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Sample records for biomedical ontology advancing

  1. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Misra,Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute,Christopher G.; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F.; Musen, Mark A.

    2006-01-23

    The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are: (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. The Center is working toward these objectives by providing tools to develop ontologies and to annotate experimental data, and by developing resources to integrate and relate existing ontologies as well as by creating repositories of biomedical data that are annotated using those ontologies. The Center is providing training workshops in ontology design, development, and usage, and is also pursuing research in ontology evaluation, quality, and use of ontologies to promote scientific discovery. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.

  2. The Ontology for Biomedical Investigations

    OpenAIRE

    Anita Bandrowski; Ryan Brinkman; Mathias Brochhausen; Brush, Matthew H.; Bill Bug; Chibucos, Marcus C.; Kevin Clancy; Mélanie Courtot; Dirk Derom; Michel Dumontier; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Frank Gibson; Alejandra Gonzalez-Beltran

    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 i...

  3. The Ontology for Biomedical Investigations

    Science.gov (United States)

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; 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

  4. 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

  5. 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

  6. The Ontology for Biomedical Investigations.

    Directory of Open Access Journals (Sweden)

    Anita Bandrowski

    Full Text Available 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

  7. Ontology-Oriented Programming for Biomedical Informatics.

    Science.gov (United States)

    Lamy, Jean-Baptiste

    2016-01-01

    Ontologies are now widely used in the biomedical domain. However, it is difficult to manipulate ontologies in a computer program and, consequently, it is not easy to integrate ontologies with databases or websites. Two main approaches have been proposed for accessing ontologies in a computer program: traditional API (Application Programming Interface) and ontology-oriented programming, either static or dynamic. In this paper, we will review these approaches and discuss their appropriateness for biomedical ontologies. We will also present an experience feedback about the integration of an ontology in a computer software during the VIIIP research project. Finally, we will present OwlReady, the solution we developed.

  8. Predicting the extension of biomedical ontologies.

    Directory of Open Access Journals (Sweden)

    Catia Pesquita

    Full Text Available Developing and extending a biomedical ontology is a very demanding task that can never be considered complete given our ever-evolving understanding of the life sciences. Extension in particular can benefit from the automation of some of its steps, thus releasing experts to focus on harder tasks. Here we present a strategy to support the automation of change capturing within ontology extension where the need for new concepts or relations is identified. Our strategy is based on predicting areas of an ontology that will undergo extension in a future version by applying supervised learning over features of previous ontology versions. We used the Gene Ontology as our test bed and obtained encouraging results with average f-measure reaching 0.79 for a subset of biological process terms. Our strategy was also able to outperform state of the art change capturing methods. In addition we have identified several issues concerning prediction of ontology evolution, and have delineated a general framework for ontology extension prediction. Our strategy can be applied to any biomedical ontology with versioning, to help focus either manual or semi-automated extension methods on areas of the ontology that need extension.

  9. Integrating systems biology models and biomedical ontologies

    Directory of Open Access Journals (Sweden)

    de Bono Bernard

    2011-08-01

    Full Text Available Abstract Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  10. Enabling Ontology Based Semantic Queries in Biomedical Database Systems.

    Science.gov (United States)

    Zheng, Shuai; Wang, Fusheng; Lu, James; Saltz, Joel

    2012-01-01

    While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations. PMID:23404054

  11. Evolution of biomedical ontologies and mappings: Overview of recent approaches.

    Science.gov (United States)

    Groß, Anika; Pruski, Cédric; Rahm, Erhard

    2016-01-01

    Biomedical ontologies are heavily used to annotate data, and different ontologies are often interlinked by ontology mappings. These ontology-based mappings and annotations are used in many applications and analysis tasks. Since biomedical ontologies are continuously updated dependent artifacts can become outdated and need to undergo evolution as well. Hence there is a need for largely automated approaches to keep ontology-based mappings up-to-date in the presence of evolving ontologies. In this article, we survey current approaches and novel directions in the context of ontology and mapping evolution. We will discuss requirements for mapping adaptation and provide a comprehensive overview on existing approaches. We will further identify open challenges and outline ideas for future developments. PMID:27642503

  12. 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.

  13. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 6, is a collection of papers that discusses the role of integrated electronics in medical systems and the usage of biological mathematical models in biological systems. Other papers deal with the health care systems, the problems and methods of approach toward rehabilitation, as well as the future of biomedical engineering. One paper discusses the use of system identification as it applies to biological systems to estimate the values of a number of parameters (for example, resistance, diffusion coefficients) by indirect means. More particularly, the i

  14. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 5, is a collection of papers that deals with application of the principles and practices of engineering to basic and applied biomedical research, development, and the delivery of health care. The papers also describe breakthroughs in health improvements, as well as basic research that have been accomplished through clinical applications. One paper examines engineering principles and practices that can be applied in developing therapeutic systems by a controlled delivery system in drug dosage. Another paper examines the physiological and materials vari

  15. 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.

  16. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning.

    Directory of Open Access Journals (Sweden)

    Robert Hoehndorf

    Full Text Available Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.

  17. Information-theoretic evaluation for computational biomedical ontologies

    CERN Document Server

    Clark, Wyatt Travis

    2014-01-01

    The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, yet evaluating their performance is difficult due to problems caused by the structure of biomedical ontologies and incomplete annotations of genes. This work proposes an information-theoretic framework to evaluate the performance of computational protein function prediction. A Bayesian network is used, structured according to the underlying ontology, to model the prior probability of a protein's function. The concepts of misinformation and remaining uncertainty are

  18. Automatic background knowledge selection for matching biomedical ontologies.

    Science.gov (United States)

    Faria, Daniel; Pesquita, Catia; Santos, Emanuel; Cruz, Isabel F; Couto, Francisco M

    2014-01-01

    Ontology matching is a growing field of research that is of critical importance for the semantic web initiative. The use of background knowledge for ontology matching is often a key factor for success, particularly in complex and lexically rich domains such as the life sciences. However, in most ontology matching systems, the background knowledge sources are either predefined by the system or have to be provided by the user. In this paper, we present a novel methodology for automatically selecting background knowledge sources for any given ontologies to match. This methodology measures the usefulness of each background knowledge source by assessing the fraction of classes mapped through it over those mapped directly, which we call the mapping gain. We implemented this methodology in the AgreementMakerLight ontology matching framework, and evaluate it using the benchmark biomedical ontology matching tasks from the Ontology Alignment Evaluation Initiative (OAEI) 2013. In each matching problem, our methodology consistently identified the sources of background knowledge that led to the highest improvements over the baseline alignment (i.e., without background knowledge). Furthermore, our proposed mapping gain parameter is strongly correlated with the F-measure of the produced alignments, thus making it a good estimator for ontology matching techniques based on background knowledge.

  19. Automatic background knowledge selection for matching biomedical ontologies.

    Directory of Open Access Journals (Sweden)

    Daniel Faria

    Full Text Available Ontology matching is a growing field of research that is of critical importance for the semantic web initiative. The use of background knowledge for ontology matching is often a key factor for success, particularly in complex and lexically rich domains such as the life sciences. However, in most ontology matching systems, the background knowledge sources are either predefined by the system or have to be provided by the user. In this paper, we present a novel methodology for automatically selecting background knowledge sources for any given ontologies to match. This methodology measures the usefulness of each background knowledge source by assessing the fraction of classes mapped through it over those mapped directly, which we call the mapping gain. We implemented this methodology in the AgreementMakerLight ontology matching framework, and evaluate it using the benchmark biomedical ontology matching tasks from the Ontology Alignment Evaluation Initiative (OAEI 2013. In each matching problem, our methodology consistently identified the sources of background knowledge that led to the highest improvements over the baseline alignment (i.e., without background knowledge. Furthermore, our proposed mapping gain parameter is strongly correlated with the F-measure of the produced alignments, thus making it a good estimator for ontology matching techniques based on background knowledge.

  20. Suggesting Missing Relations in Biomedical Ontologies Based on Lexical Regularities.

    Science.gov (United States)

    Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Karlsson, Daniel

    2016-01-01

    The number of biomedical ontologies has increased significantly in recent years. Many of such ontologies are the result of efforts of communities of domain experts and ontology engineers. The development and application of quality assurance (QA) methods should help these communities to develop useful ontologies for both humans and machines. According to previous studies, biomedical ontologies are rich in natural language content, but most of them are not so rich in axiomatic terms. Here, we are interested in studying the relation between content in natural language and content in axiomatic form. The analysis of the labels of the classes permits to identify lexical regularities (LRs), which are sets of words that are shared by labels of different classes. Our assumption is that the classes exhibiting an LR should be logically related through axioms, which is used to propose an algorithm to detect missing relations in the ontology. Here, we analyse a lexical regularity of SNOMED CT, congenital stenosis, which is reported as problematic by the SNOMED CT maintenance team. PMID:27577409

  1. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1974-01-01

    Advances in Biomedical Engineering, Volume 4, is a collection of papers that deals with gas chromatography, mass spectroscopy and the analysis of minute samples, as well as the role of the government in regulating the production, usage, safety, and efficacy of medical devices. One paper reviews the use of mass spectrometry and computer technology in relation to gas-phase analytical methods based on gas chromatograph-mass spectrometer instruments and gas chromatograph-mass spectrometer-computer analytical systems. Many health practitioners, government and private health agencies, the legal prof

  2. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

    Advances in Biomedical Engineering, Volume 3, is a collection of papers that discusses circulatory system models, linguistics in computer usage, and clinical applications on patient monitoring. One paper describes the use of comparative models of overall circulatory mechanics that include models of the cardiac pump, of the vascular systems, and of the overall systems behavior. Another paper describes a model in processing medical language data that employs an explicit semantic structure, becoming the basis for the computer-based, artificial intelligence of the system. One paper cites studies b

  3. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

    Advances in Biomedical Engineering, Volume 2, is a collection of papers that discusses the basic sciences, the applied sciences of engineering, the medical sciences, and the delivery of health services. One paper discusses the models of adrenal cortical control, including the secretion and metabolism of cortisol (the controlled process), as well as the initiation and modulation of secretion of ACTH (the controller). Another paper discusses hospital computer systems-application problems, objective evaluation of technology, and multiple pathways for future hospital computer applications. The pos

  4. Knowledge Discovery from Biomedical Ontologies in Cross Domains.

    Science.gov (United States)

    Shen, Feichen; Lee, Yugyung

    2016-01-01

    In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies.

  5. Knowledge Discovery from Biomedical Ontologies in Cross Domains

    Science.gov (United States)

    Shen, Feichen; Lee, Yugyung

    2016-01-01

    In recent years, there is an increasing demand for sharing and integration of medical data in biomedical research. In order to improve a health care system, it is required to support the integration of data by facilitating semantic interoperability systems and practices. Semantic interoperability is difficult to achieve in these systems as the conceptual models underlying datasets are not fully exploited. In this paper, we propose a semantic framework, called Medical Knowledge Discovery and Data Mining (MedKDD), that aims to build a topic hierarchy and serve the semantic interoperability between different ontologies. For the purpose, we fully focus on the discovery of semantic patterns about the association of relations in the heterogeneous information network representing different types of objects and relationships in multiple biological ontologies and the creation of a topic hierarchy through the analysis of the discovered patterns. These patterns are used to cluster heterogeneous information networks into a set of smaller topic graphs in a hierarchical manner and then to conduct cross domain knowledge discovery from the multiple biological ontologies. Thus, patterns made a greater contribution in the knowledge discovery across multiple ontologies. We have demonstrated the cross domain knowledge discovery in the MedKDD framework using a case study with 9 primary biological ontologies from Bio2RDF and compared it with the cross domain query processing approach, namely SLAP. We have confirmed the effectiveness of the MedKDD framework in knowledge discovery from multiple medical ontologies. PMID:27548262

  6. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

    OpenAIRE

    Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V.; Lawson, Andrew; Zeng, Jia; Johnson, Amber M.; Holla, Vijaykumar; Bailey, Ann M.; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda

    2015-01-01

    Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene an...

  7. Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformation.

    Science.gov (United States)

    Shaban-Nejad, Arash; Haarslev, Volker

    2015-01-01

    The issue of ontology evolution and change management is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies and interactions with other existing ontologies have been widely neglected. In our research, after revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, Represent, Legitimate and Reproduce (RLR), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general and aids in tracking and representing the changes, particularly through the use of category theory and hierarchical graph transformation. PMID:26255376

  8. Managing changes in distributed biomedical ontologies using hierarchical distributed graph transformation.

    Science.gov (United States)

    Shaban-Nejad, Arash; Haarslev, Volker

    2015-01-01

    The issue of ontology evolution and change management is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies and interactions with other existing ontologies have been widely neglected. In our research, after revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, Represent, Legitimate and Reproduce (RLR), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general and aids in tracking and representing the changes, particularly through the use of category theory and hierarchical graph transformation.

  9. Advanced Biomedical Computing Center (ABCC) | DSITP

    Science.gov (United States)

    The Advanced Biomedical Computing Center (ABCC), located in Frederick Maryland (MD), provides HPC resources for both NIH/NCI intramural scientists and the extramural biomedical research community. Its mission is to provide HPC support, to provide collaborative research, and to conduct in-house research in various areas of computational biology and biomedical research.

  10. Advanced Methods of Biomedical Signal Processing

    CERN Document Server

    Cerutti, Sergio

    2011-01-01

    This book grew out of the IEEE-EMBS Summer Schools on Biomedical Signal Processing, which have been held annually since 2002 to provide the participants state-of-the-art knowledge on emerging areas in biomedical engineering. Prominent experts in the areas of biomedical signal processing, biomedical data treatment, medicine, signal processing, system biology, and applied physiology introduce novel techniques and algorithms as well as their clinical or physiological applications. The book provides an overview of a compelling group of advanced biomedical signal processing techniques, such as mult

  11. Utilization of ontology look-up services in information retrieval for biomedical literature.

    Science.gov (United States)

    Vishnyakova, Dina; Pasche, Emilie; Lovis, Christian; Ruch, Patrick

    2013-01-01

    With the vast amount of biomedical data we face the necessity to improve information retrieval processes in biomedical domain. The use of biomedical ontologies facilitated the combination of various data sources (e.g. scientific literature, clinical data repository) by increasing the quality of information retrieval and reducing the maintenance efforts. In this context, we developed Ontology Look-up services (OLS), based on NEWT and MeSH vocabularies. Our services were involved in some information retrieval tasks such as gene/disease normalization. The implementation of OLS services significantly accelerated the extraction of particular biomedical facts by structuring and enriching the data context. The results of precision in normalization tasks were boosted on about 20%.

  12. WebMedSA: a web-based framework for segmenting and annotating medical images using biomedical ontologies

    Science.gov (United States)

    Vega, Francisco; Pérez, Wilson; Tello, Andrés.; Saquicela, Victor; Espinoza, Mauricio; Solano-Quinde, Lizandro; Vidal, Maria-Esther; La Cruz, Alexandra

    2015-12-01

    Advances in medical imaging have fostered medical diagnosis based on digital images. Consequently, the number of studies by medical images diagnosis increases, thus, collaborative work and tele-radiology systems are required to effectively scale up to this diagnosis trend. We tackle the problem of the collaborative access of medical images, and present WebMedSA, a framework to manage large datasets of medical images. WebMedSA relies on a PACS and supports the ontological annotation, as well as segmentation and visualization of the images based on their semantic description. Ontological annotations can be performed directly on the volumetric image or at different image planes (e.g., axial, coronal, or sagittal); furthermore, annotations can be complemented after applying a segmentation technique. WebMedSA is based on three main steps: (1) RDF-ization process for extracting, anonymizing, and serializing metadata comprised in DICOM medical images into RDF/XML; (2) Integration of different biomedical ontologies (using L-MOM library), making this approach ontology independent; and (3) segmentation and visualization of annotated data which is further used to generate new annotations according to expert knowledge, and validation. Initial user evaluations suggest that WebMedSA facilitates the exchange of knowledge between radiologists, and provides the basis for collaborative work among them.

  13. Advanced computational approaches to biomedical engineering

    CERN Document Server

    Saha, Punam K; Basu, Subhadip

    2014-01-01

    There has been rapid growth in biomedical engineering in recent decades, given advancements in medical imaging and physiological modelling and sensing systems, coupled with immense growth in computational and network technology, analytic approaches, visualization and virtual-reality, man-machine interaction and automation. Biomedical engineering involves applying engineering principles to the medical and biological sciences and it comprises several topics including biomedicine, medical imaging, physiological modelling and sensing, instrumentation, real-time systems, automation and control, sig

  14. The role of ontologies in biological and biomedical research: a functional perspective

    KAUST Repository

    Hoehndorf, Robert

    2015-04-10

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  15. The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

    Science.gov (United States)

    Tenenbaum, Jessica D; Whetzel, Patricia L; Anderson, Kent; Borromeo, Charles D; Dinov, Ivo D; Gabriel, Davera; Kirschner, Beth; Mirel, Barbara; Morris, Tim; Noy, Natasha; Nyulas, Csongor; Rubenson, David; Saxman, Paul R; Singh, Harpreet; Whelan, Nancy; Wright, Zach; Athey, Brian D; Becich, Michael J; Ginsburg, Geoffrey S; Musen, Mark A; Smith, Kevin A; Tarantal, Alice F; Rubin, Daniel L; Lyster, Peter

    2011-02-01

    The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health. PMID:20955817

  16. Ontology-based retrieval of bio-medical information based on microarray text corpora

    DEFF Research Database (Denmark)

    Hansen, Kim Allan; Zambach, Sine; Have, Christian Theil

    degree. We explore the possibilities of retrieving biomedical information from microarrays in Gene Expression Omnibus (GEO), of which we have indexed a sample semantically, as a rst step towards ontology based searches. Through an example we argue that it is possible to improve the retrieval......Microarray technology is often used in gene expression exper- iments. Information retrieval in the context of microarrays has mainly been concerned with the analysis of the numeric data produced; how- ever, the experiments are often annotated with textual metadata. Al- though biomedical resources...

  17. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

    Science.gov (United States)

    Dumontier, Michel; Baker, Christopher Jo; Baran, Joachim; Callahan, Alison; Chepelev, Leonid; Cruz-Toledo, José; Del Rio, Nicholas R; Duck, Geraint; Furlong, Laura I; Keath, Nichealla; Klassen, Dana; McCusker, James P; Queralt-Rosinach, Núria; Samwald, Matthias; Villanueva-Rosales, Natalia; Wilkinson, Mark D; Hoehndorf, Robert

    2014-03-06

    The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org.

  18. Extending VIVO ontology to represent research and educational resources in an academic biomedical informatics department.

    Science.gov (United States)

    Nakikj, Drashko; Weng, Chunhua

    2013-01-01

    The increasing need for interdisciplinary team sciences makes it vital for academic research departments to publicize their research and educational resources as part of "linked data" on the semantic web to facilitate research networking and recruitment. We extended an open-source ontology, VIVO, to represent the research and educational resources in an academic biomedical informatics department to enable ontology-based information storage and retrieval. Using participatory design methods, we surveyed representative types of visitors to the department web site to understand their information needs, and incorporated these needs into the ontology design. We added 114 classes and 186 properties to VIVO. Generalizability and scalability are the measures used in our theoretical evaluation.

  19. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

    Science.gov (United States)

    Kibbe, Warren A; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J; Binder, Janos X; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn M

    2015-01-01

    The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.

  20. 生物医学本体工程进展%Current Status of Biomedical Ontology Engineering

    Institute of Scientific and Technical Information of China (English)

    于彤; 崔蒙; 杨硕; 李敬华; 刘丽红; 贾李蓉

    2012-01-01

    近年来,领域本体在生物医学领域广泛应用,在知识的获取、管理和检索中发挥了积极作用.通过文献调研找出了生物医学领域中的本体,选取其中的代表性本体进行调研与分析,并讨论了存在的问题和发展趋势.%In recent years, a variety of domain ontologies have been developed in biomedical domain. They are playing an important role in the acquisition, management, and retrieval of biomedical knowledge. We identify biomedica] ontologies through literature review, and select a set of representative ontologies for investigation and analysis. We also discuss the open problems and trends in this field.

  1. A Novel Method to Transform Relational Data into Ontology in the Bio-medical Domain

    Directory of Open Access Journals (Sweden)

    V.Rajeswari

    2013-06-01

    Full Text Available Bio-Medical knowledge that has been gathered over decades, is unique in nature since large variety of data models are used in the medical field. Since this domain forms a very important aspect in the well being of the society, measures are afoot to organise the knowledge in a systematic way for interoperability and re-usability. We have discussed here an approach which makes it possible to make knowledge base available in medicinal drug industry shareable across platforms and data models. This is achieved through the application of new developments that have taken place in the computer engineering field. The work involves transforming relational data into ontology to help meet the future computing needs. With ‘cloud’ deemed to be the future computing environment for all, this work, we humbly feel will contribute towards that paradigm.

  2. Advances in Swine Biomedical Model Genomics

    Directory of Open Access Journals (Sweden)

    Joan K. Lunney

    2007-01-01

    Full Text Available This review is a short update on the diversity of swine biomedical models and the importance of genomics in their continued development. The swine has been used as a major mammalian model for human studies because of the similarity in size and physiology, and in organ development and disease progression. The pig model allows for deliberately timed studies, imaging of internal vessels and organs using standard human technologies, and collection of repeated peripheral samples and, at kill, detailed mucosal tissues. The ability to use pigs from the same litter, or cloned or transgenic pigs, facilitates comparative analyses and genetic mapping. The availability of numerous well defined cell lines, representing a broad range of tissues, further facilitates testing of gene expression, drug susceptibility, etc. Thus the pig is an excellent biomedical model for humans. For genomic applications it is an asset that the pig genome has high sequence and chromosome structure homology with humans. With the swine genome sequence now well advanced there are improving genetic and proteomic tools for these comparative analyses. The review will discuss some of the genomic approaches used to probe these models. The review will highlight genomic studies of melanoma and of infectious disease resistance, discussing issues to consider in designing such studies. It will end with a short discussion of the potential for genomic approaches to develop new alternatives for control of the most economically important disease of pigs, porcine reproductive and respiratory syndrome (PRRS, and the potential for applying knowledge gained with this virus for human viral infectious disease studies.

  3. Advances in biomedical engineering and biotechnology during 2013-2014.

    Science.gov (United States)

    Liu, Feng; Wang, Ying; Burkhart, Timothy A; González Penedo, Manuel Francisco; Ma, Shaodong

    2014-01-01

    The 3rd International Conference on Biomedical Engineering and Biotechnology (iCBEB 2014), held in Beijing from the 25th to the 28th of September 2014, is an annual conference that intends to provide an opportunity for researchers and practitioners around the world to present the most recent advances and future challenges in the fields of biomedical engineering, biomaterials, bioinformatics and computational biology, biomedical imaging and signal processing, biomechanical engineering and biotechnology, amongst others. The papers published in this issue are selected from this conference, which witnesses the advances in biomedical engineering and biotechnology during 2013-2014.

  4. SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data

    OpenAIRE

    Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; Haan, Mark de; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A.

    2015-01-01

    There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) a...

  5. Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

    Directory of Open Access Journals (Sweden)

    Sai Lakshmi Subramanian

    2015-08-01

    Full Text Available The large diversity and volume of extracellular RNA (exRNA data that will form the basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNA profiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a selection of samples from a virtual biorepository for exRNA profiling and for inclusion in the exRNA Atlas; (b retrieval of a data slice from the exRNA Atlas for integrative analysis and (c interpretation of exRNA analysis results in the context of pathways and networks. As exRNA profiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

  6. Biomedical photonics handbook therapeutics and advanced biophotonics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents recent fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers,

  7. Handbook on advanced design and manufacturing technologies for biomedical devices

    CERN Document Server

    2013-01-01

    The last decades have seen remarkable advances in computer-aided design, engineering and manufacturing technologies, multi-variable simulation tools, medical imaging, biomimetic design, rapid prototyping, micro and nanomanufacturing methods and information management resources, all of which provide new horizons for the Biomedical Engineering fields and the Medical Device Industry. Handbook on Advanced Design and Manufacturing Technologies for Biomedical Devices covers such topics in depth, with an applied perspective and providing several case studies that help to analyze and understand the key factors of the different stages linked to the development of a novel biomedical device, from the conceptual and design steps, to the prototyping and industrialization phases. Main research challenges and future potentials are also discussed, taking into account relevant social demands and a growing market already exceeding billions of dollars. In time, advanced biomedical devices will decisively change methods and resu...

  8. Formal ontology for natural language processing and the integration of biomedical databases.

    Science.gov (United States)

    Simon, Jonathan; Dos Santos, Mariana; Fielding, James; Smith, Barry

    2006-01-01

    The central hypothesis underlying this communication is that the methodology and conceptual rigor of a philosophically inspired formal ontology can bring significant benefits in the development and maintenance of application ontologies [A. Flett, M. Dos Santos, W. Ceusters, Some Ontology Engineering Procedures and their Supporting Technologies, EKAW2002, 2003]. This hypothesis has been tested in the collaboration between Language and Computing (L&C), a company specializing in software for supporting natural language processing especially in the medical field, and the Institute for Formal Ontology and Medical Information Science (IFOMIS), an academic research institution concerned with the theoretical foundations of ontology. In the course of this collaboration L&C's ontology, LinKBase, which is designed to integrate and support reasoning across a plurality of external databases, has been subjected to a thorough auditing on the basis of the principles underlying IFOMIS's Basic Formal Ontology (BFO) [B. Smith, Basic Formal Ontology, 2002. http://ontology.buffalo.edu/bfo]. The goal is to transform a large terminology-based ontology into one with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase are standardized in the framework of first-order logic. In this paper we describe how this principles-based standardization has led to a greater degree of internal coherence of the LinKBase structure, and how it has facilitated the construction of mappings between external databases using LinKBase as translation hub. We argue that the collaboration here described represents a new phase in the quest to solve the so-called "Tower of Babel" problem of ontology integration [F. Montayne, J. Flanagan, Formal Ontology: The Foundation for Natural Language Processing, 2003. http://www.landcglobal.com/]. PMID:16153885

  9. Advanced Probability Theory for Biomedical Engineers

    CERN Document Server

    Enderle, John

    2006-01-01

    This is the third in a series of short books on probability theory and random processes for biomedical engineers. This book focuses on standard probability distributions commonly encountered in biomedical engineering. The exponential, Poisson and Gaussian distributions are introduced, as well as important approximations to the Bernoulli PMF and Gaussian CDF. Many important properties of jointly Gaussian random variables are presented. The primary subjects of the final chapter are methods for determining the probability distribution of a function of a random variable. We first evaluate the prob

  10. Advances in Swine biomedical Model Genomics

    Science.gov (United States)

    This manuscript is a short update on the diversity of swine biomedical models and the importance of genomics in their continued development. The swine has been used as a major mammalian model for human studies because of the similarity in size and physiology, and in organ development and disease pro...

  11. Advancement of Women in the Biomedical Workforce: Insights for Success.

    Science.gov (United States)

    Barfield, Whitney L; Plank-Bazinet, Jennifer L; Austin Clayton, Janine

    2016-08-01

    Women continue to face unique barriers in the biomedical workforce that affect their advancement and retention in this field. The National Institutes of Health (NIH) formed the Working Group on Women in Biomedical Careers to address these issues. Through the efforts of the working group, the NIH funded 14 research grants to identify barriers or to develop and/or test interventions to support women in the biomedical workforce. The grantees that were funded through this endeavor later established the grassroots Research Partnership on Women in Biomedical Careers, and they continue to conduct research and disseminate information on the state of women in academic medicine. This Commentary explores the themes introduced in a collection of articles organized by the research partnership and published in this issue of Academic Medicine. The authors highlight the role that government plays in the advancement of women in academic medicine and highlight the findings put forward in this collection.

  12. Advances in Swine Biomedical Model Genomics

    OpenAIRE

    Lunney, Joan K.

    2007-01-01

    This review is a short update on the diversity of swine biomedical models and the importance of genomics in their continued development. The swine has been used as a major mammalian model for human studies because of the similarity in size and physiology, and in organ development and disease progression. The pig model allows for deliberately timed studies, imaging of internal vessels and organs using standard human technologies, and collection of repeated peripheral samples and, at kill, deta...

  13. DServO: A Peer-to-Peer-based Approach to Biomedical Ontology Repositories.

    Science.gov (United States)

    Mambone, Zakaria; Savadogo, Mahamadi; Some, Borlli Michel Jonas; Diallo, Gayo

    2015-01-01

    We present in this poster an extension of the ServO ontology server system, which adopts a decentralized Peer-To-Peer approach for managing multiple heterogeneous knowledge organization systems. It relies on the use of the JXTA protocol coupled with information retrieval techniques to provide a decentralized infrastructure for managing multiples instances of Ontology Repositories.

  14. Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

    Directory of Open Access Journals (Sweden)

    Hakenberg Jörg

    2009-01-01

    Full Text Available Abstract Background Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively. Results The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success than on MeSH (73% success as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate. Conclusion Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90

  15. Biomedical Applications of Advanced Multifunctional Magnetic Nanoparticles.

    Science.gov (United States)

    Long, Nguyen Viet; Yang, Yong; Teranishi, Toshiharu; Thi, Cao Minh; Cao, Yanqin; Nogami, Masayuki

    2015-12-01

    In this review, we have presented the latest results and highlights on biomedical applications of a class of noble metal nanoparticles, such as gold, silver and platinum, and a class of magnetic nanoparticles, such as cobalt, nickel and iron. Their most important related compounds are also discussed for biomedical applications for treating various diseases, typically as cancers. At present, both physical and chemical methods have been proved very successful to synthesize, shape, control, and produce metal- and oxide-based homogeneous particle systems, e.g., nanoparticles and microparticles. Therefore, we have mainly focused on functional magnetic nanoparticles for nanomedicine because of their high bioadaptability to the organs inside human body. Here, bioconjugation techniques are very crucial to link nanoparticles with conventional drugs, nanodrugs, biomolecules or polymers for biomedical applications. Biofunctionalization of engineered nanoparticles for biomedicine is shown respective to in vitro and in vivo analysis protocols that typically include drug delivery, hyperthermia therapy, magnetic resonance imaging (MRI), and recent outstanding progress in sweep imaging technique with Fourier transformation (SWIFT) MRI. The latter can be especially applied using magnetic nanoparticles, such as Co-, Fe-, Ni-based nanoparticles, α-Fe2O3, and Fe3O4 oxide nanoparticles for analysis and treatment of malignancies. Therefore, this review focuses on recent results of scientists, and related research on diagnosis and treatment methods of common and dangerous diseases by biomedical engineered nanoparticles. Importantly, nanosysems (nanoparticles) or microsystems (microparticles) or hybrid micronano systems are shortly introduced into nanomedicine. Here, Fe oxide nanoparticles ultimately enable potential and applicable technologies for tumor-targeted imaging and therapy. Finally, we have shown the latest aspects of the most important Fe-based particle systems, such as Fe,

  16. SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.

    Science.gov (United States)

    Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; de Haan, Mark; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A

    2015-01-01

    There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA's applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90 000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from

  17. SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.

    Science.gov (United States)

    Pang, Chao; Sollie, Annet; Sijtsma, Anna; Hendriksen, Dennis; Charbon, Bart; de Haan, Mark; de Boer, Tommy; Kelpin, Fleur; Jetten, Jonathan; van der Velde, Joeri K; Smidt, Nynke; Sijmons, Rolf; Hillege, Hans; Swertz, Morris A

    2015-01-01

    There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA's applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90 000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from

  18. Advances in Electronic-Nose Technologies Developed for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Alphus D. Wilson

    2011-01-01

    Full Text Available The research and development of new electronic-nose applications in the biomedical field has accelerated at a phenomenal rate over the past 25 years. Many innovative e-nose technologies have provided solutions and applications to a wide variety of complex biomedical and healthcare problems. The purposes of this review are to present a comprehensive analysis of past and recent biomedical research findings and developments of electronic-nose sensor technologies, and to identify current and future potential e-nose applications that will continue to advance the effectiveness and efficiency of biomedical treatments and healthcare services for many years. An abundance of electronic-nose applications has been developed for a variety of healthcare sectors including diagnostics, immunology, pathology, patient recovery, pharmacology, physical therapy, physiology, preventative medicine, remote healthcare, and wound and graft healing. Specific biomedical e-nose applications range from uses in biochemical testing, blood-compatibility evaluations, disease diagnoses, and drug delivery to monitoring of metabolic levels, organ dysfunctions, and patient conditions through telemedicine. This paper summarizes the major electronic-nose technologies developed for healthcare and biomedical applications since the late 1980s when electronic aroma detection technologies were first recognized to be potentially useful in providing effective solutions to problems in the healthcare industry.

  19. Ontology Engineering

    OpenAIRE

    Alterovitz, Gil; Xiang, Michael; Hill, David P; Lomax, Jane; Liu, Jonathan; Cherkassky, Michael; Dreyfuss, Jonathan; Mungall, Chris; Harris, Midori A.; Dolan, Mary E; Blake, Judith A.; Ramoni, Marco F

    2010-01-01

    Gene Ontology1 and similar biomedical ontologies are critical tools of today genetic research. These ontologies are crafted through a painstaking process of manual editing, and their organization relies on the intuition of human curators. Here we describe a method that uses information theory to automatically organize the structure of GO and optimize the distribution of the information within it. We used this approach to analyze the evolution of GO, and we identified several areas where the i...

  20. Recent advances in carbon nanodots: synthesis, properties and biomedical applications

    Science.gov (United States)

    Miao, Peng; Han, Kun; Tang, Yuguo; Wang, Bidou; Lin, Tao; Cheng, Wenbo

    2015-01-01

    Herein, a mini review is presented concerning the most recent research progress of carbon nanodots, which have emerged as one of the most attractive photoluminescent materials. Different synthetic methodologies to achieve advanced functions and better photoluminescence performances are summarized, which are mainly divided into two classes: top-down and bottom-up. The inspiring properties, including photoluminescence emission, chemiluminescence, electrochemical luminescence, peroxidase-like activity and toxicity, are discussed. Moreover, the biomedical applications in biosensing, bioimaging and drug delivery are reviewed.

  1. Advances in the Biomedical Applications of the EELA Project

    CERN Document Server

    Hernández, Vicente; Aparicio, Gabriel; Isea, Raul; Chavés, Juan Luis; Hernández, Álvaro; Mora, Henry Ricardo; Fernández, Manuel; Acero, Alicia; Montes, Esther; Mayo, Rafael

    2010-01-01

    In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the Biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computation phylogenetics. After this period, the achieved advances are summarised in this paper.

  2. Advances in the biomedical applications of the EELA Project.

    Science.gov (United States)

    Hernández, Vicente; Blanquer, Ignacio; Aparicio, Gabriel; Isea, Raúl; Chaves, Juan Luis; Hernández, Alvaro; Mora, Henry Ricardo; Fernández, Manuel; Acero, Alicia; Montes, Esther; Mayo, Rafael

    2007-01-01

    In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computational phylogenetics. After this period, the achieved advances are summarised in this paper. PMID:17476045

  3. Advances in the Biomedical Applications of the EELA Project

    OpenAIRE

    Hernández, Vicente; Blanquer, Ignacio; Aparicio, Gabriel; Isea, Raul; Chavés, Juan Luis; Hernández, Álvaro; Mora, Henry Ricardo; Fernández, Manuel; Acero, Alicia; Montes, Esther; Mayo, Rafael

    2010-01-01

    In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the Biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computation phylogenetics. After this period, the achieved advances are summarised in ...

  4. Building ontologies with basic formal ontology

    CERN Document Server

    Arp, Robert; Spear, Andrew D.

    2015-01-01

    In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now u...

  5. The Biomedical Resource Ontology (BRO) to Enable Resource Discovery in Clinical and Translational Research

    OpenAIRE

    Tenenbaum, Jessica D; Whetzel, Patricia L.; Anderson, Kent; Borromeo, Charles D; Ivo D. Dinov; Gabriel, Davera; Kirschner, Beth; Mirel, Barbara; Morris, Tim; Noy, Natasha; NYULAS, CSONGOR; Rubenson, David; Saxman, Paul R.; Singh, Harpreet; Whelan, Nancy

    2010-01-01

    The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development...

  6. Turning Informal Thesauri Into Formal Ontologies: A Feasibility Study on Biomedical Knowledge re-Use

    OpenAIRE

    Udo Hahn

    2003-01-01

    This paper reports a large-scale knowledge conversion and curation experiment. Biomedical domain knowledge from a semantically weak and shallow terminological resource, the UMLS, is transformed into a rigorous description logics format. This way, the broad coverage of the UMLS is combined with inference mechanisms for consistency and cycle checking. They are the key to proper cleansing of the knowledge directly imported from the UMLS, as well as subsequent updating, maintenance an...

  7. Advances in targeted proteomics and applications to biomedical research

    Science.gov (United States)

    Shi, Tujin; Song, Ehwang; Nie, Song; Rodland, Karin D.; Liu, Tao; Qian, Wei-Jun; Smith, Richard D.

    2016-01-01

    Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed. PMID:27302376

  8. Lipidomics as a Principal Tool for Advancing Biomedical Research

    Institute of Scientific and Technical Information of China (English)

    Sin Man Lam; Guanghou Shui

    2013-01-01

    Lipidomics,which targets at the construction of a comprehensive map of lipidome comprising the entire lipid pool within a cell or tissue,is currently emerging as an independent discipline at the interface of lipid biology,technology and medicine.The diversity and complexity of the biological lipidomes call for technical innovatin and improvement to meet the needs of various biomedical studies.The recent wave of expansion in the field of lipidomic research is mainly attributed to advances in analytical technologies,in particular,the development of new mass spectrometric and chromatographic tools for the characterization and quantification of the wide array of diverse lipid species in the cellular lipidome.Here,we review some of the key technical advances in lipidome analysis and put forth the applications of lipidomics in addressing the biological roles of lipids in numerous disease models including the metabolic syndrome,neurodegenerative diseases and infectious diseases,as well as the increasing urgency to construct the lipidome inventory for various mammalian/organism models useful for biomedical research.

  9. Recent advances in the use of gelatin in biomedical research.

    Science.gov (United States)

    Su, Kai; Wang, Chunming

    2015-11-01

    The biomacromolecule, gelatin, has increasingly been used in biomedicine-beyond its traditional use in food and cosmetics. The appealing advantages of gelatin, such as its cell-adhesive structure, low cost, off-the-shelf availability, high biocompatibility, biodegradability and low immunogenicity, among others, have made it a desirable candidate for the development of biomaterials for tissue engineering and drug delivery. Gelatin can be formulated in the form of nanoparticles, employed as size-controllable porogen, adopted as surface coating agent and mixed with synthetic or natural biopolymers forming composite scaffolds. In this article, we review recent advances in the versatile applications of gelatin within biomedical context and attempt to draw upon its advantages and potential challenges. PMID:26160110

  10. Advances in Electronic-Nose Technologies Developed for Biomedical Applications

    OpenAIRE

    Wilson, Alphus D.; Manuela Baietto

    2011-01-01

    The research and development of new electronic-nose applications in the biomedical field has accelerated at a phenomenal rate over the past 25 years. Many innovative e-nose technologies have provided solutions and applications to a wide variety of complex biomedical and healthcare problems. The purposes of this review are to present a comprehensive analysis of past and recent biomedical research findings and developments of electronic-nose sensor technologies, and to identify current and futu...

  11. Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

    Science.gov (United States)

    Panahiazar, Maryam; Sheth, Amit P; Ranabahu, Ajith; Vos, Rutger A; Leebens-Mack, Jim

    2013-01-01

    Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web technologies are being developed to make phylogenetic knowledge interpretable by web agents, thereby enabling intelligently automated, high-throughput reuse of results generated by phylogenetic research. This manuscript describes an ontology-driven, semantic problem-solving environment for phylogenetic analyses and introduces artefacts that can promote phyloinformatic efforts to promote accessibility of trees and underlying metadata. PhylOnt is an extensible ontology with concepts describing tree types and tree building methodologies including estimation methods, models and programs. In addition we present the PhylAnt platform for annotating scientific articles and NeXML files with PhylOnt concepts. The novelty of this work is the annotation of NeXML files and phylogenetic related documents with PhylOnt Ontology. This approach advances data reuse in phyloinformatics.

  12. Artificial Sight Basic Research, Biomedical Engineering, and Clinical Advances

    CERN Document Server

    Humayun, Mark S; Chader, Gerald; Greenbaum, Elias

    2008-01-01

    Artificial sight is a frontier area of modern ophthalmology combining the multidisciplinary skills of surgical ophthalmology, biomedical engineering, biological physics, and psychophysical testing. Many scientific, engineering, and surgical challenges must be surmounted before widespread practical applications can be realized. The goal of Artificial Sight is to summarize the state-of-the-art research in this exciting area, and to describe some of the current approaches and initiatives that may help patients in a clinical setting. The Editors are active researchers in the fields of artificial sight, biomedical engineering and biological physics. They have received numerous professional awards and recognition for their work. The artificial sight team at the Doheny Eye Institute, led by Dr. Mark Humayun, is a world leader in this area of biomedical engineering and clinical research. Key Features Introduces and assesses the state of the art for a broad audience of biomedical engineers, biophysicists, and clinical...

  13. Genetic Resources for Advanced Biofuel Production Described with the Gene Ontology

    Directory of Open Access Journals (Sweden)

    Trudy eTorto-Alalibo

    2014-10-01

    Full Text Available Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial Energy Gene Ontology (MENGO: http://www.mengo.biochem.vt.edu project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat, can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.

  14. Recent Advances in Shape Memory Soft Materials for Biomedical Applications.

    Science.gov (United States)

    Chan, Benjamin Qi Yu; Low, Zhi Wei Kenny; Heng, Sylvester Jun Wen; Chan, Siew Yin; Owh, Cally; Loh, Xian Jun

    2016-04-27

    Shape memory polymers (SMPs) are smart and adaptive materials able to recover their shape through an external stimulus. This functionality, combined with the good biocompatibility of polymers, has garnered much interest for biomedical applications. In this review, we discuss the design considerations critical to the successful integration of SMPs for use in vivo. We also highlight recent work on three classes of SMPs: shape memory polymers and blends, shape memory polymer composites, and shape memory hydrogels. These developments open the possibility of incorporating SMPs into device design, which can lead to vast technological improvements in the biomedical field. PMID:27018814

  15. Recent Advances in Shape Memory Soft Materials for Biomedical Applications.

    Science.gov (United States)

    Chan, Benjamin Qi Yu; Low, Zhi Wei Kenny; Heng, Sylvester Jun Wen; Chan, Siew Yin; Owh, Cally; Loh, Xian Jun

    2016-04-27

    Shape memory polymers (SMPs) are smart and adaptive materials able to recover their shape through an external stimulus. This functionality, combined with the good biocompatibility of polymers, has garnered much interest for biomedical applications. In this review, we discuss the design considerations critical to the successful integration of SMPs for use in vivo. We also highlight recent work on three classes of SMPs: shape memory polymers and blends, shape memory polymer composites, and shape memory hydrogels. These developments open the possibility of incorporating SMPs into device design, which can lead to vast technological improvements in the biomedical field.

  16. Chitin and chitosan based polyurethanes: A review of recent advances and prospective biomedical applications.

    Science.gov (United States)

    Usman, Ali; Zia, Khalid Mahmood; Zuber, Mohammad; Tabasum, Shazia; Rehman, Saima; Zia, Fatima

    2016-05-01

    Chitin and chitosan are amino polysaccharides having massive structural propensities to produce bioactive materials with innovative properties, functions and diverse applications particularly in biomedical field. The specific physico-chemical, mechanical, biological and degradation properties offer efficient way to blend these biopolymers with synthetic ones. Polyurethane (PU) gained substantial attention owing to its structure-properties relationship. The immense activities of chitin/chitosan are successfully utilized to enhance the bioactive properties of polyurethanes. This review shed a light on chitin and chitosan based PU materials with their potential applications especially focusing the bio-medical field. All the technical scientific issues have been addressed highlighting the recent advancement in the biomedical field.

  17. Designing advanced functional periodic mesoporous organosilicas for biomedical applications

    Directory of Open Access Journals (Sweden)

    Dolores Esquivel

    2014-03-01

    Full Text Available Periodic mesoporous organosilicas (PMOs, reported for the first time in 1999, constitute a new branch of organic-inorganic hybrid materials with high-ordered structures, uniform pore size and homogenous distribution of organic bridges into a silica framework. Unlike conventional mesoporous silicas, these materials offer the possibility to adjust the surface (hydrophilicity/hydrophobicity and physical properties (morphology, porosity as well as their mechanical stability through the incorporation of different functional organic moieties in their pore walls. A broad variety of PMOs has been designed for their subsequent application in many fields. More recently, PMOs have attracted growing interest in emerging areas as biology and biomedicine. This review provides a comprehensive overview of the most recent breakthroughs achieved for PMOs in biological and biomedical applications.

  18. A Semantics-Based Approach to Retrieving Biomedical Information

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik; Zambach, Sine;

    2011-01-01

    This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontol...... of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is distinct in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.......This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative...... ontologies’, i.e., ontologies providing increasingly specialised concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so called ontological semantics which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form...

  19. Toxicology ontology perspectives.

    Science.gov (United States)

    Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic; Cook, David; Dix, Ian; Escher, Sylvia; Hastings, Janna; Heard, David J; Jeliazkova, Nina; Judson, Philip; Matis-Mitchell, Sherri; Mitic, Dragana; Myatt, Glenn; Shah, Imran; Spjuth, Ola; Tcheremenskaia, Olga; Toldo, Luca; Watson, David; White, Andrew; Yang, Chihae

    2012-01-01

    The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.

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

    OpenAIRE

    Cui, Licong

    2015-01-01

    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 acr...

  1. Advancing community stakeholder engagement in biomedical HIV prevention trials: principles, practices and evidence.

    Science.gov (United States)

    Newman, Peter A; Rubincam, Clara

    2014-12-01

    Community stakeholder engagement is foundational to fair and ethically conducted biomedical HIV prevention trials. Concerns regarding the ethical engagement of community stakeholders in HIV vaccine trials and early terminations of several international pre-exposure prophylaxis trials have fueled the development of international guidelines, such as UNAIDS' good participatory practice (GPP). GPP aims to ensure that stakeholders are effectively involved in all phases of biomedical HIV prevention trials. We provide an overview of the six guiding principles in the GPP and critically examine them in relation to existing social and behavioral science research. In particular, we highlight the challenges involved in operationalizing these principles on the ground in various global contexts, with a focus on low-income country settings. Increasing integration of social science in biomedical HIV prevention trials will provide evidence to advance a science of community stakeholder engagement to support ethical and effective practices informed by local realities and sociocultural differences.

  2. Polymeric AIE-based nanoprobes for biomedical applications: recent advances and perspectives

    Science.gov (United States)

    Zhang, Xiaoyong; Wang, Ke; Liu, Meiying; Zhang, Xiqi; Tao, Lei; Chen, Yiwang; Wei, Yen

    2015-07-01

    The development of polymeric luminescent nanomaterials for biomedical applications has recently attracted a large amount of attention due to the remarkable advantages of these materials compared with small organic dyes and fluorescent inorganic nanomaterials. Among these polymeric luminescent nanomaterials, polymeric luminescent nanomaterials based on dyes with aggregation-induced emission (AIE) properties should be of great research interest due to their unique AIE properties, the designability of polymers and their multifunctional potential. In this review, the recent advances in the design and biomedical applications of polymeric luminescent nanomaterials based on AIE dyes is summarized. Various design strategies for incorporation of these AIE dyes into polymeric systems are included. The potential biomedical applications such as biological imaging, and use in biological sensors and theranostic systems of these polymeric AIE-based nanomaterials have also been highlighted. We trust this review will attract significant interest from scientists from different research fields in chemistry, materials, biology and interdisciplinary areas.

  3. 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....

  4. From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity

    Directory of Open Access Journals (Sweden)

    Mingxin Gan

    2013-01-01

    Full Text Available Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. Nevertheless, with a variety of methods available, how to choose a suitable method for a specific application becomes a problem. With this understanding, we review a majority of existing methods that rely on ontologies to calculate semantic similarity between terms. We classify existing methods into five categories: methods based on semantic distance, methods based on information content, methods based on properties of terms, methods based on ontology hierarchy, and hybrid methods. We summarize characteristics of each category, with emphasis on basic notions, advantages and disadvantages of these methods. Further, we extend our review to software tools implementing these methods and applications using these methods.

  5. Benchmarking ontologies: bigger or better?

    Directory of Open Access Journals (Sweden)

    Lixia Yao

    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.

  6. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.

    Science.gov (United States)

    Gonzalez, Graciela H; Tahsin, Tasnia; Goodale, Britton C; Greene, Anna C; Greene, Casey S

    2016-01-01

    Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine. PMID:26420781

  7. The CHRONIOUS Ontology-Driven Search Tool: Enabling Access to Focused and Up-to-Date Healthcare Literature

    CERN Document Server

    Kiefer, Stephan; Albertoni, Riccardo; Attene, Marco; Giannini, Franca; Marini, Simone; Schneider, Luc; Mesquita, Carlos; Xing, Xin; Lawo, Michael

    2011-01-01

    This paper presents an advanced search engine prototype for bibliography retrieval developed within the CHRONIOUS European IP project of the seventh Framework Program (FP7). This search engine is specifically targeted to clinicians and healthcare practitioners searching for documents related to Chronic Obstructive Pulmonary Disease (COPD) and Chronic Kidney Disease (CKD). To this aim, the presented tool exploits two pathology-specific ontologies that allow focused document indexing and retrieval. These ontologies have been developed on the top of the Middle Layer Ontology for Clinical Care (MLOCC), which provides a link with the Basic Formal Ontology, a foundational ontology used in the Open Biological and Biomedical Ontologies (OBO) Foundry. In addition link with the terms of the MeSH (Medical Subject Heading) thesaurus has been provided to guarantee the coverage with the general certified medical terms and multilingual capabilities.

  8. Towards ontology based search and knowledgesharing using domain ontologies

    DEFF Research Database (Denmark)

    Zambach, Sine

    This paper reports on work in progress. We present work on domain specific verbs and their role as relations in domain ontologies. The domain ontology which is in focus for our research is modeled in cooperation with the Danish biotech company Novo Nordic. Two of the main purposes of domain...... 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....

  9. The cognitive paradigm ontology: design and application.

    Science.gov (United States)

    Turner, Jessica A; Laird, Angela R

    2012-01-01

    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.

  10. How the UK Can Lead the Terrestrial Translation of Biomedical Advances Arising from Lunar Exploration Activities

    Science.gov (United States)

    Green, David A.

    2010-12-01

    Terrestrial translation of biomedical advances is insufficient justification for lunar exploration. However, terrestrial translation should be viewed as a critical part of the cycle of mission planning, execution and review, both in terms of the progress of space exploration, but also of sustained life on Earth. Thus, both the mission and its potential to benefit mankind are increased by the adoption of human-based exploration of the lunar surface. Whilst European biomedical sciences have grown in stature, there remains a gap between space biomedical science and terrestrial medical application. As such, an opportunity for the UK to take a sustainable leadership role exists by utilising its biomedical science community, socialised health care system (National Health Service) and defined mechanisms to determine the clinical efficacy and cost-effectiveness upon health and wellbeing (i.e. National Institute Clinical Excellence), aiding the difficult process of health care rationing. By focusing upon exploitation of the more scientifically rewarding, potentially long-term and more terrestrially analogous challenge of lunar habitation, the UK would circumnavigate the current impediments to International Space Station utilisation. Early engagement in lunar exploration would promote the UK, and its adoption of a leadership role incorporating a considered approach to the development of space biomedicine with an eye to its terrestrial value. For instance, prolonged lunar habitation could provide an `ideal controlled environment' for investigation of medical interventions, in particular multiple interactions (e.g. between exercise and nutrition), a model of accelerated aging and a number of chronic pathologies, including those related to disuse. Lunar advances could provide a springboard for individualized medicine, insights into occupational and de-centralised medicine (e.g. telemedicine) and act as a stimulus for biomedical innovation and understanding. Leadership in

  11. Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

    Science.gov (United States)

    Soldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam H

    2012-01-01

    Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data.

  12. Recent advances of cerium oxide nanoparticles in synthesis, luminescence and biomedical studies:a review

    Institute of Scientific and Technical Information of China (English)

    何立莹; 苏玉民; 蒋兰宏; 石士考

    2015-01-01

    Nanostructured cerium oxide (CeO2) commonly known as nanoceria is a rare earth metal oxide, which plays a technologi-cally important role due to its versatile applications as automobile exhaust catalysts, oxide ion conductors in solid oxide fuel cells, electrode materials for gas sensors, ultraviolet absorbents and glass-polishing materials. However, nanoceria has little or weak lumi-nescence, and therefore its uses in high-performance luminescent devices and biomedical areas are limited. In this review, we present the recent advances of nanoceria in the aspects of synthesis, luminescence and biomedical studies. The CeO2 nanoparticles can be synthesized by solution-based methods including co-precipitation, hydrothermal, microemulsion process, sol-gel techniques, combus-tion reaction and so on. Achieving controlled morphologies and enhanced luminescence efficiency of nanoceria particles are quite es-sential for its potential energy- and environment-related applications. Additionally, a new frontier for nanoceria particles in biomedi-cal research has also been opened, which involves low toxicity, retinopathy, biosensors and cancer therapy aspects. Finally, the sum-mary and outlook on the challenges and perspectives of the nanoceria particles are proposed.

  13. Advances onto the Internet of Things how ontologies make the Internet of Things meaningful

    CERN Document Server

    Re, Giuseppe

    2014-01-01

    The title of this book is a pun on the use of the preposition “onto” with the aim of recalling “Ontology”, the term commonly adopted in the computer science community to indicate the study of the formal specification for organizing knowledge. In the field of knowledge engineering, Ontologies are used for modeling concepts and relationships on some domain. The year 2013 celebrates the twentieth anniversary of the World Wide Web. The simple network of hypermedia has transformed the world of communications with enormous implications on the social relationships.  However, traditional World Wide Web is currently experiencing a challenging evolution toward the Internet of Things (IoT), today feasible thanks to the integration of pervasive technologies capable of sensing the environment.  The most important contribution of IoT regards the possibility of enabling more efficient machine-to-machine cooperation. To such aim, ontologies represent the most suitable tool to enable transfer and comprehension of in...

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

    OpenAIRE

    Skene JH Pate; Jin Heng; Zachariah Zachariah K; Nitzberg Michael; Wymore Farrell; Beauheim Catherine C; 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...

  15. The "Conflicted Dying": The Active Search for Life Extension in Advanced Cancer Through Biomedical Treatment.

    Science.gov (United States)

    Mohammed, Shan; Peter, Elizabeth; Gastaldo, Denise; Howell, Doris

    2016-03-01

    Using a poststructural perspective, we examine the subjectivities that are produced when advanced cancer patients seek life extension through biomedical treatments. Seven case studies were developed that included 20 interviews with patients, family, nurses, and physicians recruited from a tertiary hospital in Canada, 30 documents, and 5 hours of participant observation. We identify seven types of subjectivity: (a) the Desperate Subject, (b) the Cancer Expert Subject, (c) the Proactive Subject, (d) the Productive Subject, (e) the Mistrusting Subject, (f) the Model Patient Subject, and (g) the Suffering Subject. We characterize the "conflicted dying," a contemporary figure who holds multiple perspectives about seeking curative treatment despite the acknowledgment of death. Using active strategies to gain access to treatment, this figure resists traditional arrangements of power/knowledge established by health care providers. We suggest that the search for life extension is a process of shaping the self to fit certain aesthetical traits associated with surviving cancer. PMID:25711844

  16. Advances in biomedical and pharmaceutical applications of functional bacterial cellulose-based nanocomposites.

    Science.gov (United States)

    Ullah, Hanif; Wahid, Fazli; Santos, Hélder A; Khan, Taous

    2016-10-01

    Bacterial cellulose (BC) synthesized by certain species of bacteria, is a fascinating biopolymer with unique physical and mechanical properties. BC's applications range from traditional dessert, gelling, stabilizing and thickening agent in the food industry to advanced high-tech applications, such as immobilization of enzymes, bacteria and fungi, tissue engineering, heart valve prosthesis, artificial blood vessels, bone, cartilage, cornea and skin, and dental root treatment. Various BC-composites have been designed and investigated in order to enhance its biological applicability. This review focuses on the application of BC-based composites for microbial control, wound dressing, cardiovascular, ophthalmic, skeletal, and endodontics systems. Moreover, applications in controlled drug delivery, biosensors/bioanalysis, immobilization of enzymes and cells, stem cell therapy and skin tissue repair are also highlighted. This review will provide new insights for academia and industry to further assess the BC-based composites in terms of practical applications and future commercialization for biomedical and pharmaceutical purposes. PMID:27312644

  17. Advancement and applications of peptide phage display technology in biomedical science.

    Science.gov (United States)

    Wu, Chien-Hsun; Liu, I-Ju; Lu, Ruei-Min; Wu, Han-Chung

    2016-01-01

    Combinatorial phage library is a powerful research tool for high-throughput screening of protein interactions. Of all available molecular display techniques, phage display has proven to be the most popular approach. Screening phage-displayed random peptide libraries is an effective means of identifying peptides that can bind target molecules and regulate their function. Phage-displayed peptide libraries can be used for (i) B-cell and T-cell epitope mapping, (ii) selection of bioactive peptides bound to receptors or proteins, disease-specific antigen mimics, peptides bound to non-protein targets, cell-specific peptides, or organ-specific peptides, and (iii) development of peptide-mediated drug delivery systems and other applications. Targeting peptides identified using phage display technology may be useful for basic research and translational medicine. In this review article, we summarize the latest technological advancements in the application of phage-displayed peptide libraries to applied biomedical sciences.

  18. Tailoring surface topographies of polymers by using ion beam: Recent advances and the potential applications in biomedical and tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Hasebe, Terumitsu, E-mail: teru_hasebe@sakura.med.toho-u.ac.jp [Department of Radiology, Toho University, Sakura Medical Center, 564-1 Shimoshizu, Sakura, Chiba 285-8741 (Japan); Center for Science of Environment, Resources and Energy, Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522 (Japan); Nagashima, So; Yoshimoto, Yukihiro; Hotta, Atsushi; Suzuki, Tetsuya [Center for Science of Environment, Resources and Energy, Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522 (Japan)

    2012-07-01

    Ion beam technique has recently been actively employed to create various patterns on the surface of polymers. In this paper, we highlight some of the recent advances in tailoring surface topographies of polymers by using ion beam and present a brief discussion on the potential applications in biomedical and tissue engineering.

  19. Data Mining Applications Using Ontologies in Biomedicine

    CERN Document Server

    Popescu, Mihail

    2009-01-01

    Presently, a growing number of ontologies are being built and used for annotating data in biomedical research. Thanks to the tremendous amount of data being generated, ontologies are now being used in numerous ways, including connecting different databases, refining search capabilities, interpreting experimental/clinical data, and inferring knowledge. This cutting-edge resource introduces you to latest developments in bio-ontologies. The book provides you with the theoretical foundations and examples of ontologies, as well as applications of ontologies in biomedicine, from molecular levels to

  20. Quantum ontologies

    International Nuclear Information System (INIS)

    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

  1. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  2. Advanced silk material spun by a transgenic silkworm promotes cell proliferation for biomedical application.

    Science.gov (United States)

    Wang, Feng; Xu, Hanfu; Wang, Yuancheng; Wang, Riyuan; Yuan, Lin; Ding, Huan; Song, Chunnuan; Ma, Sanyuan; Peng, Zhixin; Peng, Zhangchuan; Zhao, Ping; Xia, Qingyou

    2014-12-01

    Natural silk fiber spun by the silkworm Bombyx mori is widely used not only for textile materials, but also for biofunctional materials. In the present study, we genetically engineered an advanced silk material, named hSFSV, using a transgenic silkworm, in which the recombinant human acidic fibroblast growth factor (hFGF1) protein was specifically synthesized in the middle silk gland and secreted into the sericin layer to surround the silk fiber using our previously optimized sericin1 expression system. The content of the recombinant hFGF1 in the hSFSV silk was estimated to be approximate 0.07% of the cocoon shell weight. The mechanical properties of hSFSV raw silk fiber were enhanced slightly compared to those of the wild-type raw silk fiber, probably due to the presence of the recombinant of hFGF1 in the sericin layer. Remarkably, the hSFSV raw silk significantly stimulated the cell growth and proliferation of NIH/3T3 mouse embryonic fibroblast cells, suggesting that the mitogenic activity of recombinant hFGF1 was well maintained and functioned in the sericin layer of hSFSV raw silk. These results show that the genetically engineered raw silk hSFSV could be used directly as a fine biomedical material for mass application. In addition, the strategy whereby functional recombinant proteins are expressed in the sericin layer of silk might be used to create more genetically engineered silks with various biofunctions and applications. PMID:24980060

  3. Ontology Localization

    OpenAIRE

    Espinoza Mejía, Mauricio; Montiel-Ponsoda, Elena; Aguado de Cea, G.; A. GÓMEZ-PÉREZ

    2012-01-01

    In the context of the Semantic Web, resources on the net can be enriched by well-defined, machine-understandable metadata describing their associated conceptual meaning. These metadata consisting of natural language descriptions of concepts are the focus of the activity we describe in this chapter, namely, ontology localization. In the framework of the NeOn Methodology, ontology localization is defined as the activity of adapting an ontology to a particular language and culture. This adaptati...

  4. Engineering Ontologies

    OpenAIRE

    Borst, Pim; Akkermans, Hans; Top, Jan

    1997-01-01

    We analyse the construction as well as the role of ontologies in knowledge sharing and reuse for complex industrial applications. In this article, the practical use of ontologies in large-scale applications not restricted to knowledge-based systems is demonstrated, for the domain of engineering systems modelling, simulation and design. A general and formal ontology, called PHYSSYS, for dynamic physical systems is presented and its structuring principles are discussed. We show how the PHYSSYS ...

  5. CLO : The cell line ontology

    NARCIS (Netherlands)

    Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Meehan, Terrence F.; Diehl, Alexander D.; Vempati, Uma D.; Schuerer, Stephan C.; Pang, Chao; Malone, James; Parkinson, Helen; Liu, Yue; Takatsuki, Terue; Saijo, Kaoru; Masuya, Hiroshi; Nakamura, Yukio; Brush, Matthew H.; Haendel, Melissa A.; Zheng, Jie; Stoeckert, Christian J.; Peters, Bjoern; Mungall, Christopher J.; Carey, Thomas E.; States, David J.; Athey, Brian D.; He, Yongqun

    2014-01-01

    Background: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO

  6. The ontology of medically related social entities: recent developments

    OpenAIRE

    Hicks, Amanda; Hanna, Josh; Welch, Daniel; Brochhausen, Mathias; Hogan, William R.

    2016-01-01

    Background The Ontology of Medically Related Social Entities (OMRSE) was initially developed in 2011 to provide a framework for modeling demographic data in Resource Description Framework/Web Ontology Language. It is built upon the Basic Formal Ontology and conforms to Open Biomedical Ontologies Foundry’s best practices. Description We report recent development of OMRSE which includes representations of organizations, roles, facilities, demographic data, enrollment in insurance plans, and dat...

  7. Generating Explanations for Biomedical Queries

    OpenAIRE

    Erdem, Esra; Oztok, Umut

    2013-01-01

    We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PHARMGKB, DRUGBANK, BIOGRID, CTD, SIDER, DISEASE ONTOLOGY and ORPHADATA. To appear in Theory and Practice of Logic Program...

  8. Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

    OpenAIRE

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

    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 ...

  9. 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

  10. Advances in capillary electrophoresis : In-line preconcentration for biomedical analysis. Impurity profiling of heparin

    NARCIS (Netherlands)

    van der Hoorn, Y.H.

    2015-01-01

    Capillary electrophoresis (CE) has shown to be highly suitable for the analysis of polar and ionogenic compounds in biomedical and pharmaceutical samples. Separation with CE is based on the charge-to-size ratio of analytes. The application of CE for bioanalysis may be hindered by its relatively low

  11. GoPubMed: Ontology-based literature search for the life sciences

    OpenAIRE

    Doms, Andreas

    2009-01-01

    Background: Most of our biomedical knowledge is only accessible through texts. The biomedical literature grows exponentially and PubMed comprises over 18.000.000 literature abstracts. Recently much effort has been put into the creation of biomedical ontologies which capture biomedical facts. The exploitation of ontologies to explore the scientific literature is a new area of research. Motivation: When people search, they have questions in mind. Answering questions in a domain requires the kno...

  12. 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

  13. Ontological backdrop

    DEFF Research Database (Denmark)

    Galle, Per

    2000-01-01

    In this report I keep track of ontological assumptions or implications of other OARs, introducing a system of categories and concepts that is compatible with them. The purpose was originally to keep terminology consistent throughout all OARs. However, the report also gives a condensed picture...

  14. A UML profile for the OBO relation ontology

    Science.gov (United States)

    2012-01-01

    Background Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions The use of an established and well-known graphical language in the development of biomedical ontologies provides a more

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

    Directory of Open Access Journals (Sweden)

    Skene JH Pate

    2007-09-01

    Full Text Available 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 rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD, which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1 install Apache Tomcat 2 on one's web server, (2 download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3 create an html (HyperText Markup Language file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed Ontology

  16. Ontology Requirements Specification

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; A. GÓMEZ-PÉREZ

    2012-01-01

    The goal of the ontology requirements specification activity is to state why the ontology is being built, what its intended uses are, who the end users are, and which requirements the ontology should fulfill. This chapter presents detailed methodological guidelines for specifying ontology requirements efficiently. These guidelines will help ontology engineers to capture ontology requirements and produce the ontology requirements specification document (ORSD). The ORSD will play a key role dur...

  17. Synthesis by pulsed laser ablation of 2D nanostructures for advanced biomedical sensing

    Science.gov (United States)

    Trusso, S.; Zanchi, C.; Bombelli, A.; Lucotti, A.; Tommasini, M.; de Grazia, U.; Ciusani, E.; Romito, L. M.; Ossi, P. M.

    2016-05-01

    Au nanoparticle arrays with controlled nanostructure were produced by pulsed laser ablation on glass. Such substrates were optimized for biomedical sensing by means of SERS keeping fixed all process parameters but the laser pulse (LP) number that is a key deposition parameter. It allows to fine-tune the Au surface nanostructure with a considerable improvement in the SERS response towards the detection of apomorphine in blood serum (3.3 × 10‑6 M), when LP number is increased from 1 × 104 to 2 × 104. This result is the starting point to correlate the intensity of selected SERS signals of apomorphine to its concentration in the blood of patients with Parkinson's disease.

  18. Managing Requirement Volatility in an Ontology-Driven Clinical LIMS Using Category Theory. International Journal of Telemedicine and Applications

    CERN Document Server

    Shaban-Nejad, Arash; Kassab, Mohamad; Haarslev, Volker; 10.1155/2009/917826

    2009-01-01

    Requirement volatility is an issue in software engineering in general, and in Web-based clinical applications in particular, which often originates from an incomplete knowledge of the domain of interest. With advances in the health science, many features and functionalities need to be added to, or removed from, existing software applications in the biomedical domain. At the same time, the increasing complexity of biomedical systems makes them more difficult to understand, and consequently it is more difficult to define their requirements, which contributes considerably to their volatility. In this paper, we present a novel agent-based approach for analyzing and managing volatile and dynamic requirements in an ontology-driven laboratory information management system (LIMS) designed for Web-based case reporting in medical mycology. The proposed framework is empowered with ontologies and formalized using category theory to provide a deep and common understanding of the functional and nonfunctional requirement hi...

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

    Science.gov (United States)

    Cui, Licong

    2015-01-01

    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

  20. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia

    Science.gov (United States)

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features.

  1. 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.

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

    OpenAIRE

    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 ac...

  3. Report of the 1st RCM on ''Nanoscale radiation engineering of advanced materials for potential biomedical applications''. Working document

    International Nuclear Information System (INIS)

    There are critical needs for advanced materials in the area of biomaterial engineering, primarily in generating biomaterials of enhanced specific functionalities, improved biocompatibility, and minimal natural rejection but with enhanced interfacial adhesion. These can be achieved by introduction of proper functionalities at the nanoscale dimensions and radiation techniques are uniquely suited for such a task, due to their favorable characteristics, and in most cases, not possible by other methods of synthesis. Accordingly, many of the developing and developed Member States have an interest in creating advanced materials for various health-care applications using a wide array of radiation sources and their broad expertise. The proposal for this CRP was formulated based on the requests and information received from the member states and the conclusions and recommendations of the Consultant’s meeting on “Advanced Materials on the Nano-scale Synthesized by Radiation-Induced Processes”, held on 10-14 December 2007, in Vienna. Based on these conclusions, this CRP aims to support MS to develop methodologies for the use of radiation in the synthesis, modification, and characterization of nanomaterials - nanogels, nanoparticles, nanovehicles, nanoporous membranes, and surfaces with enhanced biocompatibility for potential biomedical applications, such as cell-sheet engineering and artificial tissue construction; diagnostics and imaging; and drug delivery. Additionally, this CRP facilitates networking between radiation technologists and biomedical scientists for the development of such applications. The CRP generated a huge interest, but due to funding constrains, many good proposals had to be rejected. The first RCM of the CRP was convened in Vienna on 30 March - 03 April 2009. It was attended by 14 representatives and two observers. The participants presented and discussed the status of the field, the needs for further research, and various application possibilities

  4. Recent Advances in Biophysical/Biochemical/Biomedical Application of Raman Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    NaitengYu; XiaoyuanLi

    1995-01-01

    Examples of some important biophysical,biochemical and biomedical problems that have been uniquely solved by Raman spectroscopy will be illustrated and discussed.The first example concerns the electronic structure,metal-ligand bonding,and reactivity of metalloporphyrins,the synthetic models for the ubiquitous chromophore in hemoproteins.we will demonstrate how off-resonance scattering,electronic resonance enhanced scattering,as well as nonlinear hyper-Raman(three-photon)scattering can provide a highly complementary picture about the effective electronic symmetry and bonding of metalloporphyrins in its electronic ground and excited states.we will illustrate how the bonding information otained from the Raman effect can be useful in understanding the chemical behavior of metalloporhyrin such as its affinity toward exogenous ligand and its preference for the orientation of planar axial ligand(such as imidazole from histidine's sidechain).Some paradoxical misconception about the relationship between bond strength and ligand binding affinity will be discussed.Raman spectroscopy,particular with near infraed laser excitation to avoid fluorescence,has been applied successfully to extract significant biochemical information from intact eye lenses.The long-standing cotroversy over the exact nature of the involvement of disulfide cross-linking in lens aging and cataract formation has been settled by the Raman spectroscopy because of its ability for monitoring the sulfhydryl to disulfide reaction of an intact lens in a nondestructive and noninvasive manner.A more recent contribution to the lens biochemistry is the use of Raman spectroscopy for a clear demonstration of the biochemical changes induced by near ultraviolet light in the lens of an animal model,resembling the changes observed in human lens aging and cataract formation.

  5. Characterizing Modular Ontologies

    OpenAIRE

    Ben Abbès, Sarra; Scheuermann, Andreas; Meilender, Thomas; D'Aquin, Mathieu

    2012-01-01

    Since large monolithic ontologies are di cult to handle and reuse ontology modularization has attracted increasing attention. Several approaches and tools have been developed to support ontology modularization. Despite these e orts, a lack of knowledge about characteristics of modularly organized ontologies prevents further development. This work aims at characterizing modular ontologies. Therefore, we analyze existing modular ontologies by applying selected metrics from software engineering ...

  6. Markov Chain Ontology Analysis (MCOA

    Directory of Open Access Journals (Sweden)

    Frost H

    2012-02-01

    Full Text Available Abstract 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 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. Results 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. Conclusion 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

  7. 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.

  8. 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.)

  9. Modelling Multilinguality in Ontologies

    OpenAIRE

    Montiel-Ponsoda, Elena; Aguado de Cea, G.; A. GÓMEZ-PÉREZ; Peters, W.

    2008-01-01

    an impending need for institutions worldwide with valuable linguistic resources in different natural languages. Since most ontologies are developed in one language, obtaining multilingual ontologies implies to localize or adapt them to a concrete language and culture community. As the adaptation of the ontology conceptualization demands considerable efforts, we propose to modify the ontology terminological layer, and provide a model called Linguistic Informati...

  10. Didactical Ontologies

    Directory of Open Access Journals (Sweden)

    Steffen Mencke, Reiner Dumke

    2008-03-01

    Full Text Available Ontologies are a fundamental concept of theSemantic Web envisioned by Tim Berners-Lee [1]. Togetherwith explicit representation of the semantics of data formachine-accessibility such domain theories are the basis forintelligent next generation applications for the web andother areas of interest [2]. Their application for specialaspects within the domain of e-learning is often proposed tosupport the increasing complexity ([3], [4], [5], [6]. So theycan provide a better support for course generation orlearning scenario description [7]. By the modeling ofdidactics-related expertise and their provision for thecreators of courses many improvements like reuse, rapiddevelopment and of course increased learning performancebecome possible due to the separation from other aspects ofe-learning platforms as already proposed in [8].

  11. 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.

  12. 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

  13. 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.

  14. 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...

  15. Bringing Ontology to the Gene Ontology

    OpenAIRE

    Jennifer Williams; William Andersen

    2003-01-01

    We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinformatics applications requires explicating in machine-processible form the implicit backgrou...

  16. Advanced biomedical image analysis

    CERN Document Server

    Haidekker, Mark A

    2010-01-01

    "This book covers the four major areas of image processing: Image enhancement and restoration, image segmentation, image quantification and classification, and image visualization. Image registration, storage, and compression are also covered. The text focuses on recently developed image processing and analysis operators and covers topical research"--Provided by publisher.

  17. A Learning-Based Approach for Biomedical Word Sense Disambiguation

    Directory of Open Access Journals (Sweden)

    Hisham Al-Mubaid

    2012-01-01

    Full Text Available In the biomedical domain, word sense ambiguity is a widely spread problem with bioinformatics research effort devoted to it being not commensurate and allowing for more development. This paper presents and evaluates a learning-based approach for sense disambiguation within the biomedical domain. The main limitation with supervised methods is the need for a corpus of manually disambiguated instances of the ambiguous words. However, the advances in automatic text annotation and tagging techniques with the help of the plethora of knowledge sources like ontologies and text literature in the biomedical domain will help lessen this limitation. The proposed method utilizes the interaction model (mutual information between the context words and the senses of the target word to induce reliable learning models for sense disambiguation. The method has been evaluated with the benchmark dataset NLM-WSD with various settings and in biomedical entity species disambiguation. The evaluation results showed that the approach is very competitive and outperforms recently reported results of other published techniques.

  18. Mapping the Gene Ontology Into the Unified Medical Language System

    OpenAIRE

    Jane Lomax; McCray, Alexa T.

    2004-01-01

    We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS hi...

  19. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D; Bronzino, Joseph D

    2006-01-01

    Over the last century,medicine has come out of the "black bag" and emerged as one of the most dynamic and advanced fields of development in science and technology. Today, biomedical engineering plays a critical role in patient diagnosis, care, and rehabilitation. As such, the field encompasses a wide range of disciplines, from biology and physiology to informatics and signal processing. Reflecting the enormous growth and change in biomedical engineering during the infancy of the 21st century, The Biomedical Engineering Handbook enters its third edition as a set of three carefully focused and

  20. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

    The book will help assist a reader in the development of techniques for analysis of biomedical signals and computer aided diagnoses with a pedagogical examination of basic and advanced topics accompanied by over 350 figures and illustrations. Wide range of filtering techniques presented to address various applications. 800 mathematical expressions and equations. Practical questions, problems and laboratory exercises. Includes fractals and chaos theory with biomedical applications.

  1. Tuning Ontology Interoperability

    OpenAIRE

    Giunchiglia, Fausto; Pan, Jeff Z.; Serafini, Luciano

    2005-01-01

    The main contribution of this paper is the notion of ontology space, which allows us to move from an ontology-centric vision to a constellation-centric vision of the Web, where multiple ontologies and their interactions can be explicitly modeled and studied. This, in turn, allows us to study how OWL ontologies can interoperate, and, in particular, to provide two main results. The first is a formalization of the intended semantics of the OWL importing operator as opaque semantics. This result ...

  2. Modeling biochemical pathways in the gene ontology.

    Science.gov (United States)

    Hill, David P; D'Eustachio, Peter; Berardini, Tanya Z; Mungall, Christopher J; Renedo, Nikolai; Blake, Judith A

    2016-01-01

    The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes in the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis. PMID:27589964

  3. Ontology Languages and Engineering

    Science.gov (United States)

    Horrocks, Ian

    Ontologies and ontology based systems are rapidly becoming mainstream technologies, with RDF and OWL now being deployed in diverse application domains, and with major technology vendors starting to augment their existing systems with ontological reasoning. For example, Oracle Inc. recently enhanced its well-known database management system with modules that use RDF/OWL ontologies to support "semantic data management", and their product brochure lists numerous application areas that can benefit from this technology, including Enterprise Information Integration, KnowledgeMining, Finance, Compliance Management and Life Science Research. The design of the high quality ontologies needed to support such applications is, however, still extremely challenging. In this talk I will describe the design of OWL, show how it facilitates the development of ontology engineering tools, describe the increasingly wide range of available tools, and explain how such tools can be used to support the entire design, deployment and maintenance ontology life-cycle.

  4. Lexical Characterisation of Bio-Ontologies by the Inspection of Regularities in Labels

    OpenAIRE

    Quesada-Martinez, Manuel; Fernandez-Breis, Jesualdo Tomomas; Stevens, Robert

    2015-01-01

    Hundreds of biomedical ontologies have been produced, with many of the significant, widely used ones being developed in collaborative efforts and following a set of construction principles, which include using a systematic naming convention for their labels. Despite their success, many of these ontologies have lacked a foundation of axioms that would expose the wealth of knowledge in the ontologies to computational reasoning. Our previous results suggest that exploiting the structure on the l...

  5. Using semantic web rules to reason on an ontology of pseudogenes

    OpenAIRE

    Holford, Matthew E.; Khurana, Ekta; Cheung, Kei-Hoi; Gerstein, Mark

    2010-01-01

    Motivation: Recent years have seen the development of a wide range of biomedical ontologies. Notable among these is Sequence Ontology (SO) which offers a rich hierarchy of terms and relationships that can be used to annotate genomic data. Well-designed formal ontologies allow data to be reasoned upon in a consistent and logically sound way and can lead to the discovery of new relationships. The Semantic Web Rules Language (SWRL) augments the capabilities of a reasoner by allowing the creation...

  6. Representing NCBO Annotator results in standard RDF with the Annotation Ontology

    OpenAIRE

    Melzi, Soumia; Jonquet, Clement

    2014-01-01

    International audience; Semantic annotation is part of the Semantic Web vision. The Annotation Ontology is a model that have been proposed to represent any annotations in standard RDF. The NCBO Annotator Web service is a broadly used service for annotations in the biomedical domain, offered within the BioPortal platform and giving access to more than 350+ ontologies. This paper presents a new output format to represent the NCBO Annotator results in RDF with the Annotation Ontology. We briefly...

  7. Ontology-based multiple choice question generation.

    Science.gov (United States)

    Al-Yahya, Maha

    2014-01-01

    With recent advancements in Semantic Web technologies, a new trend in MCQ item generation has emerged through the use of ontologies. Ontologies are knowledge representation structures that formally describe entities in a domain and their relationships, thus enabling automated inference and reasoning. Ontology-based MCQ item generation is still in its infancy, but substantial research efforts are being made in the field. However, the applicability of these models for use in an educational setting has not been thoroughly evaluated. In this paper, we present an experimental evaluation of an ontology-based MCQ item generation system known as OntoQue. The evaluation was conducted using two different domain ontologies. The findings of this study show that ontology-based MCQ generation systems produce satisfactory MCQ items to a certain extent. However, the evaluation also revealed a number of shortcomings with current ontology-based MCQ item generation systems with regard to the educational significance of an automatically constructed MCQ item, the knowledge level it addresses, and its language structure. Furthermore, for the task to be successful in producing high-quality MCQ items for learning assessments, this study suggests a novel, holistic view that incorporates learning content, learning objectives, lexical knowledge, and scenarios into a single cohesive framework.

  8. Recent advances in food-packing, pharmaceutical and biomedical applications of zein and zein-based materials.

    Science.gov (United States)

    Corradini, Elisângela; Curti, Priscila S; Meniqueti, Adriano B; Martins, Alessandro F; Rubira, Adley F; Muniz, Edvani Curti

    2014-12-04

    Zein is a biodegradable and biocompatible material extracted from renewable resources; it comprises almost 80% of the whole protein content in corn. This review highlights and describes some zein and zein-based materials, focusing on biomedical applications. It was demonstrated in this review that the biodegradation and biocompatibility of zein are key parameters for its uses in the food-packing, biomedical and pharmaceutical fields. Furthermore, it was pointed out that the presence of hydrophilic-hydrophobic groups in zein chains is a very important aspect for obtaining material with different hydrophobicities by mixing with other moieties (polymeric or not), but also for obtaining derivatives with different properties. The physical and chemical characteristics and special structure (at the molecular, nano and micro scales) make zein molecules inherently superior to many other polymers from natural sources and synthetic ones. The film-forming property of zein and zein-based materials is important for several applications. The good electrospinnability of zein is important for producing zein and zein-based nanofibers for applications in tissue engineering and drug delivery. The use of zein's hydrolysate peptides for reducing blood pressure is another important issue related to the application of derivatives of zein in the biomedical field. It is pointed out that the biodegradability and biocompatibility of zein and other inherent properties associated with zein's structure allow a myriad of applications of such materials with great potential in the near future.

  9. Managing Requirement Volatility in an Ontology-Driven Clinical LIMS Using Category Theory

    Directory of Open Access Journals (Sweden)

    Arash Shaban-Nejad

    2009-01-01

    Full Text Available Requirement volatility is an issue in software engineering in general, and in Web-based clinical applications in particular, which often originates from an incomplete knowledge of the domain of interest. With advances in the health science, many features and functionalities need to be added to, or removed from, existing software applications in the biomedical domain. At the same time, the increasing complexity of biomedical systems makes them more difficult to understand, and consequently it is more difficult to define their requirements, which contributes considerably to their volatility. In this paper, we present a novel agent-based approach for analyzing and managing volatile and dynamic requirements in an ontology-driven laboratory information management system (LIMS designed for Web-based case reporting in medical mycology. The proposed framework is empowered with ontologies and formalized using category theory to provide a deep and common understanding of the functional and nonfunctional requirement hierarchies and their interrelations, and to trace the effects of a change on the conceptual framework.

  10. Ontology Assisted Query Reformulation Using Semantic and Assertion Capabilities of OWL-DL Ontologies

    CERN Document Server

    Munir, Kamran; McClatchey, Richard

    2008-01-01

    End users of recent biomedical information systems are often unaware of the storage structure and access mechanisms of the underlying data sources and can require simplified mechanisms for writing domain specific complex queries. This research aims to assist users and their applications in formulating queries without requiring complete knowledge of the information structure of underlying data sources. To achieve this, query reformulation techniques and algorithms have been developed that can interpret ontology-based search criteria and associated domain knowledge in order to reformulate a relational query. These query reformulation algorithms exploit the semantic relationships and assertion capabilities of OWL-DL based domain ontologies for query reformulation. In this paper, this approach is applied to the integrated database schema of the EU funded Health-e-Child (HeC) project with the aim of providing ontology assisted query reformulation techniques to simplify the global access that is needed to millions ...

  11. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

    Science.gov (United States)

    Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann E

    2008-09-01

    A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF. PMID:18975148

  12. Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL

    Directory of Open Access Journals (Sweden)

    Aranguren Mikel

    2007-02-01

    Full Text Available Abstract The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community.

  13. Enriching Ontologies with Multilingual Information

    OpenAIRE

    Aguado de Cea, G.; A. GÓMEZ-PÉREZ; Montiel-Ponsoda, Elena

    2009-01-01

    Organizations working in a multilingual environment demand multilingual ontologies. To solve this problem we propose LabelTranslator, a system that automatically localizes ontologies. Ontology localization consists of adapting an ontology to a concrete language and cultural community. LabelTranslator takes as input an ontology whose labels are described in a source natural language and obtains the most probable translation into a target natural language of each ontology label. Our main con...

  14. Recent advances in thromboresistant and antimicrobial polymers for biomedical applications: just say yes to nitric oxide (NO).

    Science.gov (United States)

    Wo, Yaqi; Brisbois, Elizabeth J; Bartlett, Robert H; Meyerhoff, Mark E

    2016-08-19

    Biomedical devices are essential for patient diagnosis and treatment; however, when blood comes in contact with foreign surfaces or homeostasis is disrupted, complications including thrombus formation and bacterial infections can interrupt device functionality, causing false readings and/or shorten device lifetime. Here, we review some of the current approaches for developing antithrombotic and antibacterial materials for biomedical applications. Special emphasis is given to materials that release or generate low levels of nitric oxide (NO). Nitric oxide is an endogenous gas molecule that can inhibit platelet activation as well as bacterial proliferation and adhesion. Various NO delivery vehicles have been developed to improve NO's therapeutic potential. In this review, we provide a summary of the NO releasing and NO generating polymeric materials developed to date, with a focus on the chemistry of different NO donors, the polymer preparation processes, and in vitro and in vivo applications of the two most promising types of NO donors studied thus far, N-diazeniumdiolates (NONOates) and S-nitrosothiols (RSNOs). PMID:27226170

  15. Ontology Sparse Vector Learning Algorithm for Ontology Similarity Measuring and Ontology Mapping via ADAL Technology

    Science.gov (United States)

    Gao, Wei; Zhu, Linli; Wang, Kaiyun

    2015-12-01

    Ontology, a model of knowledge representation and storage, has had extensive applications in pharmaceutics, social science, chemistry and biology. In the age of “big data”, the constructed concepts are often represented as higher-dimensional data by scholars, and thus the sparse learning techniques are introduced into ontology algorithms. In this paper, based on the alternating direction augmented Lagrangian method, we present an ontology optimization algorithm for ontological sparse vector learning, and a fast version of such ontology technologies. The optimal sparse vector is obtained by an iterative procedure, and the ontology function is then obtained from the sparse vector. Four simulation experiments show that our ontological sparse vector learning model has a higher precision ratio on plant ontology, humanoid robotics ontology, biology ontology and physics education ontology data for similarity measuring and ontology mapping applications.

  16. Advances in Biomedical Imaging, Bioengineering, and Related Technologies for the Development of Biomarkers of Pancreatic Disease: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Biomedical Imaging and Bioengineering Workshop.

    Science.gov (United States)

    Kelly, Kimberly A; Hollingsworth, Michael A; Brand, Randall E; Liu, Christina H; Singh, Vikesh K; Srivastava, Sudhir; Wasan, Ajay D; Yadav, Dhiraj; Andersen, Dana K

    2015-11-01

    A workshop sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases and the National Institute of Biomedical Imaging and Bioengineering focused on research gaps and opportunities in the development of new biomarkers of pancreatic disease. The session was held on July 22, 2015, and structured into 6 sessions: 1) Introduction and Overview; 2) Keynote Address; 3) New Approaches to the Diagnosis of Chronic Pancreatitis; 4) Biomarkers of Pain and Inflammation; 5) New Approaches to the Detection of Pancreatic Cancer; and 6) Shed Exosomes, Shed Cells, and Shed Proteins. Recent advances in the fields of pancreatic imaging, functional markers of pancreatic disease, proteomics, molecular and cellular imaging, and detection of circulating cancer cells and exosomes were reviewed. Knowledge gaps and research needs were highlighted. The development of new methods for the noninvasive determination of pancreatic pathology; the use of cellular markers of pancreatic function, inflammation, pain, and malignancy; and the refinement of methods to identify cells and cellular constituents of pancreatic cancer were discussed. The further refinement of sophisticated technical methods and the need for clinical studies to validate these new approaches in large-scale studies of patients at risk for the development of pancreatic disease were repeatedly emphasized. PMID:26465948

  17. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  18. The Ontology of Disaster.

    Science.gov (United States)

    Thompson, Neil

    1995-01-01

    Explores some key existential or ontological concepts to show their applicability to the complex area of disaster impact as it relates to health and social welfare practice. Draws on existentialist philosophy, particularly that of John Paul Sartre, and introduces some key ontological concepts to show how they specifically apply to the experience…

  19. Constructive Ontology Engineering

    Science.gov (United States)

    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…

  20. 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…

  1. Conceptual querying through ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2009-01-01

    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...... 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...... 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....

  2. Biomedical enhancements as justice.

    Science.gov (United States)

    Nam, Jeesoo

    2015-02-01

    Biomedical enhancements, the applications of medical technology to make better those who are neither ill nor deficient, have made great strides in the past few decades. Using Amartya Sen's capability approach as my framework, I argue in this article that far from being simply permissible, we have a prima facie moral obligation to use these new developments for the end goal of promoting social justice. In terms of both range and magnitude, the use of biomedical enhancements will mark a radical advance in how we compensate the most disadvantaged members of society.

  3. 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 ...

  4. Advances in porcine genomics and proteomics - a toolbox for developing the pig as a model organism for molecular biomedical research

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Larsen, Knud;

    2010-01-01

    Our current knowledge of human biology is often based on studying a wide range of animal species. In particular, for understanding human diseases, the development of adequate animal models is of immediate importance. Although genetic strains and transgenic animal model organisms like fruit fly...... (Drosophila), zebrafish and rodents are highly informative about the function of single genes and proteins, these organisms do not always closely reflect human biology, and alternative animal models are thus in great demand. The pig is a non-primate mammal that closely resembles man in anatomy, physiology...... and genetics. Pigs, although not easily kept for laboratory research, are, however, readily available for biomedical research through the large scale industrial production of pigs produced for human consumption. Recent research has facilitated the biological experimentation with pigs, and helped develop...

  5. COEUS: “semantic web in a box” for biomedical applications

    Directory of Open Access Journals (Sweden)

    Lopes Pedro

    2012-12-01

    Full Text Available Abstract Background As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. Results COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. Conclusions The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

  6. Ontological foundations for evolutionary economics: A Darwinian social ontology

    NARCIS (Netherlands)

    J.W. Stoelhorst

    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 speci

  7. OLSVis: an animated, interactive visual browser for bio-ontologies

    Directory of Open Access Journals (Sweden)

    Vercruysse Steven

    2012-07-01

    Full Text Available Abstract Background More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS. Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible. Results We created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.com Conclusions The OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method.

  8. Towards a core ontology for integrating ecological and environmental ontologies to enable improved data interoperability

    Science.gov (United States)

    Bowers, S.; Madin, J.; Jones, M.; Schildhauer, M.; Ludaescher, B.

    2007-12-01

    Research in the ecological and environmental sciences increasingly relies on the integration of traditionally small, focused studies to form larger datasets for synthetic analyses. However, a broad range of data types, structures, and semantic subtleties occur in ecological data, making data discovery and integration a difficult and time-consuming task. Our work focuses on capturing the subtleties of scientific data through semantic annotations, which involve linking ecological data to concepts and relationships in domain-specific ontologies, thereby enabling more advanced forms of data discovery and integration. A variety of ontologies related to ecological data are actively being developed, ranging from low-level and highly focused vocabularies to high-level models and classifications. However, as the number of ontologies and their included terms increase, organizing these into a coherent framework useful for data annotation becomes increasingly complex (we note that similar issues have been recognized within the molecular biology and bioinformatics communities). We describe a core ontology model for semantic annotation that provides a structured approach for integrating the growing number of ecology-relevant ontologies. The ontology defines the notion of "scientific observation" as a unifying concept for capturing the basic semantics of ecological data. Observations are distinguished at the level of the entity (e.g., location, time, thing, concept), and characteristics of an entity (e.g., height, name, color) are measured (named or classified) as data. The ontology permits observations to be related via context (such as spatial or temporal containment), further supporting the discovery and automated comparison and alignment (e.g., merging) of heterogeneous data. The core ontology also defines a set of extension points that can be used to either directly build new domain ontologies (as extension ontologies), or to provide a common basis to which existing

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Ramona L Walls

    Full Text Available 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

  11. Knowledge Management and Ontology

    Directory of Open Access Journals (Sweden)

    Tiberiu SOCACIU

    2016-07-01

    Full Text Available The knowledge society characteristic to the XXI century derives from the information society but is more than this and focuses on how information becomes knowledge. Fulminating evolution of this society has enabled intelligent devices (be they desktops, laptops, tablets, smart phones and others to be part of everyone's life. These tools not only facilitate rapid access to information, which is considered the most valuable thing today but through the multitude of applications, we can ease the decisions we make every day. In this context our approach aims at building an ontology using OWL (Web Ontology Language and RDF (Resource Description Framework in economic and a platform for working with ontologies. The platform will be represented by a web application and will allow users to extend an ontology by adding new concepts such as classes, subclasses, individual properties, but also to see ontology as a knowledge graph. Also users will be able to interact with the ontology by interrogating it using SPARQL language. Consequently, I believe that the proposed application is meant to be a useful application for viewing, querying and extending ontologies.

  12. [ ] Toward an Ontology of Finitude

    Directory of Open Access Journals (Sweden)

    Julia Hölzl

    2011-09-01

    Full Text Available Hölzl palpates an ontology of fracture. Unlike original ontologies that are concerned with essence rather than being, the ontology proposed here does not believe in its originality. This project is concerned with becoming as such rather than with its Wesen. With the indefinite striving for remaining in itself. This ontology is a fissure, fissuring itself.

  13. Biomedical photonics handbook biomedical diagnostics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers, studen

  14. Appreciating ontological struggles

    DEFF Research Database (Denmark)

    Danholt, Peter

    Appreciating ontological struggles Peter Danholt, ass. prof., Information studies, Aarhus University In the west – most of us – take for granted that we inhabit a common world, which we share with 6 billion other human beings and multiple other living beings, animals and plants. As Annemarie Mol...... a condition in the world, but as the playing out of an ontological struggle, we become able to appreciate the situation and the treatment differently and in a manner that reconsiders treatment and disease in novel ways. Importantly, when the encounter is conceived of as an ontological struggle it becomes ever...

  15. 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.

  16. FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

    OpenAIRE

    Lu, Zhiyong; Cohen, K Bretonnel; Hunter, Lawrence

    2006-01-01

    A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene’s GO annotations along with location f...

  17. Change Representation For OWL 2 Ontologies

    OpenAIRE

    Palma, R.; Haase, Peter; Corcho, Oscar; A. GÓMEZ-PÉREZ

    2009-01-01

    Ontologies are entities that evolve over time; therefore it is essential to represent and manage changes to ontologies along with the ontologies themselves. In this paper we propose a change ontology for the OWL 2 ontology language. This change ontology comprises a fine-grained taxonomy of ontology changes that considers the lowest-level atomic operations that can be performed in an ontology, but in addition also on other abstraction levels (ontology entity, composite). It thus allows to descr...

  18. Audit Validation Using Ontologies

    OpenAIRE

    Ion IVAN; Claudiu BRANDAS; Alin ZAMFIROIU

    2015-01-01

    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...

  19. Ontology Usage at ZFIN

    CERN Document Server

    Howe, Doug

    2010-01-01

    The Zebrafish Model Organism Database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. Four different ontologies are currently used to annotate data to the most specific term available facilitating a better comparison between inter-species data. In addition, ontologies are used to help users find and cluster data more quickly without the need of knowing the exact technical name for a term.

  20. Computational intelligence in biomedical imaging

    CERN Document Server

    2014-01-01

    This book provides a comprehensive overview of the state-of-the-art computational intelligence research and technologies in biomedical images with emphasis on biomedical decision making. Biomedical imaging offers useful information on patients’ medical conditions and clues to causes of their symptoms and diseases. Biomedical images, however, provide a large number of images which physicians must interpret. Therefore, computer aids are demanded and become indispensable in physicians’ decision making. This book discusses major technical advancements and research findings in the field of computational intelligence in biomedical imaging, for example, computational intelligence in computer-aided diagnosis for breast cancer, prostate cancer, and brain disease, in lung function analysis, and in radiation therapy. The book examines technologies and studies that have reached the practical level, and those technologies that are becoming available in clinical practices in hospitals rapidly such as computational inte...

  1. Secured Ontology Mapping

    Directory of Open Access Journals (Sweden)

    Manjula Shenoy.K

    2012-11-01

    Full Text Available Today’s market evolution and high volatility of business requirements put an increasing emphasis on theability for systems to accommodate the changes required by new organizational needs while maintainingsecurity objectives satisfiability. This is all the more true in case of collaboration and interoperabilitybetween different organizations and thus between their information systems. Ontology mapping has beenused for interoperability and several mapping systems have evolved to support the same. Usual solutionsdo not take care of security. That is almost all systems do a mapping of ontologies which are unsecured.We have developed a system for mapping secured ontologies using graph similarity concept. Here we giveno importance to the strings that describe ontology concepts ,properties etc. Because these strings may beencrypted in the secured ontology. Instead we use the pure graphical structure to determine mappingbetween various concepts of given two secured ontologies. The paper also gives the measure of accuracyof experiment in a tabular form in terms of precision, recall and F-measure.

  2. Advanced Fabrication Techniques for Precisely Controlled Micro and Nano Scale Environments for Complex Tissue Regeneration and Biomedical Applications

    Science.gov (United States)

    Holmes, Benjamin

    As modern medicine advances, it is still very challenging to cure joint defects due to their poor inherent regenerative capacity, complex stratified architecture, and disparate biomechanical properties. The current clinical standard for catastrophic or late stage joint degradation is a total joint implant, where the damaged joint is completely excised and replaced with a metallic or artificial joint. However, these procedures still only lasts for 10-15 years, and there are hosts of recovery complications which can occur. Thus, these studies have sought to employ advanced biomaterials and scaffold fabricated techniques to effectively regrow joint tissue, instead of merely replacing it with artificial materials. We can hypothesize here that the inclusion of biomimetic and bioactive nanomaterials with highly functional electrospun and 3D printed scaffold can improve physical characteristics (mechanical strength, surface interactions and nanotexture) enhance cellular growth and direct stem cell differentiation for bone, cartilage and vascular growth as well as cancer metastasis modeling. Nanomaterial inclusion and controlled 3D printed features effectively increased nano surface roughness, Young's Modulus and provided effective flow paths for simulated arterial blood. All of the approaches explored proved highly effective for increasing cell growth, as a result of increasing micro-complexity and nanomaterial incorporation. Additionally, chondrogenic and osteogenic differentiation, cell migration, cell to cell interaction and vascular formation were enhanced. Finally, growth-factor(gf)-loaded polymer nanospheres greatly improved vascular cell behavior, and provided a highly bioactive scaffold for mesenchymal stem cell (MSC) and human umbilical vein endothelial cell (HUVEC) co-culture and bone formation. In conclusion, electrospinning and 3D printing when combined effectively with biomimetic and bioactive nanomaterials (i.e. carbon nanomaterials, collagen, nHA, polymer

  3. Upper Ontology UMBEL in Terms of Ontology Mapping

    OpenAIRE

    Vataščinová, Jana

    2016-01-01

    The aim of the thesis is to introduce the topic of semantic web and linked data, to provide a description of the Upper Ontology UMBEL, its mappings to other ontologies, and to create new mappings to UMBEL Ontology. The source for this paper are publications and official web pages that are related to the topic. For viewing and browsing ontologies, editor Protégé is used. For mapping ontologies to UMBEL Ontology, application LogMap and UMBEL Web Services for searching for Reference Concepts are...

  4. Report of the 2nd RCM on nanoscale radiation engineering of advanced materials for potential biomedical applications

    International Nuclear Information System (INIS)

    There are critical needs for advanced materials in the area of biomaterial engineering, primarily in generating biomaterials of enhanced specific functionalities, improved biocompatibility, and minimal natural rejection but with enhanced interfacial adhesion. These can be achieved by introduction of proper functionalities at the nanoscale dimensions for which, due to their characteristics, radiation techniques are uniquely suited. Accordingly, many of the IAEA Member States (MS) have interest in creating advanced materials for various health-care applications using a wide array of radiation sources and their broad expertise. In seeking new knowledge to advance the field and tackle this specific problem, to collaborate to enhance the quality of the scientific research and improve their efficiency and effectiveness, MS had requested the support of the IAEA for such collaboration. Based on these requests, and the conclusions and recommendations of the Consultant's meeting on Advanced Materials on the Nano-scale Synthesized by Radiation-Induced Processes, held on 10-14 December 2007, the present CRP was formulated and started in 2009. The first RCM was held in 30 March – 3 April 2009, in Vienna, where the work plan for both individual participants and collaborations were discussed and accepted, as reported in the Meeting Report published as IAEA Working Material (http://www-naweb.iaea.org/napc/iachem/working_materials.html). The second RCM was held on 15-19 November 2010, Paris, France, and was attended by 17 participants (chief scientific investigators or team members) and one cost-free observer from Brazil. The participants presented their research achievements since the first RCM, centred on the main expected outputs of this CRP: a. Methodologies to prepare and characterize nanogels; nanoparticles and nanoporous membranes, as well as to synthesize and modify nanoparticle surfaces by attaching organic ligands by radiation; b. Methodologies to radiation synthesize

  5. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

    Biomedical Engineering: Health Care Systems, Technology and Techniques is an edited volume with contributions from world experts. It provides readers with unique contributions related to current research and future healthcare systems. Practitioners and researchers focused on computer science, bioinformatics, engineering and medicine will find this book a valuable reference.

  6. Adding a little reality to building ontologies for biology.

    Directory of Open Access Journals (Sweden)

    Phillip Lord

    Full Text Available BACKGROUND: Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics. The most widespread is for description of entities about which data have been collected, allowing integration and analysis across multiple resources. There are now over 60 ontologies in active use, increasingly developed as large, international collaborations. There are, however, many opinions on how ontologies should be authored; that is, what is appropriate for representation. Recently, a common opinion has been the "realist" approach that places restrictions upon the style of modelling considered to be appropriate. METHODOLOGY/PRINCIPAL FINDINGS: Here, we use a number of case studies for describing the results of biological experiments. We investigate the ways in which these could be represented using both realist and non-realist approaches; we consider the limitations and advantages of each of these models. CONCLUSIONS/SIGNIFICANCE: From our analysis, we conclude that while realist principles may enable straight-forward modelling for some topics, there are crucial aspects of science and the phenomena it studies that do not fit into this approach; realism appears to be over-simplistic which, perversely, results in overly complex ontological models. We suggest that it is impossible to avoid compromise in modelling ontology; a clearer understanding of these compromises will better enable appropriate modelling, fulfilling the many needs for discrete mathematical models within computational biology.

  7. Overview of Ontology Servers Research

    Directory of Open Access Journals (Sweden)

    Robert M. Colomb

    2007-06-01

    Full Text Available An ontology is increasingly becoming an essential tool for solving problems in many research areas. The ontology is a complex information object. It can contain millions of concepts in complex relationships. When we want to manage complex information objects, we generally turn to information systems technology. An information system intended to manage ontology is called an ontology server. The ontology server technology is at the time of writing quite immature. Therefore, this paper reviews and compares the main ontology servers that have been reported in the literatures. As a result, we point out several research questions related to server technology.

  8. Ontology-Based Search of Genomic Metadata.

    Science.gov (United States)

    Fernandez, Javier D; Lenzerini, Maurizio; Masseroli, Marco; Venco, Francesco; Ceri, Stefano

    2016-01-01

    The Encyclopedia of DNA Elements (ENCODE) is a huge and still expanding public repository of more than 4,000 experiments and 25,000 data files, assembled by a large international consortium since 2007; unknown biological knowledge can be extracted from these huge and largely unexplored data, leading to data-driven genomic, transcriptomic, and epigenomic discoveries. Yet, search of relevant datasets for knowledge discovery is limitedly supported: metadata describing ENCODE datasets are quite simple and incomplete, and not described by a coherent underlying ontology. Here, we show how to overcome this limitation, by adopting an ENCODE metadata searching approach which uses high-quality ontological knowledge and state-of-the-art indexing technologies. Specifically, we developed S.O.S. GeM (http://www.bioinformatics.deib.polimi.it/SOSGeM/), a system supporting effective semantic search and retrieval of ENCODE datasets. First, we constructed a Semantic Knowledge Base by starting with concepts extracted from ENCODE metadata, matched to and expanded on biomedical ontologies integrated in the well-established Unified Medical Language System. We prove that this inference method is sound and complete. Then, we leveraged the Semantic Knowledge Base to semantically search ENCODE data from arbitrary biologists' queries. This allows correctly finding more datasets than those extracted by a purely syntactic search, as supported by the other available systems. We empirically show the relevance of found datasets to the biologists' queries. PMID:26529777

  9. Query enhancement through the practical application of ontology: the IEDB and OBI.

    Science.gov (United States)

    Vita, Randi; Overton, James A; Greenbaum, Jason A; Sette, Alessandro; Peters, Bjoern

    2013-04-15

    Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. The Immune Epitope Database (IEDB, http://www.iedb.org) utilizes the Ontology for Biomedical Investigations (OBI) and several additional ontologies to represent immune epitope mapping experiments. Here, we describe our experiences utilizing this representation in order to provide enhanced database search functionality. We applied a simple approach to incorporate the benefits of the information captured in a formal ontology directly into the user web interface, resulting in an improved user experience with minimal changes to the database itself. The integration is easy to maintain, provides standardized terms and definitions, and allows for subsumption queries. In addition to these immediate benefits, our long-term goal is to enable true semantic integration of data and knowledge in the biomedical domain. We describe our progress towards that goal and what we perceive as the main obstacles.

  10. Engineering an Ontology for Autonomous Systems - The OASys Ontology

    OpenAIRE

    Bermejo Alonso, Julita; Sanz Bravo, Ricardo; Rodríguez, Manuel; Hernández Corbato, Carlos

    2011-01-01

    This paper describes the development of an ontology for autonomous systems, as the initial stage of a research programe on autonomous systems’ engineering within a model-based control approach. The ontology aims at providing a unified conceptual framework for the autonomous systems’ stakeholders, from developers to software engineers. The modular ontology contains both generic and domain-specific concepts for autonomous systems description and engineering. The ontology serves as the basis in a ...

  11. Ontological foundations for evolutionary economics: A Darwinian social ontology

    OpenAIRE

    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 specification of units of analysis above the level of the individual, (2) the specification of the relationship between self-organization, developmental processes, and environmental selection as drivers...

  12. A Semantics and Data-Driven Biomedical Multimedia Software System

    Directory of Open Access Journals (Sweden)

    Shih-Hsi Liu

    2010-08-01

    Full Text Available Developing a large-scale biomedical multimedia software system is always a challenging task: Satisfaction of sundry and stringent biomedical multimedia related requirements and standards; Heterogeneous software deployment and communication environments; and tangling correlation between data/contents and software functionalities, among others. This paper introduces a novel biomedical multimedia software system developed under Service-Oriented Architecture (SOA. Such a system takes the advantage of interoperability of SOA to solve the heterogeneity and correlation problems. The paper also classifies the system into services, annotation, ontologies, semantics matching, and QoS optimization aspects which may potentially solve the requirements problem: By establishing data ontology with respect to data properties, contents, QoS, and biomedical regulations and expanding service ontology to describe more functional and QoS specifications supported by services, appropriate services for processing biomedical multimedia data may be discovered, performed, tuned up or replaced as needed. Lastly, a biomedical education project that improves the performance of feature extraction and classification processed afterwards is introduced to illustrate the advantages of our software system developed under SOA.

  13. Biomedical Materials

    Institute of Scientific and Technical Information of China (English)

    CHANG Jiang; ZHOU Yanling

    2011-01-01

    @@ Biomedical materials, biomaterials for short, is regarded as "any substance or combination of substances, synthetic or natural in origin, which can be used for any period of time, as a whole or as part of a system which treats, augments, or replaces any tissue, organ or function of the body" (Vonrecum & Laberge, 1995).Biomaterials can save lives, relieve suffering and enhance the quality of life for human being.

  14. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network

    OpenAIRE

    Xiang Zuoshuang; Hur Junguk; Feldman Eva L; He Yongqun

    2011-01-01

    Abstract Background Vaccine literature indexing is poorly performed in PubMed due to limited hierarchy of Medical Subject Headings (MeSH) annotation in the vaccine field. Vaccine Ontology (VO) is a community-based biomedical ontology that represents various vaccines and their relations. SciMiner is an in-house literature mining system that supports literature indexing and gene name tagging. We hypothesize that application of VO in SciMiner will aid vaccine literature indexing and mining of va...

  15. 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...... physical and abstract world. As a next step the computer thesaurus has been created. Using the thesauri, the knowledge evolved during the PD has been described, and the set of the created concepts and relations instances has been used for the ontology model consistency checking and refinement. The Design...... of the ontology two steps could be identified: empirical research and computer implementation. Empirical research has included domain documentation analysis (Genetic Design Model System developed by Mortensen 1999), identification of the key concepts and relations between them, and categorisation of the concepts...

  16. A Framework for Multilingual Ontology Mapping

    OpenAIRE

    Trojahn, Cássia; Quaresma, Paulo; Vieira, Renata

    2008-01-01

    This paper proposes a framework for mapping multilingual Description Logics ontologies. First, the DL source ontology is translated to the target ontology language, using a lexical database or a dictionary, generating a translated ontology. The target and the translated ontologies are then used as input for the mapping process. A DL mapping ontology is generated as result of this process.

  17. Ontology-based federated data access to human studies information.

    Science.gov (United States)

    Sim, Ida; Carini, Simona; Tu, Samson W; Detwiler, Landon T; Brinkley, James; Mollah, Shamim A; Burke, Karl; Lehmann, Harold P; Chakraborty, Swati; Wittkowski, Knut M; Pollock, Brad H; Johnson, Thomas M; Huser, Vojtech

    2012-01-01

    Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed an informatics infrastructure for federated query of human studies databases, using a generalizable approach to ontology-based data access. Our approach has three main components. First, the Ontology of Clinical Research (OCRe) provides the reference semantics. Second, a data model, automatically derived from OCRe into XSD, maintains semantic synchrony of the underlying representations while facilitating data acquisition using common XML technologies. Finally, the Query Integrator issues queries distributed over the data, OCRe, and other ontologies such as SNOMED in BioPortal. We report on a demonstration of this infrastructure on data acquired from institutional systems and from ClinicalTrials.gov. PMID:23304360

  18. 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.

  19. Considerations on Construction Ontologies

    Directory of Open Access Journals (Sweden)

    Alexandru Cicortaş

    2009-01-01

    Full Text Available The paper proposes an analysis on some existent ontologies, in order to point out ways to resolve semantic heterogeneity in information systems. Authors are highlighting the tasks in a Knowledge Acquisiton System and identifying aspects related to the addition of new information to an intelligent system. A solution is proposed, as a combination of ontology reasoning services and natural languages generation. A multi-agent system will be conceived with an extractor agent, a reasoner agent and a competence management agent.

  20. Ontology-Based Federated Data Access to Human Studies Information

    OpenAIRE

    Sim, Ida; Carini, Simona; Tu, Samson W.; Detwiler, Landon T; Brinkley, James; Mollah, Shamim A.; Burke, Karl; Lehmann, Harold P.; Chakraborty, Swati; Wittkowski, Knut M.; Pollock, Brad H.; Johnson, Thomas M.; Huser, Vojtech

    2012-01-01

    Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed an informatics infrastructure for federated query of human studies databases, using a generalizable approach to ontology-based data access. Our ap...

  1. 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.

  2. Using a Novel Ontology to Inform the Discovery of Therapeutic Peptides from Animal Venoms.

    Science.gov (United States)

    Romano, Joseph D; Tatonetti, Nicholas P

    2016-01-01

    Venoms and venom-derived compounds constitute a rich and largely unexplored source of potentially therapeutic compounds. To facilitate biomedical research, it is necessary to design a robust informatics infrastructure that will allow semantic computation of venom concepts in a standardized, consistent manner. We have designed an ontology of venom-related concepts - named Venom Ontology - that reuses an existing public data source: UniProt's Tox-Prot database. In addition to describing the ontology and its construction, we have performed three separate case studies demonstrating its utility: (1) An exploration of venom peptide similarity networks within specific genera; (2) A broad overview of the distribution of available data among common taxonomic groups spanning the known tree of life; and (3) An analysis of the distribution of venom complexity across those same taxonomic groups. Venom Ontology is publicly available on BioPortal at http://bioportal.bioontology.org/ontologies/CU-VO. PMID:27570672

  3. Building Ontology Networks: How to Obtain a Particular Ontology Network Life Cycle?

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; A. GÓMEZ-PÉREZ

    2008-01-01

    To build an ontology, ontology developers should devise first a concrete plan for the ontology development, that is, they should establish the ontology life cycle. To do this, ontology developers should answer two key questions: a) which ontology life cycle model is the most appropriate for their ontology project? and b) which particular activities should be carried out in their ontology life cycle? In this paper we present a set of guidelines to help ontology developers and al...

  4. Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

    Directory of Open Access Journals (Sweden)

    Antezana Erick

    2008-04-01

    Full Text Available Abstract Background Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training. Results Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (http://odps.sourceforge.net/. Conclusions Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.

  5. Searching Biomedical Text: Towards Maximum Relevant Results

    OpenAIRE

    Galde, Ola; Sevaldsen, John Harald

    2006-01-01

    The amount of biomedical information available to users today is large and increasing. The ability to precisely retrieve desired information is vital in order to utilize available knowledge. In this work we investigated how to improve the relevance of biomedical search results. Using the Lucene Java API we applied a series of information retrieval techniques to search in biomedical data. The techniques ranged from basic stemming and stop-word removal to more advanced methods like user relevan...

  6. Dahlbeck and Pure Ontology

    Science.gov (United States)

    Mackenzie, Jim

    2016-01-01

    This article responds to Johan Dahlbeck's "Towards a pure ontology: Children's bodies and morality" ["Educational Philosophy and Theory," vol. 46 (1), 2014, pp. 8-23 (EJ1026561)]. His arguments from Nietzsche and Spinoza do not carry the weight he supposes, and the conclusions he draws from them about pedagogy would be…

  7. 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.

  8. OLS Dialog: An open-source front end to the Ontology Lookup Service

    Directory of Open Access Journals (Sweden)

    Eidhammer Ingvar

    2010-01-01

    Full Text Available Abstract Background With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data. Results In order to facilitate the location of the correct term in the correct controlled vocabulary or ontology, the Ontology Lookup Service was created. However, using the Ontology Lookup Service as a web service is not always feasible, especially for researchers without bioinformatics support. We have therefore created a Java front end to the Ontology Lookup Service, called the OLS Dialog, which can be plugged into any application requiring the annotation of data using controlled vocabulary terms, making it possible to find and use controlled vocabulary terms without requiring any additional knowledge about web services or ontology formats. Conclusions As a user-friendly open source front end to the Ontology Lookup Service, the OLS Dialog makes it straightforward to include controlled vocabulary support in third-party tools, which ultimately makes the data even more valuable to the biomedical community.

  9. Ontology-based application integration

    CERN Document Server

    Paulheim, Heiko

    2011-01-01

    Ontology-based Application Integration introduces UI-level (User Interface Level) application integration and discusses current problems which can be remedied by using ontologies. It shows a novel approach for applying ontologies in system integration. While ontologies have been used for integration of IT systems on the database and on the business logic layer, integration on the user interface layer is a novel field of research. This book also discusses how end users, not only developers, can benefit from semantic technologies. Ontology-based Application Integration presents the development o

  10. OntologyNavigator: WEB 2.0 scalable ontology based CLIR portal to IT scientific corpus for researchers

    OpenAIRE

    Kembellec, Gérald; Saleh, Imad; Sauvaget, Catherine

    2011-01-01

    International audience This work presents the architecture used in the ongoing OntologyNavigator project. It is a research tool to help advanced learners to find adapted IT papers to create scientific bibliographies. The purpose is the use of an IT representation as educational research software for researchers. We use an ontology based on the ACM's Computing Classification System in order to find scientific papers directly related to the new researcher's domain without any formal request....

  11. A strategy for building neuroanatomy ontologies.

    OpenAIRE

    Osumi-Sutherland, David; Reeve, Simon; Mungall, Christopher J.; Neuhaus, Fabian; Ruttenberg, Alan; Jefferis, Gregory S. X. E.; Armstrong, J Douglas

    2012-01-01

    Motivation: Advancing our understanding of how nervous systems work will require the ability to store and annotate 3D anatomical datasets, recording morphology, partonomy and connectivity at multiple levels of granularity from subcellular to gross anatomy. It will also require the ability to integrate this data with other datatypes including functional, genetic and electrophysiological data. The web ontology language OWL2 provides the means to solve many of these problems. Using it, one can r...

  12. 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...

  13. MEMS biomedical implants

    Institute of Scientific and Technical Information of China (English)

    Tai Yuchong

    2012-01-01

    The field of micro-electro-mechanical systems (MEMS) has advanced tremendously for the last 20 years. Most commercially noticeably, the field has successfully advanced from pressure sensors to micro physical sensors, such as accelerometers and gyros, for handheld electronics application. In parallel, MEMS has also advanced into micro total analysis system(TAS) and/or lab-on-a-chip applications. This article would discuss a relatively new but promising future direction towards MEMS biomedical implants. Specifically, Parylene C has been explored to be used as a good MEMS implant material and will be discussed in detail. Demonstrated implant devices, such as retinal and spinal cord implants, are presented in this article.

  14. Biomedical advances from tissue culture

    OpenAIRE

    Okamoto, Tetsuji; Sato, J. Denry; Barnes, David W.; Sato, Gordon H.

    2013-01-01

    The demonstration that the “dedifferentiation” of cells commonly observed in the early days of tissue culture was due to selective overgrowth of fibroblasts led to enrichment culture techniques (alternate animal and culture passage) designed to give a selective advantage to functionally differentiated tumor cells. These experiments resulted in the derivation of a large number of functionally differentiated clonal strains of a range of cell types. These results gave rise to the hypothesis that...

  15. Study on the Consciousness of Biomedical Ethics and the Influential Factors among Nursing Students in Advanced Vocational College%高职专科护生生命伦理意识及影响因素研究

    Institute of Scientific and Technical Information of China (English)

    李小雪

    2016-01-01

    目的:了解高职专科护生生命伦理意识及其影响因素,为今后高职专科院校开展生命伦理教育及研究提供依据。方法采用自设一般情况调查表、生命伦理意识问卷等对某高职专科院校550名护生的生命伦理意识水平及影响因素进行调查。结果高职专科护生生命伦理意识均分为2.78分。 t检验结果显示,护生生命伦理意识受护生学制、是否接触过相关信息、是否与老师、家人讨论过相关话题等因素影响。 Spearmen相关性分析发现护生年龄、学习成绩等对其生命伦理意识具有影响。结论高职专科护生生命伦理观尚待明确,可采用多种方式针对性地引导护生深刻理解生命伦理问题,使其拥有较积极的生命伦理意识。%Objective: To investigate the status of the consciousness of biomedical ethics and its influential factors among nursing students in advanced vocational college and to provide evidence for the development of bio-medical ethics education and research. Methods:A total of 550 nursing students from an advanced vocational col-lege were surveyed on their personal information, the consciousness of biomedical ethics and its influential factors using the self-constructed questionnaires, e. g. , general information questionnaire and consciousness of biomedic-al ethics questionnaire. Results: The mean of the consciousness of biomedical ethics among nursing students is 2. 78, which was associated with age, length of schooling, whether get the related information or not and whether discussed about the topic with teachers and families or not. Spearmen correlation analysis showed that age, grades of nursing students has effect on the consciousness of biomedical ethics. Conclusion:The views of biomedical eth-ics among nursing students in advanced vocational college need to be clarified. A variety of ways should be used to guide the nursing students to the deep understanding of ethical

  16. Ontology of the False State

    Directory of Open Access Journals (Sweden)

    Testa Italo

    2015-09-01

    Full Text Available In this paper I will argue that critical theory needs to make its socio-ontological commitments explicit, whilst on the other hand I will posit that contemporary social ontology needs to amend its formalistic approach by embodying a critical theory perspective. In the first part of my paper I will discuss how the question was posed in Horkheimer’s essays of the 1930s, which leave open two options: (1 a constructive inclusion of social ontology within social philosophy, or else (2 a program of social philosophy that excludes social ontology. Option (2 corresponds to Adorno’s position, which I argue is forced to recur to a hidden social ontology. Following option (1, I first develop a meta-critical analysis of Searle, arguing that his social ontology presupposes a notion of ‘recognition’ which it cannot account for. Furthermore, by means of a critical reading of Honneth, I argue that critical theory could incorporate a socio-ontological approach, giving value to the constitutive socio-ontological role of recognition and to the socio-ontological role of objectification. I will finish with a proposal for a socio-ontological characterization of reification which involves that the basic occurrence of recognition is to be grasped at the level of background practices.

  17. Frontiers in biomedical engineering and biotechnology.

    Science.gov (United States)

    Liu, Feng; Goodarzi, Ali; Wang, Haifeng; Stasiak, Joanna; Sun, Jianbo; Zhou, Yu

    2014-01-01

    The 2nd International Conference on Biomedical Engineering and Biotechnology (iCBEB 2013), held in Wuhan on 11–13 October 2013, is an annual conference that aims at providing an opportunity for international and national researchers and practitioners to present the most recent advances and future challenges in the fields of Biomedical Information, Biomedical Engineering and Biotechnology. The papers published by this issue are selected from this conference, which witnesses the frontier in the field of Biomedical Engineering and Biotechnology, which particularly has helped improving the level of clinical diagnosis in medical work.

  18. ONTOLOGY: UNREAL REALITY

    Directory of Open Access Journals (Sweden)

    Piotr Jaroszynski

    2014-12-01

    Full Text Available The article examines the difference between ontology and metaphysics. It shows that as soon as the composition of being from essence and existence is treated as purely mental or in a “reified” way (where essence and existence are independent elements, then essence as essence becomes a thing, and then simply becomes a being, or what is called reality. Both versions in which the real difference disappears or in which the road leads to “reification,” influence the treatment of essence as independent, where essence as thing fills the field of reality. However, if essence was only possibility, then (1 the reality also would be merely possible, (2 the realistic field of philosophical terminology would get curtailed, and (3 there would be no terms to maintain the difference between reality and possibility, between metaphysics and ontology.

  19. Mathematical modeling in biomedical imaging

    CERN Document Server

    2012-01-01

    This volume reports on recent mathematical and computational advances in optical, ultrasound, and opto-acoustic tomographies. It outlines the state-of-the-art and future directions in these fields and provides readers with the most recently developed mathematical and computational tools.  It is particularly suitable for researchers and graduate students in applied mathematics and biomedical engineering.

  20. Approaches to Ontology Based Algorithms for Clustering Text Documents

    Directory of Open Access Journals (Sweden)

    V.Sureka

    2012-09-01

    Full Text Available The advancement in digital technology and WorldWide Web has increased the usage of digitaldocuments being used for various purposes like epublishing,digital library. Increase in number oftext documents requires efficient techniques thatcan help during searching and retrieval. Documentclustering is one such technique whichautomatically organizes text documents intomeaningful groups. This paper compares theperformance of enhanced ontological algorithmsbased on K-Means and DBScan clustering.Ontology is introduced by using a concept weightwhich is calculated by considering the correlationcoefficient of the word and probability of concept.Various experiments were conducted duringperformance evaluation and the results showedthat the inclusion of ontology increased theefficiency of clustering and the performance ofontology-based DBScan algorithm is better thanthe ontology-based K-Means algorithm

  1. Ontology and geographic kinds

    OpenAIRE

    Smith, B; D M Mark

    1998-01-01

    An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they...

  2. 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…

  3. The ethics of biomedical big data

    CERN Document Server

    Mittelstadt, Brent Daniel

    2016-01-01

    This book presents cutting edge research on the new ethical challenges posed by biomedical Big Data technologies and practices. ‘Biomedical Big Data’ refers to the analysis of aggregated, very large datasets to improve medical knowledge and clinical care. The book describes the ethical problems posed by aggregation of biomedical datasets and re-use/re-purposing of data, in areas such as privacy, consent, professionalism, power relationships, and ethical governance of Big Data platforms. Approaches and methods are discussed that can be used to address these problems to achieve the appropriate balance between the social goods of biomedical Big Data research and the safety and privacy of individuals. Seventeen original contributions analyse the ethical, social and related policy implications of the analysis and curation of biomedical Big Data, written by leading experts in the areas of biomedical research, medical and technology ethics, privacy, governance and data protection. The book advances our understan...

  4. Ontology Partitioning: Clustering Based Approach

    Directory of Open Access Journals (Sweden)

    Soraya Setti Ahmed

    2015-05-01

    Full Text Available The semantic web goal is to share and integrate data across different domains and organizations. The knowledge representations of semantic data are made possible by ontology. As the usage of semantic web increases, construction of the semantic web ontologies is also increased. Moreover, due to the monolithic nature of the ontology various semantic web operations like query answering, data sharing, data matching, data reuse and data integration become more complicated as the size of ontology increases. Partitioning the ontology is the key solution to handle this scalability issue. In this work, we propose a revision and an enhancement of K-means clustering algorithm based on a new semantic similarity measure for partitioning given ontology into high quality modules. The results show that our approach produces meaningful clusters than the traditional algorithm of K-means.

  5. OntologyNavigator: WEB 2.0 scalable ontology based CLIR portal to IT scientific corpus for researchers

    CERN Document Server

    Kembellec, Gérald; Sauvaget, Catherine

    2011-01-01

    This work presents the architecture used in the ongoing OntologyNavigator project. It is a research tool to help advanced learners to find adapted IT papers to create scientific bibliographies. The purpose is the use of an IT representation as educational research software for researchers. We use an ontology based on the ACM's Computing Classification System in order to find scientific papers directly related to the new researcher's domain without any formal request. An ontology translation in French is automatically proposed and can be based on Web 2.0 enhanced by a community of users. A visualization and navigation model is proposed to make it more accessible and examples are given to show the interface of the tool. This model offers the possibility of cross language query. Users deeply interact with the translation by providing alternative translation of the node label. Customers also enrich the ontology node labels with implicit descriptors.

  6. BIG: a Grid Portal for Biomedical Data and Images

    Directory of Open Access Journals (Sweden)

    Giovanni Aloisio

    2004-06-01

    Full Text Available Modern management of biomedical systems involves the use of many distributed resources, such as high performance computational resources to analyze biomedical data, mass storage systems to store them, medical instruments (microscopes, tomographs, etc., advanced visualization and rendering tools. Grids offer the computational power, security and availability needed by such novel applications. This paper presents BIG (Biomedical Imaging Grid, a Web-based Grid portal for management of biomedical information (data and images in a distributed environment. BIG is an interactive environment that deals with complex user's requests, regarding the acquisition of biomedical data, the "processing" and "delivering" of biomedical images, using the power and security of Computational Grids.

  7. 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......, 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...

  8. Flexible sensors for biomedical technology.

    Science.gov (United States)

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes. PMID:26675174

  9. Flexible sensors for biomedical technology.

    Science.gov (United States)

    Vilela, Diana; Romeo, Agostino; Sánchez, Samuel

    2016-02-01

    Flexible sensing devices have gained a great deal of attention among the scientific community in recent years. The application of flexible sensors spans over several fields, including medicine, industrial automation, robotics, security, and human-machine interfacing. In particular, non-invasive health-monitoring devices are expected to play a key role in the improvement of patient life and in reducing costs associated with clinical and biomedical diagnostic procedures. Here, we focus on recent advances achieved in flexible devices applied on the human skin for biomedical and healthcare purposes.

  10. BIG: a Grid Portal for Biomedical Data and Images

    OpenAIRE

    Giovanni Aloisio; Maria Cristina Barba; Euro Blasi; Massimo Cafaro; Sandro Fiore; Maria Mirto

    2004-01-01

    Modern management of biomedical systems involves the use of many distributed resources, such as high performance computational resources to analyze biomedical data, mass storage systems to store them, medical instruments (microscopes, tomographs, etc.), advanced visualization and rendering tools. Grids offer the computational power, security and availability needed by such novel applications. This paper presents BIG (Biomedical Imaging Grid), a Web-based Grid portal for management of biomedic...

  11. Ontology-Based Textual Emotion Detection

    OpenAIRE

    Mohamed Haggag; Samar Fathy; Nahla Elhaggar

    2015-01-01

    Emotion Detection from text is a very important area of natural language processing. This paper shows a new method for emotion detection from text which depends on ontology. This method is depending on ontology extraction from the input sentence by using a triplet extraction algorithm by the OpenNLP parser, then make an ontology matching with the ontology base that we created by similarity and word sense disambiguation. This ontology base consists of ontologies and the emotion label related t...

  12. IT Management Using a Heavyweight CIM Ontology

    OpenAIRE

    Textor, Andreas; Stynes, Jeanne; Kroeger, Reinhold

    2011-01-01

    This paper presents an approach for ontology-based IT management based on a heavyweight (formal) ontology using the Web Ontology Language (OWL). The ontology comprises a complete OWL representation of the Common Information Model (CIM) and management rules defined in the Semantic Web Rule Language (SWRL). The ontology not only models the managed system types, but a runtime system dynamically updates model instances in the ontology that reflect values of managed system entities. This allows th...

  13. Ontology Mapping for Dynamic Multiagent Environment

    OpenAIRE

    M.Jenifer; P. S. Balamurugan; Prince, T.

    2012-01-01

    Ontologies are essential for the realization of the Semantic Web, which in turn relies on the ability of systems to identify and exploit relationships that exist between and within ontologies. As ontologies can be used to represent different domains, there is a high need for efficient ontology matching techniques that can allow information to be easily shared between different heterogeneous systems. There are various systems were proposed recently for ontology mapping. Ontology mapping is a...

  14. Biomedical engineering and nanotechnology

    International Nuclear Information System (INIS)

    This book is predominantly a compilation of papers presented in the conference which is focused on the development in biomedical materials, biomedical devises and instrumentation, biomedical effects of electromagnetic radiation, electrotherapy, radiotherapy, biosensors, biotechnology, bioengineering, tissue engineering, clinical engineering and surgical planning, medical imaging, hospital system management, biomedical education, biomedical industry and society, bioinformatics, structured nanomaterial for biomedical application, nano-composites, nano-medicine, synthesis of nanomaterial, nano science and technology development. The papers presented herein contain the scientific substance to suffice the academic directivity of the researchers from the field of biomedicine, biomedical engineering, material science and nanotechnology. Papers relevant to INIS are indexed separately

  15. [Projects to accelerate the practical use of innovative medical devices to collaborate with TWIns, Center for Advanced Biomedical Sciences, Waseda University and School of Engineering, The University of Tokyo].

    Science.gov (United States)

    Niimi, Shingo; Umezu, Mitsuo; Iseki, Hiroshi; Harada, Hiroshi Kasanuki Noboru; Mitsuishi, Mamoru; Kitamori, Takehiko; Tei, Yuichi; Nakaoka, Ryusuke; Haishima, Yuji

    2014-01-01

    Division of Medical Devices has been conducting the projects to accelerate the practical use of innovative medical devices to collaborate with TWIns, Center for Advanced Biomedical Sciences, Waseda University and School of Engineering, The University of Tokyo. The TWIns has been studying to aim at establishment of preclinical evaluation methods by "Engineering Based Medicine", and established Regulatory Science Institute for Medical Devices. School of Engineering, The University of Tokyo has been studying to aim at establishment of assessment methodology for innovative minimally invasive therapeutic devices, materials, and nanobio diagnostic devices. This report reviews the exchanges of personnel, the implement systems and the research progress of these projects.

  16. Ontology of World Politics

    Directory of Open Access Journals (Sweden)

    Angela Khristin Brown

    2014-05-01

    Full Text Available Culture division influences our lives differently in how we identify and evaluate who we are as individuals. We respond to life situations in how we interpret ourselves. How we function in society as a whole signifies invaluable differences in how we base our demeanor. Freedom of speech is a given right in American society. It is the social norm to be able to voice your opinion on diverse issues faced in our global environment. The Ontology of World Politics is a form of mediating issues of concern.Keywords: Politics, Political Opinions, World Politics

  17. A Temporal Web Ontology Language

    NARCIS (Netherlands)

    V. Milea (Viorel); F. Frasincar (Flavius); U. Kaymak (Uzay)

    2009-01-01

    textabstractThe Web Ontology Language (OWL) is the most expressive standard language for modeling ontologies on the Semantic Web. In this paper, we present a temporal extension of the very expressive fragment SHIN(D) of the OWL-DL language resulting in the tOWL language. Through a layered approach w

  18. Structural Weights in Ontology Matching

    Directory of Open Access Journals (Sweden)

    Mohammad Mehdi Keikha

    2013-10-01

    Full Text Available Ontology matching finds correspondences between similar entities of different ontologies. Two ontologies may be similar in some aspects such as structure, semantic etc. Most ontology matching systems integrate multiple matchers to extract all the similarities that two ontologies may have. Thus, we face a major problem to aggregate different similarities.Some matching systems use experimental weights for aggregation of similarities among different matchers while others use machine learning approaches and optimization algorithms to find optimal weights to assign to different matchers. However, both approaches have their own deficiencies.In this paper, we will point out the problems and shortcomings of current similarity aggregation strategies. Then, we propose a new strategy, which enables us to utilize the structural information of ontologies to get weights of matchers, for the similarity aggregation task. For achieving this goal, we create a new Ontology Matching system which it uses three available matchers, namely GMO, ISub and VDoc.We have tested our similarity aggregation strategy on the OAEI 2012 data set. Experimental results show significant improvements in accuracies of several cases, especially in matching the classes of ontologies. We will compare the performance of our similarity aggregation strategy with other well-known strategies.

  19. 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.…

  20. 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...

  1. Spintronic platforms for biomedical applications.

    Science.gov (United States)

    Freitas, P P; Cardoso, F A; Martins, V C; Martins, S A M; Loureiro, J; Amaral, J; Chaves, R C; Cardoso, S; Fonseca, L P; Sebastião, A M; Pannetier-Lecoeur, M; Fermon, C

    2012-02-01

    Since the fundamental discovery of the giant magnetoresistance many spintronic devices have been developed and implemented in our daily life (e.g. information storage and automotive industry). Lately, advances in the sensors technology (higher sensitivity, smaller size) have potentiated other applications, namely in the biological area, leading to the emergence of novel biomedical platforms. In particular the investigation of spintronics and its application to the development of magnetoresistive (MR) biomolecular and biomedical platforms are giving rise to a new class of biomedical diagnostic devices, suitable for bench top bioassays as well as point-of-care and point-of-use devices. Herein, integrated spintronic biochip platforms for diagnostic and cytometric applications, hybrid systems incorporating magnetoresistive sensors applied to neuroelectronic studies and biomedical imaging, namely magneto-encephalography and magneto-cardiography, are reviewed. Also lab-on-a-chip MR-based platforms to perform biological studies at the single molecule level are discussed. Overall the potential and main characteristics of such MR-based biomedical devices, comparing to the existing technologies while giving particular examples of targeted applications, are addressed. PMID:22146898

  2. Data Migration for Ontology Evolution

    Institute of Scientific and Technical Information of China (English)

    赵彦; 张雷; 林晨曦; 张卓; 俞勇

    2004-01-01

    Ontology is the conceptual backbone that provides meaning to data on the semantic web. However, ontology is not a static resource and may evolve over time, which often leaves the meaning of data in an undefined or inconsistent state. It is thus very important to have a method to preserve the data and its meaning when ontology changes. This paper proposed a general method that solves the problem using data migration. It analyzed some of the issues in the method including separation of ontology and data, migration specification, migration result and migration algorithm. The paper also instantiates the general mothod in RDF(S) as an example. The RDF(S) example itself is a simple but complete method for migrating RDF data when RDFS ontology changes.

  3. Solar-Terrestrial Ontology Development

    Science.gov (United States)

    McGuinness, D.; Fox, P.; Middleton, D.; Garcia, J.; Cinquni, L.; West, P.; Darnell, J. A.; Benedict, J.

    2005-12-01

    The development of an interdisciplinary virtual observatory (the Virtual Solar-Terrestrial Observatory; VSTO) as a scalable environment for searching, integrating, and analyzing databases distributed over the Internet requires a higher level of semantic interoperability than here-to-fore required by most (if not all) distributed data systems or discipline specific virtual observatories. The formalization of semantics using ontologies and their encodings for the internet (e.g. OWL - the Web Ontology Language), as well as the use of accompanying tools, such as reasoning, inference and explanation, open up both a substantial leap in options for interoperability and in the need for formal development principles to guide ontology development and use within modern, multi-tiered network data environments. In this presentation, we outline the formal methodologies we utilize in the VSTO project, the currently developed use-cases, ontologies and their relation to existing ontologies (such as SWEET).

  4. The Distributed Ontology Language (DOL): Ontology Integration and Interoperability Applied to Mathematical Formalization

    OpenAIRE

    Lange, Christoph; Kutz, Oliver; Mossakowski, Till; Grüninger, Michael

    2012-01-01

    The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper focuses on an application of DOL's meta-theoretical features in mathematical formalization: validating relationships between ontological...

  5. Multi-label literature classification based on the Gene Ontology graph

    Directory of Open Access Journals (Sweden)

    Lu Xinghua

    2008-12-01

    Full Text Available Abstract Background The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification. Results In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community. Conclusion Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate

  6. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).

    Science.gov (United States)

    He, Yongqun; Toldo, Luca; Burns, Gully; Tao, Cui; Abernethy, Darrell R

    2012-01-01

    Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in developing biomedical ontologies that represent various areas associated with vaccines and drugs. These ontologies combined with existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, MedDRA, VO, OAE, and AERO) could play significant roles on clinical and translational research. The first "Vaccine and Drug Ontology in the Study of Mechanism and Effect" workshop (VDOSME 2012) provided a platform for discussing problems and solutions in the development and application of biomedical ontologies in representing and analyzing vaccines/drugs, vaccine/drug administrations, vaccine/drug-induced immune responses (including positive host responses and adverse events), and similar topics. The workshop covered two main areas: (i) ontologies of vaccines, of drugs, and of studies thereof; and (ii) analysis of administration, mechanism and effect in terms of representations based on such ontologies. Six full-length papers included in this thematic issue focus on ontology representation and time analysis of vaccine/drug administration and host responses (including positive immune responses and adverse events), vaccine and drug adverse event text mining, and ontology-based Semantic Web applications. The workshop, together with the follow-up activities and personal meetings, provided a wonderful platform for the researchers and scientists in the vaccine and drug communities to demonstrate research progresses, share ideas, address questions, and promote collaborations for better representation and analysis of vaccine and drug-related terminologies and clinical and research data.

  7. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

    Science.gov (United States)

    Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

  8. Biomedical applications of nisin.

    Science.gov (United States)

    Shin, J M; Gwak, J W; Kamarajan, P; Fenno, J C; Rickard, A H; Kapila, Y L

    2016-06-01

    Nisin is a bacteriocin produced by a group of Gram-positive bacteria that belongs to Lactococcus and Streptococcus species. Nisin is classified as a Type A (I) lantibiotic that is synthesized from mRNA and the translated peptide contains several unusual amino acids due to post-translational modifications. Over the past few decades, nisin has been used widely as a food biopreservative. Since then, many natural and genetically modified variants of nisin have been identified and studied for their unique antimicrobial properties. Nisin is FDA approved and generally regarded as a safe peptide with recognized potential for clinical use. Over the past two decades the application of nisin has been extended to biomedical fields. Studies have reported that nisin can prevent the growth of drug-resistant bacterial strains, such as methicillin-resistant Staphylococcus aureus, Streptococcus pneumoniae, Enterococci and Clostridium difficile. Nisin has now been shown to have antimicrobial activity against both Gram-positive and Gram-negative disease-associated pathogens. Nisin has been reported to have anti-biofilm properties and can work synergistically in combination with conventional therapeutic drugs. In addition, like host-defence peptides, nisin may activate the adaptive immune response and have an immunomodulatory role. Increasing evidence indicates that nisin can influence the growth of tumours and exhibit selective cytotoxicity towards cancer cells. Collectively, the application of nisin has advanced beyond its role as a food biopreservative. Thus, this review will describe and compare studies on nisin and provide insight into its future biomedical applications.

  9. Prospective Integration of Cultural Consideration in Biomedical Research for Patients with Advanced Cancer: Recommendations from an International Conference on Malignant Bowel Obstruction in Palliative Care

    OpenAIRE

    Fineberg, Iris Cohen; Grant, Marcia; Aziz, Noreen M.; Payne, Richard; Kagawa-Singer, Marjorie; Dunn, Geoffrey P.; Kinzbrunner, Barry M.; Palos, Guadalupe; Shinagawa, Susan Matsuko; Krouse, Robert S.

    2007-01-01

    In the setting of an international conference on malignant bowel obstruction as a model for randomized control trials (RCT) in palliative care, we discuss the importance of incorporating prospective cultural considerations in research design. The approach commonly used in biomedical research has traditionally valued the RCT as the ultimate “way of knowing” about how to best treat a medical condition. The foremost limitation of this approach is the lack of recognition of the impact of cultural...

  10. Handbook of metadata, semantics and ontologies

    CERN Document Server

    Sicilia, Miguel-Angel

    2013-01-01

    Metadata research has emerged as a discipline cross-cutting many domains, focused on the provision of distributed descriptions (often called annotations) to Web resources or applications. Such associated descriptions are supposed to serve as a foundation for advanced services in many application areas, including search and location, personalization, federation of repositories and automated delivery of information. Indeed, the Semantic Web is in itself a concrete technological framework for ontology-based metadata. For example, Web-based social networking requires metadata describing people and

  11. Bridge Ontology:A Multi-Ontologies-Based Approach for Semantic Annotation

    Institute of Scientific and Technical Information of China (English)

    WANG Peng; XU Bao-wen; LU Jian-jiang; LI Yan-hui; JIANG Jian-hua

    2004-01-01

    Representing the relationships between ontologies is the key problem of semantic annotations based on multi-ontologies.Traditional approaches only had the ability of denoting the simple concept subsumption relations between ontologies.Through analyzing and classifying the relationships between ontologies, the idea of bridge ontology was proposed, which had the powerful capability of expressing the complex relationships between concepts and relationships between relations in multi-ontologies.Meanwhile, a new approach employing bridge ontology was proposed to deal with the multi-ontologies-based semantic annotation problem.The bridge ontology is a peculiar ontology, which can be created and maintained conveniently, and is effective in the multi-ontologies-based semantic annotation.The approach using bridge ontology has the advantages of low-cost, scalable, robust in the web circumstance, and avoiding the unnecessary ontology extending and integration.

  12. Ontology for E-Learning: A Case Study

    Science.gov (United States)

    Colace, Francesco; De Santo, Massimo; Gaeta, Matteo

    2009-01-01

    Purpose: The development of adaptable and intelligent educational systems is widely considered one of the great challenges in scientific research. Among key elements for building advanced training systems, an important role is played by methodologies chosen for knowledge representation. In this scenario, the introduction of ontology formalism can…

  13. Logical implications for regulatory relations represented by verbs in biomedical texts

    DEFF Research Database (Denmark)

    Zambach, Sine

    Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However, some relations are used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular their usage expressed as verbs in diffe......Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However, some relations are used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular their usage expressed as verbs...

  14. Ontology Research and Development. Part 2 - A Review of Ontology Mapping and Evolving.

    Science.gov (United States)

    Ding, Ying; Foo, Schubert

    2002-01-01

    Reviews ontology research and development, specifically ontology mapping and evolving. Highlights include an overview of ontology mapping projects; maintaining existing ontologies and extending them as appropriate when new information or knowledge is acquired; and ontology's role and the future of the World Wide Web, or Semantic Web. (Contains 55…

  15. A cognitive science perspective on legal ontologies

    NARCIS (Netherlands)

    J. Breuker; R. Hoekstra

    2011-01-01

    We can trace five origins of ontology engineering, and all five still play a major role in ontology engineering. Each of these roots gives a different perspective on content and use of ontologies. Philosophical ontology is concerned with "reality"; Information science with systematic terminology; Ar

  16. Multilingual Lexical Semantic Resources for Ontology Translation

    OpenAIRE

    Declerck, T.; A. GÓMEZ-PÉREZ; Vela, O.; Gantner, Z.; Manzano-Macho, D.

    2006-01-01

    We describe the integration of some multilingual language resources in ontological descriptions, with the purpose of providing ontologies, which are normally using concept labels in just one (natural) language, with multilingual facility in their design and use in the context of Semantic Web applications, supporting both the semantic annotation of textual documents with multilingual ontology labels and ontology extraction from multilingual text sources.

  17. OWL 2 Web Ontology Language: XML serialization

    NARCIS (Netherlands)

    B. Motik; P. Patel-Schneider; S. Bechhofer; B. Cuenca Grau; A. Fokoue; R. Hoekstra; B. Parsia

    2008-01-01

    The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information writ

  18. Biomedical technology

    CERN Document Server

    Wriggers, Peter

    2015-01-01

    During the last years computational methods lead to new approaches that can be applied within medical practice. Based on the tremendous advances in medical imaging and high-performance computing, virtual testing is able to help in medical decision processes or implant designs. Current challenges in medicine and engineering are related to the application of computational methods to clinical medicine and the study of biological systems at different scales. Additionally manufacturers will be able to use computational tools and methods to predict the performance of their medical devices in virtual patients. The physical and animal testing procedures could be reduced by virtual prototyping of medical devices. Here simulations can enhance the performance of alternate device designs for a range of virtual patients. This will lead to a refinement of designs and to safer products. This book summarizes different aspects of approaches to enhance function, production, initialization and complications of different types o...

  19. Cosmological Ontology and Epistemology

    CERN Document Server

    Page, Don N

    2014-01-01

    In cosmology, we would like to explain our observations and predict future observations from theories of the entire universe. Such cosmological theories make ontological assumptions of what entities exist and what their properties and relationships are. One must also make epistemological assumptions or metatheories of how one can test cosmological theories. Here I shall propose a Bayesian analysis in which the likelihood of a complete theory is given by the normalized measure it assigns to the observation used to test the theory. In this context, a discussion is given of the trade-off between prior probabilities and likelihoods, of the measure problem of cosmology, of the death of Born's rule, of the Boltzmann brain problem, of whether there is a better principle for prior probabilities than mathematical simplicity, and of an Optimal Argument for the Existence of God.

  20. Process and Tool Support for Ontology-Aware Life Support System Development and Integration Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Recent advances in ontology development support a rich description of entities that are modeled within a domain and how these entities relate to each other....

  1. Ontology mapping and data discovery for the translational investigator.

    Science.gov (United States)

    Wynden, Rob; Weiner, Mark G; Sim, Ida; Gabriel, Davera; Casale, Marco; Carini, Simona; Hastings, Shannon; Ervin, David; Tu, Samson; Gennari, John H; Anderson, Nick; Mobed, Ketty; Lakshminarayanan, Prakash; Massary, Maggie; Cucina, Russ J

    2010-03-01

    An integrated data repository (IDR) containing aggregations of clinical, biomedical, economic, administrative, and public health data is a key component of an overall translational research infrastructure. But most available data repositories are designed using standard data warehouse architecture that employs arbitrary data encoding standards, making queries across disparate repositories difficult. In response to these shortcomings we have designed a Health Ontology Mapper (HOM) that translates terminologies into formal data encoding standards without altering the underlying source data. We believe the HOM system promotes inter-institutional data sharing and research collaboration, and will ultimately lower the barrier to developing and using an IDR.

  2. Ontological semantics for data privacy compliance: the NEURONA ontology

    OpenAIRE

    Casellas, Núria; Nieto, Juan-Emilio; Meroño, Albert; Roig, Antoni; Torralba, Sergi; Reyes, Mario; Casanovas, Pompeu

    2010-01-01

    Ponència presentada Intelligent Privacy Management, AAAI Spring-Symposium (2010) This paper describes the analysis of the requirements and the knowledge acquisition process for the development of a legal ontology for the representation of data protection knowledge in the framework of the NEURONA project. This modular ontology is used in the NEURONA application to reason about the correctness of the measures of protection applied to these data files by an organization. In this sense the us...

  3. Biomedical devices and their applications

    CERN Document Server

    2004-01-01

    This volume introduces readers to the basic concepts and recent advances in the field of biomedical devices. The text gives a detailed account of novel developments in drug delivery, protein electrophoresis, estrogen mimicking methods and medical devices. It also provides the necessary theoretical background as well as describing a wide range of practical applications. The level and style make this book accessible not only to scientific and medical researchers but also to graduate students.

  4. Institutionalising Ontology-Based Semantic Integration

    OpenAIRE

    Schorlemmer, Marco; Kalfoglou, Yannis

    2008-01-01

    We address what is still a scarcity of general mathematical foundations for ontology-based semantic integration underlying current knowledge engineering methodologies in decentralised and distributed environments. After recalling the first-order ontology-based approach to semantic integration and a formalisation of ontological commitment, we propose a general theory that uses a syntax-and interpretation-independent formulation of language, ontology, and ontological commitment in terms of inst...

  5. Enhanced Search Method for Ontology Classification

    OpenAIRE

    Je Min Kim; Soon Hyen Kwon; Young Tack Park

    2012-01-01

    The web ontology language (OWL) has become a W3C recommendation to publish and share ontologies on the semantic web. In order to infer implicit information (classification, satisfiability and realization) of OWL ontology, a number of OWL reasoners have been introduced. Ontology classification is to compute a partial ordering or hierarchy of named concepts in the ontology using the subsumption testing. Most of the reasoners use both top-down and bottom-up searches using subsumption testing for...

  6. An architecture for scaling ontology networks

    OpenAIRE

    Adamou, Alessandro

    2013-01-01

    Constructing ontology networks typically occurs at design time at the hands of knowledge engineers who assemble their components statically. There are, however, use cases where ontology networks need to be assembled upon request and processed at runtime, without altering the stored ontologies and without tampering with one another. These are what we call "virtual [ontology] networks", and keeping track of how an ontology changes in each virtual network is called "multiplexing". Issues may...

  7. AceWiki: Collaborative Ontology Management in Controlled Natural Language

    CERN Document Server

    Kuhn, Tobias

    2008-01-01

    AceWiki is a prototype that shows how a semantic wiki using controlled natural language - Attempto Controlled English (ACE) in our case - can make ontology management easy for everybody. Sentences in ACE can automatically be translated into first-order logic, OWL, or SWRL. AceWiki integrates the OWL reasoner Pellet and ensures that the ontology is always consistent. Previous results have shown that people with no background in logic are able to add formal knowledge to AceWiki without being instructed or trained in advance.

  8. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Engineering Fundamentals, the first volume of the handbook, presents material from respected scientists with diverse backgrounds in physiological systems, biomechanics, biomaterials, bioelectric phenomena, and neuroengineering. More than three dozen specific topics are examined, including cardia

  9. Concept Approximation between Fuzzy Ontologies

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Fuzzy ontologies are efficient tools to handle fuzzy and uncertain knowledge on the semantic web; but there are heterogeneity problems when gaining interoperability among different fuzzy ontologies. This paper uses concept approximation between fuzzy ontologies based on instances to solve the heterogeneity problems. It firstly proposes an instance selection technology based on instance clustering and weighting to unify the fuzzy interpretation of different ontologies and reduce the number of instances to increase the efficiency. Then the paper resolves the problem of computing the approximations of concepts into the problem of computing the least upper approximations of atom concepts. It optimizes the search strategies by extending atom concept sets and defining the least upper bounds of concepts to reduce the searching space of the problem. An efficient algorithm for searching the least upper bounds of concept is given.

  10. Iterated Ontology Revision by Reinterpretation

    OpenAIRE

    Özçep, Özgür Lütfü

    2016-01-01

    Iterated applications of belief change operators are essential for different scenarios such as that of ontology evolution where new information is not presented at once but only in piecemeal fashion within a sequence. I discuss iterated applications of so called reinterpretation operators that trace conflicts between ontologies back to the ambiguous of symbols and that provide conflict resolution strategies with bridging axioms. The discussion centers on adaptations of the classical iteration...

  11. A Temporal Web Ontology Language

    OpenAIRE

    Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

    2009-01-01

    textabstractThe Web Ontology Language (OWL) is the most expressive standard language for modeling ontologies on the Semantic Web. In this paper, we present a temporal extension of the very expressive fragment SHIN(D) of the OWL-DL language resulting in the tOWL language. Through a layered approach we introduce 3 extensions: i) Concrete Domains, that allows the representation of restrictions using concrete domain binary predicates, ii) Temporal Representation, that introduces timepoints, relat...

  12. Social ontologi og metodologisk individualisme

    DEFF Research Database (Denmark)

    Baldursson, Einar Baldvin

    2013-01-01

    spørgsmålet om hvorvidt metode fordrer en bestemt ontologi, gives eksempler på social metodologi. Dermed etableres et afsæt for en konkret vurdering af, om der er - og i givet fald hvilken - sammenhæng mellem ontologi og metodologi (Red.).for at modellering og simulation åbner muligheden for at afprøvning og...

  13. Realist Magic : Objects, Ontology, Causality

    OpenAIRE

    Morton, Timothy

    2013-01-01

    Object-oriented ontology offers a startlingly fresh way to think about causality that takes into account developments in physics since 1900. Causality, argues, Object Oriented Ontology (OOO), is aesthetic. In this book, Timothy Morton explores what it means to say that a thing has come into being, that it is persisting, and that it has ended. Drawing from examples in physics, biology, ecology, art, literature and music, Morton demonstrates the counterintuitive yet elegant explanatory power of...

  14. Musical Ontology: Critical, not Metaphysical

    Directory of Open Access Journals (Sweden)

    Jonathan A. Neufeld

    2014-01-01

    Full Text Available The ontology of musical works often sets the boundaries within which evaluation of musical works and performances takes place. Questions of ontology are therefore often taken to be prior to and apart from the evaluative questions considered by either performers as they present works to audiences or an audience’s critical reflection on a performance. In this paper I argue that, while the ontology of musical works may well set the boundaries of legitimate evaluation, ontological questions should not be considered as prior to or apart from critical evaluation. Rather, ontological claims are a type of critical evaluation made within musical practices. I argue that philosophers of music might learn from the debate in political philosophy about the difficulty of setting the limits of public reason in a way that remains open to a plurality of legitimate evaluative perspectives. Just as pre-political or metaphysical identification of the boundaries of public reason fail to accommodate the fact of pluralism in contemporary democratic politics, so too does a metaphysical identification of the boundaries of legitimate evaluation of musical works and performances fail to accommodate the fact of pluralism in contemporary musical practices. I apply John Rawls’s formulation of political liberalism, arguing that musical ontology should be critical, not metaphysical.

  15. Guidelines for a Dynamic Ontology - Integrating Tools of Evolution and Versioning in Ontology

    OpenAIRE

    Pittet, Perrine; Nicolle, Christophe; Cruz, Christophe

    2011-01-01

    International audience Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This paper presents a new way to manage the lifecycle of an ontology incorporating both versioning tools and evolution process. This solution, called VersionGraph, is integrated in the source ontology since its creation in order to make...

  16. Optimizing biomedical science learning in a veterinary curriculum: a review.

    Science.gov (United States)

    Warren, Amy L; Donnon, Tyrone

    2013-01-01

    As veterinary medical curricula evolve, the time dedicated to biomedical science teaching, as well as the role of biomedical science knowledge in veterinary education, has been scrutinized. Aside from being mandated by accrediting bodies, biomedical science knowledge plays an important role in developing clinical, diagnostic, and therapeutic reasoning skills in the application of clinical skills, in supporting evidence-based veterinary practice and life-long learning, and in advancing biomedical knowledge and comparative medicine. With an increasing volume and fast pace of change in biomedical knowledge, as well as increased demands on curricular time, there has been pressure to make biomedical science education efficient and relevant for veterinary medicine. This has lead to a shift in biomedical education from fact-based, teacher-centered and discipline-based teaching to applicable, student-centered, integrated teaching. This movement is supported by adult learning theories and is thought to enhance students' transference of biomedical science into their clinical practice. The importance of biomedical science in veterinary education and the theories of biomedical science learning will be discussed in this article. In addition, we will explore current advances in biomedical teaching methodologies that are aimed to maximize knowledge retention and application for clinical veterinary training and practice.

  17. 基于非本体资源重用重构的本体构建研究%Study on Ontologies Building Based on Reusing and Reengineering of Non-ontological Resources

    Institute of Scientific and Technical Information of China (English)

    段瑞龙; 宋文; 张士男

    2012-01-01

    To truly realize the semantic web, ontologies have to be rich and renewable in time. In order that ontologies can be developed faster and renewed timely, saving time and resources, ontology practitioners turn to non-ontological resources in ontologies building. The paper starts with the scientific definition and classification of non-ontological resources. Then it outlines the research progress of non-ontological resource reuse, non-ontological resource reengineering, and patterns for re-engineering non-ontological resources into ontologies. Based on the former study, the paper advances the entire process of reusing and reengineering non-ontological resources in ontologies building, in the hope of throwing more light on building ontologies using non-ontological resources.%要真正实现语义网,必须有丰富且及时更新的本体。为了加快本体开发速度、节约时间和资源、实现本体的及时更新,本体构建者开始重用非本体资源进行本体构建。文章首先对非本体资源进行了科学的定义和分类,接着概述了非本体资源重用、重构和重构非本体资源构建本体的模式目前的研究水平,并在此基础上提出了重用、重构非本体资源进行本体构建的全部流程,以求对利用非本体资源构建本体提供借鉴。

  18. ``Force,'' ontology, and language

    Science.gov (United States)

    Brookes, David T.; Etkina, Eugenia

    2009-06-01

    We introduce a linguistic framework through which one can interpret systematically students’ understanding of and reasoning about force and motion. Some researchers have suggested that students have robust misconceptions or alternative frameworks grounded in everyday experience. Others have pointed out the inconsistency of students’ responses and presented a phenomenological explanation for what is observed, namely, knowledge in pieces. We wish to present a view that builds on and unifies aspects of this prior research. Our argument is that many students’ difficulties with force and motion are primarily due to a combination of linguistic and ontological difficulties. It is possible that students are primarily engaged in trying to define and categorize the meaning of the term “force” as spoken about by physicists. We found that this process of negotiation of meaning is remarkably similar to that engaged in by physicists in history. In this paper we will describe a study of the historical record that reveals an analogous process of meaning negotiation, spanning multiple centuries. Using methods from cognitive linguistics and systemic functional grammar, we will present an analysis of the force and motion literature, focusing on prior studies with interview data. We will then discuss the implications of our findings for physics instruction.

  19. Biomedical applications of nisin.

    Science.gov (United States)

    Shin, J M; Gwak, J W; Kamarajan, P; Fenno, J C; Rickard, A H; Kapila, Y L

    2016-06-01

    Nisin is a bacteriocin produced by a group of Gram-positive bacteria that belongs to Lactococcus and Streptococcus species. Nisin is classified as a Type A (I) lantibiotic that is synthesized from mRNA and the translated peptide contains several unusual amino acids due to post-translational modifications. Over the past few decades, nisin has been used widely as a food biopreservative. Since then, many natural and genetically modified variants of nisin have been identified and studied for their unique antimicrobial properties. Nisin is FDA approved and generally regarded as a safe peptide with recognized potential for clinical use. Over the past two decades the application of nisin has been extended to biomedical fields. Studies have reported that nisin can prevent the growth of drug-resistant bacterial strains, such as methicillin-resistant Staphylococcus aureus, Streptococcus pneumoniae, Enterococci and Clostridium difficile. Nisin has now been shown to have antimicrobial activity against both Gram-positive and Gram-negative disease-associated pathogens. Nisin has been reported to have anti-biofilm properties and can work synergistically in combination with conventional therapeutic drugs. In addition, like host-defence peptides, nisin may activate the adaptive immune response and have an immunomodulatory role. Increasing evidence indicates that nisin can influence the growth of tumours and exhibit selective cytotoxicity towards cancer cells. Collectively, the application of nisin has advanced beyond its role as a food biopreservative. Thus, this review will describe and compare studies on nisin and provide insight into its future biomedical applications. PMID:26678028

  20. Biomedical ethics and the biomedical engineer: a review.

    Science.gov (United States)

    Saha, S; Saha, P S

    1997-01-01

    Biomedical engineering is responsible for many of the dramatic advances in modern medicine. This has resulted in improved medical care and better quality of life for patients. However, biomedical technology has also contributed to new ethical dilemmas and has challenged some of our moral values. Bioengineers often lack adequate training in facing these moral and ethical problems. These include conflicts of interest, allocation of scarce resources, research misconduct, animal experimentation, and clinical trials for new medical devices. This paper is a compilation of our previous published papers on these topics, and it summarizes many complex ethical issues that a bioengineer may face during his or her research career or professional practice. The need for ethics training in the education of a bioengineering student is emphasized. We also advocate the adoption of a code of ethics for bioengineers.

  1. 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.

  2. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

    Science.gov (United States)

    Hastings, Janna; Jeliazkova, Nina; Owen, Gareth; Tsiliki, Georgia; Munteanu, Cristian R; Steinbeck, Christoph; Willighagen, Egon

    2015-01-01

    Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.

  3. Ontology design patterns to disambiguate relations between genes and gene products in GENIA

    Directory of Open Access Journals (Sweden)

    Hoehndorf Robert

    2011-10-01

    Full Text Available Abstract Motivation Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences. Results We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. Availability Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.

  4. Prospective integration of cultural consideration in biomedical research for patients with advanced cancer: recommendations from an international conference on malignant bowel obstruction in palliative care.

    Science.gov (United States)

    Fineberg, Iris Cohen; Grant, Marcia; Aziz, Noreen M; Payne, Richard; Kagawa-Singer, Marjorie; Dunn, Geoffrey P; Kinzbrunner, Barry M; Palos, Guadalupe; Shinagawa, Susan Matsuko; Krouse, Robert S

    2007-07-01

    In the setting of an international conference on malignant bowel obstruction as a model for randomized controlled trials (RCTs) in palliative care, we discuss the importance of incorporating prospective cultural considerations into research design. The approach commonly used in biomedical research has traditionally valued the RCT as the ultimate "way of knowing" about how to best treat a medical condition. The foremost limitation of this approach is the lack of recognition of the impact of cultural viewpoints on research outcomes. We propose that interest relevant to cultural viewpoints should be emphasized in conceptualizing and interpreting research questions, designs, and results. In addition to recognizing our cultural biases as individuals and researchers, we recommend two major shifts in designing and implementing RCTs: 1) inclusion of a multidisciplinary team of researchers to inform the diversity of perspectives and expertise brought to the research, and 2) use of mixed methods of inquiry, reflecting both deductive and inductive modes of inference. PMID:17532174

  5. Ontology Mapping for a New Database Integration Model Using an Ontology-driven Mediated Warehousing Approach

    Directory of Open Access Journals (Sweden)

    Ali Ahmed

    2014-04-01

    Full Text Available Ontology mapping is a technique that has become very useful for matching semantics between ontologies or schemas that were designed independently of each other. The main goal of the ontology mapping is to enable interoperability between applications in distributed information systems based on heterogeneous ontologies. To achieve this goal it is necessary to formally define mapping rules between local data sources and ontologies and the notion of a mapping between ontologies. In this study, the authors proposed a new mapping approach, so that the ontologies have to be linked to actual information sources in order to support the integration process. In this approach, first, for each incorporated information source, a local ontology is generated to describe its semantics as well as the resulting mappings between the source and the local ontology, then the local ontologies are mapped to a global ontology using the mapping rule.

  6. Role of Ontology in Information Retrieval

    Institute of Scientific and Technical Information of China (English)

    WU Dan; WANG Hui-lin

    2006-01-01

    Based on the comparison between ontology and thesaurus, and the analysis of an ontology-based Information Retrieval (IR) model, the potential advantages that ontology may contribute to IR are analyzed. Then a general architecture of ontology-based Information Retrieval System (IRS) and the approach of constructing it are presented. Based on the researches, the role of ontology in IR is summarized from four aspects and a typical system called Textpresso is analyzed. Finally, a conclusion is drawn that utilizing ontology is the trend of IR and can really improve the IRS.

  7. Cohesion Metrics for Ontology Design and Application

    Directory of Open Access Journals (Sweden)

    Haining Yao

    2005-01-01

    Full Text Available Recently, domain specific ontology development has been driven by research on the Semantic Web. Ontologies have been suggested for use in many application areas targeted by the Semantic Web, such as dynamic web service composition and general web service matching. Fundamental characteristics of these ontologies must be determined in order to effectively make use of them: for example, Sirin, Hendler and Parsia have suggested that determining fundamental characteristics of ontologies is important for dynamic web service composition. Our research examines cohesion metrics for ontologies. The cohesion metrics examine the fundamental quality of cohesion as it relates to ontologies.

  8. 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

  9. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham Iii, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  10. A Review of Biomedical Centrifugal Microfluidic Platforms

    Directory of Open Access Journals (Sweden)

    Minghui Tang

    2016-02-01

    Full Text Available Centrifugal microfluidic or lab-on-a-disc platforms have many advantages over other microfluidic systems. These advantages include a minimal amount of instrumentation, the efficient removal of any disturbing bubbles or residual volumes, and inherently available density-based sample transportation and separation. Centrifugal microfluidic devices applied to biomedical analysis and point-of-care diagnostics have been extensively promoted recently. This paper presents an up-to-date overview of these devices. The development of biomedical centrifugal microfluidic platforms essentially covers two categories: (i unit operations that perform specific functionalities, and (ii systems that aim to address certain biomedical applications. With the aim to provide a comprehensive representation of current development in this field, this review summarizes progress in both categories. The advanced unit operations implemented for biological processing include mixing, valving, switching, metering and sequential loading. Depending on the type of sample to be used in the system, biomedical applications are classified into four groups: nucleic acid analysis, blood analysis, immunoassays, and other biomedical applications. Our overview of advanced unit operations also includes the basic concepts and mechanisms involved in centrifugal microfluidics, while on the other hand an outline on reported applications clarifies how an assembly of unit operations enables efficient implementation of various types of complex assays. Lastly, challenges and potential for future development of biomedical centrifugal microfluidic devices are discussed.

  11. Comparing categories among geographic ontologies

    Science.gov (United States)

    Kavouras, Marinos; Kokla, Margarita; Tomai, Eleni

    2005-03-01

    Numerous attempts have been made to generate semantic "mappings" between different ontologies, or create aligned/integrated ones. An essential step towards their success is the ability to compare the categories involved. This paper introduces a systematic methodology for comparing categories met in geographic ontologies. The methodology explores/extracts semantic information provided by categories' definitions. The first step towards this goal is the recognition of syntactic and lexical patterns in definitions, which help to identify (a) semantic properties such as purpose, location, cover, and (b) semantic relations such as hypernym, part of, has-parts, etc. At the second step, a similarity measure among categories is applied, in order to explore how (the) extracted properties and relations interrelate. This framework enables us to (a) better understand the impact of context in cross-ontology "mappings", (b) evaluate the "quality" of definitions as to whether they respect mere ontological aspects (such as unambiguous taxonomies), and (c) deal more effectively with the problem of semantic translation among geographic ontologies.

  12. PhysiomeSpace: digital library service for biomedical data.

    Science.gov (United States)

    Testi, Debora; Quadrani, Paolo; Viceconti, Marco

    2010-06-28

    Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client-server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community. PMID:20478910

  13. PhysiomeSpace: digital library service for biomedical data.

    Science.gov (United States)

    Testi, Debora; Quadrani, Paolo; Viceconti, Marco

    2010-06-28

    Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client-server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community.

  14. Biomedical optical imaging

    CERN Document Server

    Fujimoto, James G

    2009-01-01

    Biomedical optical imaging is a rapidly emerging research area with widespread fundamental research and clinical applications. This book gives an overview of biomedical optical imaging with contributions from leading international research groups who have pioneered many of these techniques and applications. A unique research field spanning the microscopic to the macroscopic, biomedical optical imaging allows both structural and functional imaging. Techniques such as confocal and multiphoton microscopy provide cellular level resolution imaging in biological systems. The integration of this tech

  15. Introduction to biomedical engineering

    CERN Document Server

    Enderle, John

    2011-01-01

    Introduction to Biomedical Engineering is a comprehensive survey text for biomedical engineering courses. It is the most widely adopted text across the BME course spectrum, valued by instructors and students alike for its authority, clarity and encyclopedic coverage in a single volume. Biomedical engineers need to understand the wide range of topics that are covered in this text, including basic mathematical modeling; anatomy and physiology; electrical engineering, signal processing and instrumentation; biomechanics; biomaterials science and tissue engineering; and medical and engineering e

  16. An ontology for sensor networks

    Science.gov (United States)

    Compton, Michael; Neuhaus, Holger; Bermudez, Luis; Cox, Simon

    2010-05-01

    Sensors and networks of sensors are important ways of monitoring and digitizing reality. As the number and size of sensor networks grows, so too does the amount of data collected. Users of such networks typically need to discover the sensors and data that fit their needs without necessarily understanding the complexities of the network itself. The burden on users is eased if the network and its data are expressed in terms of concepts familiar to the users and their job functions, rather than in terms of the network or how it was designed. Furthermore, the task of collecting and combining data from multiple sensor networks is made easier if metadata about the data and the networks is stored in a format and conceptual models that is amenable to machine reasoning and inference. While the OGC's (Open Geospatial Consortium) SWE (Sensor Web Enablement) standards provide for the description and access to data and metadata for sensors, they do not provide facilities for abstraction, categorization, and reasoning consistent with standard technologies. Once sensors and networks are described using rich semantics (that is, by using logic to describe the sensors, the domain of interest, and the measurements) then reasoning and classification can be used to analyse and categorise data, relate measurements with similar information content, and manage, query and task sensors. This will enable types of automated processing and logical assurance built on OGC standards. The W3C SSN-XG (Semantic Sensor Networks Incubator Group) is producing a generic ontology to describe sensors, their environment and the measurements they make. The ontology provides definitions for the structure of sensors and observations, leaving the details of the observed domain unspecified. This allows abstract representations of real world entities, which are not observed directly but through their observable qualities. Domain semantics, units of measurement, time and time series, and location and mobility

  17. 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.

  18. Research on Forging Die Design Ontology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenlei; FAN Yushun

    2006-01-01

    Forging die design is heavily dependent on engineers' experiences. But traditional AI technologies can barely provide a standard knowledge representation style for knowledge transferring. This paper introduces ontology into forging die design. 3-layer forging die design ontology is built, which includes Meta-ontology, Domain-ontology and Bottom ontology. Further, by conceptualization, the concepts and their relations are formally addressed by primitives such as Term, Relation and Function etc, which are explicitly expressed by concept tree. Bottom ontology uses Knowledge Item and Prototype to represent and capture general knowledge for knowledge reuse and share. Forging die design ontology building approach is discussed for standard knowledge representation, knowledge mine and knowledge driven CAD design etc. And OWL language is employed for integration among different domain ontologies integration. Finally a locomotive forging die KBE system is presented to demonstrate this approach.

  19. A Statistical Amalgamation Approach for Ontologies

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2012-02-01

    Full Text Available As ontology is subjective and varies in different domains, the amount of ontologies turns out to be huge but with poor compatibility. Mainstream method for ontology integration is mostly achieved by establishing mappings between ontologies. In this essay, the author put forward another way of ontology merging. After statistic machine learning on concept relations, the frequency of different ontologies appeared in concept relations reveals certainty factor and help to build a large-scale concept relations network including the statistic information and domain categories, so that the conceptions conveyed by different ontologies can be fused together and the merging concept space turns to be relatively objective. And the experiments results also help to demonstrate the feasibility of the ontology merging.

  20. Biomedical engineering principles

    CERN Document Server

    Ritter, Arthur B; Valdevit, Antonio; Ascione, Alfred N

    2011-01-01

    Introduction: Modeling of Physiological ProcessesCell Physiology and TransportPrinciples and Biomedical Applications of HemodynamicsA Systems Approach to PhysiologyThe Cardiovascular SystemBiomedical Signal ProcessingSignal Acquisition and ProcessingTechniques for Physiological Signal ProcessingExamples of Physiological Signal ProcessingPrinciples of BiomechanicsPractical Applications of BiomechanicsBiomaterialsPrinciples of Biomedical Capstone DesignUnmet Clinical NeedsEntrepreneurship: Reasons why Most Good Designs Never Get to MarketAn Engineering Solution in Search of a Biomedical Problem

  1. Fundamental of biomedical engineering

    CERN Document Server

    Sawhney, GS

    2007-01-01

    About the Book: A well set out textbook explains the fundamentals of biomedical engineering in the areas of biomechanics, biofluid flow, biomaterials, bioinstrumentation and use of computing in biomedical engineering. All these subjects form a basic part of an engineer''s education. The text is admirably suited to meet the needs of the students of mechanical engineering, opting for the elective of Biomedical Engineering. Coverage of bioinstrumentation, biomaterials and computing for biomedical engineers can meet the needs of the students of Electronic & Communication, Electronic & Instrumenta

  2. Ontology-based Cloud Services Representation

    Directory of Open Access Journals (Sweden)

    Abdullah Ali

    2014-07-01

    Full Text Available The advancement of cloud computing has enabled service providers to provide diversity of cloud services to users with different attributes at a range of costs. Finding the suitable service from the increasing numbers of cloud services that satisfy the user requirements such as performance, cost and security has become a big challenge. The variety on services description none uniformed naming conventions and the heterogeneous types and features of cloud services led to make the cloud service discovery a hard problem. Therefore, an intelligent service discovery system is necessary for searching and retrieving appropriate services accurately and quickly. Many studies have been conducted to discover the cloud services using different techniques, such as ontology model and agents technology. The existing ontology for cloud services does not cover the cloud concepts and it is intended to be used for specific tasks only. This study represents the cloud concepts in a comprehensive way that can be used for cloud services discovery or cloud computing management.

  3. Science Fiction and Ontologies of Leadership

    Directory of Open Access Journals (Sweden)

    Jana Vizmuller-Zocco

    2014-12-01

    Full Text Available The role of leadership in science fiction receives a particular analysis which is based on what can be termed transhumanist novels published in Italy between 2008 and 2013. The main purpose of this study is to answer the following question: What happens to (the nature of leadership in a technologically-driven society? Four novels form the backbone of the description of futuristic leadership. The four conclusions drawn from this analysis regarding the nature of leadership in a technologically-driven society point to a much greater need for leadership studies to pay attention to technological advances (and the philosophical underpinnings of, specifically, transhumanism. The impact of nano-bio-technology affecting the role of leaders, followers, goals, alignment, commitment has ontological repercussions on the manner in which (augmented and unaugmented humans deal with each other. If early augmented humans/cyborgs and any other sentient beings are in fact comparable to Giambattista Vico’s brutes, and if his corsi e ricorsi (ebbs and flows of human history can apply to non-human, sentient beings’ history, then the work is cut out for all disciplines, but especially for those which deal with ontologies of leadership.

  4. Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics.

    Science.gov (United States)

    Percha, Bethany; Altman, Russ B

    2013-01-01

    The biomedical literature presents a uniquely challenging text mining problem. Sentences are long and complex, the subject matter is highly specialized with a distinct vocabulary, and producing annotated training data for this domain is time consuming and expensive. In this environment, unsupervised text mining methods that do not rely on annotated training data are valuable. Here we investigate the use of random indexing, an automated method for producing vector-space semantic representations of words from large, unlabeled corpora, to address the problem of term normalization in sentences describing drugs and genes. We show that random indexing produces similarity scores that capture some of the structure of PHARE, a manually curated ontology of pharmacogenomics concepts. We further show that random indexing can be used to identify likely word candidates for inclusion in the ontology, and can help localize these new labels among classes and roles within the ontology.

  5. Developing ontologies in OWL: An observational study

    OpenAIRE

    Dzbor, Martin; Motta, Enrico; Buil-Aranda, C.; Gómez-Pérez, José Manuel; Görlitz, Olaf; Lewen, Holger

    2006-01-01

    As is known in the human-computer interaction (HCI) domain, interactions involve the user, the technology, and the ways they work together. We expand these notions to human-ontology interaction with the aim to investigate how users interact with the networked ontologies in a realistic ontology lifecycle. In this paper, we describe a user study that we have carried out in order to improve our understanding of the level of support provided by current ontology engineering tools in the context en...

  6. Grouping axioms for more coherent ontology descriptions

    OpenAIRE

    Williams, Sandra; Power, Richard

    2010-01-01

    Ontologies and datasets for the Semantic Web are encoded in OWL formalisms that are not easily comprehended by people. To make ontologies accessible to human domain experts, several research groups have developed ontology verbalisers using Natural Language Generation. In practice ontologies are usually composed of simple axioms, so that realising them separately is relatively easy; there remains however the problem of producing texts that are coherent and efficient. We describe in this paper ...

  7. CHARACTER RECOGNITION APPROACH BASED ON ONTOLOGY

    OpenAIRE

    Hacene Belhadef; Aicha Eutamene; Mohamed Khireddine Kholadi

    2011-01-01

    In this paper, we present a general description of a new character recognition process based on ontology, semantically annotated by a domain expert. Such process is based essentially on a matching step between two ontologies, the first represents a domain ontology, containing the typographical description of different characters represent an alphabet of a well definite language (Latin for example), the second ontology, describes the document in question in the form of concepts where each conc...

  8. Justification Patterns for OWL DL Ontologies

    OpenAIRE

    Nguyen, Tu Anh T.; Power, Richard; Piwek, Paul; Williams, Sandra

    2011-01-01

    For debugging OWL-DL ontologies, natural language explanations of inconsistencies and undesirable entailments are of great help. From such explanations, ontology developers can learn why an ontology gives rise to specific entailments. Unfortunately, commonly used tableaux-based reasoning services do not provide a basis for such explanations, since they rely on a refutation proof strategy and normalising transformations that are difficult for human ontology editors to understand. For this reas...

  9. BAMS Neuroanatomical Ontology: Design and Implementation

    OpenAIRE

    Mihail Bota; Swanson, Larry W.

    2008-01-01

    We describe in this paper the structure and main features of a domain specific ontology for neuroscience, the BAMS Neuroanatomical Ontology. The ontology includes a complete set of concepts that describe the parts of the rat nervous system, a growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts. The ontology is linked with a complex representation of structural and physiological variables used to classify neurons, w...

  10. Domain-Specific Ontology of Botany

    Institute of Scientific and Technical Information of China (English)

    Fang Gu; Cun-Gen Cao; Yue-Fei Sui; Wen Tian

    2004-01-01

    Domain-specific ontologies are greatly useful in knowledge acquisition, sharing and analysis. In this paper, botany-specific ontology for acquiring and analyzing botanical knowledge is presented. The ontology is represented in a set of well-defined categories, and each concept is viewed as an instance of certain category. The authors also introduce botany-specific axioms, an integral part of the ontology, for checking and reasoning with the acquired knowledge. Consistency, completeness and redundancy of the axioms are discussed.

  11. Ontologies used for Competence Management

    Directory of Open Access Journals (Sweden)

    Victoria Iordan

    2008-05-01

    Full Text Available Developing multi-agent systems requires an adequate modeling of knowledge inorder that the agents and the human person are able to understand and accept the conceptsof domain area in the same way. Ontologies allow developing an coherent framework for aspecified domain. Based on the concepts used ant the relations between them, the agentsare able to understand, reason and act in the domain in order to accomplish their goalsand finally the system functions. Based on appropriate ontologies defined for a particulardomain, a multi-agent system that allows managing, searching and matching the usercompetences with the existent competences is presented.

  12. SWRL: Rule Acquisition Using Ontology

    OpenAIRE

    Plinere, D; Borisovs, A

    2009-01-01

    Nowadays rule-based systems are very common. The use of ontology-based systems is becoming ever more popular, especially in addition to the rule-based one. The most widely used ontology development platform is Protégé. Protégé provides a knowledge acquisition tool, but still the main issue of the ontologybased rule system is rule acquisition. This paper presents an approach to using SWRL rules Tab, a plug-in to Protégé, for rule acquisition. SWRL rules Tab transforms conj...

  13. 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

  14. Historical and Conceptual Foundation of Diagrammatical Ontology

    DEFF Research Database (Denmark)

    Øhrstrøm, Peter; Uckelman, Sara L.; Schärfe, Henrik

    2007-01-01

    and philosophical background for Jacob Lorhard’s invention of the word ‘ontology’ as well as the scientific status of ontology in the 16th and 17th century. We also consider the use of Ramean style diagrams and diagrammatic ontology in general. A modern implementation of Lorhard’s ontology is discussed...

  15. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

    Hage, W.R. van; Isaac, A.; Aleksovski, Z.

    2007-01-01

    Ontology matching exists to solve practical problems. Hence, methodologies to find and evaluate solutions for ontology matching should be centered on practical problems. In this paper we propose two statistically-founded evaluation techniques to assess ontology-matching performance that are based on

  16. 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 techniq

  17. Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study

    OpenAIRE

    Moreau, Tristan; Gibaud, Bernard

    2015-01-01

    Different non-invasive neuroimaging modalities and multi-level analysis of human connectomics datasets yield a great amount of heterogeneous data which are hard to integrate into an unified representation. Biomedical ontologies can provide a suitable integrative framework for domain knowledge as well as a tool to facilitate information retrieval, data sharing and data comparisons across scales, modalities and species. Especially, it is urgently needed to fill the gap between neurobiology and ...

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

    Science.gov (United States)

    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.

  19. Visualization and simulation of complex flows in biomedical engineering

    CERN Document Server

    Imai, Yohsuke; Ishikawa, Takuji; Oliveira, Mónica

    2014-01-01

    This book focuses on the most recent advances in the application of visualization and simulation methods to understand the flow behavior of complex fluids used in biomedical engineering and other related fields. It shows the physiological flow behavior in large arteries, microcirculation, respiratory systems and in biomedical microdevices.

  20. Using Ontologies for the E-learning System in Healthcare Human Resources Management

    OpenAIRE

    Lidia BAJENARU; Ana-Maria BOROZAN; Ion SMEUREANU

    2015-01-01

    This paper provides a model for the use of ontology in e-learning systems for structuring educational content in the domain of healthcare human resources management (HHRM) in Romania. In this respect we propose an effective method to improve the learning system by providing personalized learning paths created using ontology and advanced educational strategies to provide a personalized learning content for the medical staff. Personalization of e-learning process for the chosen target group wil...

  1. Biomedical applications engineering tasks

    Science.gov (United States)

    Laenger, C. J., Sr.

    1976-01-01

    The engineering tasks performed in response to needs articulated by clinicians are described. Initial contacts were made with these clinician-technology requestors by the Southwest Research Institute NASA Biomedical Applications Team. The basic purpose of the program was to effectively transfer aerospace technology into functional hardware to solve real biomedical problems.

  2. 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.

  3. An ontological approach to logistics

    NARCIS (Netherlands)

    Daniele, Laura; Ferreira Pires, Luis; Zelm, M.; Sinderen, van M.J.; Doumeingts, G.

    2013-01-01

    In today’s global market, the competitiveness of enterprises is strongly dictated by their ability to collaborate with other enterprises. Ontologies enable common understanding of concepts and have been acknowledged as a powerful means to foster collaboration, both within the boundaries of an indivi

  4. A Mobile Army of Ontologies

    DEFF Research Database (Denmark)

    Juul, Jesper

    2015-01-01

    their cultural position(s). The following scholars have agreed to participate the event: Pawel Grabarczyk (“Games Within Games: How to Properly Individuate Game Modes?”), Stefano Gualeni (“Augmented Ontologies and Games”), Jesper Juul: (“A Mobile Army of Ontologies”), Veli-Matti Karhulahti (“Videogame...

  5. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  6. Towards quantitative measures in applied ontology

    CERN Document Server

    Hoehndorf, Robert; Gkoutos, Georgios V

    2012-01-01

    Applied ontology is a relatively new field which aims to apply theories and methods from diverse disciplines such as philosophy, cognitive science, linguistics and formal logics to perform or improve domain-specific tasks. To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated. We propose that results in applied ontology must be evaluated within their domain of application, based on some ontology-based task within the domain, and discuss quantitative measures which would facilitate the objective evaluation and comparison of research results in applied ontology.

  7. The Evaluation of Ontology Matching versus Text

    OpenAIRE

    Andreea-Diana MIHIS

    2010-01-01

    Lately, the ontologies have become more and more complex, and they are used in different domains. Some of the ontologies are domain independent; some are specific to a domain. In the case of text processing and information retrieval, it is important to identify the corresponding ontology to a specific text. If the ontology is of a great scale, only a part of it may be reflected in the natural language text. This article presents metrics which evaluate the degree in which an ontology matches a...

  8. BAMS neuroanatomical ontology: design and implementation

    Directory of Open Access Journals (Sweden)

    Mihail Bota

    2008-05-01

    Full Text Available We describe in this paper the structure and main features of a domain specific ontology for neuroscience, the BAMS Neuroanatomical Ontology. The ontology includes a complete set of concepts that describe the parts of the rat nervous system, a growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts. The ontology is linked with a complex representation of structural and physiological variables used to classify neurons, which is encoded in BAMS. BAMS Neuroanatomical Ontology is accessible on the web and includes an interface that allows browsing terms, viewing criteria for classification, and accessing associated information.

  9. Engineering β-sheet peptide assemblies for biomedical applications.

    Science.gov (United States)

    Yu, Zhiqiang; Cai, Zheng; Chen, Qiling; Liu, Menghua; Ye, Ling; Ren, Jiaoyan; Liao, Wenzhen; Liu, Shuwen

    2016-03-01

    Hydrogels have been widely studied in various biomedical applications, such as tissue engineering, cell culture, immunotherapy and vaccines, and drug delivery. Peptide-based nanofibers represent a promising new strategy for current drug delivery approaches and cell carriers for tissue engineering. This review focuses on the recent advances in the use of self-assembling engineered β-sheet peptide assemblies for biomedical applications. The applications of peptide nanofibers in biomedical fields, such as drug delivery, tissue engineering, immunotherapy, and vaccines, are highlighted. The current challenges and future perspectives for self-assembling peptide nanofibers in biomedical applications are discussed.

  10. Signal and image analysis for biomedical and life sciences

    CERN Document Server

    Sun, Changming; Pham, Tuan D; Vallotton, Pascal; Wang, Dadong

    2014-01-01

    With an emphasis on applications of computational models for solving modern challenging problems in biomedical and life sciences, this book aims to bring collections of articles from biologists, medical/biomedical and health science researchers together with computational scientists to focus on problems at the frontier of biomedical and life sciences. The goals of this book are to build interactions of scientists across several disciplines and to help industrial users apply advanced computational techniques for solving practical biomedical and life science problems. This book is for users in t

  11. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it\\'s also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  12. Micro and Nano Manipulations for Biomedical Applications

    CERN Document Server

    Yih, Tachung C

    2007-01-01

    Taking bio-device research and development to "the next level," this book covers the latest advances in biomedical microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS). The book presents new developments in the synthesis and use of metallic nanoparticles in bio-sensing and drug delivery, including quantum dots semiconductors nanocrystals.

  13. Ontology-Based Semantic Cache in AOKB

    Institute of Scientific and Technical Information of China (English)

    郑红; 陆汝钤; 金芝; 胡思康

    2002-01-01

    When querying on a large-scale knowledge base, a major technique of im-proving performance is to preload knowledge to minimize the number of roundtrips to theknowledge base. In this paper, an ontology-based semantic cache is proposed for an agentand ontology-oriented knowledge base (AOKB). In AOKB, an ontology is the collection of re-lationships between a group of knowledge units (agents and/or other sub-ontologies). Whenloading some agent A, its relationships with other knowledge units are examined, and thosewho have a tight semantic tie with A will be preloaded at the same time, including agents andsub-ontologies in the same ontology where A is. The preloaded agents and ontologies are savedat a semantic cache located in the memory. Test results show that up to 50% reduction inrunning time is achieved.

  14. Essentials in Ontology Engineering: Methodologies, Languages, and Tools

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; García-Castro, Raúl; Villazón-Terrazas, B.; A. GÓMEZ-PÉREZ

    2011-01-01

    In the beginning of the 90s, ontology development was similar to an art: ontology developers did not have clear guidelines on how to build ontologies but only some design criteria to be followed. Work on principles, methods and methodologies, together with supporting technologies and languages, made ontology development become an engineering discipline, the so-called Ontology Engineering. Ontology Engineering refers to the set of activities that concern the ontology development process and th...

  15. Semantic Cooperation and Knowledge Reuse by Using Autonomous Ontologies

    OpenAIRE

    Zhao, Yuting; Wang, Kewen; Topor, Rodney; Pan, Jeff Z.; Giunchiglia, Fausto

    2007-01-01

    Several proposals have been put forward to support distributed agent cooperation in the SemanticWeb, by allowing concepts and roles in one ontology be reused in another ontology. In general, these proposals reduce the autonomy of each ontology by defining the semantics of the ontology to depend on the semantics of the other ontologies. We propose a new framework for managing autonomy in a set of cooperating ontologies (or ontology space). In this framework, each language entity concept/role/i...

  16. Biomedical engineering: A platform for research and innovation in ultrasound

    Science.gov (United States)

    Holland, Christy K.

    2001-05-01

    An undergraduate or graduate degree in biomedical engineering prepares students to solve problems at the interface between engineering and medicine. Biomedical engineering encompasses evolving areas such as advanced medical imaging for diagnosis and treatment of disease, tissue engineering for designing and manufacturing biological implants for damaged or diseased tissues and organs, and bioinformatics for determining which genes play a major role in health and disease. Biomedical engineering academic programs produce graduates with the ability to pursue successful careers in the biomedical device industry or to obtain advanced degrees leading to careers in biomedical engineering research, medicine, law or business. Biomedical engineering majors take courses in biology, anatomy, physics, chemistry, engineering, mathematics and medical product design and value life-long learning. Students learn to work effectively in interdisciplinary teams comprised of individuals with diverse social, cultural and technical backgrounds. Biomedical engineering is becoming increasingly important in imaging and image-guided research. Some examples of innovative ultrasound technology under development are ultrasound devices to accelerate the dissolution of blood clots, advanced surgical instruments with ultrasound guidance and ultrasound contrast agents for targeted drug delivery. Biomedical engineering is a great career choice for technically minded individuals who endeavor to work on applied problems that are medically relevant.

  17. An ontology for component-based models of water resource systems

    Science.gov (United States)

    Elag, Mostafa; Goodall, Jonathan L.

    2013-08-01

    Component-based modeling is an approach for simulating water resource systems where a model is composed of a set of components, each with a defined modeling objective, interlinked through data exchanges. Component-based modeling frameworks are used within the hydrologic, atmospheric, and earth surface dynamics modeling communities. While these efforts have been advancing, it has become clear that the water resources modeling community in particular, and arguably the larger earth science modeling community as well, faces a challenge of fully and precisely defining the metadata for model components. The lack of a unified framework for model component metadata limits interoperability between modeling communities and the reuse of models across modeling frameworks due to ambiguity about the model and its capabilities. To address this need, we propose an ontology for water resources model components that describes core concepts and relationships using the Web Ontology Language (OWL). The ontology that we present, which is termed the Water Resources Component (WRC) ontology, is meant to serve as a starting point that can be refined over time through engagement by the larger community until a robust knowledge framework for water resource model components is achieved. This paper presents the methodology used to arrive at the WRC ontology, the WRC ontology itself, and examples of how the ontology can aid in component-based water resources modeling by (i) assisting in identifying relevant models, (ii) encouraging proper model coupling, and (iii) facilitating interoperability across earth science modeling frameworks.

  18. 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. PMID:26873781

  19. Handbook of biomedical optics

    CERN Document Server

    Boas, David A

    2011-01-01

    Biomedical optics holds tremendous promise to deliver effective, safe, non- or minimally invasive diagnostics and targeted, customizable therapeutics. Handbook of Biomedical Optics provides an in-depth treatment of the field, including coverage of applications for biomedical research, diagnosis, and therapy. It introduces the theory and fundamentals of each subject, ensuring accessibility to a wide multidisciplinary readership. It also offers a view of the state of the art and discusses advantages and disadvantages of various techniques.Organized into six sections, this handbook: Contains intr

  20. Biomedical Engineering Desk Reference

    CERN Document Server

    Ratner, Buddy D; Schoen, Frederick J; Lemons, Jack E; Dyro, Joseph; Martinsen, Orjan G; Kyle, Richard; Preim, Bernhard; Bartz, Dirk; Grimnes, Sverre; Vallero, Daniel; Semmlow, John; Murray, W Bosseau; Perez, Reinaldo; Bankman, Isaac; Dunn, Stanley; Ikada, Yoshito; Moghe, Prabhas V; Constantinides, Alkis

    2009-01-01

    A one-stop Desk Reference, for Biomedical Engineers involved in the ever expanding and very fast moving area; this is a book that will not gather dust on the shelf. It brings together the essential professional reference content from leading international contributors in the biomedical engineering field. Material covers a broad range of topics including: Biomechanics and Biomaterials; Tissue Engineering; and Biosignal Processing* A hard-working desk reference providing all the essential material needed by biomedical and clinical engineers on a day-to-day basis * Fundamentals, key techniques,

  1. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  2. Powering biomedical devices

    CERN Document Server

    Romero, Edwar

    2013-01-01

    From exoskeletons to neural implants, biomedical devices are no less than life-changing. Compact and constant power sources are necessary to keep these devices running efficiently. Edwar Romero's Powering Biomedical Devices reviews the background, current technologies, and possible future developments of these power sources, examining not only the types of biomedical power sources available (macro, mini, MEMS, and nano), but also what they power (such as prostheses, insulin pumps, and muscular and neural stimulators), and how they work (covering batteries, biofluids, kinetic and ther

  3. Graphene based materials for biomedical applications

    Directory of Open Access Journals (Sweden)

    Yuqi Yang

    2013-10-01

    Full Text Available Graphene, a single layer 2-dimensional structure nanomaterial with unique physicochemical properties (e.g. high surface area, excellent electrical conductivity, strong mechanical strength, unparalleled thermal conductivity, remarkable biocompatibility and ease of functionalization, has received increasing attention in physical, chemical and biomedical fields. This article selectively reviews current advances of graphene based materials for biomedical applications. In particular, graphene based biosensors for small biomolecules (glucose, dopamine etc., proteins and DNA detection have been summarized; graphene based bioimaging, drug delivery, and photothermal therapy applications have been described in detail. Future perspectives and possible challenges in this rapidly developing area are also discussed.

  4. Developing biomedical devices design, innovation and protection

    CERN Document Server

    Andreoni, Giuseppe; Colombo, Barbara

    2013-01-01

    During the past two decades incredible progress has been achieved in the instruments and devices used in the biomedical field. This progress stems from continuous scientific research that has taken advantage of many findings and advances in technology made available by universities and industry. Innovation is the key word, and in this context legal protection and intellectual property rights (IPR) are of crucial importance. This book provides students and practitioners with the fundamentals for designing biomedical devices and explains basic design principles. Furthermore, as an aid to the dev

  5. WEB MINING BASED FRAMEWORK FOR ONTOLOGY LEARNING

    Directory of Open Access Journals (Sweden)

    C.Ramesh

    2015-07-01

    Full Text Available Today, the notion of Semantic Web has emerged as a prominent solution to the problem of organizing the immense information provided by World Wide Web, and its focus on supporting a better co-operation between humans and machines is noteworthy. Ontology forms the major component of Semantic Web in its realization. However, manual method of ontology construction is time-consuming, costly, error-prone and inflexible to change and in addition, it requires a complete participation of knowledge engineer or domain expert. To address this issue, researchers hoped that a semi-automatic or automatic process would result in faster and better ontology construction and enrichment. Ontology learning has become recently a major area of research, whose goal is to facilitate construction of ontologies, which reduces the effort in developing ontology for a new domain. However, there are few research studies that attempt to construct ontology from semi-structured Web pages. In this paper, we present a complete framework for ontology learning that facilitates the semi-automation of constructing and enriching web site ontology from semi structured Web pages. The proposed framework employs Web Content Mining and Web Usage mining in extracting conceptual relationship from Web. The main idea behind this concept was to incorporate the web author's ideas as well as web users’ intentions in the ontology development and its evolution.

  6. Self-organizing ontology of biochemically relevant small molecules

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2012-01-01

    Full Text Available Abstract Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology

  7. Semantics-driven modelling of user preferences for information retrieval in the biomedical domain.

    Science.gov (United States)

    Gladun, Anatoly; Rogushina, Julia; Valencia-García, Rafael; Béjar, Rodrigo Martínez

    2013-03-01

    A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

  8. Jacob's Ladder and Scientific Ontologies

    CERN Document Server

    Stern, Julio Michael

    2013-01-01

    The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget's central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is based on Heinz von Foerster's fundamental metaphor of - objects as tokens for eigen-solutions, and is also supported by formal inference methods of Bayesian statistics. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the definition or identification of chemical elements. Some of von Foerster's epistemological imperatives provide general guidelines of development and argumentation. Keywords: Chemical elements; Cognitive constructivism; Development of cognitive structures; Eigen-solutions; External symbol grounding; Objective knowledge; Ontology alignments; Scientific ontologies.

  9. Sensors for biomedical applications

    NARCIS (Netherlands)

    Bergveld, Piet

    1986-01-01

    This paper considers the impact during the last decade of modern IC technology, microelectronics, thin- and thick-film technology, fibre optic technology, etc. on the development of sensors for biomedical applications.

  10. Geographic Ontologies, Gazetteers and Multilingualism

    OpenAIRE

    Robert Laurini

    2015-01-01

    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 wh...

  11. Social Ontology and Social Cognition

    OpenAIRE

    Lo Presti, Patrizio

    2013-01-01

    The aim of this paper is to show that there is a reciprocal dependency relationship between social cognition and social ontology. It is argued that, on the one hand, the existence conditions of socially meaningful objects and of social groups are about subjects’ social cognitive processes and interactive patterns and, on the other hand, social cognitive processes and interactive patterns are modulated by socially meaningful objects and social groups. I proceed from a historically informed dis...

  12. Biomedical signal processing

    CERN Document Server

    Akay, Metin

    1994-01-01

    Sophisticated techniques for signal processing are now available to the biomedical specialist! Written in an easy-to-read, straightforward style, Biomedical Signal Processing presents techniques to eliminate background noise, enhance signal detection, and analyze computer data, making results easy to comprehend and apply. In addition to examining techniques for electrical signal analysis, filtering, and transforms, the author supplies an extensive appendix with several computer programs that demonstrate techniques presented in the text.

  13. Sharing big biomedical data

    OpenAIRE

    Toga, Arthur W.; Dinov, Ivo D.

    2015-01-01

    Background The promise of Big Biomedical Data may be offset by the enormous challenges in handling, analyzing, and sharing it. In this paper, we provide a framework for developing practical and reasonable data sharing policies that incorporate the sociological, financial, technical and scientific requirements of a sustainable Big Data dependent scientific community. Findings Many biomedical and healthcare studies may be significantly impacted by using large, heterogeneous and incongruent data...

  14. 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.

  15. The relevance of ontological commitments

    CERN Document Server

    Echenique-Robba, Pablo

    2014-01-01

    In this introductory note, I describe my particular view of the notion of ontological commitments as honest and pragmatic working hypotheses that assume the existence (out there) of certain entities represented by the symbols in our theory. I argue that this is not naive, in the sense that it does not entail the belief that the hypotheses could ever be proved to be true (or false), but it is nevertheless justified by the success and predictive power of the theory that contains the concepts assumed to exist. I also claim that the ontological commitments one holds (even if tacitly so) have a great influence on what kind of science is produced, how it is used, and how it is understood. Not only I justify this claim, but I also propose a sketch of a possible falsification of it. As a natural conclusion, I defend the importance of identifying, clarifying and making explicit one's ontological commitments if fruitful scientific discussions are to be had. Finally, I compare my point of view with that of some philosop...

  16. gOntt: a Tool for Scheduling Ontology Development Projects

    OpenAIRE

    A. GÓMEZ-PÉREZ; Suárez-Figueroa, Mari Carmen; Vigo, Martin

    2009-01-01

    The Ontology Engineering field lacks tools that guide ontology developers to plan and schedule their ontology development projects. gOntt helps ontology developers in two ways: (a) to schedule ontology projects; and (b) to execute such projects based on the schedule and using the NeOn Methodology.

  17. A novel approach for connecting temporal-ontologies with blood flow simulations.

    Science.gov (United States)

    Weichert, F; Mertens, C; Walczak, L; Kern-Isberner, G; Wagner, M

    2013-06-01

    In this paper an approach for developing a temporal domain ontology for biomedical simulations is introduced. The ideas are presented in the context of simulations of blood flow in aneurysms using the Lattice Boltzmann Method. The advantages in using ontologies are manyfold: On the one hand, ontologies having been proven to be able to provide medical special knowledge e.g., key parameters for simulations. On the other hand, based on a set of rules and the usage of a reasoner, a system for checking the plausibility as well as tracking the outcome of medical simulations can be constructed. Likewise, results of simulations including data derived from them can be stored and communicated in a way that can be understood by computers. Later on, this set of results can be analyzed. At the same time, the ontologies provide a way to exchange knowledge between researchers. Lastly, this approach can be seen as a black-box abstraction of the internals of the simulation for the biomedical researcher as well. This approach is able to provide the complete parameter sets for simulations, part of the corresponding results and part of their analysis as well as e.g., geometry and boundary conditions. These inputs can be transferred to different simulation methods for comparison. Variations on the provided parameters can be automatically used to drive these simulations. Using a rule base, unphysical inputs or outputs of the simulation can be detected and communicated to the physician in a suitable and familiar way. An example for an instantiation of the blood flow simulation ontology and exemplary rules for plausibility checking are given.

  18. Combining Ontology Development Methodologies and Semantic Web Platforms for E-government Domain Ontology Development

    CERN Document Server

    Dombeu, Jean Vincent Fonou; 10.5121/ijwest.2011.2202

    2011-01-01

    One of the key challenges in electronic government (e-government) is the development of systems that can be easily integrated and interoperated to provide seamless services delivery to citizens. In recent years, Semantic Web technologies based on ontology have emerged as promising solutions to the above engineering problems. However, current research practicing semantic development in e-government does not focus on the application of available methodologies and platforms for developing government domain ontologies. Furthermore, only a few of these researches provide detailed guidelines for developing semantic ontology models from a government service domain. This research presents a case study combining an ontology building methodology and two state-of-the-art Semantic Web platforms namely Protege and Java Jena ontology API for semantic ontology development in e-government. Firstly, a framework adopted from the Uschold and King ontology building methodology is employed to build a domain ontology describing th...

  19. 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......The term 'ontology' has been used in many ways and across different communities. In th following we will introduce ontologies as an explication of some shared vocabulary or conceptualization of a specific subject matter. The main problem with the use of a shared vocabulary according to a specific...... 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...

  20. Context Ontology Implementation for Smart Home

    CERN Document Server

    Van Nguyen, Tam; Nguyen, Huy; Choi, Deokjai; Lee, Chilwoo

    2010-01-01

    Context awareness is one of the important fields in ubiquitous computing. Smart Home, a specific instance of ubiquitous computing, provides every family with opportunities to enjoy the power of hi-tech home living. Discovering that relationship among user, activity and context data in home environment is semantic, therefore, we apply ontology to model these relationships and then reason them as the semantic information. In this paper, we present the realization of smart home's context-aware system based on ontology. We discuss the current challenges in realizing the ontology context base. These challenges can be listed as collecting context information from heterogeneous sources, such as devices, agents, sensors into ontology, ontology management, ontology querying, and the issue related to environment database explosion.

  1. 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.

  2. Manpower development for the biomedical industry space.

    Science.gov (United States)

    Goh, James C H

    2013-01-01

    The Biomedical Sciences (BMS) Cluster is one of four key pillars of the Singapore economy. The Singapore Government has injected research funding for basic and translational research to attract companies to carry out their commercial R&D activities. To further intensify the R&D efforts, the National Research Foundation (NRF) was set up to coordinate the research activities of different agencies within the larger national framework and to fund strategic R&D initiatives. In recent years, funding agencies began to focus on support of translational and clinical research, particularly those with potential for commercialization. Translational research is beginning to have traction, in particular research funding for the development of innovation medical devices. Therefore, the Biomedical Sciences sector is projected to grow which means that there is a need to invest in human capital development to achieve sustainable growth. In support of this, education and training programs to strengthen the manpower capabilities for the Biomedical Sciences industry have been developed. In recent years, undergraduate and graduate degree courses in biomedical engineering/bioengineering have been developing at a rapid rate. The goal is to train students with skills to understand complex issues of biomedicine and to develop and implement of advanced technological applications to these problems. There are a variety of career opportunities open to graduates in biomedical engineering, however regardless of the type of career choices, students must not only focus on achieving good grades. They have to develop their marketability to employers through internships, overseas exchange programs, and involvement in leadership-type activities. Furthermore, curriculum has to be developed with biomedical innovation in mind and ensure relevance to the industry. The objective of this paper is to present the NUS Bioengineering undergraduate program in relation to manpower development for the biomedical

  3. Ontology Design Patterns: Adoption Challenges and Solutions

    OpenAIRE

    Hammar, Karl

    2014-01-01

    Ontology Design Patterns (ODPs) are intended to guide non-experts in performing ontology engineering tasks successfully. While being the topic of significant research efforts, the uptake of these ideas outside the academic community is limited. This paper summarises some issues preventing broader adoption of Ontology Design Patterns among practitioners, suggests research directions that may help overcome these issues, and presents early results of work in these directions.

  4. Ontology Design Patterns: Improving Findability and Composition

    OpenAIRE

    Hammar, Karl

    2014-01-01

    Ontology Design Patterns (ODPs) are intended to guide non-experts in performing ontology engineering tasks successfully. While being the topic of significant research efforts, the uptake of these ideas outside the academic community is limited. This paper summarises issues preventing broader adoption of Ontology Design Patterns among practitioners, with an emphasis on finding and composing such patterns, and presents early results of work aiming to overcome these issues.

  5. An Ontology For Mobile Situation Aware Systems

    OpenAIRE

    Paul F O'Brien

    2008-01-01

    This paper introduces a novel design artefact, namely a generic situation management ontology based on situation theory. This ontology contributes to the foundation knowledge base of mobile service delivery systems for future research and systems design. It demonstrates the applicability, and feasibility of using situation theory in the design of reactive information systems. The support within the ontology for context based filtering for situation detection also contributes to the efficiency...

  6. NOA: a novel Network Ontology Analysis method

    OpenAIRE

    Wang, Jiguang; Huang, Qiang; Liu, Zhi-Ping; Wang, Yong; Wu, Ling-Yun; Chen, Luonan; Zhang, Xiang-Sun

    2011-01-01

    Gene ontology analysis has become a popular and important tool in bioinformatics study, and current ontology analyses are mainly conducted in individual gene or a gene list. However, recent molecular network analysis reveals that the same list of genes with different interactions may perform different functions. Therefore, it is necessary to consider molecular interactions to correctly and specifically annotate biological networks. Here, we propose a novel Network Ontology Analysis (NOA) meth...

  7. Agent-based argumentation for ontology alignments

    OpenAIRE

    Laera, Loredana; Tamma, Valentina; Bench-Capon, Trevor; Euzenat, Jérôme

    2006-01-01

    laera2006a International audience When agents communicate they do not necessarily use the same vocabulary or ontology. For them to interact successfully they must find correspondences between the terms used in their ontologies. While many proposals for matching two agent ontologies have been presented in the literature, the resulting alignment may not be satisfactory to both agents and can become the object of further negotiation between them. This paper describes our work constructing ...

  8. Semantic Plagiarism Detection System Using Ontology Mapping

    Directory of Open Access Journals (Sweden)

    Manjula Shenoy K

    2012-06-01

    Full Text Available Plagiarism detection can play an important role in detecting stealing of original ideas in papers, journals and internet web sites. Checking these manually is simply impossible nowadays due to existence of large digital repository. Ontology is a way of describing documents semantics. Ontology mapping can resolve semantic heterogeneity in documents. Our paper proposes an automatic system for semantic plagiarism detection based on ontology mapping.

  9. A Marketplace for Ontologies and Ontology-Based Tools and Applications in the Life Sciences

    Energy Technology Data Exchange (ETDEWEB)

    McEntire, R; Goble, C; Stevens, R; Neumann, E; Matuszek, P; Critchlow, T; Tarczy-Hornoch, P

    2005-06-30

    This paper describes a strategy for the development of ontologies in the life sciences, tools to support the creation and use of those ontologies, and a framework whereby these ontologies can support the development of commercial applications within the field. At the core of these efforts is the need for an organization that will provide a focus for ontology work that will engage researchers as well as drive forward the commercial aspects of this effort.

  10. Querying Ontology Based Database Using OntoQL (an Ontology Query Language)

    OpenAIRE

    Jean, Stéphane; Aït-Ameur, Yamine; Pierra, Guy

    2006-01-01

    International audience Nowadays, ontologies are used in several research domains by offering the means to describe and represent concepts of information sources. Therefore, several approaches and systems storing ontologies and their instances in the same repository (database) have been proposed. As a consequence, defining a query language to support ontology-based database (OBDB) becomes a challenge for the database community. In this paper, we present OntoQL, an ontology query language fo...

  11. A core ontology of fishery and its use in the fishery ontology service project

    OpenAIRE

    Gangemi, Aldo; Fisseha, Frehiwot; Keizer, Johannes; Lehmann, Jos; Liang, Anita; Pettman, Ian; Sini, Margerita; Taconet, Marc

    2004-01-01

    Ontology creation and document indexing are well-known, critical bottlenecks for integrating semantic services and in general for bootstrapping the Semantic Web. For certain domains or communities, legacy terminologies and indexing methods exist which can be reused effectively. In the Fishery Ontology Project (FOS), we have reengineered and aligned legacy thesauri by using formal ontological methods, and we are deploying the resulting ontology library (currently including more than 35,000 cla...

  12. 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.

  13. Content-Specific Auditing of a Large Scale Anatomy Ontology

    Science.gov (United States)

    Kalet, Ira J.; Mejino, Jose L. V.; Wang, Vania; Whipple, Mark; Brinkley, James F.

    2009-01-01

    Biomedical ontologies are envisioned to be useable in a range of research and clinical applications. The requirements for such uses include formal consistency, adequacy of coverage, and possibly other domain specific constraints. In this report we describe a case study that illustrates how application specific requirements may be used to identify modeling problems as well as data entry errors in ontology building and evolution. We have begun a project to use the UW Foundational Model of Anatomy (FMA) in a clinical application in radiation therapy planning. This application focuses mainly (but not exclusively) on the representation of the lymphatic system in the FMA, in order to predict the spread of tumor cells to regional metastatic sites. This application requires that the downstream relations associated with lymphatic system components must only be to other lymphatic chains or vessels, must be at the appropriate level of granularity, and that every path through the lymphatic system must terminate at one of the two well known trunks of the lymphatic system. It is possible through a programmable query interface to the FMA to write small programs that systematically audit the FMA for compliance with these constraints. We report on the design of some of these programs, and the results we obtained by applying them to the lymphatic system. The algorithms and approach are generalizable to other network organ systems in the FMA such as arteries and veins. In addition to illustrating exact constraint checking methods, this work illustrates how the details of an application may reflect back a requirement to revise the design of the ontology itself. PMID:19248842

  14. INFORMATION SYSTEMS: NEW ONTOLOGIES-BASED SCENARIOS

    Directory of Open Access Journals (Sweden)

    Susana Herrea

    2006-11-01

    Full Text Available While ontology is still a fertile area of research in the field of Philosophy, Ontologies currently stands for research, development, and application fields in disciplines related with computing, information and knowledge. Information Systems (IS are essentially knowledge artifacts that capture and represent knowledge in certain domains. Considering that ontologies is generally used to specify and communicate knowledge in a domain, and the growing recognition that ontological principles and concepts can be fruitfully applied to the IS field, one could say that an IS has its own implicit ontology when attributing meaning to the symbols used. Explicitly, however, ontology may play different roles in an IS. The scenarios presented in this article allow visualizing the roles that ontologies are now playing or will play in the near future in IS. There is a wide range of uses for ontologies in the different scenarios - they vary from the conceptual analysis of IS modeling techniques to their use as support for IS design, development and application. Our knowledge on the roles played by ontologies in IS is expected to be expanded.

  15. Logical Development of the Cell Ontology

    Directory of Open Access Journals (Sweden)

    Blake Judith A

    2011-01-01

    Full Text Available Abstract Background The Cell Ontology (CL is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL. Results Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types. Conclusion Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.

  16. 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…

  17. A Process for Engineer Domain Ontology: An Experience in Developing Business Analysis Ontology

    OpenAIRE

    Atanasova, Irena

    2011-01-01

    During the last years several works have been aimed to improve ontology technological as-pects, like representation language and inference mechanisms. This paper presents a discussion on the process and product of an experience in developing ontology for the public sector whose organization requires a strong knowledge management. This process is applied to engineer and develop ontology for Business analysis domain.

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

    Science.gov (United States)

    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…

  19. Ontology Research and Development. Part 1-A Review of Ontology Generation.

    Science.gov (United States)

    Ding, Ying; Foo, Schubert

    2002-01-01

    Discusses the role of ontology in knowledge representation, including enabling content-based access, interoperability, communications, and new levels of service on the Semantic Web; reviews current ontology generation studies and projects as well as problems facing such research; and discusses ontology mapping, information extraction, natural…

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

    Science.gov (United States)

    d'Aquin, Mathieu; Noy, Natalya F

    2012-03-01

    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.

  1. Membership Function Assignment for Elements of Single OWL Ontology

    OpenAIRE

    Verhodubs, Olegs

    2014-01-01

    This paper develops the idea of membership function assignment for OWL (Web Ontology Language) ontology elements in order to subsequently generate fuzzy rules from this ontology. The task of membership function assignment for OWL ontology elements had already been partially described, but this concerned the case, when several OWL ontologies of the same domain were available, and they were merged into a single ontology. The purpose of this paper is to present the way of membership function ass...

  2. Searching and ranking ontologies on the Semantic Web

    OpenAIRE

    Thomas, Edward; Alani, Harith; Sleeman, Derek; Brewster, Christopher

    2005-01-01

    The number of ontologies available online is increasing constantly. Tools that are capable of searching, retrieving, and ranking ontologies are becoming crucial to facilitate ontology search and reuse. In this document, we describe OntoSearch, which is a tool for capturing and searching ontologies on the Semantic web. We also briefly describe AKTiveRank which is used to rank OWL ontologies based on certain ontology-structure analysis..

  3. Faceted Lightweight Ontologies: a Formalization and some Experiments

    OpenAIRE

    Farazi, Mohammad Shahjahan Feroz

    2010-01-01

    While classifications are heavily used to categorize web content, the evolution of the web foresees a more formal structure -- ontology - which can serve this purpose. Ontologies are core artifacts of the Semantic Web which enable machines to use inference rules to conduct automated reasoning on data. Lightweight ontologies bridge the gap between classifications and ontologies. A lightweight ontology (LO) is an ontology representing a backbone taxonomy where the concept of the child node is m...

  4. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

    Directory of Open Access Journals (Sweden)

    Kim Jung-jae

    2011-10-01

    Full Text Available Abstract Background The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge. Results We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task. Conclusions Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.

  5. Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study

    Directory of Open Access Journals (Sweden)

    Tristan eMoreau

    2015-04-01

    Full Text Available Different non-invasive neuroimaging modalities and multi-level analysis of human connectomics datasets yield a great amount of heterogeneous data which are hard to integrate into an unified representation. Biomedical ontologies can provide a suitable integrative framework for domain knowledge as well as a tool to facilitate information retrieval, data sharing and data comparisons across scales, modalities and species. Especially, it is urgently needed to fill the gap between neurobiology and in vivo human connectomics in order to better take into account the reality highlighted in Magnetic Resonance Imaging (MRI and relate it to existing brain knowledge. The aim of this study was to create a neuroanatomical ontology, called Human Connectomics Ontology (HCO, in order to represent macroscopic gray matter regions connected with fiber bundles assessed by diffusion tractography and to annotate MRI connectomics datasets acquired in the living human brain. First a neuroanatomical view called NEURO-DL-FMA was extracted from the reference ontology Foundational Model of Anatomy (FMA in order to construct a gross anatomy ontology of the brain. HCO extends NEURO-DL-FMA by introducing entities (such as MR_Node and MR_Route and object properties such as tracto_connects pertaining to MR connectivity. The Web Ontology Language Description Logics (OWL DL formalism was used in order to enable reasoning with common reasoning engines. Moreover, an experimental work was achieved in order to demonstrate how the HCO could be effectively used to address complex queries concerning in vivo MRI connectomics datasets. Indeed, neuroimaging datasets of five healthy subjects were annotated with terms of the HCO and a multi-level analysis of the connectivity patterns assessed by diffusion tractography of the right medial Brodmann Area 6 was achieved using a set of queries. This approach can facilitate comparison of data across scales, modalities and species.

  6. Ontology-Driven Information Integration

    Science.gov (United States)

    Tissot, Florence; Menzel, Chris

    2005-01-01

    Ontology-driven information integration (ODII) is a method of computerized, automated sharing of information among specialists who have expertise in different domains and who are members of subdivisions of a large, complex enterprise (e.g., an engineering project, a government agency, or a business). In ODII, one uses rigorous mathematical techniques to develop computational models of engineering and/or business information and processes. These models are then used to develop software tools that support the reliable processing and exchange of information among the subdivisions of this enterprise or between this enterprise and other enterprises.

  7. Concepts, ontologies, and knowledge representation

    CERN Document Server

    Jakus, Grega; Omerovic, Sanida; Tomažic, Sašo

    2013-01-01

    Recording knowledge in a common framework that would make it possible to seamlessly share global knowledge remains an important challenge for researchers. This brief examines several ideas about the representation of knowledge addressing this challenge. A widespread general agreement is followed that states uniform knowledge representation should be achievable by using ontologies populated with concepts. A separate chapter is dedicated to each of the three introduced topics, following a uniform outline: definition, organization, and use. This brief is intended for those who want to get to know

  8. 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.

  9. How do Ontology Mappings Change in the Life Sciences?

    CERN Document Server

    Gross, Anika; Thor, Andreas; Rahm, Erhard

    2012-01-01

    Mappings between related ontologies are increasingly used to support data integration and analysis tasks. Changes in the ontologies also require the adaptation of ontology mappings. So far the evolution of ontology mappings has received little attention albeit ontologies change continuously especially in the life sciences. We therefore analyze how mappings between popular life science ontologies evolve for different match algorithms. We also evaluate which semantic ontology changes primarily affect the mappings. We further investigate alternatives to predict or estimate the degree of future mapping changes based on previous ontology and mapping transitions.

  10. Towards a Formalized Ontology-Based Requirements Model

    Institute of Scientific and Technical Information of China (English)

    JIANG Dan-dong; ZHANG Shen-sheng; WANG Ying-lin

    2005-01-01

    The goal of this paper is to take a further step towards an ontological approach for representing requirements information. The motivation for ontologies was discussed. The definitions of ontology and requirements ontology were given. Then, it presented a collection of informal terms, including four subject areas. It also discussed the formalization process of ontology. The underlying meta-ontology was determined, and the formalized requirements ontology was analyzed. This formal ontology is built to serve as a basis for requirements model. Finally, the implementation of software system was given.

  11. A framework for using reference ontologies as a foundation for the semantic web.

    Science.gov (United States)

    Brinkley, James F; Suciu, Dan; Detwiler, Landon T; Gennari, John H; Rosse, Cornelius

    2006-01-01

    The semantic web is envisioned as an evolving set of local ontologies that are gradually linked together into a global knowledge network. Many such local "application" ontologies are being built, but it is difficult to link them together because of incompatibilities and lack of adherence to ontology standards. "Reference" ontologies are an emerging ontology type that attempt to represent deep knowledge of basic science in a principled way that allows them to be re-used in multiple ways, just as the basic sciences are re-used in clinical applications. As such they have the potential to be a foundation for the semantic web if methods can be developed for deriving application ontologies from them. We describe a computational framework for this purpose that is generalized from the database concept of "views", and describe the research issues that must be solved to implement such a framework. We argue that the development of such a framework is becoming increasingly feasible due to a convergence of advances in several fields.

  12. Constructing a semantic predication gold standard from the biomedical literature

    Directory of Open Access Journals (Sweden)

    Kilicoglu Halil

    2011-12-01

    Full Text Available Abstract Background Semantic relations increasingly underpin biomedical text mining and knowledge discovery applications. The success of such practical applications crucially depends on the quality of extracted relations, which can be assessed against a gold standard reference. Most such references in biomedical text mining focus on narrow subdomains and adopt different semantic representations, rendering them difficult to use for benchmarking independently developed relation extraction systems. In this article, we present a multi-phase gold standard annotation study, in which we annotated 500 sentences randomly selected from MEDLINE abstracts on a wide range of biomedical topics with 1371 semantic predications. The UMLS Metathesaurus served as the main source for conceptual information and the UMLS Semantic Network for relational information. We measured interannotator agreement and analyzed the annotations closely to identify some of the challenges in annotating biomedical text with relations based on an ontology or a terminology. Results We obtain fair to moderate interannotator agreement in the practice phase (0.378-0.475. With improved guidelines and additional semantic equivalence criteria, the agreement increases by 12% (0.415 to 0.536 in the main annotation phase. In addition, we find that agreement increases to 0.688 when the agreement calculation is limited to those predications that are based only on the explicitly provided UMLS concepts and relations. Conclusions While interannotator agreement in the practice phase confirms that conceptual annotation is a challenging task, the increasing agreement in the main annotation phase points out that an acceptable level of agreement can be achieved in multiple iterations, by setting stricter guidelines and establishing semantic equivalence criteria. Mapping text to ontological concepts emerges as the main challenge in conceptual annotation. Annotating predications involving biomolecular

  13. SELECTION OF ONTOLOGY FOR WEB SERVICE DESCRIPTION LANGUAGE TO ONTOLOGY WEB LANGUAGE CONVERSION

    Directory of Open Access Journals (Sweden)

    J. Mannar Mannan

    2014-01-01

    Full Text Available Semantic web is to extend the current human readable web to encoding some of the semantic of resources in a machine processing form. As a Semantic web component, Semantic Web Services (SWS uses a mark-up that makes the data into detailed and sophisticated machine readable way. One such language is Ontology Web Language (OWL. Existing conventional web service annotation can be changed to semantic web service by mapping Web Service Description Language (WSDL with the semantic annotation of OWL-S. In this conversion of WSDL to OWL process, the ontology plays a vital role. Ontology can be stored and retrieved from local repository and selecting the appropriate ontology is a complicated process and this can be achieved by Ontology Searching and Property Matching (OSPM engine. Ontology is stored in the local repository as ontology document and exact matching of ontology for the requested query can be searched using semantic similarity ranking method. High ranked classes of ontology will undergo property matching; here requested concept will be matched with the resulting property. OSPM engine act as the backbone for selecting an exact ontology and reduce the conflict that occurs while selecting the ontology for annotation purpose.

  14. Model driven engineering and ontology development

    CERN Document Server

    Gasevic, Dragan; Devedzic, Vladan; Bézivin, Jean; Selic, Bran

    2009-01-01

    Describes technologies, tools, and standards like XML, RDF, OWL, MDA, and UML. This book describes OMG's ODM (Ontology Definition Metamodel) initiative, a specification which is in the form of an OMG language like UML. It also covers applications and practical aspects of developing ontologies using MDA-based languages.

  15. 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; 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.

  16. 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.

  17. 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.

  18. Ontology Design Patterns as Interfaces (invited)

    Science.gov (United States)

    Janowicz, K.

    2015-12-01

    In recent years ontology design patterns (ODP) have gained popularity among knowledge engineers. ODPs are modular but self-contained building blocks that are reusable and extendible. They minimize the amount of ontological commitments and thereby are easier to integrate than large monolithic ontologies. Typically, patterns are not directly used to annotate data or to model certain domain problems but are combined and extended to form data and purpose-driven local ontologies that serve the needs of specific applications or communities. By relying on a common set of patterns these local ontologies can be aligned to improve interoperability and enable federated queries without enforcing a top-down model of the domain. In previous work, we introduced ontological views as layer on top of ontology design patterns to ease the reuse, combination, and integration of patterns. While the literature distinguishes multiple types of patterns, e.g., content patterns or logical patterns, we propose to use them as interfaces here to guide the development of ontology-driven systems.

  19. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  20. Taking a view on bio-ontologies

    NARCIS (Netherlands)

    S. Jupp; A. Gibson; J. Malone; H. Parkinson; R. Stevens

    2012-01-01

    We present a technique for separating knowledge representation from application specific views that are currently often conflated within bio-ontologies. Many ontologies contain information for two tasks; one to represent the knowledge of some field of interest and another to support an application t

  1. Cell mechanics in biomedical cavitation

    Science.gov (United States)

    Wang, Qianxi; Manmi, Kawa; Liu, Kuo-Kang

    2015-01-01

    Studies on the deformation behaviours of cellular entities, such as coated microbubbles and liposomes subject to a cavitation flow, become increasingly important for the advancement of ultrasonic imaging and drug delivery. Numerical simulations for bubble dynamics of ultrasound contrast agents based on the boundary integral method are presented in this work. The effects of the encapsulating shell are estimated by adapting Hoff's model used for thin-shell contrast agents. The viscosity effects are estimated by including the normal viscous stress in the boundary condition. In parallel, mechanical models of cell membranes and liposomes as well as state-of-the-art techniques for quantitative measurement of viscoelasticity for a single cell or coated microbubbles are reviewed. The future developments regarding modelling and measurement of the material properties of the cellular entities for cutting-edge biomedical applications are also discussed. PMID:26442142

  2. Biomedical Perspective of Electrochemical Nanobiosensor

    Institute of Scientific and Technical Information of China (English)

    Priti Singh; Shailendra Kumar Pandey; Jyoti Singh; Sameer Srivastava; Sadhana Sachan; Sunil Kumar Singh

    2016-01-01

    Electrochemical biosensor holds great promise in the biomedical area due to its enhanced specificity, sensi-tivity, label-free nature and cost effectiveness for rapid point-of-care detection of diseases at bedside. In this review, we are focusing on the working principle of electrochemical biosensor and how it can be employed in detecting biomarkers of fatal diseases like cancer, AIDS, hepatitis and cardiovascular diseases. Recent advances in the development of implantable biosensors and exploration of nanomaterials in fabrication of electrodes with increasing the sensitivity of biosensor for quick and easy detection of biomolecules have been elucidated in detail. Electrochemical-based detection of heavy metal ions which cause harmful effect on human health has been discussed. Key challenges associated with the electrochemical sensor and its future perspectives are also addressed.

  3. Reactive Leadership: Divining, Developing, and Demonstrating Community Ontologies

    Science.gov (United States)

    Graybeal, J.

    2008-12-01

    The Marine Metadata Interoperability Project (known as MMI, on the web at http://marinemetadata.org) was formed to provide leadership in metadata practices to the marine science community. In 2004 this meant finding and writing about resources and best practices, which until then were all but invisible. In 2008 the scope is far wider, encompassing comprehensive guidance, collaborative community environments, and introduction and demonstration of advanced technologies to an increasingly interested scientific domain. MMI's technical leadership, based on experiences gained in the hydrologic community, emphasized the role ontologies could play in marine science. An early MMI workshop successfully incorporated a large number of community vocabularies, tools to harmonize them in a common ontological format, and the mapping of terms from vocabularies expressed in that format. That 2005 workshop demonstrated the connections to be made among different community vocabularies, and was well regarded by participants, but did not lead to widespread adoption of the tools, technologies, or even the vocabularies. Ontology development efforts for marine sensors and platforms showed intermittent progress, but again were not adopted or pushed toward completion. It is now 2008, and the marine community is increasingly attentive to a wide range of interoperability issues. A large part of the community has at least heard of "semantic interoperability", and many understand its critical role in finding and working with data. Demand for specific solutions, and for workable approaches, is becoming more vocal in the marine community. Yet there is still no encompassing model in place for achieving semantic interoperability, only simple operational registries have been set up for oceanographic community vocabularies, and only a few isolated applications demonstrate how semantic barriers can be overcome. Why has progress been so slow? Are good answers on the horizon? And if we build it, will the

  4. 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...... becomes easier with a visual representation. An idea is to use the expressive power that a 3D representation to provide visualization for the user. In this paper we propose a new method for positioning the elements of the visualized concept lattice in the 3D world based on Operations Research (OR) methods...... should be feasible for on-line processing and what-if analysis of ontologies....

  5. 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...... becomes easier with a visual representation. An idea is to use the expressive power that a 3D representation to provide visualization for the user. In this paper we propose a new method for positioning the elements of the visualized concept lattice in the 3D world based on Operations Research (OR) methods...... should be feasible for on-line processing and what-if analysis of ontologies....

  6. Towards an Ontology for Reef Islands

    Science.gov (United States)

    Duce, Stephanie

    Reef islands are complex, dynamic and vulnerable environments with a diverse range of stake holders. Communication and data sharing between these different groups of stake holders is often difficult. An ontology for the reef island domain would improve the understanding of reef island geomorphology and improve communication between stake holders as well as forming a platform from which to move towards interoperability and the application of Information Technology to forecast and monitor these environments. This paper develops a small, prototypical reef island domain ontology, based on informal, natural language relations, aligned to the DOLCE upper-level ontology, for 20 fundamental terms within the domain. A subset of these terms and their relations are discussed in detail. This approach reveals and discusses challenges which must be overcome in the creation of a reef island domain ontology and which could be relevant to other ontologies in dynamic geospatial domains.

  7. An Ontology-Based Collaborative Design System

    Science.gov (United States)

    Su, Tieming; Qiu, Xinpeng; Yu, Yunlong

    A collaborative design system architecture based on ontology is proposed. In the architecture, OWL is used to construct global shared ontology and local ontology; both of them are machine-interpretable. The former provides a semantic basis for the communication among designers so as to make the designers share the common understanding of knowledge. The latter which describes knowledge of designer’s own is the basis of design by reasoning. SWRL rule base comprising rules defined based on local ontology is constructed to enhance the reasoning capability of local knowledge base. The designers can complete collaborative design at a higher level based on the local knowledge base and the global shared ontology, which enhances the intelligence of design. Finally, a collaborative design case is presented and analyzed.

  8. 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....

  9. A Category Theoretic Model of RDF Ontology

    Directory of Open Access Journals (Sweden)

    S. Aliyu

    2015-07-01

    Full Text Available Ontology languages are used in modelling the semantics of concepts within a particular domain and the relationships between those concepts. The Semantic Web standard provides a number of modelling languages that differ in their level of expressivity and are organized in a Semantic Web Stack in such a way that each language level builds on the expressivity of the other. There are several problems when one attempts to use independently developed ontologies. When existing ontologies are adapted for new purposes it requires that certain operations are performed on them. These operations are currently performed in a semi-automated manner. This paper seeks to model categorically the syntax and semantics of RDF ontology as a step towards the formalization of ontological operations using category theory.

  10. [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. PMID:22921289

  11. FROG - Fingerprinting Genomic Variation Ontology.

    Directory of Open Access Journals (Sweden)

    E Abinaya

    Full Text Available Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies. FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  12. Ontological Representation of Academic Programs

    Directory of Open Access Journals (Sweden)

    Richard Hackelbusch

    2006-10-01

    Full Text Available Using legal terminology, academic institutions release teaching and examination regulations to form the statutory framework of academic programs. This terminology is one reason why students often do not know how to satisfy the program requirements laid down by the corresponding institutions. This can result in needlessly long study times. Frequent changes of those regulations and parallel valid different regulations forming the statutory framework of programs leading to the same degrees may aggravate those problems. Furthermore, academic boards have to supply an amount of courses which fits the students’ actual demand. This is a difficult task because there is only little information available for forecasting. In this paper, we present an ontology to handle these problems. It allows semantic representations of examination regulations and academic programs. Based upon this ontology, decision support systems can be implemented which can help students to decide how to satisfy the corresponding program regulations or which can help academic boards to forecast the students’ demand on certain courses.

  13. FROG - Fingerprinting Genomic Variation Ontology.

    Science.gov (United States)

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  14. An Ontology-Driven Method for Hierarchical Mining of Temporal Patterns: Application to HIV Drug Resistance Research

    OpenAIRE

    Raj, Rashmi; O’Connor, Martin J.; Das, Amar K.

    2007-01-01

    Many biomedical research databases contain time-oriented data resulting from longitudinal, time-series and time-dependent study designs, knowledge of which is not handled explicitly by most data-analytic methods. To make use of such knowledge about research data, we have developed an ontology-driven temporal mining method, called ChronoMiner. Most mining algorithms require data be inputted in a single table. ChronoMiner, in contrast, can search for interesting temporal patterns among multiple...

  15. The Development Process of the Semantic Web and Web Ontology

    Directory of Open Access Journals (Sweden)

    K.Vanitha

    2011-08-01

    Full Text Available This paper deals with the semantic web and web ontology. The existing ontology development processes are not catered towards casual web ontology development, a notion analogous to standard web page development. Ontologies have become common on the World-Wide Web[2]. Key features of this process include easy and rapid creation of ontological skeletons, searching and linking to existing ontologies and a natural language-based technique to improve presentation of ontologies[6]. Ontologies, however, vary greatly in size, scope and semantics. They can range from generic upper-level ontologies to domain-specific schemas. The success of the Semantic Web is based on the existance of numerous distributed ontologies, using which users can annotate their data, thereby enabling shared machine readable content. This paper elaborates the stages in a casual ontology development process.

  16. Geo-Ontologies Are Scale Dependent

    Science.gov (United States)

    Frank, A. U.

    2009-04-01

    Philosophers aim at a single ontology that describes "how the world is"; for information systems we aim only at ontologies that describe a conceptualization of reality (Guarino 1995; Gruber 2005). A conceptualization of the world implies a spatial and temporal scale: what are the phenomena, the objects and the speed of their change? Few articles (Reitsma et al. 2003) seem to address that an ontology is scale specific (but many articles indicate that ontologies are scale-free in another sense namely that they are scale free in the link densities between concepts). The scale in the conceptualization can be linked to the observation process. The extent of the support of the physical observation instrument and the sampling theorem indicate what level of detail we find in a dataset. These rules apply for remote sensing or sensor networks alike. An ontology of observations must include scale or level of detail, and concepts derived from observations should carry this relation forward. A simple example: in high resolution remote sensing image agricultural plots and roads between them are shown, at lower resolution, only the plots and not the roads are visible. This gives two ontologies, one with plots and roads, the other with plots only. Note that a neighborhood relation in the two different ontologies also yield different results. References Gruber, T. (2005). "TagOntology - a way to agree on the semantics of tagging data." Retrieved October 29, 2005., from http://tomgruber.org/writing/tagontology-tagcapm-talk.pdf. Guarino, N. (1995). "Formal Ontology, Conceptual Analysis and Knowledge Representation." International Journal of Human and Computer Studies. Special Issue on Formal Ontology, Conceptual Analysis and Knowledge Representation, edited by N. Guarino and R. Poli 43(5/6). Reitsma, F. and T. Bittner (2003). Process, Hierarchy, and Scale. Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information ScienceInternational Conference

  17. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  18. Integrated nanobiosensor technology for biomedical application

    OpenAIRE

    Choi, Chulhee

    2012-01-01

    Chulhee Choi1,21Department of Bio and Brain Engineering, 2Graduate School of Medical Science and Engineering, 3KI for the BioCentury 4Optical Bioimaging Center, KAIST, Daejeon, Republic of KoreaAbstract: Advances in nanotechnology have led to the development of nanoscale biosensors that have exquisite sensitivity and versatility. The biomedical application of nanobiosensors is wide; moreover, the future impact of nanobiosensor systems for point-of-care diagnostics will be unmatched. The ultim...

  19. [Big data, medical language and biomedical terminology systems].

    Science.gov (United States)

    Schulz, Stefan; López-García, Pablo

    2015-08-01

    A variety of rich terminology systems, such as thesauri, classifications, nomenclatures and ontologies support information and knowledge processing in health care and biomedical research. Nevertheless, human language, manifested as individually written texts, persists as the primary carrier of information, in the description of disease courses or treatment episodes in electronic medical records, and in the description of biomedical research in scientific publications. In the context of the discussion about big data in biomedicine, we hypothesize that the abstraction of the individuality of natural language utterances into structured and semantically normalized information facilitates the use of statistical data analytics to distil new knowledge out of textual data from biomedical research and clinical routine. Computerized human language technologies are constantly evolving and are increasingly ready to annotate narratives with codes from biomedical terminology. However, this depends heavily on linguistic and terminological resources. The creation and maintenance of such resources is labor-intensive. Nevertheless, it is sensible to assume that big data methods can be used to support this process. Examples include the learning of hierarchical relationships, the grouping of synonymous terms into concepts and the disambiguation of homonyms. Although clear evidence is still lacking, the combination of natural language technologies, semantic resources, and big data analytics is promising. PMID:26077872

  20. Semantator: semantic annotator for converting biomedical text to linked data.

    Science.gov (United States)

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

    2013-10-01

    More than 80% of biomedical data is embedded in plain text. The unstructured nature of these text-based documents makes it challenging to easily browse and query the data of interest in them. One approach to facilitate browsing and querying biomedical text is to convert the plain text to a linked web of data, i.e., converting data originally in free text to structured formats with defined meta-level semantics. In this paper, we introduce Semantator (Semantic Annotator), a semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through Semantator, information of interest can be either annotated manually or semi-automatically using plug-in information extraction tools. The annotated results will be stored in RDF and can be queried using the SPARQL query language. In addition, semantic reasoners can be directly applied to the annotated data for consistency checking and knowledge inference. Semantator has been released online and was used by the biomedical ontology community who provided positive feedbacks. Our evaluation results indicated that (1) Semantator can perform the annotation functionalities as designed; (2) Semantator can be adopted in real applications in clinical and transactional research; and (3) the annotated results using Semantator can be easily used in Semantic-web-based reasoning tools for further inference.

  1. Biomedical Engineering in Modern Society

    Science.gov (United States)

    Attinger, E. O.

    1971-01-01

    Considers definition of biomedical engineering (BME) and how biomedical engineers should be trained. State of the art descriptions of BME and BME education are followed by a brief look at the future of BME. (TS)

  2. 基于叙词表的海洋领域本体构建研究%Thesaurus-based Ontological Construction Using Ocean Domain Ontology

    Institute of Scientific and Technical Information of China (English)

    周军根; 刘柏嵩

    2012-01-01

    With a view of better conduct ocean management, this paper applies some concepts in ontology to the ocean management area, and explores the methods for ontological establishment. From the ocean status in quo and based on the existing "Ocean Thesaurus", the ontology construction method is proposed. Under the guidance of the introduced method the ocean domain ontology is constructed for ocean management. This ontology solves effectively the coordination and information sharing for different administrative departments and advances the ocean management techniques.%为有效地进行海洋管理,将本体思想引入该领域,研究构建了海洋领域本体.从海洋领域的实际情况入手,并在专家构建的《海洋主题词表》的基础上,提出一种基于叙词表的本体构建方法.在此方法的指导下,构建了海洋领域本体.该本体能效解决我国各部门协调和信息共享问题,促进我国海洋信息管理的发展.

  3. Biomedical applications of photochemistry

    OpenAIRE

    Chan, BP

    2010-01-01

    Photochemistry is the study of photochemical reactions between light and molecules. Recently, there have been increasing interests in using photochemical reactions in the fields of biomaterials and tissue engineering. This work revisits the components and mechanisms of photochemistry and reviews biomedical applications of photochemistry in various disciplines, including oncology, molecular biology, and biosurgery, with particular emphasis on tissue engineering. Finally, potential toxicities a...

  4. Anatomy for Biomedical Engineers

    Science.gov (United States)

    Carmichael, Stephen W.; Robb, Richard A.

    2008-01-01

    There is a perceived need for anatomy instruction for graduate students enrolled in a biomedical engineering program. This appeared especially important for students interested in and using medical images. These students typically did not have a strong background in biology. The authors arranged for students to dissect regions of the body that…

  5. Implantable CMOS Biomedical Devices

    Directory of Open Access Journals (Sweden)

    Toshihiko Noda

    2009-11-01

    Full Text Available The results of recent research on our implantable CMOS biomedical devices are reviewed. Topics include retinal prosthesis devices and deep-brain implantation devices for small animals. Fundamental device structures and characteristics as well as in vivo experiments are presented.

  6. Bevalac biomedical facility

    International Nuclear Information System (INIS)

    This paper describes the physical layout of the Bevalac Facility and the research programs carried out at the facility. Beam time on the Bevalac is divided between two disciplines: one-third for biomedical research and two-thirds for nuclear science studies. The remainder of the paper discusses the beam delivery system including dosimetry, beam sharing and beam scanning

  7. Biomedical applications in EELA.

    Science.gov (United States)

    Cardenas, Miguel; Hernández, Vicente; Mayo, Rafael; Blanquer, Ignacio; Perez-Griffo, Javier; Isea, Raul; Nuñez, Luis; Mora, Henry Ricardo; Fernández, Manuel

    2006-01-01

    The current demand for Grid Infrastructures to bring collabarating groups between Latina America and Europe has created the EELA proyect. This e-infrastructure is used by Biomedical groups in Latina America and Europe for the studies of ocnological analisis, neglected diseases, sequence alignments and computation plygonetics. PMID:16823158

  8. Biomedical technology prosperity game{trademark}

    Energy Technology Data Exchange (ETDEWEB)

    Berman, M.; Boyack, K.W.; Wesenberg, D.L.

    1996-07-01

    Prosperity Games{trademark} are an outgrowth and adaptation of move/countermove and seminar War Games. Prosperity Games{trademark} are simulations that explore complex issues in a variety of areas including economics, politics, sociology, environment, education and research. These issues can be examined from a variety of perspectives ranging from a global, macroeconomic and geopolitical viewpoint down to the details of customer/supplier/market interactions in specific industries. All Prosperity Games{trademark} are unique in that both the game format and the player contributions vary from game to game. This report documents the Biomedical Technology Prosperity Game{trademark} conducted under the sponsorship of Sandia National Laboratories, the Defense Advanced Research Projects Agency, and the Koop Foundation, Inc. Players were drawn from all stakeholders involved in biomedical technologies including patients, hospitals, doctors, insurance companies, legislators, suppliers/manufacturers, regulators, funding organizations, universities/laboratories, and the legal profession. The primary objectives of this game were to: (1) Identify advanced/critical technology issues that affect the cost and quality of health care. (2) Explore the development, patenting, manufacturing and licensing of needed technologies that would decrease costs while maintaining or improving quality. (3) Identify policy and regulatory changes that would reduce costs and improve quality and timeliness of health care delivery. (4) Identify and apply existing resources and facilities to develop and implement improved technologies and policies. (5) Begin to develop Biomedical Technology Roadmaps for industry and government cooperation. The deliberations and recommendations of these players provided valuable insights as to the views of this diverse group of decision makers concerning biomedical issues. Significant progress was made in the roadmapping of key areas in the biomedical technology field.

  9. A new gene ontology-based measure for the functional similarity of gene products

    Institute of Scientific and Technical Information of China (English)

    QI Guo-long; QIAN Shi-yu; FANG Ji-qian

    2013-01-01

    Background Although biomedical ontologies have standardized the representation of gene products across species and databases,a method for determining the functional similarities of gene products has not yet been developed.Methods We proposed a new semantic similarity measure based on Gene Ontology that considers the semantic influences from all of the ancestor terms in a graph.Our measure was compared with Resnik's measure in two applications,which were based on the association of the measure used with the gene co-expression and the proteinprotein interactions.Results The results showed a considerable association between the semantic similarity and the expression correlation and between the semantic similarity and the protein-protein interactions,and our measure performed the best overall.Conclusion These results revealed the potential value of our newly proposed semantic similarity measure in studying the functional relevance of gene products.

  10. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  11. Anthropological Component of Descartes’ Ontology

    Directory of Open Access Journals (Sweden)

    Anatolii M. Malivskyi

    2014-06-01

    Full Text Available The purpose of the article is to outline and comprehend the Descartes’ theory about anthropological component of ontology as the most important part of his philosophy. The accomplishment of this purpose covers the successive solution of the following tasks: 1 review of the research literature concerning the problem of human’s presence and the individual nature of truth; 2 emphasize the ambivalence of the basic intention of his legacy; 3 justify the thesis about constitutivity of human’s presence and comprehend passions as the form of disclosure of ontology’s anthropological component. Methodology. The use of the euristic potential of phenomenology, postpositivism and postmodernism makes it possible to emphasize the multiple-layer and multiple-meaning classical philosophy works, to comprehend the limitation and scarcity of the naïve-enlightening vision of human nature and to look for a new reception of European classics that provides the overcoming of established nihilism and pessimism concerning the interpretation of human nature. Scientific novelty. It is the first time that anthropological component of Descartes’ ontology became an object of particular attention. It previously lacked attention because of following main reasons: 1 traditional underestimating of the fact of Descartes’ legacy incompleteness as an unrealized anthropological project and 2 lack of proper attention to the individual nature of truth. The premise for its constructive overcoming is the attention to ambivalence of the basic intention and the significance of ethics in the philosopher’s legacy. His texts and research literature allow confirming the constitutive nature of human’s presence and passions as the key form of disclosure of the ontology anthropological component. Conclusions. The established tradition of interpretation the Descartes’ philosophizing nature as the filiation process of impersonal knowledge loses its cogency these days. The

  12. DermO; an ontology for the description of dermatologic disease

    KAUST Repository

    Fisher, Hannah M.

    2016-06-13

    Background There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working terminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. Results We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. Conclusions DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domains.

  13. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotate...

  14. Vattimo and the Possibilities of Nihilistic Ontology

    Directory of Open Access Journals (Sweden)

    Myroslav Feodosijevič Hryschko

    2010-04-01

    Full Text Available Gianni Vattimo’s “nihilistic ontology” is immediately distinguished by its resolute anti-metaphysics. Thus, instead of what Vattimo construes as the definitive tropes of metaphysics, i.e., temporal permanence, necessity, foundationalism, etc., the possibility of nihilistic ontology must maintain a critical exigency regarding these tropes. According to this imperative, Vattimo seeks to equate nihilistic ontology with a hermeneutic ontology. This text examines this equation, attempting to separate the continuity between nihilism and hermeneutics, according to the latter’s commitment to a variation of anthropocentrism evinced in concepts such as the effectivity of the particular content of a history, which in turn belies a nihilism that has posited history and man as contingent. Rather, what is at stake in a nihilistic ontology, consistent with Vattimo’s reading, is a radically minimal ontology dedicated to the contingency of Being itself, thus excising the privileged ontological status of man that characterizes the hermeneutic ontology, a privileging analogous to the very metaphysical foundationalism that nihilism is to obviate.

  15. CiTO, the Citation Typing Ontology

    Directory of Open Access Journals (Sweden)

    Shotton David

    2010-06-01

    Full Text Available Abstract CiTO, the Citation Typing Ontology, is an ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its publication and peer review status. This paper describes CiTO and illustrates its usefulness both for the annotation of bibliographic reference lists and for the visualization of citation networks. The latest version of CiTO, which this paper describes, is CiTO Version 1.6, published on 19 March 2010. CiTO is written in the Web Ontology Language OWL, uses the namespace http://purl.org/net/cito/, and is available from http://purl.org/net/cito/. This site uses content negotiation to deliver to the user an OWLDoc Web version of the ontology if accessed via a Web browser, or the OWL ontology itself if accessed from an ontology management tool such as Protégé 4 (http://protege.stanford.edu/. Collaborative work is currently under way to harmonize CiTO with other ontologies describing bibliographies and the rhetorical structure of scientific discourse.

  16. SEMANTIC INTEGRATION FOR AUTOMATIC ONTOLOGY MAPPING

    Directory of Open Access Journals (Sweden)

    Siham AMROUCH

    2013-11-01

    Full Text Available In the last decade, ontologies have played a key technology role for information sharing and agents interoperability in different application domains. In semantic web domain, ontologies are efficiently used to face the great challenge of representing the semantics of data, in order to bring the actual web to its full power and hence, achieve its objective. However, using ontologies as common and shared vocabularies requires a certain degree of interoperability between them. To confront this requirement, mapping ontologies is a solution that is not to be avoided. In deed, ontology mapping build a meta layer that allows different applications and information systems to access and share their informations, of course, after resolving the different forms of syntactic, semantic and lexical mismatches. In the contribution presented in this paper, we have integrated the semantic aspect based on an external lexical resource, wordNet, to design a new algorithm for fully automatic ontology mapping. This fully automatic character features the main difference of our contribution with regards to the most of the existing semi-automatic algorithms of ontology mapping, such as Chimaera, Prompt, Onion, Glue, etc. To better enhance the performances of our algorithm, the mapping discovery stage is based on the combination of two sub-modules. The former analysis the concept’s names and the later analysis their properties. Each one of these two sub-modules is it self based on the combination of lexical and semantic similarity measures.

  17. 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,…

  18. 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.

  19. The Usability-Error Ontology

    DEFF Research Database (Denmark)

    Elkin, Peter L.; Beuscart-zephir, Marie-Catherine; Pelayo, Sylvia;

    2013-01-01

    will grow over time to support an increasing number of HIT system types. In this manuscript, we present this Ontology of Usability Error Types and specifically address Computerized Physician Order Entry (CPOE), Electronic Health Records (EHR) and Revenue Cycle HIT systems.......Clinical Systems have become standard partners with clinicians in the care of patients. As these systems become integral parts of the clinical workflow, they have the potential to help improve patient outcomes, however they have also in some cases have led to adverse events and has resulted...... in patients coming to harm. Often the root cause analysis of these adverse events can be traced back to Usability Errors in the Health Information Technology (HIT) or its interaction with users. Interoperability of the documentation of HIT related Usability Errors in a consistent fashion can improve our...

  20. Biomedical signals, imaging, and informatics

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Signals, Imaging, and Informatics, the third volume of the handbook, presents material from respected scientists with diverse backgrounds in biosignal processing, medical imaging, infrared imaging, and medical informatics.More than three dozen specific topics are examined, including biomedical s

  1. Oceanographic ontology-based spatial knowledge query

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The construction of oceanographic ontologies is fundamental to the "digital ocean". Therefore, on the basis of introduction of new concept of oceanographic ontology, an oceanographic ontology-based spatial knowledge query (OOBSKQ) method was proposed and developed. Because the method uses a natural language to describe query conditions and the query result is highly integrated knowledge,it can provide users with direct answers while hiding the complicated computation and reasoning processes, and achieves intelligent,automatic oceanographic spatial information query on the level of knowledge and semantics. A case study of resource and environmental application in bay has shown the implementation process of the method and its feasibility and usefulness.

  2. DOMAIN ONTOLOGY DEVELOPMENT FOR COMMUNICABLE DISEASES

    Directory of Open Access Journals (Sweden)

    Iti Mathur

    2013-02-01

    Full Text Available Web has become the very first resource to search for any kind of information. With the emergence of semantic web, our search queries have started generating more informed results. Ontologies are at the core of any semantic web application. They help in rapid development of distributed systems by providing information on the fly. This key feature of distribution and sharing of information has made ontologies as a new knowledge representation mechanism. A mechanism which is strongly backed by a sound inference system. In this paper, we shall discuss the development, verification and validation of an ontology in a health domain.

  3. 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.

  4. 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...... and evolution. In this paper, we present a product line based reuseoriented ontology development methodology which integrates ontology development with design by reuse and design for reuse. The basic building block in our approach is the meta-ontology. In the first stage, reengineering of existing ontologies...... 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...

  5. Ontology Evaluation:Consideration of Criteria, Approaches and Layers

    Directory of Open Access Journals (Sweden)

    Akram Fathian Dastgerdi

    2012-03-01

    Full Text Available Ontology is commonly used as a structure capturing knowledge about a certain area via providing relevant concepts and relations between them. Nowadays, because of the increase in designing ontologies in different domains, it is important to describe some criteria for selecting the most appropriate ontology. The purpose of this paper is to discuss the ontology evaluation criteria, approaches and layers. At first, different evaluation stages in ontology evaluation were explained. Then the most important approaches to ontology evaluation were described: included gold standard, task-based, data-driven and criteria based evaluation. Another part of this paper was about ontology evaluation criteria such as those mentioned by experts of ontology domain as well as the criteria that proposed by US National Center for ontological Research. Lastly, the levels of ontology evaluation, involved lexical, vocabulary, or data layer, hierarchy or taxonomy layer, other semantic relations layer, context or application level, syntactic level, structure, architecture and design layer were characterized.

  6. Optical Polarizationin Biomedical Applications

    CERN Document Server

    Tuchin, Valery V; Zimnyakov, Dmitry A

    2006-01-01

    Optical Polarization in Biomedical Applications introduces key developments in optical polarization methods for quantitative studies of tissues, while presenting the theory of polarization transfer in a random medium as a basis for the quantitative description of polarized light interaction with tissues. This theory uses the modified transfer equation for Stokes parameters and predicts the polarization structure of multiple scattered optical fields. The backscattering polarization matrices (Jones matrix and Mueller matrix) important for noninvasive medical diagnostic are introduced. The text also describes a number of diagnostic techniques such as CW polarization imaging and spectroscopy, polarization microscopy and cytometry. As a new tool for medical diagnosis, optical coherent polarization tomography is analyzed. The monograph also covers a range of biomedical applications, among them cataract and glaucoma diagnostics, glucose sensing, and the detection of bacteria.

  7. Toxicology of Biomedical Polymers

    Directory of Open Access Journals (Sweden)

    P. V. Vedanarayanan

    1987-04-01

    Full Text Available This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasised since in our country, at present, there are no regulations covering the manufacturing and marketing of medical devices. Finally the question of the general and subtle long term systemic toxicity of biomedical polymers have been brought to attention with the suggestion that this question needs to be resolved permanently by appropriate studies.

  8. Ontology enrichment by discovering multi-relational association rules from ontological knowledge bases

    OpenAIRE

    d'Amato, Claudia; Staab, Steffen; Tettamanzi, Andrea G. B.; Van Minh, Tran; Gandon, Fabien

    2016-01-01

    International audience In the Semantic Web context, OWL ontologies represent the con-ceptualization of domains of interest while the corresponding as-sertional knowledge is given by the heterogeneous Web resources referring to them. Being strongly decoupled, ontologies and assertion can be out-of-sync. An ontology can be incomplete, noisy and sometimes inconsistent with regard to the actual usage of its conceptual vocabulary in the assertions. Data mining can support the discovery of hidde...

  9. A Process for Engineer Domain Ontology: An Experience in Developing Business Analysis Ontology

    Directory of Open Access Journals (Sweden)

    Irena ATANASOVA

    2011-01-01

    Full Text Available During the last years several works have been aimed to improve ontology technological as-pects, like representation language and inference mechanisms. This paper presents a discussion on the process and product of an experience in developing ontology for the public sector whose organization requires a strong knowledge management. This process is applied to engineer and develop ontology for Business analysis domain.

  10. 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.

  11. Multilingual Biomedical Dictionary

    OpenAIRE

    Daumke, Philipp; Markó, Kornél; Poprat, Michael; Schulz, Stefan

    2005-01-01

    We present a unique technique to create a multilingual biomedical dictionary, based on a methodology called Morpho-Semantic indexing. Our approach closes a gap caused by the absence of free available multilingual medical dictionaries and the lack of accuracy of non-medical electronic translation tools. We first explain the underlying technology followed by a description of the dictionary interface, which makes use of a multilingual subword thesaurus and of statistical inform...

  12. Multilingual biomedical dictionary.

    Science.gov (United States)

    Daumke, Philipp; Markó, Kornél; Poprat, Michael; Schulz, Stefan

    2005-01-01

    We present a unique technique to create a multilingual biomedical dictionary, based on a methodology called Morpho-Semantic indexing. Our approach closes a gap caused by the absence of free available multilingual medical dictionaries and the lack of accuracy of non-medical electronic translation tools. We first explain the underlying technology followed by a description of the dictionary interface, which makes use of a multilingual subword thesaurus and of statistical information from a domain-specific, multilingual corpus.

  13. Toxicology of Biomedical Polymers

    OpenAIRE

    P. V. Vedanarayanan; A. C. Fernandez

    1987-01-01

    This paper deals with the various types of polymers, used in the fabrication of medical devices, their diversity of applications and toxic hazards which may arise out of their application. The potential toxicity of monomers and the various additives used in the manufacture of biomedical polymers have been discussed along with hazards which may arise out of processing of devices such as sterilization. The importance of quality control and stringent toxicity evaluation methods have been emphasi...

  14. EmotionsOnto: an ontology for developing affective applications

    OpenAIRE

    López Gil, Juan Miguel; García González, Roberto; Gil Iranzo, Rosa María; Collazos Ordóñez, César A.

    2014-01-01

    EmotionsOnto is a generic ontology for describing emotions and their detection and expression systems taking contextual and multimodal elements into account. The ontology is proposed as a way to develop an easily computerizable and flexible formal model. Moreover, it is based on the Web Ontology Language (OWL) standard, which also makes ontologies easily shareable and extensible. Once formalized as an ontology, the knowledge about emotions can be used in order to make computers more personali...

  15. Towards an Ontology based integrated Framework for Semantic Web

    OpenAIRE

    Ibrahim, Nora Y.; Mokhtar, Sahar A.; Harb, Hany M.

    2013-01-01

    This Ontologies are widely used as a means for solving the information heterogeneity problems on the web because of their capability to provide explicit meaning to the information. They become an efficient tool for knowledge representation in a structured manner. There is always more than one ontology for the same domain. Furthermore, there is no standard method for building ontologies, and there are many ontology building tools using different ontology languages. Because of these reasons, in...

  16. LabelTranslator: A Tool to Automatically Localize an Ontology

    OpenAIRE

    Espinoza, M; A. GÓMEZ-PÉREZ; E. Mena

    2008-01-01

    This demo proposal briefly presents LabelTranslator, a system that suggests translations of ontology labels, with the purpose of localizing ontologies. LabelTranslator takes as input an ontology whose labels are described in a source natural language and obtains the most probable translation of each ontology label into a target natural language.Our main contribution is the automatization of this process, which reduces human efforts to localize manually the ontology.

  17. Generating Natural Language Explanations For Entailments In Ontologies

    OpenAIRE

    Nguyen, Tu

    2013-01-01

    Building an error-free and high-quality ontology in OWL (Web Ontology Language)---the latest standard ontology language endorsed by the World Wide Web Consortium---is not an easy task for domain experts, who usually have limited knowledge of OWL and logic. One sign of an erroneous ontology is the occurrence of undesired inferences (or entailments), often caused by interactions among (apparently innocuous) axioms within the ontology. This suggests the need for a tool that allows developers to ...

  18. Towards an Upper-Level Ontology for Molecular Biology

    OpenAIRE

    Schulz, Stefan; Beisswanger, Elena; Wermter, Joachim; Hahn, Udo

    2006-01-01

    There is a growing need for the general-purpose description of the basic ontological entities in the life sciences domain. Up until now, upper-level models are mainly purpose-driven, such as the GENIA ontology, originally devised as a vocabulary for corpus annotation. As an alternative, we here present BioTop, a description-logic-based top-level ontology for molecular biology, as an ontologically more conscious re-design of the GENIA ontology.

  19. 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 ...... 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....

  20. Usage of the Jess Engine, Rules and Ontology to Query a Relational Database

    Science.gov (United States)

    Bak, Jaroslaw; Jedrzejek, Czeslaw; Falkowski, Maciej

    We present a prototypical implementation of a library tool, the Semantic Data Library (SDL), which integrates the Jess (Java Expert System Shell) engine, rules and ontology to query a relational database. The tool extends functionalities of previous OWL2Jess with SWRL implementations and takes full advantage of the Jess engine, by separating forward and backward reasoning. The optimization of integration of all these technologies is an advancement over previous tools. We discuss the complexity of the query algorithm. As a demonstration of capability of the SDL library, we execute queries using crime ontology which is being developed in the Polish PPBW project.

  1. Aproximaciones a la ontología del arte (Approaches to the Ontology of Art)

    OpenAIRE

    Vélez León, Paulo

    2006-01-01

    El presenta trabajo describe y caracteriza de manera breve y concisa lo que podría ser una ontología del arte. En la primera sección se presentan las dificultades actuales, así como las nociones y preguntas principales de la ontología. En la sección segunda, en base de los aportes del NCOR, se bosqueja las definiciones y caracterizaciones actuales de la ontología, se hace especial hincapié, en la ontología aplicada. En la tercera y cuarta sección se caracteriza y configura lo que podría...

  2. User centered and ontology based information retrieval system for life sciences

    Directory of Open Access Journals (Sweden)

    Sy Mohameth-François

    2012-01-01

    Full Text Available Abstract Background Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. Results This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. Conclusions The ontology based information retrieval system described in this paper (OBIRS is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens

  3. Gene-based and semantic structure of the Gene Ontology as a complex network

    Science.gov (United States)

    Coronnello, Claudia; Tumminello, Michele; Miccichè, Salvatore

    2016-09-01

    The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The Gene Ontology (GO) is constantly evolving over time. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. Here we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium. Moreover, the GO is a natural example of bipartite network of terms and genes. Here we are interested in studying the properties of the projected network of terms, i.e. a gene-based weighted network of GO terms, in which a link between any two terms is set if at least one gene is annotated in both terms. One aim of the present paper is to compare the structural properties of the semantic and the gene-based network. The relative importance of terms is very similar in the two networks, but the community structure changes. We show that in some cases GO terms that appear to be distinct from a semantic point of view are instead connected, and appear in the same community when considering their gene content. The identification of such gene-based communities of terms might therefore be the basis of a simple protocol aiming at improving the semantic structure of GO. Information about terms that share large gene content might also be important from a biomedical point of view, as it might reveal how genes over-expressed in a certain term also affect other biological processes, molecular functions and cellular components not directly linked according to GO semantics.

  4. Computable visually observed phenotype ontological framework for plants

    Directory of Open Access Journals (Sweden)

    Schaeffer Mary

    2011-06-01

    Full Text Available Abstract Background The ability to search for and precisely compare similar phenotypic appearances within and across species has vast potential in plant science and genetic research. The difficulty in doing so lies in the fact that many visual phenotypic data, especially visually observed phenotypes that often times cannot be directly measured quantitatively, are in the form of text annotations, and these descriptions are plagued by semantic ambiguity, heterogeneity, and low granularity. Though several bio-ontologies have been developed to standardize phenotypic (and genotypic information and permit comparisons across species, these semantic issues persist and prevent precise analysis and retrieval of information. A framework suitable for the modeling and analysis of precise computable representations of such phenotypic appearances is needed. Results We have developed a new framework called the Computable Visually Observed Phenotype Ontological Framework for plants. This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in a machine-interpretable form. This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery. The framework was applied to two different plant species with semantic rules mined and an ontology constructed. Rule quality was evaluated and showed high quality rules for most semantics. This framework also facilitates automatic annotation of phenotype images and can be adopted by different plant communities to aid in their research. Conclusions The Computable Visually Observed Phenotype Ontological Framework for plants has been developed for more efficient and accurate management of visually observed phenotypes, which play a significant role in plant genomics research. The

  5. 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

  6. 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.

  7. 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...

  8. How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

    Science.gov (United States)

    Krallinger, Martin; Leitner, Florian; Vazquez, Miguel; Salgado, David; Marcelle, Christophe; Tyers, Mike; Valencia, Alfonso; Chatr-aryamontri, Andrew

    2012-01-01

    There is an increasing interest in developing ontologies and controlled vocabularies to improve the efficiency and consistency of manual literature curation, to enable more formal biocuration workflow results and ultimately to improve analysis of biological data. Two ontologies that have been successfully used for this purpose are the Gene Ontology (GO) for annotating aspects of gene products and the Molecular Interaction ontology (PSI-MI) used by databases that archive protein-protein interactions. The examination of protein interactions has proven to be extremely promising for the understanding of cellular processes. Manual mapping of information from the biomedical literature to bio-ontology terms is one of the most challenging components in the curation pipeline. It requires that expert curators interpret the natural language descriptions contained in articles and infer their semantic equivalents in the ontology (controlled vocabulary). Since manual curation is a time-consuming process, there is strong motivation to implement text-mining techniques to automatically extract annotations from free text. A range of text mining strategies has been devised to assist in the automated extraction of biological data. These strategies either recognize technical terms used recurrently in the literature and propose them as candidates for inclusion in ontologies, or retrieve passages that serve as evidential support for annotating an ontology term, e.g. from the PSI-MI or GO controlled vocabularies. Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information Extraction Systems in Biology) challenge. Special emphasis is given to protein-protein interaction data and PSI-MI terms referring to interaction detection methods.

  9. GFVO: the Genomic Feature and Variation Ontology.

    Science.gov (United States)

    Baran, Joachim; Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

    2015-01-01

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology's GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  10. Topological Properties in Ontology-based Applications

    OpenAIRE

    Serrano, Miguel Á.; Gómez Romero, Juan; Patricio Guisado, Miguel Ángel; García, Jesús; Molina, José M.

    2011-01-01

    Proceedings of: 11th International Conference on Intelligent Systems Design and Applications, Córdoba, Spain, 22 – 24 November, 2011. Representation and reasoning with spatial properties is essential in several application domains where ontologies are being successfully applied; e.g., Information Fusion systems. This requires a full characterization of the semantics of relations such as adjacent, included, overlapping, etc. Nevertheless, ontologies are not expressive enough to direct...

  11. Sustainability economics, ontology and the capability approach

    OpenAIRE

    Martins, Nuno O.

    2011-01-01

    Copyright © 2011 Elsevier B.V. All rights reserved. The relationship between sustainability economics and the capability approach has recently been explored. Here I shall discuss this relationship, and argue that a study of the ontology underlying the capability approach can help us to see more clearly the interconnections between sustainability economics and the capability approach. In particular, the interpretations of the capability approach as an ontological exercise, which have recent...

  12. A HUMAN RESOURCE ONTOLOGY FOR RECRUITMENT PROCESS

    OpenAIRE

    Ionela MANIU; George MANIU

    2009-01-01

    In this paper we propose a model of ontology for the human resource domain. We emphasize the benefits resulting from the application of Semantic Web technologies in the recruitment process. We use currently available standards and classifications to develop a human resource ontology which gives us means for semantic annotation of job postings and applications. Furthermore, we outline the process of semantic matching which improves the quality of query results. Finally, we propose the architec...

  13. Making methodology a matter of process ontology

    DEFF Research Database (Denmark)

    Revsbæk, Line

    2016-01-01

    This paper presents a practice of doing qualitative interview analysis from the insights of the process ontology in G. H. Mead’s Philosophy of the Present (1932). The paper presents two cases of analyzing in the present while listening to recorded interview material eliciting researcher’s case...... study and otherwise related experiences creating case narratives inclusive of researcher’s reflexive voice. The paper presents an auto-ethnographic approach to data analysis based on process theory ontology....

  14. Ontological Groundwork for Hermeneutics: Heidegger and Gadamer

    OpenAIRE

    Zehragül Aşkın; Hüseyin Çellik

    2015-01-01

    Heidegger transformed Schleiermacher and Dielthey’s hermeneutic approaches epistemological and procedural implications on an ontological basis and in Time and Being by using “hermeneutic cycle” he have brought a thinking experience in to hermeneutics. Heideggerian pretense claims that understanding has an ontological not epistemological basis. This claim had a broad repercussion in Gadamer who have brought his thesis about universality of hermeneutics in philosophy. Heidegger and Gadamer’s im...

  15. Ontological Supply Chain Management: Concepts, Applications, Extensions

    OpenAIRE

    Ilter, H. Kemal

    2013-01-01

    SCOM: Multi-Layer Ontological Model for Supply Chain Systems© aims to create a model for tracking and tracing products, agents, flows and operations of a supply chain with an upper ontology.  It will hopefully let us to track or trace most properties in not-usual supply chains such as interstellar supply chains (eg. raw materials from the planet Mars), health-related supply chains (eg. blood products), food management (eg. genetic structures of agricultural products), envir...

  16. Integrating Ontology into Semantic File Systems

    OpenAIRE

    Ngo, Ba-Hung; Bac, Christian; SILBER-CHAUSSUMIER, Frédérique

    2007-01-01

    Semantic file systems enhance standard file systems with the ability of file searching based on file semantics. In this paper, we propose to integrate the support for ontologies into a file system to build efficient semantic file systems whose file semantics can be shared between users, applications and semantic file systems themselves. We call it ontology-based file system. We identify three existing types of file semantics: property-based, content-based and context-based semantics and adopt...

  17. Energy Ontologies: Wind, Biomass, and Fossil Transportation

    OpenAIRE

    Heidi Scott

    2016-01-01

    This article uses literary sources to draw ontological distinctions among three distinct energy sources: wind power, biomass, and fossil fuels. The primary aim is to demonstrate how radically our fossil fuel regime has changed human ontology in the last two centuries during which we have entered the Anthropocene. Because this radical transformation contains myriad elements, this article will focus on transportation: the speed, quality, and quantity of travel permitted by successive energy sou...

  18. Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL

    OpenAIRE

    Aranguren Mikel; Bechhofer Sean; Lord Phillip; Sattler Ulrike; Stevens Robert

    2007-01-01

    Abstract The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a...

  19. Microposts Ontology Construction Via Concept Extraction

    Directory of Open Access Journals (Sweden)

    Beenu Yadav

    2012-08-01

    Full Text Available The social networking website Facebook offers to its users a feature called “status updates” (or just “status”, which allows users to create Microposts directed to all their contacts, or a subset thereof. Readers can respond to Microposts, or in addition to that also click a “Like” button to show their appreciation for a certain Micropost. Adding semantic meaning in the sense of unambiguous intended ideas to such Microposts. We can make a start towards semantic web by adding semantic annotation to web resources. Ontology are used to specify meaning of annotations. Ontology provide a vocabulary for representing and communicating knowledge about some topic and a set of semantic relationships that hold among the terms in that vocabulary. For increasing the efficiency of ontology based application there is a need to develop a mechanism that reduces the manual work in developing ontology. In this paper, we proposed Microposts’ ontology construction. In this paper we present a method that extracts meaningfulknowledge from microposts shared in social platforms. This process involves different steps for the analysis of such microposts (extraction of keywords, named entities and their matching to ontological concepts.

  20. Ontological Modeling for Integrated Spacecraft Analysis

    Science.gov (United States)

    Wicks, Erica

    2011-01-01

    Current spacecraft work as a cooperative group of a number of subsystems. Each of these requiresmodeling software for development, testing, and prediction. It is the goal of my team to create anoverarching software architecture called the Integrated Spacecraft Analysis (ISCA) to aid in deploying the discrete subsystems' models. Such a plan has been attempted in the past, and has failed due to the excessive scope of the project. Our goal in this version of ISCA is to use new resources to reduce the scope of the project, including using ontological models to help link the internal interfaces of subsystems' models with the ISCA architecture.I have created an ontology of functions specific to the modeling system of the navigation system of a spacecraft. The resulting ontology not only links, at an architectural level, language specificinstantiations of the modeling system's code, but also is web-viewable and can act as a documentation standard. This ontology is proof of the concept that ontological modeling can aid in the integration necessary for ISCA to work, and can act as the prototype for future ISCA ontologies.

  1. An Approach to Support Collaborative Ontology Construction.

    Science.gov (United States)

    Tahar, Kais; Schaaf, Michael; Jahn, Franziska; Kücherer, Christian; Paech, Barbara; Herre, Heinrich; Winter, Alfred

    2016-01-01

    The increasing number of terms used in textbooks for information management (IM) in hospitals makes it difficult for medical informatics students to grasp IM concepts and their interrelations. Formal ontologies which comprehend and represent the essential content of textbooks can facilitate the learning process in IM education. The manual construction of such ontologies is time-consuming and thus very expensive [3]. Moreover, most domain experts lack skills in using a formal language like OWL [2] and usually have no experience with standard editing tools like Protégé http://protege.stanford.edu [4,5]. This paper presents an ontology modeling approach based on Excel2OWL, a self-developed tool which efficiently supports domain experts in collaboratively constructing ontologies from textbooks. This approach was applied to classic IM textbooks, resulting in an ontology called SNIK. Our method facilitates the collaboration between domain experts and ontologists in the development process. Furthermore, the proposed approach enables ontologists to detect modeling errors and also to evaluate and improve the quality of the resulting ontology rapidly. This approach allows us to visualize the modeled textbooks and to analyze their semantics automatically. Hence, it can be used for e-learning purposes, particularly in the field of IM in hospitals. PMID:27577406

  2. An Approach to Support Collaborative Ontology Construction.

    Science.gov (United States)

    Tahar, Kais; Schaaf, Michael; Jahn, Franziska; Kücherer, Christian; Paech, Barbara; Herre, Heinrich; Winter, Alfred

    2016-01-01

    The increasing number of terms used in textbooks for information management (IM) in hospitals makes it difficult for medical informatics students to grasp IM concepts and their interrelations. Formal ontologies which comprehend and represent the essential content of textbooks can facilitate the learning process in IM education. The manual construction of such ontologies is time-consuming and thus very expensive [3]. Moreover, most domain experts lack skills in using a formal language like OWL [2] and usually have no experience with standard editing tools like Protégé http://protege.stanford.edu [4,5]. This paper presents an ontology modeling approach based on Excel2OWL, a self-developed tool which efficiently supports domain experts in collaboratively constructing ontologies from textbooks. This approach was applied to classic IM textbooks, resulting in an ontology called SNIK. Our method facilitates the collaboration between domain experts and ontologists in the development process. Furthermore, the proposed approach enables ontologists to detect modeling errors and also to evaluate and improve the quality of the resulting ontology rapidly. This approach allows us to visualize the modeled textbooks and to analyze their semantics automatically. Hence, it can be used for e-learning purposes, particularly in the field of IM in hospitals.

  3. Ontology Based Feature Driven Development Life Cycle

    Directory of Open Access Journals (Sweden)

    Farheen Siddiqui

    2012-01-01

    Full Text Available The upcoming technology support for semantic web promises fresh directions for Software Engineering community. Also semantic web has its roots in knowledge engineering that provoke software engineers to look for application of ontology applications throughout the Software Engineering lifecycle. The internal components of a semantic web are "light weight", and may be of less quality standards than the externally visible modules. In fact the internal components are generated from external (ontological component. That's the reason agile development approaches such as feature driven development are suitable for applications internal component development. As yet there is no particular procedure that describes the role of ontology in FDD processes. Therefore we propose an ontology based feature driven development for semantic web application that can be used form application model development to feature design and implementation. Features are precisely defined in the OWL-based domain model. Transition from OWL based domain model to feature list is directly defined in transformation rules. On the other hand the ontology based overall model can be easily validated through automated tools. Advantages of ontology-based feature Driven development are also discussed.

  4. 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.

  5. A Conceptual Model for Ontology Based Learning

    Directory of Open Access Journals (Sweden)

    Touraj Banirostam

    2012-11-01

    Full Text Available Utilizing learning features by many fields like education, artificial intelligence, and multi-agent systems, leads to generation of various definitions for this concept. In this article, these field’s significant definitions for learning will be presented, and their key concepts in each field will be described. Using the mentioned features in different learning definitions, ontology will get presented for the concept of learning. In the ontology, the main ontological concepts and their relations have been represented. Also a conceptual model for learning based on presented ontology will be proposed by means of model and modeling description. Then concepts of presented definitions are going to be shown in proposed model and after that, the model’s functionality will be discuss. Twelve main characteristics have been used to describe the proposed model’s functionality. Utilizing learning ontology to improve the proposed conceptual model can be used also as a guide to model learning and also can be useful in different learning models’ comparison. So that the key concepts which can be used for considered learning model will be determined. Furthermore, an example based on proposed ontology and definition features is explained.

  6. Biomedical applications of dipeptides and tripeptides.

    Science.gov (United States)

    Santos, Sara; Torcato, Inês; Castanho, Miguel A R B

    2012-01-01

    Peptides regulate many physiological processes, acting at some sites as endocrine or paracrine signals and at others as neurotransmitters or growth factors, for instance. These molecules represent a major evolution in medical and industrial fields, as it is becoming mandatory to design and exploit molecules that do not necessarily fit the description of classical drug classes. The list of peptides with potential biomedical applications is huge and is growing each year. These biomedical applications range from uses as drugs to flavor-active peptides as ingredients in natural health products, nutraceuticals and functional foods. Among the peptide family, dipeptides and tripeptides are very appealing for drug discovery and development because of their cost-effectiveness, possibility of oral administration, and simplicity to perform molecular structural and quantitative structure-activity studies. Our objective is to review different actual and future uses of dipeptides and tripeptides as well as the major advances and obstacles in this growing area. PMID:23193593

  7. Construction of an annotated corpus to support biomedical information extraction

    Directory of Open Access Journals (Sweden)

    McNaught John

    2009-10-01

    Full Text Available Abstract Background Information Extraction (IE is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC, consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining. Initial experiments have also shown that the corpus may

  8. Using Ontologies for the E-learning System in Healthcare Human Resources Management

    Directory of Open Access Journals (Sweden)

    Lidia BAJENARU

    2015-01-01

    Full Text Available This paper provides a model for the use of ontology in e-learning systems for structuring educational content in the domain of healthcare human resources management (HHRM in Romania. In this respect we propose an effective method to improve the learning system by providing personalized learning paths created using ontology and advanced educational strategies to provide a personalized learning content for the medical staff. Personalization of e-learning process for the chosen target group will be achieved by setting up learning path for each user according to his profile. This will become possible using: domain ontology, learning objects, modeling student knowledge. Developing an ontology-based system for competence management allows complex interactions, providing intelligent interfacing. This is a new approach for the healthcare system managers in permanent training based on e-learning technologies and specific ontologies in a complex area that needs urgent modernization and efficiency to meet the public health economic, social and political context of Romania.

  9. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach.

    Science.gov (United States)

    Imam, Fahim T; Larson, Stephen D; Bandrowski, Anita; Grethe, Jeffery S; Gupta, Amarnath; Martone, Maryann E

    2012-01-01

    An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships. The knowledge models defined in the NIFSTD ontologies enable an effective concept-based search over heterogeneous types of web-accessible information entities in NIF's production system. NIFSTD covers major domains in neuroscience, including diseases, brain anatomy, cell types, sub-cellular anatomy, small molecules, techniques, and resource descriptors. Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. We present here on the structure, design principles, community engagement, and the current state of NIFSTD ontologies.

  10. Biological and Biomedical Coatings Handbook Processing and Characterization

    CERN Document Server

    Zhang, Sam

    2011-01-01

    Written in a versatile, contemporary style that will benefit both novice and expert alike, Biological and Biomedical Coatings Handbook, Two-Volume Set covers the state of the art in the development and implementation of advanced thin films and coatings in the biological field. Consisting of two volumes--Processing and Characterization and Applications--this handbook details the latest understanding of advances in the design and performance of biological and biomedical coatings, covering a vast array of material types, including bio-ceramics, polymers, glass, chitosan, and nanomaterials. Contri

  11. Rank Based Clustering For Document Retrieval From Biomedical Databases

    Directory of Open Access Journals (Sweden)

    Jayanthi Manicassamy

    2009-09-01

    Full Text Available Now a day's, search engines are been most widely used for extracting information's from various resources throughout the world. Where, majority of searches lies in the field of biomedical for retrieving related documents from various biomedical databases. Currently search engines lacks in document clustering and representing relativeness level of documents extracted from the databases. In order to overcome these pitfalls a text based search engine have been developed for retrieving documents from Medline and PubMed biomedical databases. The search engine has incorporated page ranking bases clustering concept which automatically represents relativeness on clustering bases. Apart from this graph tree construction is made for representing the level of relatedness of the documents that are networked together. This advance functionality incorporation for biomedical document based search engine found to provide better results in reviewing related documents based on relativeness.

  12. 安全本体研究进展%Research Progress in Security Ontology

    Institute of Scientific and Technical Information of China (English)

    高建波; 张保稳; 陈晓桦

    2012-01-01

    Ontology is applied in various domains,including intelligence system, computer sciences,information technology, and biomedical sciences et al. The analysis of ontology becomes the core of knowledge representation system in different domains. At the same time the study of ontology facilitates knowledge sharing and reuse. Applying ontology in information security makes security ontology (SO). This paper mainly described the following aspects of SO: present and history of SO,principle,method,and meanings of building SO, existing SO and its categories, dedcription language and application of SO. Then according to above analysis, this article concluded its structural system,depicted knowledge representation and reasoning ability of SO,and pointed out there is a long way to go in building of SO,ontology evaluation, ontology learning,and application of SO.%本体概念已经被广泛地应用到人工智能系统、计算机科学、信息技术、生物医学等众多学科领域.对不同领域的本体分析构成了该领域知识表示体系的核心,同时本体研究促进了知识的共享和重用.将本体的概念应用在信息安全领域就形成了安全本体.主要从以下几个方面描述了安全本体:安全本体研究的现状及发展过程,构建安全本体的原则、方法和意义,现有的安全本体及分类,安全本体的描述语言,安全本体的应用.接着依据对现有的安全本体及其应用的分析,总结了安全本体的结构体系,描述了安全本体的知识表示及推理能力,并指出在构建安全本体、本体评估、本体学习和安全本体的应用等方面依然有待完善.

  13. Ontological Matchmaking in Recommender Systems

    CERN Document Server

    Bonifati, Angela; Sileo, Domenica; Summa, Gianvito

    2010-01-01

    The electronic marketplace offers great potential for the recommendation of supplies. In the so called recommender systems, it is crucial to apply matchmaking strategies that faithfully satisfy the predicates specified in the demand, and take into account as much as possible the user preferences. We focus on real-life ontology-driven matchmaking scenarios and identify a number of challenges, being inspired by such scenarios. A key challenge is that of presenting the results to the users in an understandable and clear-cut fashion in order to facilitate the analysis of the results. Indeed, such scenarios evoke the opportunity to rank and group the results according to specific criteria. A further challenge consists of presenting the results to the user in an asynchronous fashion, i.e. the 'push' mode, along with the 'pull' mode, in which the user explicitly issues a query, and displays the results. Moreover, an important issue to consider in real-life cases is the possibility of submitting a query to multiple p...

  14. BIMS: Biomedical Information Management System

    OpenAIRE

    Mora, Oscar; Bisbal, Jesús

    2013-01-01

    In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research projects. The main goal is to facilitate the clinicians' job in data entry, and researcher's tasks in data management, in high data quality biomedical research projects. The BIMS architecture has been designed following the two-level modeling paradigm, a promising...

  15. Principles of Biomedical Engineering

    CERN Document Server

    Madihally, Sundararajan V

    2010-01-01

    Describing the role of engineering in medicine today, this comprehensive volume covers a wide range of the most important topics in this burgeoning field. Supported with over 145 illustrations, the book discusses bioelectrical systems, mechanical analysis of biological tissues and organs, biomaterial selection, compartmental modeling, and biomedical instrumentation. Moreover, you find a thorough treatment of the concept of using living cells in various therapeutics and diagnostics.Structured as a complete text for students with some engineering background, the book also makes a valuable refere

  16. Statistics in biomedical research

    Directory of Open Access Journals (Sweden)

    González-Manteiga, Wenceslao

    2007-06-01

    Full Text Available The discipline of biostatistics is nowadays a fundamental scientific component of biomedical, public health and health services research. Traditional and emerging areas of application include clinical trials research, observational studies, physiology, imaging, and genomics. The present article reviews the current situation of biostatistics, considering the statistical methods traditionally used in biomedical research, as well as the ongoing development of new methods in response to the new problems arising in medicine. Clearly, the successful application of statistics in biomedical research requires appropriate training of biostatisticians. This training should aim to give due consideration to emerging new areas of statistics, while at the same time retaining full coverage of the fundamentals of statistical theory and methodology. In addition, it is important that students of biostatistics receive formal training in relevant biomedical disciplines, such as epidemiology, clinical trials, molecular biology, genetics, and neuroscience.La Bioestadística es hoy en día una componente científica fundamental de la investigación en Biomedicina, salud pública y servicios de salud. Las áreas tradicionales y emergentes de aplicación incluyen ensayos clínicos, estudios observacionales, fisología, imágenes, y genómica. Este artículo repasa la situación actual de la Bioestadística, considerando los métodos estadísticos usados tradicionalmente en investigación biomédica, así como los recientes desarrollos de nuevos métodos, para dar respuesta a los nuevos problemas que surgen en Medicina. Obviamente, la aplicación fructífera de la estadística en investigación biomédica exige una formación adecuada de los bioestadísticos, formación que debería tener en cuenta las áreas emergentes en estadística, cubriendo al mismo tiempo los fundamentos de la teoría estadística y su metodología. Es importante, además, que los estudiantes de

  17. Biomedical Sensors and Instruments

    CERN Document Server

    Tagawa, Tatsuo

    2011-01-01

    The living body is a difficult object to measure: accurate measurements of physiological signals require sensors and instruments capable of high specificity and selectivity that do not interfere with the systems under study. As a result, detailed knowledge of sensor and instrument properties is required to be able to select the "best" sensor from one of the many designed to meet these challenges. From the underlying principles to practical applications, this updated edition of Biomedical Sensors and Instruments provides an easy-to-understand introduction to the various kinds of biome

  18. Biomedical photonics handbook

    CERN Document Server

    Vo-Dinh, Tuan

    2003-01-01

    1.Biomedical Photonics: A Revolution at the Interface of Science and Technology, T. Vo-DinhPHOTONICS AND TISSUE OPTICS2.Optical Properties of Tissues, J. Mobley and T. Vo-Dinh3.Light-Tissue Interactions, V.V. Tuchin 4.Theoretical Models and Algorithms in Optical Diffusion Tomography, S.J. Norton and T. Vo-DinhPHOTONIC DEVICES5.Laser Light in Biomedicine and the Life Sciences: From the Present to the Future, V.S. Letokhov6.Basic Instrumentation in Photonics, T. Vo-Dinh7.Optical Fibers and Waveguides for Medical Applications, I. Gannot and

  19. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

    Biomedical Signals and Systems is meant to accompany a one-semester undergraduate signals and systems course. It may also serve as a quick-start for graduate students or faculty interested in how signals and systems techniques can be applied to living systems. The biological nature of the examples allows for systems thinking to be applied to electrical, mechanical, fluid, chemical, thermal and even optical systems. Each chapter focuses on a topic from classic signals and systems theory: System block diagrams, mathematical models, transforms, stability, feedback, system response, control, time

  20. 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...