ontology research papers 2012

ontology research papers 2012




Uberon, an integrative multi-species anatomy ontology
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Abstract 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

goseq: Gene Ontology testing for RNA-seq datasets
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This document gives an introduction to the use of the goseq R Bioconductor package

Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models
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The diversity of modeling approaches in computational neuroscience makes model sharing, retrieval, reuse and reproducibility difficult and even sometimes impossible. To address this problem, standardized languages have been developed by and for the community, such

Completeness guarantees for incomplete ontology reasoners: Theory and practice
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Abstract To achieve scalability of query answering, the developers of Semantic Web applications are often forced to use incomplete OWL 2 reasoners, which fail to derive all answers for at least one query, ontology, and data set. The lack of completeness

The language of gene ontology: a Zipf s law analysis
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Background Most major genome projects and sequence databases provide a GO annotation of their data, either automatically or through human annotators, creating a large corpus of data written in the language of GO. Texts written in natural language show a statistical

On the feasibility of using OWL 2 DL reasoners for ontology matching problems
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Abstract. In this paper we discuss the feasibility of using OWL 2 DL reasoners to diagnose the integration of large-scale ontologies via mappings. To this end, we have extended our ontology matching system LOGMAP with complete OWL 2 DL reasoning and diagnosis

Developing an Ontology for Sharing Biobank Data based on the BBMRI Minimum Data Set MIABIS
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ABSTRACT Sharing data about heterogeneous collections of specimens stored in biobanks is an important topic with respect to making optimal use of sparse resources. Based on a minimum data set for biobank data sharing created by the European Biobanking and

Domain-Aware Ontology Matching
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The inherent heterogeneity of datasets on the Semantic Web has created a need to interlink them, and several tools have emerged that automate this task. In this paper we are interested in what happens if we enrich these matching tools with knowledge of the

Summarize gene annotations based on collective ontology annotations
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As computational and high throughput analyses have been widely used in interpreting gene functions, the number of gene annotations and resultant metadata describing the conditions for each annotation has increased dramatically. To standardize these annotations, genes

Improving Access to Software Architecture Knowledge An Ontology-based Search Approach
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ABSTRACT Every software has an architecture, but in most cases it is poorly documented. That s especially true in virtual community for software development, where creating and updating documents is not a high priority activity and architectural knowledge remain

The cognitive paradigm ontology: design and application
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ABSTRACT 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 (eg, the Stroop

Ontology-based Solution for Data Warehousing in Genetic Neurological Disease
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ABSTRACT In the field of genetic disorder of the nervous system, there is a huge amount of information available on the Internet. Extracting relevant information from these heterogeneous sources is a complex task usually dedicated to data warehouse. Heterogeneity can be related to the

Exploiting the UMLS Metathesaurus in the Ontology Alignment Evaluation Initiative
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Abstract. In this paper we describe how the UMLS Metathesaurus-the most comprehensive effort for integrating medical thesauri and ontologies-is being used within the context of the Ontology Alignment Evaluation Initiative (OAEI). We also present the obtained results in

An ontology-based exploration of the concepts and relationships in the activities and participation component of the international classification of functioning,
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Abstract Background: The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related issues, aimed at describing and measuring health and disability at both individual and population levels. Here we discuss

Tightly integrated probabilistic description logic programs for representing ontology mappings
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Abstract Creating mappings between ontologies is a common way of approaching the semantic heterogeneity problem on the Semantic Web. To fit into the landscape of Semantic Web languages, a suitable, logic-based representation formalism for mappings is needed.

OWL 2 Profiles: An Introduction to Lightweight Ontology Languages
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This chapter gives an extended introduction to the lightweight profiles OWL EL, OWL QL, and OWL RL of the Web Ontology Language OWL. The three ontology language standards are sublanguages of OWL DL that are restricted in ways that significantly simplify

ZooAnimals. owl: A didactically sound example-ontology for teaching description logics in OWL 2
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A didactically sound example-ontology for teaching description logics in OWL 2 Daniel Schober 1*, Niels Grewe 2, Johannes Rhl 2, Martin Boeker 1 1Institute of Medical Biometry and Medical Informatics (IMBI), University Medical Center, Freiburg, Germany

COMPARING ONTOLOGY LANGUAGES FOR MODEL REPRESENTATION OF THE SITBACONTOLOGY VIA A CONTROLLED EXPERIMENT-RESEARCH
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In recent years, we can see increased use of ontology languages, such as Frames [Minsky, representing knowledge. Knowledge representation has become necessary in various

COMPREHENSIVE ONTOLOGY COGNITIVE ASSISTED VISUALIZATION TOOLS-A SURVEY
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ABSTRACT Comprehensive Ontology is used in different contexts with different authors. Ontology comprehension is a collection of techniques that facilitate the understanding of ontologies. These tools are being applied for further development in various disciplines for

Large-scale interactive ontology matching: Algorithms and implementation
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Abstract. In this paper we present the ontology matching system LogMap 2, a much improved version of its predecessor LogMap. LogMap 2 supports user interaction during the matching process, which is essential for use cases requiring very accurate mappings.

On the interaction of existential rules and equality constraints in ontology querying
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Ontological query processing is an exciting research topic in database theory, knowledge representation, and logic programming. In many cases, ontological constraints are expressed over an extensional database by extending traditional Datalog rules to allow

Automated System for Software Project Cost Estimation Based on Ontology Engineering
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ABSTRACT in this paper, ontology based software automated system for project cost estimation is proposed. The system uses the ONTOCOM cost estimation model. The system is implemented using Microsoft visual studio ASP. Net C#. It is cost effective and can run

The mouse pathology ontology, MPATH; structure and applica-tions
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ABSTRACT The advent of large scale pathology-based phenotyping of mice requires a relatively simple nomenclature and coding system that can be integrated into data collection platforms (computerized medical record keeping systems) to enable the pathologist to

Modular combination of reasoners for ontology classification
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Abstract. Classification is a fundamental reasoning task in ontology design, and there is currently a wide range of reasoners highly optimised for classification of SROIQ ontologies. Existing reasoners, however, do not exploit the fact that most of the axioms in many

NeuroNames: an ontology for the BrainInfo portal to neuroscience on the web
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is a growing portal to neuroscientific information on the Web. It is indexed by NeuroNames, an ontology designed to compensate for ambiguities in neuroanatomical nomenclature. The 20-year old ontology continues to evolve toward

An ontology and a REST API for sequence based microbial typing data
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In the Microbial typing field, the need to have a common understanding of the concepts described and the ability to share results within the community is an increasingly important requisite for the continued development of portable and accurate sequence-based typing

An evaluation of ontology matching in geo-service applications
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ABSTRACT Matching between concepts describing the meaning of services representing heterogeneous information sources is a key operation in many application domains, including web service coordination, data integration, peer-to-peer information sharing,

A formal semantics for weighted ontology mappings
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Ontology mappings are often assigned a weight or confidence factor by matchers. Nonetheless, few semantic accounts have been given so far for such weights. This paper presents a formal semantics for weighted mappings between different ontologies. It is

Ontology-Based Governance of Data-Aware Processes
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In this paper we show how one can use the technology developed recently for Ontology- Based Data Access (OBDA) to govern data-aware processes through ontologies. In particular, we consider processes executed over a relational database which issue calls to

Three semantics for the core of the distributed ontology language
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Abstract. The Distributed Ontology Language DOL, which is currently being standardised as ISO WD 17347 within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3, aims at providing a unified framework for (1) ontologies formalised in

An Approach to Developing an Ontology that Represents Knowledge Embedded in Filmed Materials.
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ABSTRACT This paper introduces the reader to the approach we are taking to develop an ontology that could be used to represent the knowledge inherent in filmed materials. Such an ontology could be used as the semantic basis for multimedia retrieval systems. The

Semantics of the distributed ontology language: Institutes and Institutions
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OWL is a popular language for ontologies. Yet, the restriction to a decidable description logic often hinders ontology designers from expressing knowledge that cannot (or can only in quite complicated ways) be expressed in a description logic. A practice to deal with this

Data linking with ontology alignment
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It is a trend to publish RDF data on the web, so that users can share information semantically. Then, linking isolated data sets together is highly needed. I would like to reduce the comparison scale by isolating the types of resources to be compared, so that it

You Say Ordinary, We Say Gifted: How Ontology Can Help Mitigate Cultural Variation in the Social Sciences
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Persson s (2012a) article offers a timely contribution to the science of giftedness through questioning the validity of research emerging from within this paradigm. Using evidence from a number of disciplines he demonstrates that what is regarded as gifted behaviour in

A region-based ontology of the brain ventricular system and its relation to schizophrenia
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Abstract This chapter describes an initial region-based formalisation of some concepts about neuroanatomy into ontological and epistemic terms, as part of a major effort into the formalisation of the knowledge contained in neuroimages of patients with schizophrenia.

Pathway Synthesis Using the Act Ontology
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Abstract We describe here the Act Ontology, a formalism for uniformly describing biochemical function, and its use in building an enzymatic pathway synthesizer. A formal description of biochemical function allows us to reason about it, and for the particular case

Using Ontology-based Approaches to Representing Speech Transcripts for Automated Speech Scoring
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Abstract This paper presents a thesis proposal on approaches to automatically scoring non- native speech from second language tests. Current speech scoring systems assess speech by primarily using acoustic features such as fluency and pronunciation; however content

Visualizing and Editing Ontology Fragments with OWLGrEd
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ABSTRACT. The OWLGrEd ontology editor allows graphical visualization and authoring of OWL 2.0 ontologies using a compact yet intuitive presentation that combines UML class diagram notation with textual Manchester syntax for class expressions. Here we show, how to

Quest, an OWL 2 QL reasoner for Ontology-Based Data Access
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Abstract. Ontology Based Data Access (OBDA) has drawn considerable attention from the OWL and RDF communities. In OBDA, instance data is accessed by means of mappings, which state the relationship between the data in a data source (eg, an RDBMSs) and the

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS
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Background It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic

Markov Chain Ontology Analysis (MCOA)
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Background 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

A legal case OWL ontology with an instantiation of Popov v. Hayashi
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Abstract The paper provides an OWL ontology for legal cases with an instantiation of the legal case Popov v. Hayashi. The ontology makes explicit the conceptual knowledge of the legal case domain, supports reasoning about the domain, and can be used to annotate

Mixing open and closed world assumption in ontology-based data access: Non-uniform data complexity
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Abstract. When using ontologies to access instance data, it can be useful to make a closed world assumption (CWA) for some predicates and an open world assumption (OWA) for others. The main problem with such a setup is that conjunctive query (CQ) answering

Structured chemical class definitions and automated matching for chemical ontology evolution
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Ontologies encode the knowledge of human experts in order to allow computers to automate common tasks in a domain. They are hierarchically organised and backed by computational logic which allows automated inferences of the implicit consequences of explicitly stated

SurfShop: combing a product ontology with topic model results for online window-shopping.
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Abstract At present, online shopping is typically a search-oriented activity where a user gains access to products which best match their query. Instead, we propose a surf-oriented online shopping paradigm, which links associated products allowing users to wander

Quest, a system for ontology based data access
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Abstract. Ontology Based Data Access (OBDA) has drawn considerable attention from the OWL and RDF communities. In OBDA, instance data is accessed by means of mappings, which state the relationship between the data in a data source (eg, an RDBMSs) and the

YAM++: A multi-strategy based approach for Ontology matching task
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In this paper, we present the capability of our ontology matching tool YAM++. We show that YAM++ is able to discover mappings between entities of given two ontologies by using machine learning approach. Besides, we also demonstrate that if the training data are not

LoLa: A Modular Ontology of Logics, Languages, and Translations
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Abstract. The Distributed Ontology Language (DOL), currently being standardised within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3, aims at providing a unified framework for (1) ontologies formalised in heterogeneous logics,(2)

From Polygons and Timestamps to Dynamic Geographic Features: Grounding a Spatio-temporal Geo-ontology
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This paper presents a knowledge representation approach to modelling and manipulating spatio-temporal data and to grounding a spatio-temporal geographic ontology upon the data. This approach has been developed in the form of a definition-based ontological

Category theoretic ontology for representation of assessment scales and consensus guidelines in elderly care
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Kazem Sadegh-Zadeh s approach1 to medical language is a first true and complete attempt to provide concrete and detail insight into clinical practice and medical decision-making based on practiced morality and normative ethics. His language of medicine is combined

Incorporating the Ontology Paradigm into a Mainstream Programming Environment
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The emergence of the Semantic Web have revived the interest in knowledge engineering and ontologies. Different paradigms often share challenges and solutions, and can complement and mutually improve each other. This paper presents a simple and agile

Ontology Constraints in Incomplete and Complete Data
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Ontology and other logical languages are built around the idea that axioms enable the inference of new facts about the available data. In some circumstances, however, the data is meant to be complete in certain ways, and deducing new facts may be undesirable.

Towards a Framework for Service Ontology Evaluation
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ABSTRACT Though there has been a tremendous proliferation in the economic activities involving services, service science as a body of knowledge is still at its infancy. The need for a new service science discipline can be justified by looking at some of the distinguishing

Domain-independent entity coreference for linking ontology instances
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The objective of entity coreference is to determine if different mentions (eg, person names, place names, database records, ontology instances, etc.) refer to the same real word object. Entity coreference algorithms can be used to detect duplicate database records and to

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