

Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.

Science.gov (United States)

Nigam, Rajni; Munzenmaier, Diane H; Worthey, Elizabeth A; Dwinell, Melinda R; Shimoyama, Mary; Jacob, Howard J

2013-11-22

The Rat Genome Database (RGD) ( http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed. The Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######). As rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This

Development of a Ground Vehicle Maneuver Ontology to Support the Common Operational Picture

National Research Council Canada - National Science Library

Richmond, Paul W; Blais, Curtis L; Goerger, Niki C

2006-01-01

.... This paper describes both the Mobility-COP, from which warfighters can assess the ability of forces to maneuver effectively under multiple environmental and tactical conditions, and a formal ontology...

An ontology design pattern for surface water features

Science.gov (United States)

Sinha, Gaurav; Mark, David; Kolas, Dave; Varanka, Dalia; Romero, Boleslo E.; Feng, Chen-Chieh; Usery, E. Lynn; Liebermann, Joshua; Sorokine, Alexandre

2014-01-01

Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities exist due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology for other more context-dependent ontologies. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex or specialized surface water ontologies. A fundamental distinction is made in this ontology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is implemented in OWL, but Description Logic axioms and a detailed explanation is provided in this paper. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. Also provided is a discussion of why there is a need to complement the pattern with other ontologies, especially the previously developed Surface Network pattern. Finally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through an annotated geospatial dataset and sample queries using the classes of the Surface Water pattern.

Constructing a Geology Ontology Using a Relational Database

Science.gov (United States)

Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

2013-12-01

In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances

Two obvious intuitions : Ontology-mapping needs background knowledge and approximation

NARCIS (Netherlands)

Van Harmelen, Frank

2007-01-01

Ontology mapping (or: ontology alignment, or integration) is one of the most active areas the Semantic Web area. An increasing amount of ontologies are becoming available in recent years, and if the Semantic Web is to be taken seriously, the problem of ontology mapping must be solved. Numerous

Nuclear component design ontology building based on ASME codes

International Nuclear Information System (INIS)

Bao Shiyi; Zhou Yu; He Shuyan

2005-01-01

The adoption of ontology analysis in the study of concept knowledge acquisition and representation for the nuclear component design process based on computer-supported cooperative work (CSCW) makes it possible to share and reuse numerous concept knowledge of multi-disciplinary domains. A practical ontology building method is accordingly proposed based on Protege knowledge model in combination with both top-down and bottom-up approaches together with Formal Concept Analysis (FCA). FCA exhibits its advantages in the way it helps establish and improve taxonomic hierarchy of concepts and resolve concept conflict occurred in modeling multi-disciplinary domains. With Protege-3.0 as the ontology building tool, a nuclear component design ontology based ASME codes is developed by utilizing the ontology building method. The ontology serves as the basis to realize concept knowledge sharing and reusing of nuclear component design. (authors)

Where to search top-K biomedical ontologies?

Science.gov (United States)

Oliveira, Daniela; Butt, Anila Sahar; Haller, Armin; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2018-03-20

Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

Ontology - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available gzip) consists of some directories (see the following table). Data file File name: ontology....tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/ontology.tar.gz File size: 9...he NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. O...ples Data item Description ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes). onto...logy/meo/meo_fma_mapping.ttl An ontology mapping files t

Quality control for terms and definitions in ontologies and taxonomies

Directory of Open Access Journals (Sweden)

Rüegg Alexander

2006-04-01

Full Text Available Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO, the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

Ontology Enabled Generation of Embedded Web Services

DEFF Research Database (Denmark)

Hansen, Klaus Marius; Zhang, Weishan; Soares, Goncalo Teofilo Afonso Pinheiro

2008-01-01

Web services are increasingly adopted as a service provision mechanism in pervasive computing environments. Implementing web services on networked, embedded devices raises a number of challenges, for example efficiency of web services, handling of variability and dependencies of hardware...... and software platforms, and of devices state and context changes. To address these challenges, we developed a Web service compiler, Limbo, in which Web Ontology Language (OWL) ontologies are used to make the Limbo compiler aware of its compilation context, such as targeted hardware and software. At the same...... time, knowledge on device details, platform dependencies, and resource/power consumption is built into the supporting ontologies, which are used to configure Limbo for generating resource efficient web service code. A state machine ontology is used to generate stub code to facilitate handling of state...

Information Pre-Processing using Domain Meta-Ontology and Rule Learning System

Science.gov (United States)

Ranganathan, Girish R.; Biletskiy, Yevgen

Around the globe, extraordinary amounts of documents are being created by Enterprises and by users outside these Enterprises. The documents created in the Enterprises constitute the main focus of the present chapter. These documents are used to perform numerous amounts of machine processing. While using thesedocuments for machine processing, lack of semantics of the information in these documents may cause misinterpretation of the information, thereby inhibiting the productiveness of computer assisted analytical work. Hence, it would be profitable to the Enterprises if they use well defined domain ontologies which will serve as rich source(s) of semantics for the information in the documents. These domain ontologies can be created manually, semi-automatically or fully automatically. The focus of this chapter is to propose an intermediate solution which will enable relatively easy creation of these domain ontologies. The process of extracting and capturing domain ontologies from these voluminous documents requires extensive involvement of domain experts and application of methods of ontology learning that are substantially labor intensive; therefore, some intermediate solutions which would assist in capturing domain ontologies must be developed. This chapter proposes a solution in this direction which involves building a meta-ontology that will serve as an intermediate information source for the main domain ontology. This chapter proposes a solution in this direction which involves building a meta-ontology as a rapid approach in conceptualizing a domain of interest from huge amount of source documents. This meta-ontology can be populated by ontological concepts, attributes and relations from documents, and then refined in order to form better domain ontology either through automatic ontology learning methods or some other relevant ontology building approach.

Self-adaptation of Ontologies to Folksonomies in Semantic Web

OpenAIRE

Francisco Echarte; José Javier Astrain; Alberto Córdoba; Jesús Villadangos

2008-01-01

Ontologies and tagging systems are two different ways to organize the knowledge present in the current Web. In this paper we propose a simple method to model folksonomies, as tagging systems, with ontologies. We show the scalability of the method using real data sets. The modeling method is composed of a generic ontology that represents any folksonomy and an algorithm to transform the information contained in folksonomies to the generic ontology. The method allows representing folksonomies at...

Complex Topographic Feature Ontology Patterns

Science.gov (United States)

Varanka, Dalia E.; Jerris, Thomas J.

2015-01-01

Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

A document-centric approach for developing the tolAPC ontology.

Science.gov (United States)

Blfgeh, Aisha; Warrender, Jennifer; Hilkens, Catharien M U; Lord, Phillip

2017-11-28

There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different "formalisms" to represent and share their data - by the far most common, however, is the "office file" either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.

Introduction to Semantic Web Ontology Languages

NARCIS (Netherlands)

Antoniou, Grigoris; Franconi, Enrico; Van Harmelen, Frank

2005-01-01

The aim of this chapter is to give a general introduction to some of the ontology languages that play a prominent role on the Semantic Web, and to discuss the formal foundations of these languages. Web ontology languages will be the main carriers of the information that we will want to share and

An overview of the ontological basis of African jurisprudence | Agbo ...

African Journals Online (AJOL)

Life for the African is encapsulated in his understanding of the concept of ontology in which 'beings' and 'forces' are hierarchically ordered. A distortion of this order affects the African's 'vital force' and consequent 'vital rank'. This understanding underlies the African conception of law and juridical restitution as regulating ...

Inferring ontology graph structures using OWL reasoning

KAUST Repository

Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

2018-01-01

' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies

Duelling Ontologies: Might Vitalism Offer Balance and Value?

Science.gov (United States)

Richards, Dennis; Emmanuel, Elizabeth; Grace, Sandra

This article is part of a project investigating chiropractors' beliefs on the role of vitalism in their philosophical and practice approaches and how that might contribute to addressing current epidemics of non-communicable diseases. It aims to present atomism, reductionism, materialism and mechanism as fundamental ontologies in biomedicine and to examine what role these might play in its struggle to deal with these epidemics; to present vitalism as a fundamental ontology existing in chiropractic along with these ontologies of biomedicine; and to discuss how imbalances in the use of these ontologies and practices stemming from them might be contributing to difficulties in addressing these epidemics. The use of more balanced approaches by chiropractors involving not only mechanistic biomedical ontologies but also an increased focus on vitalism might offer value in addressing these epidemics and should be investigated. Copyright © 2017 Elsevier Inc. All rights reserved.

OAE: The Ontology of Adverse Events.

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He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry

2014-01-01

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term 'adverse event' denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. For example, using the data extracted from the Vaccine Adverse Event Reporting System (VAERS), OAE was used to analyse vaccine adverse events associated with the administrations of different types of influenza vaccines. OAE has also been used to represent and classify the vaccine adverse events cited in package inserts of FDA-licensed human vaccines in the USA. OAE is a biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e

An Ontology-Underpinned Emergency Response System for Water Pollution Accidents

Directory of Open Access Journals (Sweden)

Xiaoliang Meng

2018-02-01

Full Text Available With the unceasing development and maturation of environment geographic information system, the response to water pollution accidents has been digitalized through the combination of monitoring sensors, management servers, and application software. However, most of these systems only achieve the basic and general geospatial data management and functional process tasks by adopting mechanistic water-quality models. To satisfy the sustainable monitoring and real-time emergency response application demand of the government and public users, it is a hotspot to study how to make the water pollution information being semantic and make the referred applications intelligent. Thus, the architecture of the ontology-underpinned emergency response system for water pollution accidents is proposed in this paper. This paper also makes a case study for usability testing of the water ontology models, and emergency response rules through an online water pollution emergency response system. The system contributes scientifically to the safety and sustainability of drinking water by providing emergency response and decision-making to the government and public in a timely manner.

A collaborative recommendation framework for ontology evaluation and reuse

OpenAIRE

Cantador, Iván; Fernández Sánchez, Miriam; Castells, Pablo

2006-01-01

This is an electronic version of the paper presented at the International Workshop on Recommender Systems, held in Riva del Garda on 2006 Ontology evaluation can be defined as assessing the quality and the adequacy of an ontology for being used in a spe-cific context, for a specific goal. Although ontology reuse is being extensively addressed by the Semantic Web community, the lack of appropriate support tools and automatic techniques for the evaluation of certain ontology features are oft...

Application of Ontologies for Big Earth Data

Science.gov (United States)

Huang, T.; Chang, G.; Armstrong, E. M.; Boening, C.

2014-12-01

Connected data is smarter data! Earth Science research infrastructure must do more than just being able to support temporal, geospatial discovery of satellite data. As the Earth Science data archives continue to expand across NASA data centers, the research communities are demanding smarter data services. A successful research infrastructure must be able to present researchers the complete picture, that is, datasets with linked citations, related interdisciplinary data, imageries, current events, social media discussions, and scientific data tools that are relevant to the particular dataset. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts designed to improve discovery and application of Earth Science data. The SWEET ontologies collection was initially developed to capture the relationships between keywords in the NASA Global Change Master Directory (GCMD). Over the years this popular ontologies collection has expanded to cover over 200 ontologies and 6000 concepts to enable scalable classification of Earth system science concepts and Space science. This presentation discusses the semantic web technologies as the enabling technology for data-intensive science. We will discuss the application of the SWEET ontologies as a critical component in knowledge-driven research infrastructure for some of the recent projects, which include the DARPA Ontological System for Context Artifact and Resources (OSCAR), 2013 NASA ACCESS Virtual Quality Screening Service (VQSS), and the 2013 NASA Sea Level Change Portal (SLCP) projects. The presentation will also discuss the benefits in using semantic web technologies in developing research infrastructure for Big Earth Science Data in an attempt to "accommodate all domains and provide the necessary glue for information to be cross-linked, correlated, and discovered in a semantically rich manner." [1] [1] Savas Parastatidis: A platform for all that we know

Specifying Geographic Information - Ontology, Knowledge Representation, and Formal Constraints

DEFF Research Database (Denmark)

Christensen, Jesper Vinther

2007-01-01

as in the private sector. The theoretical background is the establishment of a representational system, which ontologically comprises a representation of notions in the "real world" and notions which include the representation of these. Thus, the thesis leans towards a traditional division between modeling...... of domains and conceptualization of these. The thesis contributes a formalization of what is understood by domain models and conceptual models, when the focus is on geographic information. Moreover, it is shown how specifications for geographic information are related to this representational system...... of requirements and rules, building on terms from the domain and concept ontologies. In combination with the theoretical basis the analysis is used for developing an underlying model of notions, which defines the individual elements in a specification and the relations between them. In the chapters of the thesis...

Construction of Engineering Ontologies for Knowledge Sharing and Reuse

NARCIS (Netherlands)

Borst, Willem Nico; Borst, W.N.

1997-01-01

This thesis describes an investigation into the practical use of ontologies for the development of information systems. Ontologies are formal descriptions of shared knowledge in a domain. An ontology can be used as a specification of an information system because it specifies the knowledge that is

Towards Ontological Foundations for Agent Modeling Concepts using UFO

NARCIS (Netherlands)

Guizzardi, G.; Wagner, Gerd

Foundational ontologies provide the basic concepts upon which any domain-specific ontology is built. This paper presents a new foundational ontology, UFO, and shows how it can be used as a foundation of agent concepts and for evaluating agent-oriented modeling methods. UFO is derived from a

On Automatic Modeling and Use of Domain-specific Ontologies

DEFF Research Database (Denmark)

Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

2005-01-01

In this paper, we firstly introduce an approach to the modeling of a domain-specific ontology for use in connection with a given document collection. Secondly, we present a methodology for deriving conceptual similarity from the domain-specific ontology. Adopted for ontology representation is a s...

The Relationship between User Expertise and Structural Ontology Characteristics

Science.gov (United States)

Waldstein, Ilya Michael

2014-01-01

Ontologies are commonly used to support application tasks such as natural language processing, knowledge management, learning, browsing, and search. Literature recommends considering specific context during ontology design, and highlights that a different context is responsible for problems in ontology reuse. However, there is still no clear…

GeoSciGraph: An Ontological Framework for EarthCube Semantic Infrastructure

Science.gov (United States)

Gupta, A.; Schachne, A.; Condit, C.; Valentine, D.; Richard, S.; Zaslavsky, I.

2015-12-01

The CINERGI (Community Inventory of EarthCube Resources for Geosciences Interoperability) project compiles an inventory of a wide variety of earth science resources including documents, catalogs, vocabularies, data models, data services, process models, information repositories, domain-specific ontologies etc. developed by research groups and data practitioners. We have developed a multidisciplinary semantic framework called GeoSciGraph semantic ingration of earth science resources. An integrated ontology is constructed with Basic Formal Ontology (BFO) as its upper ontology and currently ingests multiple component ontologies including the SWEET ontology, GeoSciML's lithology ontology, Tematres controlled vocabulary server, GeoNames, GCMD vocabularies on equipment, platforms and institutions, software ontology, CUAHSI hydrology vocabulary, the environmental ontology (ENVO) and several more. These ontologies are connected through bridging axioms; GeoSciGraph identifies lexically close terms and creates equivalence class or subclass relationships between them after human verification. GeoSciGraph allows a community to create community-specific customizations of the integrated ontology. GeoSciGraph uses the Neo4J,a graph database that can hold several billion concepts and relationships. GeoSciGraph provides a number of REST services that can be called by other software modules like the CINERGI information augmentation pipeline. 1) Vocabulary services are used to find exact and approximate terms, term categories (community-provided clusters of terms e.g., measurement-related terms or environmental material related terms), synonyms, term definitions and annotations. 2) Lexical services are used for text parsing to find entities, which can then be included into the ontology by a domain expert. 3) Graph services provide the ability to perform traversal centric operations e.g., finding paths and neighborhoods which can be used to perform ontological operations like

Towards Self-managed Pervasive Middleware using OWL/SWRL ontologies

DEFF Research Database (Denmark)

Zhang, Weishan; Hansen, Klaus Marius

2008-01-01

Self-management for pervasive middleware is important to realize the Ambient Intelligence vision. In this paper, we present an OWL/SWRL context ontologies based self-management approach for pervasive middleware where OWL ontology is used as means for context modeling. The context ontologies....../SWRL context ontologies based self-management approach with the self-diagnosis in Hydra middleware, using device state machine and other dynamic context information, for example web service calls. The evaluations in terms of extensibility, performance and scalability show that this approach is effective...

Fuzzy knowledge bases integration based on ontology

OpenAIRE

Ternovoy, Maksym; Shtogrina, Olena

2012-01-01

the paper describes the approach for fuzzy knowledge bases integration with the usage of ontology. This approach is based on metadata-base usage for integration of different knowledge bases with common ontology. The design process of metadata-base is described.

ExO: An Ontology for Exposure Science

Science.gov (United States)

An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them. Ontologies are critically important for specifying data of interest in a consistent manner, thereby enablin...

Geographic Ontologies, Gazetteers and Multilingualism

Directory of Open Access Journals (Sweden)

Robert Laurini

2015-01-01

Full Text Available Different languages imply different visions of space, so that terminologies are different in geographic ontologies. In addition to their geometric shapes, geographic features have names, sometimes different in diverse languages. In addition, the role of gazetteers, as dictionaries of place names (toponyms, is to maintain relations between place names and location. The scope of geographic information retrieval is to search for geographic information not against a database, but against the whole Internet: but the Internet stores information in different languages, and it is of paramount importance not to remain stuck to a unique language. In this paper, our first step is to clarify the links between geographic objects as computer representations of geographic features, ontologies and gazetteers designed in various languages. Then, we propose some inference rules for matching not only types, but also relations in geographic ontologies with the assistance of gazetteers.

An Ontology Driven Information Architecture for Big Data and Diverse Domains

Science.gov (United States)

Hughes, John S.; Crichton, Dan; Hardman, Sean; Joyner, Ron; Ramirez, Paul

2013-04-01

The Planetary Data System's has just released the PDS4 system for first use. Its architecture is comprised of three principle parts, an ontology that captures knowledge from the planetary science domain, a federated registry/repository system for product identification, versioning, tracking, and storage, and a REST-based service layer for search, retrieval, and distribution. An ontology modeling tool is used to prescriptively capture product definitions that adhere to object-oriented principles and that are compliant with specific registry, archive, and data dictionary reference models. The resulting information model is product centric, allowing all information to be packaged into products and tracked in the registry. The flexibility required in a diverse domain is provided through the use of object-oriented extensions and a hierarchical governance scheme with common, discipline, and mission levels. Finally all PDS4 data standards are generated or derived from the information model. The federated registry provides identification, versioning, and tracking functionality across federated repositories and is configured for deployment using configuration files generated from the ontology. Finally a REST-based service layer provides for metadata harvest, product transformation, packaging, and search, and portal hosting. A model driven architecture allows the data and software engineering teams to develop in parallel with minimal team interaction. The resulting software remains relatively stable as the domain evolves. Finally the development of a single shared ontology promotes interoperability and data correlation and helps meet the expectations of modern scientists for science data discovery, access and use. This presentation will provide an overview of PDS4 focusing on the data standards, how they were developed, how they are now being used, and will present some of the lessons learned while developing in a diverse scientific community. Copyright 2013 California

A four stage approach for ontology-based health information system design.

Science.gov (United States)

Kuziemsky, Craig E; Lau, Francis

2010-11-01

To describe and illustrate a four stage methodological approach to capture user knowledge in a biomedical domain area, use that knowledge to design an ontology, and then implement and evaluate the ontology as a health information system (HIS). A hybrid participatory design-grounded theory (GT-PD) method was used to obtain data and code them for ontology development. Prototyping was used to implement the ontology as a computer-based tool. Usability testing evaluated the computer-based tool. An empirically derived domain ontology and set of three problem-solving approaches were developed as a formalized model of the concepts and categories from the GT coding. The ontology and problem-solving approaches were used to design and implement a HIS that tested favorably in usability testing. The four stage approach illustrated in this paper is useful for designing and implementing an ontology as the basis for a HIS. The approach extends existing ontology development methodologies by providing an empirical basis for theory incorporated into ontology design. Copyright © 2010 Elsevier B.V. All rights reserved.

Operational Plan Ontology Model for Interconnection and Interoperability

Science.gov (United States)

Long, F.; Sun, Y. K.; Shi, H. Q.

2017-03-01

Aiming at the assistant decision-making system’s bottleneck of processing the operational plan data and information, this paper starts from the analysis of the problem of traditional expression and the technical advantage of ontology, and then it defines the elements of the operational plan ontology model and determines the basis of construction. Later, it builds up a semi-knowledge-level operational plan ontology model. Finally, it probes into the operational plan expression based on the operational plan ontology model and the usage of the application software. Thus, this paper has the theoretical significance and application value in the improvement of interconnection and interoperability of the operational plan among assistant decision-making systems.

KneeTex: an ontology-driven system for information extraction from MRI reports.

Science.gov (United States)

Spasić, Irena; Zhao, Bo; Jones, Christopher B; Button, Kate

2015-01-01

In the realm of knee pathology, magnetic resonance imaging (MRI) has the advantage of visualising all structures within the knee joint, which makes it a valuable tool for increasing diagnostic accuracy and planning surgical treatments. Therefore, clinical narratives found in MRI reports convey valuable diagnostic information. A range of studies have proven the feasibility of natural language processing for information extraction from clinical narratives. However, no study focused specifically on MRI reports in relation to knee pathology, possibly due to the complexity of knee anatomy and a wide range of conditions that may be associated with different anatomical entities. In this paper we describe KneeTex, an information extraction system that operates in this domain. As an ontology-driven information extraction system, KneeTex makes active use of an ontology to strongly guide and constrain text analysis. We used automatic term recognition to facilitate the development of a domain-specific ontology with sufficient detail and coverage for text mining applications. In combination with the ontology, high regularity of the sublanguage used in knee MRI reports allowed us to model its processing by a set of sophisticated lexico-semantic rules with minimal syntactic analysis. The main processing steps involve named entity recognition combined with coordination, enumeration, ambiguity and co-reference resolution, followed by text segmentation. Ontology-based semantic typing is then used to drive the template filling process. We adopted an existing ontology, TRAK (Taxonomy for RehAbilitation of Knee conditions), for use within KneeTex. The original TRAK ontology expanded from 1,292 concepts, 1,720 synonyms and 518 relationship instances to 1,621 concepts, 2,550 synonyms and 560 relationship instances. This provided KneeTex with a very fine-grained lexico-semantic knowledge base, which is highly attuned to the given sublanguage. Information extraction results were evaluated

Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

Science.gov (United States)

Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

2013-01-01

Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

Towards exergaming commons: composing the exergame ontology for publishing open game data.

Science.gov (United States)

Bamparopoulos, Giorgos; Konstantinidis, Evdokimos; Bratsas, Charalampos; Bamidis, Panagiotis D

2016-01-01

It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collection and analysis of game metrics data. In light of this and initiatives like the Quantified Self, there is an emerging need to open the data produced by health games and their associated metrics in order for them to be evaluated by the research community in an attempt to quantify their potential health, cognitive and physiological benefits. We have developed an ontology that describes exergames using the Web Ontology Language (OWL); it is available at http://purl.org/net/exergame/ns#. After an investigation of key components of exergames, relevant ontologies were incorporated, while necessary classes and properties were defined to model these components. A JavaScript framework was also developed in order to apply the ontology to online exergames. Finally, a SPARQL Endpoint is provided to enable open data access to potential clients through the web. Exergame components include details for players, game sessions, as well as, data produced during these game-playing sessions. The description of the game includes elements such as goals, game controllers and presentation hardware used; what is more, concepts from already existing ontologies are reused/repurposed. Game sessions include information related to the player, the date and venue where the game was played, as well as, the results/scores that were produced/achieved. These games are subsequently played by 14 users in multiple game sessions and the results derived from these sessions are published in a triplestore as open data. We model concepts related to exergames by providing a standardized structure for reference and comparison. This is the first work that publishes data from actual exergame sessions on the web, facilitating the integration and analysis of the data, while allowing open data access through

Towards an ontology for data quality in integrated chronic disease management: a realist review of the literature.

Science.gov (United States)

Liaw, S T; Rahimi, A; Ray, P; Taggart, J; Dennis, S; de Lusignan, S; Jalaludin, B; Yeo, A E T; Talaei-Khoei, A

2013-01-01

Effective use of routine data to support integrated chronic disease management (CDM) and population health is dependent on underlying data quality (DQ) and, for cross system use of data, semantic interoperability. An ontological approach to DQ is a potential solution but research in this area is limited and fragmented. Identify mechanisms, including ontologies, to manage DQ in integrated CDM and whether improved DQ will better measure health outcomes. A realist review of English language studies (January 2001-March 2011) which addressed data quality, used ontology-based approaches and is relevant to CDM. We screened 245 papers, excluded 26 duplicates, 135 on abstract review and 31 on full-text review; leaving 61 papers for critical appraisal. Of the 33 papers that examined ontologies in chronic disease management, 13 defined data quality and 15 used ontologies for DQ. Most saw DQ as a multidimensional construct, the most used dimensions being completeness, accuracy, correctness, consistency and timeliness. The majority of studies reported tool design and development (80%), implementation (23%), and descriptive evaluations (15%). Ontological approaches were used to address semantic interoperability, decision support, flexibility of information management and integration/linkage, and complexity of information models. DQ lacks a consensus conceptual framework and definition. DQ and ontological research is relatively immature with little rigorous evaluation studies published. Ontology-based applications could support automated processes to address DQ and semantic interoperability in repositories of routinely collected data to deliver integrated CDM. We advocate moving to ontology-based design of information systems to enable more reliable use of routine data to measure health mechanisms and impacts. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Science.gov (United States)

Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

2013-01-01

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

Construction of mammographic examination process ontology using bottom-up hierarchical task analysis.

Science.gov (United States)

Yagahara, Ayako; Yokooka, Yuki; Jiang, Guoqian; Tsuji, Shintarou; Fukuda, Akihisa; Nishimoto, Naoki; Kurowarabi, Kunio; Ogasawara, Katsuhiko

2018-03-01

Describing complex mammography examination processes is important for improving the quality of mammograms. It is often difficult for experienced radiologic technologists to explain the process because their techniques depend on their experience and intuition. In our previous study, we analyzed the process using a new bottom-up hierarchical task analysis and identified key components of the process. Leveraging the results of the previous study, the purpose of this study was to construct a mammographic examination process ontology to formally describe the relationships between the process and image evaluation criteria to improve the quality of mammograms. First, we identified and created root classes: task, plan, and clinical image evaluation (CIE). Second, we described an "is-a" relation referring to the result of the previous study and the structure of the CIE. Third, the procedural steps in the ontology were described using the new properties: "isPerformedBefore," "isPerformedAfter," and "isPerformedAfterIfNecessary." Finally, the relationships between tasks and CIEs were described using the "isAffectedBy" property to represent the influence of the process on image quality. In total, there were 219 classes in the ontology. By introducing new properties related to the process flow, a sophisticated mammography examination process could be visualized. In relationships between tasks and CIEs, it became clear that the tasks affecting the evaluation criteria related to positioning were greater in number than those for image quality. We developed a mammographic examination process ontology that makes knowledge explicit for a comprehensive mammography process. Our research will support education and help promote knowledge sharing about mammography examination expertise.

Benchmarking the Applicability of Ontology in Geographic Object-Based Image Analysis

Directory of Open Access Journals (Sweden)

Sachit Rajbhandari

2017-11-01

Full Text Available In Geographic Object-based Image Analysis (GEOBIA, identification of image objects is normally achieved using rule-based classification techniques supported by appropriate domain knowledge. However, GEOBIA currently lacks a systematic method to formalise the domain knowledge required for image object identification. Ontology provides a representation vocabulary for characterising domain-specific classes. This study proposes an ontological framework that conceptualises domain knowledge in order to support the application of rule-based classifications. The proposed ontological framework is tested with a landslide case study. The Web Ontology Language (OWL is used to construct an ontology in the landslide domain. The segmented image objects with extracted features are incorporated into the ontology as instances. The classification rules are written in Semantic Web Rule Language (SWRL and executed using a semantic reasoner to assign instances to appropriate landslide classes. Machine learning techniques are used to predict new threshold values for feature attributes in the rules. Our framework is compared with published work on landslide detection where ontology was not used for the image classification. Our results demonstrate that a classification derived from the ontological framework accords with non-ontological methods. This study benchmarks the ontological method providing an alternative approach for image classification in the case study of landslides.

New concepts for building vocabulary for cell image ontologies

Directory of Open Access Journals (Sweden)

Plant Anne L

2011-12-01

Full Text Available Abstract Background There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Results Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical

New concepts for building vocabulary for cell image ontologies.

Science.gov (United States)

Plant, Anne L; Elliott, John T; Bhat, Talapady N

2011-12-21

There are significant challenges associated with the building of ontologies for cell biology experiments including the large numbers of terms and their synonyms. These challenges make it difficult to simultaneously query data from multiple experiments or ontologies. If vocabulary terms were consistently used and reused across and within ontologies, queries would be possible through shared terms. One approach to achieving this is to strictly control the terms used in ontologies in the form of a pre-defined schema, but this approach limits the individual researcher's ability to create new terms when needed to describe new experiments. Here, we propose the use of a limited number of highly reusable common root terms, and rules for an experimentalist to locally expand terms by adding more specific terms under more general root terms to form specific new vocabulary hierarchies that can be used to build ontologies. We illustrate the application of the method to build vocabularies and a prototype database for cell images that uses a visual data-tree of terms to facilitate sophisticated queries based on a experimental parameters. We demonstrate how the terminology might be extended by adding new vocabulary terms into the hierarchy of terms in an evolving process. In this approach, image data and metadata are handled separately, so we also describe a robust file-naming scheme to unambiguously identify image and other files associated with each metadata value. The prototype database http://sbd.nist.gov/ consists of more than 2000 images of cells and benchmark materials, and 163 metadata terms that describe experimental details, including many details about cell culture and handling. Image files of interest can be retrieved, and their data can be compared, by choosing one or more relevant metadata values as search terms. Metadata values for any dataset can be compared with corresponding values of another dataset through logical operations. Organizing metadata for cell imaging

NeOn Methodology for Building Ontology Networks: Specification, Scheduling and Reuse

OpenAIRE

Suárez-Figueroa, Mari Carmen

2010-01-01

A new ontology development paradigm has started; its emphasis lies on the reuse and possible subsequent reengineering of knowledge resources, on the collaborative and argumentative ontology development, and on the building of ontology networks; this new trend is the opposite of building new ontologies from scratch. To help ontology developers in this new paradigm, it is important to provide strong methodological support. This thesis presents some contributions to the methodological area of...

Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

Science.gov (United States)

He, Yongqun

2014-07-01

While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

An Ontology Design Pattern for Surface Water Features

Energy Technology Data Exchange (ETDEWEB)

Sinha, Gaurav [Ohio University; Mark, David [University at Buffalo (SUNY); Kolas, Dave [Raytheon BBN Technologies; Varanka, Dalia [U.S. Geological Survey, Rolla, MO; Romero, Boleslo E [University of California, Santa Barbara; Feng, Chen-Chieh [National University of Singapore; Usery, Lynn [U.S. Geological Survey, Rolla, MO; Liebermann, Joshua [Tumbling Walls, LLC; Sorokine, Alexandre [ORNL

2014-01-01

Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities can be found due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology. It can then be used to systematically incor-porate concepts that are specific to a culture, language, or scientific domain. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex surface water ontologies. A fundamental distinction is made in this on-tology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is imple-mented in OWL, but Description Logic axioms and a detailed explanation is provided. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. A discussion about why there is a need to complement the pattern with other ontologies, es-pecially the previously developed Surface Network pattern is also provided. Fi-nally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through a few queries and annotated geospatial datasets.

An Ontology-centered Approach for Designing an Interactive Competence Management System for IT Companies

Directory of Open Access Journals (Sweden)

Stefan TRAUSAN-MATU

2009-01-01

Full Text Available The paper presents a generic framework for an intelligent information system of competence management based on ontologies for information technology companies. In a first step it will be applied in an information technology (IT small enterprise and then its applicability will be verified for other organizations of the same type. The work presented in the paper is performed under the project "CONTO – Ontology-based Competencies Management in Information Technology" funded by the Romanian Ministry of Education and Research, involving two universities, a research institute and an IT private company. A competence management system (CMS, in our vision has to achieve three functions: (a to support the complete and systematic acquisition of knowledge about the competence of the members of an enterprise; (b to provide the knowledge about competences and their owners; (c to apply the available knowledge to serve a purpose. The core of the competence management information system is an ontology that plays the role of the declarative knowledge repository containing the basic concepts (such as: company-job, competence, domain, group, person etc. and their relationships with other concepts, instances and properties. The Protégé environment was used for the development of this ontology. The structure of the ontology is conceived so that description logics can be used to represent the concept definitions of the application domain in a structured and formally well-understood way. Knowledge acquisition is performed in our approach by enriching the ontology, according to the requirements of the IT company. An advantage of using an ontology-based system is the possibility of the identification of new relations among concepts based on inferences starting from the existing knowledge. The user can choose to query instances of one type of concept. The paper also presents some use-cases.

Towards ontology based search and knowledgesharing using domain ontologies

DEFF Research Database (Denmark)

Zambach, Sine

verbs for relations in the ontology modeling. For this work we use frequency lists from a biomedical text corpus of different genres as well as a study of the relations used in other biomedical text mining tools. In addition, we discuss how these relations can be used in broarder perspective....

SWARMs Ontology: A Common Information Model for the Cooperation of Underwater Robots

Science.gov (United States)

Li, Xin; Bilbao, Sonia; Martín-Wanton, Tamara; Bastos, Joaquim; Rodriguez, Jonathan

2017-01-01

In order to facilitate cooperation between underwater robots, it is a must for robots to exchange information with unambiguous meaning. However, heterogeneity, existing in information pertaining to different robots, is a major obstruction. Therefore, this paper presents a networked ontology, named the Smart and Networking Underwater Robots in Cooperation Meshes (SWARMs) ontology, to address information heterogeneity and enable robots to have the same understanding of exchanged information. The SWARMs ontology uses a core ontology to interrelate a set of domain-specific ontologies, including the mission and planning, the robotic vehicle, the communication and networking, and the environment recognition and sensing ontology. In addition, the SWARMs ontology utilizes ontology constructs defined in the PR-OWL ontology to annotate context uncertainty based on the Multi-Entity Bayesian Network (MEBN) theory. Thus, the SWARMs ontology can provide both a formal specification for information that is necessarily exchanged between robots and a command and control entity, and also support for uncertainty reasoning. A scenario on chemical pollution monitoring is described and used to showcase how the SWARMs ontology can be instantiated, be extended, represent context uncertainty, and support uncertainty reasoning. PMID:28287468

Developing Learning Materials Using an Ontology of Mathematical Logic

Science.gov (United States)

Boyatt, Russell; Joy, Mike

2012-01-01

Ontologies describe a body of knowledge and give formal structure to a domain by describing concepts and their relationships. The construction of an ontology provides an opportunity to develop a shared understanding and a consistent vocabulary to be used for a given activity. This paper describes the construction of an ontology for an area of…

Uberon, an integrative multi-species anatomy ontology

Science.gov (United States)

2012-01-01

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

Annotating breast cancer microarray samples using ontologies

Science.gov (United States)

Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

2008-01-01

As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

Ontology-centric integration and navigation of the dengue literature.

Science.gov (United States)

Rajapakse, Menaka; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Schreiber, Mark J; Baker, Christopher J O

2008-10-01

Uninhibited access to the unstructured information distributed across the web and in scientific literature databases continues to be beyond the reach of scientists and health professionals. To address this challenge we have developed a literature driven, ontology-centric navigation infrastructure consisting of a content acquisition engine, a domain-specific ontology (in OWL-DL) and an ontology instantiation pipeline delivering sentences derived by domain-specific text mining. A visual query tool for reasoning over A-box instances in the populated ontology is presented and used to build conceptual queries that can be issued to the knowledgebase. We have deployed this generic infrastructure to facilitate data integration and knowledge sharing in the domain of dengue, which is one of the most prevalent viral diseases that continue to infect millions of people in the tropical and subtropical regions annually. Using our unique methodology we illustrate simplified search and discovery on dengue information derived from distributed resources and aggregated according to dengue ontology. Furthermore we apply data mining to the instantiated ontology to elucidate trends in the mentions of dengue serotypes in scientific abstracts since 1974.

Løgstrup’s Ontological Ethics

DEFF Research Database (Denmark)

Rabjerg, Bjørn

2017-01-01

aim is to provide a coherent exposition of Løgstrup’s ethics. However, the result is not a normative ethics upon which we may act, but rather a descriptive diagnosis of interdependence as the basic ontological condition of human social life, where the sovereign expressions of life may enable us to act.......The article explores K. E. Løgstrup’s ontological ethics, understood as an ethics rooted in interdependence. Interdependence, the fact that human beings always hold power over each other, has two very different aspects, which I will call negative and positive, each of them in turn leading...... to different aspects of ontological ethics. By negative and positive I mean the two opposing possibilities of all human interaction that we can either destroy the other person’s life (to a greater or smaller degree) or cause the other person’s life to flourish. We can either be a blessing in the other person’s...

Comparison of reasoners for large ontologies in the OWL 2 EL profile

NARCIS (Netherlands)

Dentler, K.; Cornet, R.; ten Teije, A.C.M.; de Keizer, N.F.

2011-01-01

This paper provides a survey to and a comparison of state-of-the-art Semantic Web reasoners that succeed in classifying large ontologies expressed in the tractable OWL 2 EL profile. Reasoners are characterized along several dimensions: The first dimension comprises underlying reasoning

Visual syntax of UML class and package diagram constructs as an ontology

CSIR Research Space (South Africa)

Thomas, A

2015-11-01

Full Text Available and package diagrams are two diagrams of UML. The motivation for this work is twofold; UML lacks a formal visual syntax specification and ontologies are under-explored for visual syntax specifications. The work in this paper, therefore, explores using...

Ontology for cell-based geographic information

Science.gov (United States)

Zheng, Bin; Huang, Lina; Lu, Xinhai

2009-10-01

Inter-operability is a key notion in geographic information science (GIS) for the sharing of geographic information (GI). That requires a seamless translation among different information sources. Ontology is enrolled in GI discovery to settle the semantic conflicts for its natural language appearance and logical hierarchy structure, which are considered to be able to provide better context for both human understanding and machine cognition in describing the location and relationships in the geographic world. However, for the current, most studies on field ontology are deduced from philosophical theme and not applicable for the raster expression in GIS-which is a kind of field-like phenomenon but does not physically coincide to the general concept of philosophical field (mostly comes from the physics concepts). That's why we specifically discuss the cell-based GI ontology in this paper. The discussion starts at the investigation of the physical characteristics of cell-based raster GI. Then, a unified cell-based GI ontology framework for the recognition of the raster objects is introduced, from which a conceptual interface for the connection of the human epistemology and the computer world so called "endurant-occurrant window" is developed for the better raster GI discovery and sharing.

Semi Automatic Ontology Instantiation in the domain of Risk Management

Science.gov (United States)

Makki, Jawad; Alquier, Anne-Marie; Prince, Violaine

One of the challenging tasks in the context of Ontological Engineering is to automatically or semi-automatically support the process of Ontology Learning and Ontology Population from semi-structured documents (texts). In this paper we describe a Semi-Automatic Ontology Instantiation method from natural language text, in the domain of Risk Management. This method is composed from three steps 1 ) Annotation with part-of-speech tags, 2) Semantic Relation Instances Extraction, 3) Ontology instantiation process. It's based on combined NLP techniques using human intervention between steps 2 and 3 for control and validation. Since it heavily relies on linguistic knowledge it is not domain dependent which is a good feature for portability between the different fields of risk management application. The proposed methodology uses the ontology of the PRIMA1 project (supported by the European community) as a Generic Domain Ontology and populates it via an available corpus. A first validation of the approach is done through an experiment with Chemical Fact Sheets from Environmental Protection Agency2.

OntoPop: An Ontology Population System for the Semantic Web

Science.gov (United States)

Thongkrau, Theerayut; Lalitrojwong, Pattarachai

The development of ontology at the instance level requires the extraction of the terms defining the instances from various data sources. These instances then are linked to the concepts of the ontology, and relationships are created between these instances for the next step. However, before establishing links among data, ontology engineers must classify terms or instances from a web document into an ontology concept. The tool for help ontology engineer in this task is called ontology population. The present research is not suitable for ontology development applications, such as long time processing or analyzing large or noisy data sets. OntoPop system introduces a methodology to solve these problems, which comprises two parts. First, we select meaningful features from syntactic relations, which can produce more significant features than any other method. Second, we differentiate feature meaning and reduce noise based on latent semantic analysis. Experimental evaluation demonstrates that the OntoPop works well, significantly out-performing the accuracy of 49.64%, a learning accuracy of 76.93%, and executes time of 5.46 second/instance.

Ontological Choices and the Value-Free Ideal

NARCIS (Netherlands)

Ludwig, D.J.

2015-01-01

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

Ontological Choices and the Value-Free Ideal

NARCIS (Netherlands)

Ludwig, David

2016-01-01

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

In search of a primitive ontology for relativistic quantum field theory

Energy Technology Data Exchange (ETDEWEB)

Lam, Vincent [University of Lausanne, CH-1015 Lausanne (Switzerland)

2014-07-01

There is a recently much discussed approach to the ontology of quantum mechanics according to which the theory is ultimately about entities in 3-dimensional space and their temporal evolution. Such an ontology postulating from the start matter localized in usual physical space or spacetime, by contrast to an abstract high-dimensional space such as the configuration space of wave function realism, is called primitive ontology in the recent literature on the topic and finds its roots in Bell's notion of local beables. The main motivation for a primitive ontology lies in its explanatory power: the primitive ontology allows for a direct account of the behaviour and properties of familiar macroscopic objects. In this context, it is natural to look for a primitive ontology for relativistic quantum field theory (RQFT). The aim of this talk is to critically discuss this interpretative move within RQFT, in particular with respect to the foundational issue of the existence of unitarily inequivalent representations. Indeed the proposed primitive ontologies for RQFT rely either on a Fock space representation or a wave functional representation, which are strictly speaking only unambiguously available for free systems in flat spacetime. As a consequence, it is argued that these primitive ontologies constitute only effective ontologies and are hardly satisfying as a fundamental ontology for RQFT.

Metadata and Ontologies in Learning Resources Design

Science.gov (United States)

Vidal C., Christian; Segura Navarrete, Alejandra; Menéndez D., Víctor; Zapata Gonzalez, Alfredo; Prieto M., Manuel

Resource design and development requires knowledge about educational goals, instructional context and information about learner's characteristics among other. An important information source about this knowledge are metadata. However, metadata by themselves do not foresee all necessary information related to resource design. Here we argue the need to use different data and knowledge models to improve understanding the complex processes related to e-learning resources and their management. This paper presents the use of semantic web technologies, as ontologies, supporting the search and selection of resources used in design. Classification is done, based on instructional criteria derived from a knowledge acquisition process, using information provided by IEEE-LOM metadata standard. The knowledge obtained is represented in an ontology using OWL and SWRL. In this work we give evidence of the implementation of a Learning Object Classifier based on ontology. We demonstrate that the use of ontologies can support the design activities in e-learning.

Towards a Consistent and Scientifically Accurate Drug Ontology.

Science.gov (United States)

Hogan, William R; Hanna, Josh; Joseph, Eric; Brochhausen, Mathias

2013-01-01

Our use case for comparative effectiveness research requires an ontology of drugs that enables querying National Drug Codes (NDCs) by active ingredient, mechanism of action, physiological effect, and therapeutic class of the drug products they represent. We conducted an ontological analysis of drugs from the realist perspective, and evaluated existing drug terminology, ontology, and database artifacts from (1) the technical perspective, (2) the perspective of pharmacology and medical science (3) the perspective of description logic semantics (if they were available in Web Ontology Language or OWL), and (4) the perspective of our realism-based analysis of the domain. No existing resource was sufficient. Therefore, we built the Drug Ontology (DrOn) in OWL, which we populated with NDCs and other classes from RxNorm using only content created by the National Library of Medicine. We also built an application that uses DrOn to query for NDCs as outlined above, available at: http://ingarden.uams.edu/ingredients. The application uses an OWL-based description logic reasoner to execute end-user queries. DrOn is available at http://code.google.com/p/dr-on.

Kernel Methods for Mining Instance Data in Ontologies

Science.gov (United States)

Bloehdorn, Stephan; Sure, York

The amount of ontologies and meta data available on the Web is constantly growing. The successful application of machine learning techniques for learning of ontologies from textual data, i.e. mining for the Semantic Web, contributes to this trend. However, no principal approaches exist so far for mining from the Semantic Web. We investigate how machine learning algorithms can be made amenable for directly taking advantage of the rich knowledge expressed in ontologies and associated instance data. Kernel methods have been successfully employed in various learning tasks and provide a clean framework for interfacing between non-vectorial data and machine learning algorithms. In this spirit, we express the problem of mining instances in ontologies as the problem of defining valid corresponding kernels. We present a principled framework for designing such kernels by means of decomposing the kernel computation into specialized kernels for selected characteristics of an ontology which can be flexibly assembled and tuned. Initial experiments on real world Semantic Web data enjoy promising results and show the usefulness of our approach.

Platonic wholes and quantum ontology

CERN Document Server

Woszczek, Marek

2015-01-01

The subject of the book is a reconsideration of the internalistic model of composition of the Platonic type, more radical than traditional, post-Aristotelian externalistic compositionism, and its application in the field of the ontology of quantum theory. At the centre of quantum ontology is nonseparability. Quantum wholes are atemporal wholes governed by internalistic logic and they are primitive, global physical entities, requiring an extreme relativization of the fundamental notions of mechanics. That ensures quantum theory to be fully consistent with the relativistic causal structure, with

Root justifications for ontology repair

CSIR Research Space (South Africa)

Moodley, K

2011-08-01

Full Text Available stream_source_info Moodley_2011.pdf.txt stream_content_type text/plain stream_size 32328 Content-Encoding ISO-8859-1 stream_name Moodley_2011.pdf.txt Content-Type text/plain; charset=ISO-8859-1 Root Justi cations... the ontology, based on the no- tion of root justi cations [8, 9]. In Section 5, we discuss the implementation of a Prot eg e3 plugin which demonstrates our approach to ontology repair. In this section we also discuss some experimental results comparing...

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning

KAUST Repository

Slater, Luke

2016-04-19

Ontologies are widely used in biology and biomedicine for the annotation and integration of data, and hundreds of ontologies have been developed for this purpose. These ontologies also constitute large volumes of formalized domain knowledge, usually expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within them relies on the use of automated reasoning. We have developed Aber-OWL, an ontology repository that provides OWL EL reasoning to answer queries and verify the consistency of ontologies. Aber-OWL also provides a set of web services which provide ontology-based access to scientific literature in Pubmed and Pubmed Central, SPARQL query expansion to retrieve linked data, and integration with Bio2RDF. Here, we report on our experiences with Aber-OWL and outline a roadmap for future development. Aber-OWL is freely available at http://aber-owl.net.

Application of Ontology Technology in Health Statistic Data Analysis.

Science.gov (United States)

Guo, Minjiang; Hu, Hongpu; Lei, Xingyun

2017-01-01

Research Purpose: establish health management ontology for analysis of health statistic data. Proposed Methods: this paper established health management ontology based on the analysis of the concepts in China Health Statistics Yearbook, and used protégé to define the syntactic and semantic structure of health statistical data. six classes of top-level ontology concepts and their subclasses had been extracted and the object properties and data properties were defined to establish the construction of these classes. By ontology instantiation, we can integrate multi-source heterogeneous data and enable administrators to have an overall understanding and analysis of the health statistic data. ontology technology provides a comprehensive and unified information integration structure of the health management domain and lays a foundation for the efficient analysis of multi-source and heterogeneous health system management data and enhancement of the management efficiency.

PAV ontology: provenance, authoring and versioning.

Science.gov (United States)

Ciccarese, Paolo; Soiland-Reyes, Stian; Belhajjame, Khalid; Gray, Alasdair Jg; Goble, Carole; Clark, Tim

2013-11-22

Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as Dublin Core Terms (DC Terms) and the W3C Provenance Ontology (PROV-O) are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. In particular, to track authoring and versioning information of web resources, PROV-O provides a basic methodology but not any specific classes and properties for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV, namespace http://purl.org/pav/): a lightweight ontology for capturing "just enough" descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the W3C PROV-O ontology to support broader interoperability. The initial design of the PAV ontology was driven by requirements from the AlzSWAN project with further requirements incorporated later from other projects detailed in this paper. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related

Application of Pareto optimization method for ontology matching in nuclear reactor domain

International Nuclear Information System (INIS)

Meenachi, N. Madurai; Baba, M. Sai

2017-01-01

This article describes the need for ontology matching and describes the methods to achieve the same. Efforts are put in the implementation of the semantic web based knowledge management system for nuclear domain which necessitated use of the methods for development of ontology matching. In order to exchange information in a distributed environment, ontology mapping has been used. The constraints in matching the ontology are also discussed. Pareto based ontology matching algorithm is used to find the similarity between two ontologies in the nuclear reactor domain. Algorithms like Jaro Winkler distance, Needleman Wunsch algorithm, Bigram, Kull Back and Cosine divergence are employed to demonstrate ontology matching. A case study was carried out to analysis the ontology matching in diversity in the nuclear reactor domain and same was illustrated.

Application of Pareto optimization method for ontology matching in nuclear reactor domain

Energy Technology Data Exchange (ETDEWEB)

Meenachi, N. Madurai [Indira Gandhi Centre for Atomic Research, HBNI, Tamil Nadu (India). Planning and Human Resource Management Div.; Baba, M. Sai [Indira Gandhi Centre for Atomic Research, HBNI, Tamil Nadu (India). Resources Management Group

2017-12-15

This article describes the need for ontology matching and describes the methods to achieve the same. Efforts are put in the implementation of the semantic web based knowledge management system for nuclear domain which necessitated use of the methods for development of ontology matching. In order to exchange information in a distributed environment, ontology mapping has been used. The constraints in matching the ontology are also discussed. Pareto based ontology matching algorithm is used to find the similarity between two ontologies in the nuclear reactor domain. Algorithms like Jaro Winkler distance, Needleman Wunsch algorithm, Bigram, Kull Back and Cosine divergence are employed to demonstrate ontology matching. A case study was carried out to analysis the ontology matching in diversity in the nuclear reactor domain and same was illustrated.

Using AberOWL for fast and scalable reasoning over BioPortal ontologies

KAUST Repository

Slater, Luke

2016-08-08

Background: Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided. Methods: We apply the AberOWL infrastructure to provide automated reasoning-based access to all accessible and consistent ontologies in BioPortal (368 ontologies). We perform an extensive performance evaluation to determine query times, both for queries of different complexity and for queries that are performed in parallel over the ontologies. Results and conclusions: We demonstrate that, with the exception of a few ontologies, even complex and parallel queries can now be answered in milliseconds, therefore allowing automated reasoning to be used on a large scale, to run in parallel, and with rapid response times.

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

Directory of Open Access Journals (Sweden)

Gregorio Sergio E

2009-05-01

Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

Designing Network-based Business Model Ontology

DEFF Research Database (Denmark)

Hashemi Nekoo, Ali Reza; Ashourizadeh, Shayegheh; Zarei, Behrouz

2015-01-01

Survival on dynamic environment is not achieved without a map. Scanning and monitoring of the market show business models as a fruitful tool. But scholars believe that old-fashioned business models are dead; as they are not included the effect of internet and network in themselves. This paper...... is going to propose e-business model ontology from the network point of view and its application in real world. The suggested ontology for network-based businesses is composed of individuals` characteristics and what kind of resources they own. also, their connections and pre-conceptions of connections...... such as shared-mental model and trust. However, it mostly covers previous business model elements. To confirm the applicability of this ontology, it has been implemented in business angel network and showed how it works....

The Russian Quest for Ontological Security

DEFF Research Database (Denmark)

Pedersen, Jonas Gejl

This paper argues that Russia’s decision to militarily intervene in the Kosovo crisis (1999) arose out of ontological, alongside material, insecurity. Whereas states’ material security essentially deals with national survival, ontological security concerns safety of the ‘national Self......’. By supplementing the existing theories of geopolitics and regime security with the conceptual lens of ontological security, my interpretivist case study demonstrates why Russia, despite great risk and material costs, decided to militarily intervene and traces how Russian senses of ‘national Self’ were...... fundamentally reconstructed during intervention. I find that the anxiety arising from a future scenario of an already weak post-Soviet ‘Russian Self’ gradually being engulfed by a confident ‘Western Self’ played a significant role in Russia’s decision to occupy Slatina airbase. My analysis paradoxically shows...

Six scenarios of exploiting an ontology based, mobilized learning environment

NARCIS (Netherlands)

Kismihók, G.; Szabó, I.; Vas, R.

2012-01-01

In this article, six different exploitation possibilities of an educational ontology based, mobilized learning management system are presented. The focal point of this system is the educational ontology model. The first version of this educational ontology model serves as a foundation for curriculum

Effects of an ontology display with history representation on organizational memory information systems.

Science.gov (United States)

Hwang, Wonil; Salvendy, Gavriel

2005-06-10

Ontologies, as a possible element of organizational memory information systems, appear to support organizational learning. Ontology tools can be used to share knowledge among the members of an organization. However, current ontology-viewing user interfaces of ontology tools do not fully support organizational learning, because most of them lack proper history representation in their display. In this study, a conceptual model was developed that emphasized the role of ontology in the organizational learning cycle and explored the integration of history representation in the ontology display. Based on the experimental results from a split-plot design with 30 participants, two conclusions were derived: first, appropriately selected history representations in the ontology display help users to identify changes in the ontologies; and second, compatibility between types of ontology display and history representation is more important than ontology display and history representation in themselves.

Querying archetype-based EHRs by search ontology-based XPath engineering.

Science.gov (United States)

Kropf, Stefan; Uciteli, Alexandr; Schierle, Katrin; Krücken, Peter; Denecke, Kerstin; Herre, Heinrich

2018-05-11

Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards. The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist. The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.

An ontologically founded architecture for information systems in clinical and epidemiological research.

Science.gov (United States)

Uciteli, Alexandr; Groß, Silvia; Kireyev, Sergej; Herre, Heinrich

2011-08-09

This paper presents an ontologically founded basic architecture for information systems, which are intended to capture, represent, and maintain metadata for various domains of clinical and epidemiological research. Clinical trials exhibit an important basis for clinical research, and the accurate specification of metadata and their documentation and application in clinical and epidemiological study projects represents a significant expense in the project preparation and has a relevant impact on the value and quality of these studies.An ontological foundation of an information system provides a semantic framework for the precise specification of those entities which are presented in this system. This semantic framework should be grounded, according to our approach, on a suitable top-level ontology. Such an ontological foundation leads to a deeper understanding of the entities of the domain under consideration, and provides a common unifying semantic basis, which supports the integration of data and the interoperability between different information systems.The intended information systems will be applied to the field of clinical and epidemiological research and will provide, depending on the application context, a variety of functionalities. In the present paper, we focus on a basic architecture which might be common to all such information systems. The research, set forth in this paper, is included in a broader framework of clinical research and continues the work of the IMISE on these topics.

The design ontology

DEFF Research Database (Denmark)

Storga, Mario; Andreasen, Mogens Myrup; Marjanovic, Dorian

2010-01-01

The article presents the research of the nature, building and practical role of a Design Ontology as a potential framework for the more efficient product development (PD) data-, information- and knowledge- description, -explanation, -understanding and -reusing. In the methodology for development ...

C2 Domain Ontology within Our Lifetime

Science.gov (United States)

2009-06-01

25] Masolo, C., et al: The WonderWeb Library of Foundational Ontologies Prelimary Report, WonderWeb Deliverable D17, ISTC -CNR, May 2003. [26...www.ifomis.org/bfo/BFO  [25] Masolo, C., et al: The WonderWeb Library of Foundational Ontologies Prelimary Report, WonderWeb Deliverable D17, ISTC -CNR

Ontologies and Information Systems: A Literature Survey

Science.gov (United States)

2011-06-01

Falcon-AO (LMO + GMO ) [146], and RiMOM [317]. Meta-matching systems include APFEL [76] and eTuner [286]. There also exist frameworks that provide a set...Jian, N., Qu, Y. and Wang, Q. 2005. GMO : A graph matching for ontologies. In Proceedings of the K-CAPWorkshop on Integrating Ontologies, Banff

Critical Ontology for an Enactive Music Pedagogy

Science.gov (United States)

van der Schyff, Dylan; Schiavio, Andrea; Elliott, David J.

2016-01-01

An enactive approach to music education is explored through the lens of critical ontology. Assumptions central to Western academic music culture are critically discussed; and the concept of "ontological education" is introduced as an alternative framework. We argue that this orientation embraces more primordial ways of knowing and being,…

Individual Building Extraction from TerraSAR-X Images Based on Ontological Semantic Analysis

Directory of Open Access Journals (Sweden)

Rong Gui

2016-08-01

Full Text Available Accurate building information plays a crucial role for urban planning, human settlements and environmental management. Synthetic aperture radar (SAR images, which deliver images with metric resolution, allow for analyzing and extracting detailed information on urban areas. In this paper, we consider the problem of extracting individual buildings from SAR images based on domain ontology. By analyzing a building scattering model with different orientations and structures, the building ontology model is set up to express multiple characteristics of individual buildings. Under this semantic expression framework, an object-based SAR image segmentation method is adopted to provide homogeneous image objects, and three categories of image object features are extracted. Semantic rules are implemented by organizing image object features, and the individual building objects expression based on an ontological semantic description is formed. Finally, the building primitives are used to detect buildings among the available image objects. Experiments on TerraSAR-X images of Foshan city, China, with a spatial resolution of 1.25 m × 1.25 m, have shown the total extraction rates are above 84%. The results indicate the ontological semantic method can exactly extract flat-roof and gable-roof buildings larger than 250 pixels with different orientations.

Multimedia ontology representation and applications

CERN Document Server

Chaudhury, Santanu; Ghosh, Hiranmay

2015-01-01

The result of more than 15 years of collective research, Multimedia Ontology: Representation and Applications provides a theoretical foundation for understanding the nature of media data and the principles involved in its interpretation. The book presents a unified approach to recent advances in multimedia and explains how a multimedia ontology can fill the semantic gap between concepts and the media world. It relays real-life examples of implementations in different domains to illustrate how this gap can be filled.The book contains information that helps with building semantic, content-based

Completeness, supervenience and ontology

International Nuclear Information System (INIS)

Maudlin, Tim W E

2007-01-01

In 1935, Einstein, Podolsky and Rosen raised the issue of the completeness of the quantum description of a physical system. What they had in mind is whether or not the quantum description is informationally complete, in that all physical features of a system can be recovered from it. In a collapse theory such as the theory of Ghirardi, Rimini and Weber, the quantum wavefunction is informationally complete, and this has often been taken to suggest that according to that theory the wavefunction is all there is. If we distinguish the ontological completeness of a description from its informational completeness, we can see that the best interpretations of the GRW theory must postulate more physical ontology than just the wavefunction

Completeness, supervenience and ontology

Energy Technology Data Exchange (ETDEWEB)

Maudlin, Tim W E [Department of Philosophy, Rutgers University, 26 Nichol Avenue, New Brunswick, NJ 08901-1411 (United States)

2007-03-23

In 1935, Einstein, Podolsky and Rosen raised the issue of the completeness of the quantum description of a physical system. What they had in mind is whether or not the quantum description is informationally complete, in that all physical features of a system can be recovered from it. In a collapse theory such as the theory of Ghirardi, Rimini and Weber, the quantum wavefunction is informationally complete, and this has often been taken to suggest that according to that theory the wavefunction is all there is. If we distinguish the ontological completeness of a description from its informational completeness, we can see that the best interpretations of the GRW theory must postulate more physical ontology than just the wavefunction.

Reconciliation of ontology and terminology to cope with linguistics.

Science.gov (United States)

Baud, Robert H; Ceusters, Werner; Ruch, Patrick; Rassinoux, Anne-Marie; Lovis, Christian; Geissbühler, Antoine

2007-01-01

To discuss the relationships between ontologies, terminologies and language in the context of Natural Language Processing (NLP) applications in order to show the negative consequences of confusing them. The viewpoints of the terminologist and (computational) linguist are developed separately, and then compared, leading to the presentation of reconciliation among these points of view, with consideration of the role of the ontologist. In order to encourage appropriate usage of terminologies, guidelines are presented advocating the simultaneous publication of pragmatic vocabularies supported by terminological material based on adequate ontological analysis. Ontologies, terminologies and natural languages each have their own purpose. Ontologies support machine understanding, natural languages support human communication, and terminologies should form the bridge between them. Therefore, future terminology standards should be based on sound ontology and do justice to the diversities in natural languages. Moreover, they should support local vocabularies, in order to be easily adaptable to local needs and practices.

From Patient Discharge Summaries to an Ontology for Psychiatry.

Science.gov (United States)

Richard, Marion; Aimé, Xavier; Jaulent, Marie-Christine; Krebs, Marie-Odile; Charlet, Jean

2017-01-01

Psychiatry aims at detecting symptoms, providing diagnoses and treating mental disorders. We developed ONTOPSYCHIA, an ontology for psychiatry in three modules: social and environmental factors of mental disorders, mental disorders, and treatments. The use of ONTOPSYCHIA, associated with dedicated tools, will facilitate semantic research in Patient Discharge Summaries (PDS). To develop the first module of the ontology we propose a PDS text analysis in order to explicit psychiatry concepts. We decided to set aside classifications during the construction of the modu le, to focus only on the information contained in PDS (bottom-up approach) and to return to domain classifications solely for the enrichment phase (top-down approach). Then, we focused our work on the development of the LOVMI methodology (Les Ontologies Validées par Méthode Interactive - Ontologies Validated by Interactive Method), which aims to provide a methodological framework to validate the structure and the semantic of an ontology.

Organizational Knowledge Transfer Using Ontologies and a Rule-Based System

Science.gov (United States)

Okabe, Masao; Yoshioka, Akiko; Kobayashi, Keido; Yamaguchi, Takahira

In recent automated and integrated manufacturing, so-called intelligence skill is becoming more and more important and its efficient transfer to next-generation engineers is one of the urgent issues. In this paper, we propose a new approach without costly OJT (on-the-job training), that is, combinational usage of a domain ontology, a rule ontology and a rule-based system. Intelligence skill can be decomposed into pieces of simple engineering rules. A rule ontology consists of these engineering rules as primitives and the semantic relations among them. A domain ontology consists of technical terms in the engineering rules and the semantic relations among them. A rule ontology helps novices get the total picture of the intelligence skill and a domain ontology helps them understand the exact meanings of the engineering rules. A rule-based system helps domain experts externalize their tacit intelligence skill to ontologies and also helps novices internalize them. As a case study, we applied our proposal to some actual job at a remote control and maintenance office of hydroelectric power stations in Tokyo Electric Power Co., Inc. We also did an evaluation experiment for this case study and the result supports our proposal.

Validating EHR clinical models using ontology patterns.

Science.gov (United States)

Martínez-Costa, Catalina; Schulz, Stefan

2017-12-01

Clinical models are artefacts that specify how information is structured in electronic health records (EHRs). However, the makeup of clinical models is not guided by any formal constraint beyond a semantically vague information model. We address this gap by advocating ontology design patterns as a mechanism that makes the semantics of clinical models explicit. This paper demonstrates how ontology design patterns can validate existing clinical models using SHACL. Based on the Clinical Information Modelling Initiative (CIMI), we show how ontology patterns detect both modeling and terminology binding errors in CIMI models. SHACL, a W3C constraint language for the validation of RDF graphs, builds on the concept of "Shape", a description of data in terms of expected cardinalities, datatypes and other restrictions. SHACL, as opposed to OWL, subscribes to the Closed World Assumption (CWA) and is therefore more suitable for the validation of clinical models. We have demonstrated the feasibility of the approach by manually describing the correspondences between six CIMI clinical models represented in RDF and two SHACL ontology design patterns. Using a Java-based SHACL implementation, we found at least eleven modeling and binding errors within these CIMI models. This demonstrates the usefulness of ontology design patterns not only as a modeling tool but also as a tool for validation. Copyright © 2017 Elsevier Inc. All rights reserved.

KaBOB: ontology-based semantic integration of biomedical databases.

Science.gov (United States)

Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

2015-04-23

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for

Automated Ontology Alignment with Fuselets for Community of Interest (COI) Integration

National Research Council Canada - National Science Library

Starz, James; Roberts, Joe

2008-01-01

Discusses the ontology alignment problem by presenting a tool called Ontrapro-the Ontology Translation Protocol, which allows users to apply a myriad of ontology alignment algorithms in an iterative fashion...

An Approach to Folksonomy-Based Ontology Maintenance for Learning Environments

Science.gov (United States)

Gasevic, D.; Zouaq, Amal; Torniai, Carlo; Jovanovic, J.; Hatala, Marek

2011-01-01

Recent research in learning technologies has demonstrated many promising contributions from the use of ontologies and semantic web technologies for the development of advanced learning environments. In spite of those benefits, ontology development and maintenance remain the key research challenges to be solved before ontology-enhanced learning…

Logical Characterisation of Ontology Construction using Fuzzy Description Logics

DEFF Research Database (Denmark)

Badie, Farshad; Götzsche, Hans

had the extension of ontologies with Fuzzy Logic capabilities which plan to make proper backgrounds for ontology driven reasoning and argumentation on vague and imprecise domains. This presentation conceptualises learning from fuzzy classes using the Inductive Logic Programming framework. Then......, employs Description Logics in characterising and analysing fuzzy statements. And finally, provides a conceptual framework describing fuzzy concept learning in ontologies using the Inductive Logic Programming....

Ontology matters: a commentary on contribution to cultural historical activity

Science.gov (United States)

Martin, Jenny

2017-10-01

This commentary promotes discussion on the imaginary provided by Sanaz Farhangi in her article entitled, Contribution to activity: a lens for understanding students' potential and agency in physics education. The commentary is concerned with aligning ontological assumptions in research accounts of learning and development with transformative aims. A broad definition of ontology as the theory of existence is preferred. Sociocultural approaches share relational ontology as a common foundation. I agree with scholars elaborating Vygotsky's Transformative Activist Stance that a relational ontology does not imply activism. However, I argue that relational ontology provides a necessary and sufficient theoretical grounding for intentional transformation. I draw upon positioning theory to elaborate the moral aspects of language use and to illustrate that a theory of being as relational already eliminates the transcendental position. I draw on Farhangi's article to further the discussion on the necessity and sufficiency of relational ontology and associated grammars in accounting for activism.

Recent changes in the Building Topology Ontology

DEFF Research Database (Denmark)

Rasmussen, Mads Holten; Pauwels, Pieter; Lefrancois, Maxime

The Building Topology Ontology (BOT) was in early 2017 suggested to the W3C community group for Linked Building Data as a simple ontology covering the core concepts of a building. Since it was first announced it has been extended to cover a building site, elements hosted by other elements, zones...

Aspect OntoMaven - Aspect-Oriented Ontology Development and Configuration With OntoMaven

OpenAIRE

Paschke, Adrian; Schaefermeier, Ralph

2015-01-01

In agile ontology-based software engineering projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The contribution of this paper is a new design artifact called OntoMaven combined with a unified approach to ontology modularization, aspect-oriented ontology development, which was inspired by aspect-oriented programming. OntoMaven adopts the Apache Maven-based d...

Ontology modularization to improve semantic medical image annotation.

Science.gov (United States)

Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul

2011-02-01

Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results. Copyright © 2010 Elsevier Inc. All rights reserved.

Toward a formal ontology for narrative

Directory of Open Access Journals (Sweden)

Ciotti, Fabio

2016-03-01

Full Text Available In this paper the rationale and the first draft of a formal ontology for modeling narrative texts are presented. Building on the semiotic and structuralist narratology, and on the work carried out in the late 1980s by Giuseppe Gigliozzi in Italy, the focus of my research are the concepts of character and of narrative world/space. This formal model is expressed in the OWL 2 ontology language. The main reason to adopt a formal modeling approach is that I consider the purely probabilistic-quantitative methods (now widespread in digital literary studies inadequate. An ontology, on one hand provides a tool for the analysis of strictly literary texts. On the other hand (though beyond the scope of the present work, its formalization can also represent a significant contribution towards grounding the application of storytelling methods outside of scholarly contexts.

Summarizing an Ontology: A "Big Knowledge" Coverage Approach.

Science.gov (United States)

Zheng, Ling; Perl, Yehoshua; Elhanan, Gai; Ochs, Christopher; Geller, James; Halper, Michael

2017-01-01

Maintenance and use of a large ontology, consisting of thousands of knowledge assertions, are hampered by its scope and complexity. It is important to provide tools for summarization of ontology content in order to facilitate user "big picture" comprehension. We present a parameterized methodology for the semi-automatic summarization of major topics in an ontology, based on a compact summary of the ontology, called an "aggregate partial-area taxonomy", followed by manual enhancement. An experiment is presented to test the effectiveness of such summarization measured by coverage of a given list of major topics of the corresponding application domain. SNOMED CT's Specimen hierarchy is the test-bed. A domain-expert provided a list of topics that serves as a gold standard. The enhanced results show that the aggregate taxonomy covers most of the domain's main topics.

Ontology Maintenance using Textual Analysis

Directory of Open Access Journals (Sweden)

Yassine Gargouri

2003-10-01

Full Text Available Ontologies are continuously confronted to evolution problem. Due to the complexity of the changes to be made, a maintenance process, at least a semi-automatic one, is more and more necessary to facilitate this task and to ensure its reliability. In this paper, we propose a maintenance ontology model for a domain, whose originality is to be language independent and based on a sequence of text processing in order to extract highly related terms from corpus. Initially, we deploy the document classification technique using GRAMEXCO to generate classes of texts segments having a similar information type and identify their shared lexicon, agreed as highly related to a unique topic. This technique allows a first general and robust exploration of the corpus. Further, we apply the Latent Semantic Indexing method to extract from this shared lexicon, the most associated terms that has to be seriously considered by an expert to eventually confirm their relevance and thus updating the current ontology. Finally, we show how the complementarity between these two techniques, based on cognitive foundation, constitutes a powerful refinement process.

MIRO: guidelines for minimum information for the reporting of an ontology.

Science.gov (United States)

Matentzoglu, Nicolas; Malone, James; Mungall, Chris; Stevens, Robert

2018-01-18

Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation. We propose the Minimum Information for Reporting an Ontology (MIRO) guidelines as a means to facilitate a higher degree of completeness and consistency between ontology documentation, including published papers, and ultimately a higher standard of report quality. A draft of the MIRO guidelines was circulated for public comment in the form of a questionnaire, and we subsequently collected 110 responses from ontology authors, developers, users and reviewers. We report on the feedback of this consultation, including comments on each guideline, and present our analysis on the relative importance of each MIRO information item. These results were used to update the MIRO guidelines, mainly by providing more detailed operational definitions of the individual items and assigning degrees of importance. Based on our revised version of MIRO, we conducted a review of 15 recently published ontology description reports from three important journals in the Semantic Web and Biomedical domain and analysed them for compliance with the MIRO guidelines. We found that only 41.38% of the information items were covered by the majority of the papers (and deemed important by the survey respondents) and a large number of important items are not covered at all, like those related to testing and versioning policies. We believe that the community-reviewed MIRO guidelines can contribute to improving significantly the quality of ontology description reports and other documentation, in particular by increasing consistent

OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system.

Science.gov (United States)

Senderov, Viktor; Simov, Kiril; Franz, Nico; Stoev, Pavel; Catapano, Terry; Agosti, Donat; Sautter, Guido; Morris, Robert A; Penev, Lyubomir

2018-01-18

The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy. OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System. A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses. OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.

An ontology based trust verification of software license agreement

Science.gov (United States)

Lu, Wenhuan; Li, Xiaoqing; Gan, Zengqin; Wei, Jianguo

2017-08-01

When we install software or download software, there will show up so big mass document to state the rights and obligations, for which lots of person are not patient to read it or understand it. That would may make users feel distrust for the software. In this paper, we propose an ontology based verification for Software License Agreement. First of all, this work proposed an ontology model for domain of Software License Agreement. The domain ontology is constructed by proposed methodology according to copyright laws and 30 software license agreements. The License Ontology can act as a part of generalized copyright law knowledge model, and also can work as visualization of software licenses. Based on this proposed ontology, a software license oriented text summarization approach is proposed which performances showing that it can improve the accuracy of software licenses summarizing. Based on the summarization, the underline purpose of the software license can be explicitly explored for trust verification.

Ontology-Based Retrieval of Spatially Related Objects for Location Based Services

Science.gov (United States)

Haav, Hele-Mai; Kaljuvee, Aivi; Luts, Martin; Vajakas, Toivo

Advanced Location Based Service (LBS) applications have to integrate information stored in GIS, information about users' preferences (profile) as well as contextual information and information about application itself. Ontology engineering provides methods to semantically integrate several data sources. We propose an ontology-driven LBS development framework: the paper describes the architecture of ontologies and their usage for retrieval of spatially related objects relevant to the user. Our main contribution is to enable personalised ontology driven LBS by providing a novel approach for defining personalised semantic spatial relationships by means of ontologies. The approach is illustrated by an industrial case study.

A fuzzy ontology modeling for case base knowledge in diabetes mellitus domain

Directory of Open Access Journals (Sweden)

Shaker El-Sappagh

2017-06-01

Full Text Available Knowledge-Intensive Case-Based Reasoning Systems (KI-CBR mainly depend on ontologies. Ontology can play the role of case-base knowledge. The combination of ontology and fuzzy logic reasoning is critical in the medical domain. Case-base representation based on fuzzy ontology is expected to enhance the semantic and storage of CBR knowledge-base. This paper provides an advancement to the research of diabetes diagnosis CBR by proposing a novel case-base fuzzy OWL2 ontology (CBRDiabOnto. This ontology can be considered as the first fuzzy case-base ontology in the medical domain. It is based on a case-base fuzzy Extended Entity Relation (EER data model. It contains 63 (fuzzy classes, 54 (fuzzy object properties, 138 (fuzzy datatype properties, and 105 fuzzy datatypes. We populated the ontology with 60 cases and used SPARQL-DL for its query. The evaluation of CBRDiabOnto shows that it is accurate, consistent, and cover terminologies and logic of diabetes mellitus diagnosis.

Cross document ontology based information for multimedia retrieval

NARCIS (Netherlands)

Reidsma, Dennis; Kuper, Jan; Declerck, T.; Saggion, H.; Cunningham, H.; Ganter, B.; de Moor, A.

2003-01-01

This paper describes the MUMIS project, which applies ontology based Information Extraction to improve the results of Information Retrieval in multimedia archives. It makes use of a domain specific ontology, multilingual lexicons and reasoning algorithms to automatically create a semantic annotation

Annotating Evidence Based Clinical Guidelines : A Lightweight Ontology

NARCIS (Netherlands)

Hoekstra, R.; de Waard, A.; Vdovjak, R.; Paschke, A.; Burger, A.; Romano, P.; Marshall, M.S.; Splendiani, A.

2012-01-01

This paper describes a lightweight ontology for representing annotations of declarative evidence based clinical guidelines. We present the motivation and requirements for this representation, based on an analysis of several guidelines. The ontology provides the means to connect clinical questions

Ontological Issues and the Possible Development of Cultural Psychology.

Science.gov (United States)

Pérez-Campos, Gilberto

2017-12-01

Ontological issues have a bad reputation within mainstream psychology. This paper, however, is an attempt to argue that ontological reflection may play an important role in the development of cultural psychology. A cross-reading of two recent papers on the subject (Mammen & Mironenko, Integrative Psychological and Behavioral Science, 49(4), 681-713, 2015; Simão Integrative Psychological and Behavioral Science, 50, 568-585, 2016), aimed at characterizing their respective approaches to ontological issues, sets the stage for a presentation of Cornelius Castoriadis' ontological reflections. On this basis, a dialogue is initiated with E.E. Boesch's Symbolic Activity Theory that could contribute to a more refined understanding of human psychological functioning in its full complexity.

[Towards a structuring fibrillar ontology].

Science.gov (United States)

Guimberteau, J-C

2012-10-01

Over previous decades and centuries, the difficulty encountered in the manner in which the tissue of our bodies is organised, and structured, is clearly explained by the impossibility of exploring it in detail. Since the creation of the microscope, the perception of the basic unity, which is the cell, has been essential in understanding the functioning of reproduction and of transmission, but has not been able to explain the notion of form; since the cells are not everywhere and are not distributed in an apparently balanced manner. The problems that remain are those of form and volume and also of connection. The concept of multifibrillar architecture, shaping the interfibrillar microvolumes in space, represents a solution to all these questions. The architectural structures revealed, made up of fibres, fibrils and microfibrils, from the mesoscopic to the microscopic level, provide the concept of a living form with structural rationalism that permits the association of psychochemical molecular biodynamics and quantum physics: the form can thus be described and interpreted, and a true structural ontology is elaborated from a basic functional unity, which is the microvacuole, the intra and interfibrillar volume of the fractal organisation, and the chaotic distribution. Naturally, new, less linear, less conclusive, and less specific concepts will be implied by this ontology, leading one to believe that the emergence of life takes place under submission to forces that the original form will have imposed and oriented the adaptive finality. Copyright © 2012. Published by Elsevier SAS.

Global Warming and Geographically Scalar Climatic Objects Exist: An Ontologically Realist and Object-Oriented Analysis of the Daymet TMAX Climate Summaries for North America

Science.gov (United States)

Jackson, C. P.

2017-12-01

The scientific materialist worldview, what Peter Unger refers to as the Scientiphical worldview, or Scientiphicalism, has been utterly catastrophic for mesoscale objects in general, but, with its closely associated twentieth-century formal logic, this has been especially true for notoriously vague things like climate change, coastlines, mountains and dust storms. That is, any so-called representations or references ultimately suffer the same ontological demise as their referents, no matter how well-defined their boundaries may in fact be. Against this reductionist metaphysics, climatic objects are discretized within three separate ontologically realist systems, Graham Harman's object-oriented philosophy, or ontology (OOO), Markus Gabriel's ontology of fields of sense (OFS) and Tristan Garcia's two systems and new order of time, so as to make an ontological case for any geographically scalar object, beginning with pixels, as well as any notoriously vague thing they are said to represent. Four-month overlapping TMAX seasonals were first developed from the Oak Ridge National Laboratory (ORNL) Daymet climate temperature maximum (TMAX) monthly summaries (1980-2016) for North America and segmented within Trimble's eCognition Developer using the simple and widely familiar quadtree algorithm with a scale parameter of four, in this example. The regression coefficient was then calculated for the resulting 37-year climatic objects and an equally simple classification was applied. The same segmentation and classification was applied to the Daymet annual summaries, as well, for comparison. As was expected, the mean warming and cooling trends are lowest for the annual summary TMAX climatic objects. However, the Fall (SOND) season has the largest and smallest areas of warming and cooling, respectively, and the highest mean trend for warming objects. Conversely, Spring (MAMJ) has the largest and smallest areas undergoing cooling and warming, respectively. Finally, Summer (JJAS

Ontology Assisted Formal Specification Extraction from Text

Directory of Open Access Journals (Sweden)

Andreea Mihis

2010-12-01

Full Text Available In the field of knowledge processing, the ontologies are the most important mean. They make possible for the computer to understand better the natural language and to make judgments. In this paper, a method which use ontologies in the semi-automatic extraction of formal specifications from a natural language text is proposed.

The missions and means framework as an ontology