WorldWideScience

Sample records for life science ontologies

  1. OBML - Ontologies in Biomedicine and Life Sciences.

    Science.gov (United States)

    Herre, Heinrich; Hoehndorf, Robert; Kelso, Janet; Loebe, Frank; Schulz, Stefan

    2011-08-09

    The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2nd in a series of meetings organized by the Working Group "Ontologies in Biomedicine and Life Sciences" of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences - from public health to clinical care and molecular biology - is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation.The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue.An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology

  2. 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.

  3. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    Science.gov (United States)

    2011-01-01

    Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA. Conclusions GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches. PMID:21914205

  4. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    Directory of Open Access Journals (Sweden)

    Kirsten Toralf

    2011-09-01

    Full Text Available Abstract Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA. Conclusions GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.

  5. GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

    OpenAIRE

    Kirsten Toralf; Gross Anika; Hartung Michael; Rahm Erhard

    2011-01-01

    Abstract Background Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. Results We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and ...

  6. COnto-Diff: generation of complex evolution mappings for life science ontologies.

    Science.gov (United States)

    Hartung, Michael; Groß, Anika; Rahm, Erhard

    2013-02-01

    Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Sample ontology, GOstat and ontology term enrichment Data detail Data name Sample on...tology, GOstat and ontology term enrichment DOI 10.18908/lsdba.nbdc01389-006.V002 Version V2 10.18908/lsdba....t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

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

    OpenAIRE

    2012-01-01

    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. H...

  9. Recognizing lexical and semantic change patterns in evolving life science ontologies to inform mapping adaptation.

    Science.gov (United States)

    Dos Reis, Julio Cesar; Dinh, Duy; Da Silveira, Marcos; Pruski, Cédric; Reynaud-Delaître, Chantal

    2015-03-01

    Mappings established between life science ontologies require significant efforts to maintain them up to date due to the size and frequent evolution of these ontologies. In consequence, automatic methods for applying modifications on mappings are highly demanded. The accuracy of such methods relies on the available description about the evolution of ontologies, especially regarding concepts involved in mappings. However, from one ontology version to another, a further understanding of ontology changes relevant for supporting mapping adaptation is typically lacking. This research work defines a set of change patterns at the level of concept attributes, and proposes original methods to automatically recognize instances of these patterns based on the similarity between attributes denoting the evolving concepts. This investigation evaluates the benefits of the proposed methods and the influence of the recognized change patterns to select the strategies for mapping adaptation. The summary of the findings is as follows: (1) the Precision (>60%) and Recall (>35%) achieved by comparing manually identified change patterns with the automatic ones; (2) a set of potential impact of recognized change patterns on the way mappings is adapted. We found that the detected correlations cover ∼66% of the mapping adaptation actions with a positive impact; and (3) the influence of the similarity coefficient calculated between concept attributes on the performance of the recognition algorithms. The experimental evaluations conducted with real life science ontologies showed the effectiveness of our approach to accurately characterize ontology evolution at the level of concept attributes. This investigation confirmed the relevance of the proposed change patterns to support decisions on mapping adaptation. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. 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

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

    Lifescience Database Archive (English)

    Full Text Available ng environment for metagenome analyses. ontology/mdbv/mdbv.rdf A vocabulary for describing data schema in Mi...crobial phenotypes. ontology/mccv/mccv.ttl Structured controlled vocabulary for d.... ontology/insdc/nucleotide.ttl A vocabulary for describing metadata of INSDC entries. About This Database D

  12. A cognitive science perspective on legal ontologies

    NARCIS (Netherlands)

    Breuker, J.; Hoekstra, R.; Sartor, G.; Casanovas, P.; Biasiotti, M.; Fernández-Barrera, M.

    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;

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

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; Gómez-Pérez, A.

    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...

  14. User Centered and Ontology Based Information Retrieval System for Life Sciences

    CERN Document Server

    Ranwez, Sylvie; Sy, Mohameth-François; Montmain, Jacky; Crampes, Michel

    2010-01-01

    Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of retrieved documents and no explanation for their adequacy to the query. Users may thus be confused by the selection and have no idea how to adapt their query so that the results match their expectations. This paper describes a request method and an environment based on aggregating models to assess the relevance of documents annotated by concepts of ontology. The selection of documents is then 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 exploration of data corpus.

  15. Life sciences

    Energy Technology Data Exchange (ETDEWEB)

    Day, L. (ed.)

    1991-04-01

    This document is the 1989--1990 Annual Report for the Life Sciences Divisions of the University of California/Lawrence Berkeley Laboratory. Specific progress reports are included for the Cell and Molecular Biology Division, the Research Medicine and Radiation Biophysics Division (including the Advanced Light Source Life Sciences Center), and the Chemical Biodynamics Division. 450 refs., 46 figs. (MHB)

  16. 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.

  17. Scaffolding in Mobile Science Enquiry-based Learning Using Ontologies

    Directory of Open Access Journals (Sweden)

    Sohaib Ahmed

    2012-08-01

    Full Text Available The use of ontologies has become increasingly widespread in many areas, particularly in technology enhanced learning. They appear promising in supporting knowledge representation and learning content creation for domains of interest. In this paper, we show how ontology-based scaffolding has helped mobile learners to perform scientific enquiry investigations. Enquiry-based learning aims to provide educational activities and tools to assists students to learn science by doing science. In this study, a design science research approach was taken to creating an ontology-driven application for a science content domain, which has been evaluated with high school science students. The results showed the significant value of ontologies in scaffolding learning content in such enquiry-based learning environments. With this application, students were found to learn science in more meaningful and engaged ways as well as developing positive attitudes towards mobile learning.

  18. Scaffolding in Mobile Science Enquiry-based Learning Using Ontologies

    OpenAIRE

    Sohaib Ahmed; David Parsons; Mandia Mentis

    2012-01-01

    The use of ontologies has become increasingly widespread in many areas, particularly in technology enhanced learning. They appear promising in supporting knowledge representation and learning content creation for domains of interest. In this paper, we show how ontology-based scaffolding has helped mobile learners to perform scientific enquiry investigations. Enquiry-based learning aims to provide educational activities and tools to assists students to learn science by doing science. In this s...

  19. 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.

  20. Ontologies, taxonomies and thesauri in systems science and systematics

    CERN Document Server

    Currás, Emilia

    2010-01-01

    The originality of this book, which deals with such a new subject matter, lies in the application of methods and concepts never used before - such as ontologies and taxonomies, as well as thesauri - to the ordering of knowledge based on primary information. Chapters in the book also examine the study of ontologies, taxonomies and thesauri from the perspective of systematics and general systems theory. Ontologies, Taxonomies and Thesauri in Systems Science and Systematics will be extremely useful to those operating within the network of related fields, which includes documentation and informati

  1. Deely on Consequences of Semiotic Ontology of Science, and Religion

    DEFF Research Database (Denmark)

    Brier, Søren

    to be the concept of science or, which Deely always underlined, meant Peircean postmodern semiotic pragmaticist realism. Ontologically this meant that the universe is not only self-organizing driven by irreversible thermodynamics’ forming of dissipative structures or objective information organization...

  2. ODISEES: Ontology-Driven Interactive Search Environment for Earth Sciences

    Science.gov (United States)

    Rutherford, Matthew T.; Huffer, Elisabeth B.; Kusterer, John M.; Quam, Brandi M.

    2015-01-01

    This paper discusses the Ontology-driven Interactive Search Environment for Earth Sciences (ODISEES) project currently being developed to aid researchers attempting to find usable data among an overabundance of closely related data. ODISEES' ontological structure relies on a modular, adaptable concept modeling approach, which allows the domain to be modeled more or less as it is without worrying about terminology or external requirements. In the model, variables are individually assigned semantic content based on the characteristics of the measurements they represent, allowing intuitive discovery and comparison of data without requiring the user to sift through large numbers of data sets and variables to find the desired information.

  3. Semantics, ontologies and eScience for the geosciences

    OpenAIRE

    Reitsma, Femke; Laxton, John; Ballard, Stuart; Kuhn, Werner; Abdelmoty, Alia

    2009-01-01

    Semantics, ontologies and eScience are key areas of research that aim to deal with the growing volume, number of sources and heterogeneity of geoscience data, information and knowledge. Following a workshop held at the eScience Institute in Edinburgh on the 7–9th of March 2008, this paper discusses some of the significant research topics and challenges for enhancing geospatial computing using semantic and grid technologies.

  4. Semantics, ontologies and eScience for the geosciences

    Science.gov (United States)

    Reitsma, Femke; Laxton, John; Ballard, Stuart; Kuhn, Werner; Abdelmoty, Alia

    2009-04-01

    Semantics, ontologies and eScience are key areas of research that aim to deal with the growing volume, number of sources and heterogeneity of geoscience data, information and knowledge. Following a workshop held at the eScience Institute in Edinburgh on the 7-9th of March 2008, this paper discusses some of the significant research topics and challenges for enhancing geospatial computing using semantic and grid technologies.

  5. Advancing science through mining libraries, ontologies, and communities.

    Science.gov (United States)

    Evans, James A; Rzhetsky, Andrey

    2011-07-08

    Life scientists today cannot hope to read everything relevant to their research. Emerging text-mining tools can help by identifying topics and distilling statements from books and articles with increased accuracy. Researchers often organize these statements into ontologies, consistent systems of reality claims. Like scientific thinking and interchange, however, text-mined information (even when accurately captured) is complex, redundant, sometimes incoherent, and often contradictory: it is rooted in a mixture of only partially consistent ontologies. We review work that models scientific reason and suggest how computational reasoning across ontologies and the broader distribution of textual statements can assess the certainty of statements and the process by which statements become certain. With the emergence of digitized data regarding networks of scientific authorship, institutions, and resources, we explore the possibility of accounting for social dependences and cultural biases in reasoning models. Computational reasoning is starting to fill out ontologies and flag internal inconsistencies in several areas of bioscience. In the not too distant future, scientists may be able to use statements and rich models of the processes that produced them to identify underexplored areas, resurrect forgotten findings and ideas, deconvolute the spaghetti of underlying ontologies, and synthesize novel knowledge and hypotheses.

  6. Transition from Critical Ontology To Metaphysical Foundations of Natural Science

    Directory of Open Access Journals (Sweden)

    Juan Csno De Pablo

    2015-03-01

    Full Text Available The Critique of Pure Reason out lines an a priori ontology of nature. We find in the Critique the category of substance, which is totally a priori. However, the metaphysical principles of natural science come from the notion of matter, which is empirical. This article shows the transition carried out by Kant between two areas of knowledge. For this purpose, we will relate two Kantian texts: Prologomena to Any Future Metaphysics Which Shall Lay Claim to Being a Science and Metaphysical Foundations of Natural Science.

  7. Providing the Missing Link: the Exposure Science Ontology ...

    Science.gov (United States)

    Although knowledge-discovery tools are new to the exposure science community, these tools are critical for leveraging exposure information to design health studies and interpret results for improved public health decisions. Standardized ontologies define relationships, allow for automated reasoning, and facilitate meta-analyses. ExO will facilitate development of biologically relevant exposure metrics, design of in vitro toxicity tests, and incorporation of information on susceptibility and background exposures for risk assessment. In this approach, there are multiple levels of organization, from the global environment down through ecosystems, communities, indoor spaces, populations, organisms, tissues, and cells. We anticipate that the exposure science and environmental health community will adopt and contribute to this work, as wide acceptance is key to integration and federated searching of exposure data to support environmental and public health research. In particular, we anticipate acceptance of the concept that exposure science provides the spatial/temporal narrative about the intensity (concentration) of a stressor at the boundary between two systems: one functioning as an “environment” (stressor) and one functioning as a target (receptor). An agreed-upon exposure ontology with clear definitions and relationships should help to facilitate decision-making, study design and prioritization of research initiatives by enhancing the capacity for data colle

  8. Construction informatics - Issues in engineering, computer science and ontology

    DEFF Research Database (Denmark)

    Eir, Asger

    2004-01-01

    . With origin in civil engineering and design issues, the study was directed towards computer science oriented theories in an attempt to introduce such theories in modelling and clarification of the domain. This strategy turned out to be a strength for the study and this thesis. However, it also discovered some...... problems in carrying out such a truly interdisciplinary Ph.D. study. Per Galle s and Dines Bjørner's common background in computer science has been essential for the success of this study. The original title of the Ph.D. project was Design and application of a civil engineering ontology. However, it became....... The issues of the thesis are treated from three angles: from computer science, from civil engineering and design theory, and from philosophy. It is characteristic for the thesis that these angles are all present in analysis and argumentation. The philosophical aspect is a natural ingredient as construction...

  9. Construction informatics - Issues in engineering, computer science and ontology

    DEFF Research Database (Denmark)

    Eir, Asger

    2004-01-01

    . With origin in civil engineering and design issues, the study was directed towards computer science oriented theories in an attempt to introduce such theories in modelling and clarification of the domain. This strategy turned out to be a strength for the study and this thesis. However, it also discovered some...... problems in carrying out such a truly interdisciplinary Ph.D. study. Per Galle s and Dines Bjørner's common background in computer science has been essential for the success of this study. The original title of the Ph.D. project was Design and application of a civil engineering ontology. However, it became....... The issues of the thesis are treated from three angles: from computer science, from civil engineering and design theory, and from philosophy. It is characteristic for the thesis that these angles are all present in analysis and argumentation. The philosophical aspect is a natural ingredient as construction...

  10. Ontologies: Semantic Nirvana for Earth Science Model Interoperability? (Invited)

    Science.gov (United States)

    Graybeal, J.

    2009-12-01

    The Challenge: When we build a given model, we do so to meet today's needs. If the model is good, new people will want to use it in new ways. That tests how well the model can work in new contexts: new user groups, new science domains, or new data providers or data users. We can say a model is interoperable if it works well in each new case, with few or no changes. Here we deal with perhaps the least-addressed part of model interoperability: semantic interoperability, the ability of models to understand the meaning of each other's data. The Scenario: A model has been built that uses observational data, and creates output data sets. In subsequent years, the model must (a) be connected to another model and exchange data with it; (b) be evaluated and used by a scientist in another domain; (c) document its outputs for two different repositories that use different keywords; and (d) identify and incorporate new observation streams as they come on-line. All these steps are mostly done manually today, and explanations about the data exchanged in similar form. Can we make them more efficient, or even automated, by leveraging good semantic practices? A problem in each case is the use of local or community naming conventions that are not known to all parties. How can this be improved? The Reality: Many models use the standard name conventions and vocabularies specified by the netCDF COARDS Climate and Forecast conventions. These provide a good basic level of 'semantic interoperability', and for this reason alone Earth science models are semantically far ahead of most other Earth science data systems. Yet these conventions aren't always used, aren't always sufficient, and don't help us interoperate with lots of existing systems. What are the issues for semantic interoperability in modeling, how do ontologies and other semantic capabilities help us fix them, and are ontologies worth the trouble?

  11. A Posteriori Ontology Engineering for Data-Driven Science

    Energy Technology Data Exchange (ETDEWEB)

    Gessler, Damian Dg; Joslyn, Cliff A.; Verspoor, Karin M.

    2013-05-28

    Science—and biology in particular—has a rich tradition in categorical knowledge management. This continues today in the generation and use of formal ontologies. Unfortunately, the link between hard data and ontological content is predominately qualitative, not quantitative. The usual approach is to construct ontologies of qualitative concepts, and then annotate the data to the ontologies. This process has seen great value, yet it is laborious, and the success to which ontologies are managing and organizing the full information content of the data is uncertain. An alternative approach is the converse: use the data itself to quantitatively drive ontology creation. Under this model, one generates ontologies at the time they are needed, allowing them to change as more data influences both their topology and their concept space. We outline a combined approach to achieve this, taking advantage of two technologies, the mathematical approach of Formal Concept Analysis (FCA) and the semantic web technologies of the Web Ontology Language (OWL).

  12. Mapping the entangled ontology of science teachers’ lived experience

    DEFF Research Database (Denmark)

    Daugbjerg, Peer Schrøder; de Freitas, E.; Valero, Paola

    2015-01-01

    In this paper we investigate how the bodily activity of teaching, along with the embodied aspect of lived experience, relates to science teachers’ ways of dealing with bodies as living organisms which are both the subject matter as well as the site or vehicle of learning. More precisely, the foll......In this paper we investigate how the bodily activity of teaching, along with the embodied aspect of lived experience, relates to science teachers’ ways of dealing with bodies as living organisms which are both the subject matter as well as the site or vehicle of learning. More precisely......, the following questions are pursued: (1) In what ways do primary science teachers refer to the lived and living body in teaching and learning? (2) In what ways do primary science teachers tap into past experiences in which the body figured prominently in order to teach students about living organisms? We draw...... on the relational ontology and intra-action of Karen Barad (J Women Cult Soc 28(3): 801, 2003) as she argues for a “relational ontology” that sees a relation as a dynamic flowing entanglement of a matter and meaning. We combine this with the materialist phenomenological studies of embodiment by SungWon Hwang...

  13. The Ontological Reversal: A Figure of Thought of Importance for Science Education.

    Science.gov (United States)

    Dahlin, Bo

    2003-01-01

    Investigated whether the "ontological reversal" described by E. Husserl, the tendency to view abstract mathematical models of phenomena as more real than the phenomena themselves, is present in the reasoning of pre-service science teachers. Findings for 23 pre-service teachers indicate the presence of the ontological reversal as a figure of…

  14. The Ontological Reversal: A Figure of Thought of Importance for Science Education.

    Science.gov (United States)

    Dahlin, Bo

    2003-01-01

    Investigated whether the "ontological reversal" described by E. Husserl, the tendency to view abstract mathematical models of phenomena as more real than the phenomena themselves, is present in the reasoning of pre-service science teachers. Findings for 23 pre-service teachers indicate the presence of the ontological reversal as a figure…

  15. The Ontological Reversal: A Figure of Thought of Importance for Science Education.

    Science.gov (United States)

    Dahlin, Bo

    2003-01-01

    Investigated whether the "ontological reversal" described by E. Husserl, the tendency to view abstract mathematical models of phenomena as more real than the phenomena themselves, is present in the reasoning of pre-service science teachers. Findings for 23 pre-service teachers indicate the presence of the ontological reversal as a figure…

  16. Life sciences and environmental sciences

    Energy Technology Data Exchange (ETDEWEB)

    1992-02-01

    The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER`s mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

  17. Life sciences and environmental sciences

    Energy Technology Data Exchange (ETDEWEB)

    1992-02-01

    The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.

  18. ExO: An Ontology for Exposure Science

    Science.gov (United States)

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

  19. ExO: An Ontology for Exposure Science

    Science.gov (United States)

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

  20. Providing the Missing Link: the Exposure Science Ontology ExO

    Science.gov (United States)

    Although knowledge-discovery tools are new to the exposure science community, these tools are critical for leveraging exposure information to design health studies and interpret results for improved public health decisions. Standardized ontologies define relationships, allow for ...

  1. Providing the Missing Link: the Exposure Science Ontology ExO

    Science.gov (United States)

    Although knowledge-discovery tools are new to the exposure science community, these tools are critical for leveraging exposure information to design health studies and interpret results for improved public health decisions. Standardized ontologies define relationships, allow for ...

  2. Mapping the entangled ontology of science teachers' lived experience

    Science.gov (United States)

    Daugbjerg, Peer S.; de Freitas, Elizabeth; Valero, Paola

    2015-09-01

    In this paper we investigate how the bodily activity of teaching, along with the embodied aspect of lived experience, relates to science teachers' ways of dealing with bodies as living organisms which are both the subject matter as well as the site or vehicle of learning. More precisely, the following questions are pursued: (1) In what ways do primary science teachers refer to the lived and living body in teaching and learning? (2) In what ways do primary science teachers tap into past experiences in which the body figured prominently in order to teach students about living organisms? We draw on the relational ontology and intra-action of Karen Barad (J Women Cult Soc 28(3): 801, 2003) as she argues for a "relational ontology" that sees a relation as a dynamic flowing entanglement of a matter and meaning. We combine this with the materialist phenomenological studies of embodiment by SungWon Hwang and Wolff-Michael Roth (Scientific and mathematical bodies, Sense Publishers, Rotterdam, 2011), as they address how the teachers and students are present in the classroom with/in their "living and lived bodies". Our aim is to use theoretical insights from these two different but complementary approaches to map the embodiment of teachers' experiences and actions. We build our understanding of experience on the work of John Dewey (Experience and education, Simon & Schuster, New York, 1938) and also Jean Clandinin and Michael Connelly (Handbook of qualitative research, Sage Publications, California, 2000), leading us to propose three dimensions: settings, relations and continuity. This means that bodies and settings are mutually entailed in the present relation, and furthermore that the past as well as the present of these bodies and settings—their continuity—is also part of the present relation. We analyse the entanglement of lived experience and embodied teaching using these three proposed dimensions of experience. Analysing interviews and observations of three Danish

  3. IS ONTOLOGY NECESSARY FOR MODERN SCIENCE: HISTORICAL PERSPECTIVE AND ACTUALITY OF THE PROBLEM

    Directory of Open Access Journals (Sweden)

    Lyudmila Pavlovna SIDOROVA

    2014-01-01

    Full Text Available Image modification of ontology in the history of philos-ophy and science is discussed in the article. It focuses on the reasons of de-ontologization of knowledge in natural sciences and intellectual tradition of the 20th century on the whole. It studies the influence of ne-okantian and positivistic philosophy on the develop-ment of “constructivist”, “antirealistic” discourse in scientific cognition. Phenomenology of E. Husserl and quantum physics are considered as sources of new ontology project.

  4. Life of Science

    DEFF Research Database (Denmark)

    Engelhardt, Robin; Margot Ricard, Lykke

    Learning Lab Denmark, København. 2003 Short description: In connection to the conference Changes and Challenges the White Book "Life of Science" was published. Member states of the European Union as well as applying countries were invited to contribute to the book with texts in order to present...... inspiring cases of concrete educational strategies for improving learning, teaching and recruitment in the fields of science and technology. Abstract: The aim of this white book is to present some of the most inspiring examples of Science and Technology Education in Europe. In creating the white book, we...

  5. Text Mining to inform construction of Earth and Environmental Science Ontologies

    Science.gov (United States)

    Schildhauer, M.; Adams, B.; Rebich Hespanha, S.

    2013-12-01

    There is a clear need for better semantic representation of Earth and environmental concepts, to facilitate more effective discovery and re-use of information resources relevant to scientists doing integrative research. In order to develop general-purpose Earth and environmental science ontologies, however, it is necessary to represent concepts and relationships that span usage across multiple disciplines and scientific specialties. Traditional knowledge modeling through ontologies utilizes expert knowledge but inevitably favors the particular perspectives of the ontology engineers, as well as the domain experts who interacted with them. This often leads to ontologies that lack robust coverage of synonymy, while also missing important relationships among concepts that can be extremely useful for working scientists to be aware of. In this presentation we will discuss methods we have developed that utilize statistical topic modeling on a large corpus of Earth and environmental science articles, to expand coverage and disclose relationships among concepts in the Earth sciences. For our work we collected a corpus of over 121,000 abstracts from many of the top Earth and environmental science journals. We performed latent Dirichlet allocation topic modeling on this corpus to discover a set of latent topics, which consist of terms that commonly co-occur in abstracts. We match terms in the topics to concept labels in existing ontologies to reveal gaps, and we examine which terms are commonly associated in natural language discourse, to identify relationships that are important to formally model in ontologies. Our text mining methodology uncovers significant gaps in the content of some popular existing ontologies, and we show how, through a workflow involving human interpretation of topic models, we can bootstrap ontologies to have much better coverage and richer semantics. Because we base our methods directly on what working scientists are communicating about their

  6. An Ontology-Based Resource Selection Service on Science Cloud

    Science.gov (United States)

    Yoo, Hyunjeong; Hur, Cinyoung; Kim, Seoyoung; Kim, Yoonhee

    Cloud computing requires scalable and cooperative sharing the resources in various organizations by dynamic configuring a virtual organization according to user's requirements. Ontology-based representation of Cloud computing environment would be able to conceptualize common attributes among Cloud resources and to describe relations among them semantically. However, mutual compatibility among organizations is limited because a method applying ontology to Cloud is not established yet.

  7. Life Sciences MIS

    Science.gov (United States)

    Dittman, R. A.; Marks, V.

    1983-01-01

    Management Information System, MIS, provides Life Sciences Projects Division at Johnson Space Center with automated system for project managment. MIS utilizes Tektronix 4027 color graphics display terminal and form-fillout capability. User interface with MIS data base is through series of forms.

  8. Designing and Implementing Basic Sciences Ontology Based on Concepts and Relationships of Relevant Thesauri

    Directory of Open Access Journals (Sweden)

    Molouk Sadat Hosseini Beheshti

    2015-05-01

    Full Text Available Currently, the main portion of knowledge is stored in electronic texts and documents and for transferring that knowledge effectively, we must use proper methods to gather and retrieve relevant information. Ontologies provide means to produce structured documents and use intelligent search instead of keyword search. Ontology defines the common words and concepts used to describe and represent an area of knowledge. However, developing ontologies is a time consuming and labor work, so many ontology developers try to facilitate and speed up this process by reusing other resources. In fact, thesaurus contains semantic information and hierarchical structure that make it an appropriate resource for ontology construction. Therefore, we determined to use the thesauri previously developed at Iranian Research Institute for Information Science and Technology (IRANDOC to construct ontology in basic sciences domain. At first, we synchronized common concepts in thesauri before integrating them as a macro thesaurus and removed inconsistencies. To reduce the amount of time and human resources which were needed for synchronizing process, Thesaurus Synchronizer was developed to illustrate differences between matched cases of two thesauri. It provides powerful tools for demonstrating differences and suggestions for each of the existing matters. Thus, domain experts synchronized each two thesaurus semi-automatically. Then we merged thesauri and transform the data format into ISO 25964 standard. The conceptual model have been designed based on the terms and their relationships in the integrated thesaurus and the concept maps that were designed by domain experts for each of basic sciences (Chemistry, Physics, Biology, Geology and Mathematics. We used the methodology called METHONTOLOGY in this stage. The main activity in this methodology is conceptualization and it enables the construction of ontologies at the knowledge level. Ultimately, the ontology was generated by

  9. Performing ontology.

    Science.gov (United States)

    Aspers, Patrik

    2015-06-01

    Ontology, and in particular, the so-called ontological turn, is the topic of a recent themed issue of Social Studies of Science (Volume 43, Issue 3, 2013). Ontology, or metaphysics, is in philosophy concerned with what there is, how it is, and forms of being. But to what is the science and technology studies researcher turning when he or she talks of ontology? It is argued that it is unclear what is gained by arguing that ontology also refers to constructed elements. The 'ontological turn' comes with the risk of creating a pseudo-debate or pseudo-activity, in which energy is used for no end, at the expense of empirical studies. This text rebuts the idea of an ontological turn as foreshadowed in the texts of the themed issue. It argues that there is no fundamental qualitative difference between the ontological turn and what we know as constructivism.

  10. Efficient Management of Biomedical Ontology Versions

    Science.gov (United States)

    Kirsten, Toralf; Hartung, Michael; Groß, Anika; Rahm, Erhard

    Ontologies have become very popular in life sciences and other domains. They mostly undergo continuous changes and new ontology versions are frequently released. However, current analysis studies do not consider the ontology changes reflected in different versions but typically limit themselves to a specific ontology version which may quickly become obsolete. To allow applications easy access to different ontology versions we propose a central and uniform management of the versions of different biomedical ontologies. The proposed database approach takes concept and structural changes of succeeding ontology versions into account thereby supporting different kinds of change analysis. Furthermore, it is very space-efficient by avoiding redundant storage of ontology components which remain unchanged in different versions. We evaluate the storage requirements and query performance of the proposed approach for the Gene Ontology.

  11. An Ontology of Gene

    OpenAIRE

    Masuya, Hiroshi; Mizoguchi, Riichiro

    2012-01-01

    The concept of a gene was established in the era of classical genetics and is now essential for life science for elucidating the molecular basis of the coding of genetic information necessary to realize the body of an organism and its biological functions. However, an ontology fully representing multiple aspects of a gene is still not available. In this study, we dissected the biological and ontological definitions of bearers of genetic information, including genes and alleles. Based on this ...

  12. Life of Science

    DEFF Research Database (Denmark)

    Engelhardt, Robin; Margot Ricard, Lykke

    Learning Lab Denmark, København. 2003 Short description: In connection to the conference Changes and Challenges the White Book "Life of Science" was published. Member states of the European Union as well as applying countries were invited to contribute to the book with texts in order to present i...... occurred, and the challenges we currently face in Scienceand Technology Education. We extend our deepest gratitude to all who contributed to the volume.......Learning Lab Denmark, København. 2003 Short description: In connection to the conference Changes and Challenges the White Book "Life of Science" was published. Member states of the European Union as well as applying countries were invited to contribute to the book with texts in order to present...... inspiring cases of concrete educational strategies for improving learning, teaching and recruitment in the fields of science and technology. Abstract: The aim of this white book is to present some of the most inspiring examples of Science and Technology Education in Europe. In creating the white book, we...

  13. Work flows in life science

    NARCIS (Netherlands)

    Wassink, Ingo

    2010-01-01

    The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab

  14. Work flows in life science

    NARCIS (Netherlands)

    Wassink, I.

    2010-01-01

    The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab

  15. Space shuttle and life sciences

    Science.gov (United States)

    Mason, J. A.

    1977-01-01

    During the 1980's, some 200 Spacelab missions will be flown on space shuttle in earth-orbit. Within these 200 missions, it is planned that at least 20 will be dedicated to life sciences research, projects which are yet to be outlined by the life sciences community. Objectives of the Life Sciences Shuttle/Spacelab Payloads Program are presented. Also discussed are major space life sciences programs including space medicine and physiology, clinical medicine, life support technology, and a variety of space biology topics. The shuttle, spacelab, and other life sciences payload carriers are described. Concepts for carry-on experiment packages, mini-labs, shared and dedicated spacelabs, as well as common operational research equipment (CORE) are reviewed. Current NASA planning and development includes Spacelab Mission Simulations, an Announcement of Planning Opportunity for Life Sciences, and a forthcoming Announcement of Opportunity for Flight Experiments which will together assist in forging a Life Science Program in space.

  16. Data-driven Ontology Development: A Case Study at NASA's Atmospheric Science Data Center

    Science.gov (United States)

    Hertz, J.; Huffer, E.; Kusterer, J.

    2012-12-01

    Well-founded ontologies are key to enabling transformative semantic technologies and accelerating scientific research. One example is semantically enabled search and discovery, making scientific data accessible and more understandable by accurately modeling a complex domain. The ontology creation process remains a challenge for many anxious to pursue semantic technologies. The key may be that the creation process -- whether formal, community-based, automated or semi-automated -- should encompass not only a foundational core and supplemental resources but also a focus on the purpose or mission the ontology is created to support. Are there tools or processes to de-mystify, assess or enhance the resulting ontology? We suggest that comparison and analysis of a domain-focused ontology can be made using text engineering tools for information extraction, tokenizers, named entity transducers and others. The results are analyzed to ensure the ontology reflects the core purpose of the domain's mission and that the ontology integrates and describes the supporting data in the language of the domain - how the science is analyzed and discussed among all users of the data. Commonalities and relationships among domain resources describing the Clouds and Earth's Radiant Energy (CERES) Bi-Directional Scan (BDS) datasets from NASA's Atmospheric Science Data Center are compared. The domain resources include: a formal ontology created for CERES; scientific works such as papers, conference proceedings and notes; information extracted from the datasets (i.e., header metadata); and BDS scientific documentation (Algorithm Theoretical Basis Documents, collection guides, data quality summaries and others). These resources are analyzed using the open source software General Architecture for Text Engineering, a mature framework for computational tasks involving human language.

  17. Ontology of Space Physics for e-Science Applications Based on ISO 19156

    Science.gov (United States)

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

    2014-12-01

    A structural, ontological presentation of the discipline domain concepts and their relationships is a powerful e-science tool: it enables data search and discovery by content of the observations. Even a simple classification of the concepts using the parent-child hierarchies enables analyses by association, thus bringing a greater insight in the data. Ontology specifications have been put to many uses in space physics, primarily to harmonize data analysis across multiple data resources and thus facilitate interoperability. Among the multitude of ontology writeups, the SPASE data model stands out as a prominent, highly detailed collection of keywords for heliophysics. We will present an ontology design that draws its strengths from SPASE and further enhances it with a greater structural organization of the keyword vocabularies, in particular related to wave phenomena, as well as describes a variety of events and activities in the Sun-Earth system beyond the quiet-time behaviour. The new ontology is being developed for the Near Earth Space Data Infrastructure for e-Science (ESPAS) project funded by the 7th European Framework, whose data model is based on a suite of ISO 19156 standards for Observations and Measurements (O&M). The O&M structure and language have driven the ESPAS ontology organization, with the Observed Property vocabulary as its cornerstone. The ontology development has progressed beyond the O&M framework to include domain-specific components required to describe the space physics concepts in a dictionary-controlled, unambiguous manner. Not surprisingly, wave phenomena and events presented the greatest challenge to the ESPAS ontology team as they demanded characterization of processes involved in the wave generation, propagation, modification, and reception, as well as the propagation medium itself. One of the notable outcomes of this effort is the ability of the new ontology schema to accommodate and categorize, for example, the URSI standard

  18. Toward a Social Ontology for Science Education: Introducing Deleuze and Guattari's Assemblages

    Science.gov (United States)

    Bazzul, Jesse; Kayumova, Shakhnoza

    2016-01-01

    This essay's main objective is to develop a theoretical, ontological basis for critical, social justice-oriented science education. Using Deleuze and Guattari's notion of assemblages, rhizomes, and arborescent structures, this article challenges authoritarian institutional practices, as well as the subject of these practices, and offers a way for…

  19. Science for Life and Living.

    Science.gov (United States)

    Bybee, Rodger W.; Landes, Nancy M.

    1990-01-01

    Described is an elementary school science program developed by the Biological Sciences Curriculum Study entitled "Science for Life and Living: Integrating Science, Technology and Health." Discussed are the rationale, unifying themes, organization, teaching model, implementation, development, production, and support for this program. (CW)

  20. Life Sciences and employability

    Directory of Open Access Journals (Sweden)

    Wynand J. Boshoff

    2012-03-01

    Full Text Available This article addresses unemployment in rural areas. South Africa is also characterised by skills shortage and high unemployment figures, especially in rural areas as compared to urban areas. The institutional reality of education is that every rural village hosts a high school which is primarily engaged in preparing learners for further studies, whilst the Further Training Colleges (previously known as technical colleges are mainly located in the larger centres. It is with this scenario as a backdrop that the possible role of high schools to alleviate the problem is being argued. It is clear that rural employers do not expect from school leavers to be in possession of applicable knowledge, but rather to be in possession of the ability as well as certain personal characteristics that would make them employable. Unfortunately, however, this is not always found in young persons who have completed their schooling successfully. Life Sciences educators can render a valuable service should certain nontraditional approaches be incorporated into the teaching practice. This will enable them to contribute to solving one of South Africa’s serious problems.

  1. Physics of the Life Sciences

    CERN Document Server

    Newman, Jay

    2008-01-01

    Originally developed for the author's course at Union College, this text is designed for life science students who need to understand the connections of fundamental physics to modern biology and medicine. Almost all areas of modern life sciences integrally involve physics in both experimental techniques and in basic understanding of structure and function. Physics of the Life Sciences is not a watered-down, algebra-based engineering physics book with sections on relevant biomedical topics added as an afterthought. This authoritative and engaging text, which is designed to be covered in a two-semester course, was written with a thoroughgoing commitment to the needs and interests of life science students. Although covering most of the standard topics in introductory physics in a more or less traditional sequence, the author gives added weight and space to concepts and applications of greater relevance to the life sciences. Students benefit from occasional sidebars using calculus to derive fundamental relations,...

  2. CODEX: exploration of semantic changes between ontology versions.

    Science.gov (United States)

    Hartung, Michael; Gross, Anika; Rahm, Erhard

    2012-03-15

    Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways.

  3. Integrating Vygotsky's theory of relational ontology into early childhood science education

    Science.gov (United States)

    Kirch, Susan A.

    2014-03-01

    In Science Education during Early Childhood: A Cultural- Historical Perspective, Wolff-Michael Roth, Maria Inês Mafra Goulart and Katerina Plakitsi explore the practical application of Vygotsky's relational ontological theory of human development to early childhood science teaching and teacher development. In this review, I interrogate how Roth et al. conceptualize "emergent curriculum" within the Eurocentric cultural-historical traditions of early childhood education that evolved primarily from the works of Vygotsky and Piaget and compare it to the conceptualizations from other prominent early childhood researchers and curriculum developers. I examine the implications of the authors' interpretation of emergence for early childhood science education and teacher preparation.

  4. Ontology-Driven Provenance Management in eScience: An Application in Parasite Research

    Science.gov (United States)

    Sahoo, Satya S.; Weatherly, D. Brent; Mutharaju, Raghava; Anantharam, Pramod; Sheth, Amit; Tarleton, Rick L.

    Provenance, from the French word "provenir", describes the lineage or history of a data entity. Provenance is critical information in scientific applications to verify experiment process, validate data quality and associate trust values with scientific results. Current industrial scale eScience projects require an end-to-end provenance management infrastructure. This infrastructure needs to be underpinned by formal semantics to enable analysis of large scale provenance information by software applications. Further, effective analysis of provenance information requires well-defined query mechanisms to support complex queries over large datasets. This paper introduces an ontology-driven provenance management infrastructure for biology experiment data, as part of the Semantic Problem Solving Environment (SPSE) for Trypanosoma cruzi (T.cruzi). This provenance infrastructure, called T.cruzi Provenance Management System (PMS), is underpinned by (a) a domain-specific provenance ontology called Parasite Experiment ontology, (b) specialized query operators for provenance analysis, and (c) a provenance query engine. The query engine uses a novel optimization technique based on materialized views called materialized provenance views (MPV) to scale with increasing data size and query complexity. This comprehensive ontology-driven provenance infrastructure not only allows effective tracking and management of ongoing experiments in the Tarleton Research Group at the Center for Tropical and Emerging Global Diseases (CTEGD), but also enables researchers to retrieve the complete provenance information of scientific results for publication in literature.

  5. Science and Creativity: The Importance of Ontology for Scientific Understanding

    Science.gov (United States)

    Martin, Lee

    2010-01-01

    The history of science presented by Hisham B. Ghassib (2010) on his article, "Where Does Creativity Fit into a Productivist Industrial Model of Knowledge Production?," reveals the significance of knowledge generating action throughout human history. Ghassib's (2010) paper explores the embedded nature of scientific practise and in doing so offers…

  6. Life Sciences Data Archive (LSDA)

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA's Life Sciences Data Archive (LSDA) is an active archive that provides information and data from 1961 (Mercury Project) through current flight and flight analog...

  7. 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...

  8. 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

  9. Hysteria, race, and phlogiston. A model of ontological elimination in the human sciences.

    Science.gov (United States)

    Ludwig, David

    2014-03-01

    Elimination controversies are ubiquitous in philosophy and the human sciences. For example, it has been suggested that human races, hysteria, intelligence, mental disorder, propositional attitudes such as beliefs and desires, the self, and the super-ego should be eliminated from the list of respectable entities in the human sciences. I argue that eliminativist proposals are often presented in the framework of an oversimplified "phlogiston model" and suggest an alternative account that describes ontological elimination on a gradual scale between criticism of empirical assumptions and conceptual choices.

  10. NASA Space Life Sciences

    Science.gov (United States)

    Hayes, Judith

    2009-01-01

    This slide presentation reviews the requirements that NASA has for the medical service of a crew returning to earth after long duration space flight. The scenarios predicate a water landing. Two scenarios are reviewed that outline the ship-board medical operations team and the ship board science reseach team. A schedule for the each crew upon landing is posited for each of scenarios. The requirement for a heliport on board the ship is reviewed and is on the requirement for a helicopter to return the Astronauts to the Baseline Data Collection Facility (BDCF). The ideal is to integrate the medical and science requirements, to minimize the risks and Inconveniences to the returning astronauts. The medical support that is required for all astronauts returning from long duration space flight (30 days or more) is reviewed. The personnel required to support the team is outlined. The recommendations for medical operations and science research for crew support are stated.

  11. Life sciences domain analysis model.

    Science.gov (United States)

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H; Klemm, Juli D

    2012-01-01

    Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science.

  12. Life Sciences Data Archive (LSDA)

    Science.gov (United States)

    Fitts, M.; Johnson-Throop, Kathy; Thomas, D.; Shackelford, K.

    2008-01-01

    In the early days of spaceflight, space life sciences data were been collected and stored in numerous databases, formats, media-types and geographical locations. While serving the needs of individual research teams, these data were largely unknown/unavailable to the scientific community at large. As a result, the Space Act of 1958 and the Science Data Management Policy mandated that research data collected by the National Aeronautics and Space Administration be made available to the science community at large. The Biomedical Informatics and Health Care Systems Branch of the Space Life Sciences Directorate at JSC and the Data Archive Project at ARC, with funding from the Human Research Program through the Exploration Medical Capability Element, are fulfilling these requirements through the systematic population of the Life Sciences Data Archive. This program constitutes a formal system for the acquisition, archival and distribution of data for Life Sciences-sponsored experiments and investigations. The general goal of the archive is to acquire, preserve, and distribute these data using a variety of media which are accessible and responsive to inquiries from the science communities.

  13. A Method for Evaluating and Standardizing Ontologies

    Science.gov (United States)

    Seyed, Ali Patrice

    2012-01-01

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

  14. A Method for Evaluating and Standardizing Ontologies

    Science.gov (United States)

    Seyed, Ali Patrice

    2012-01-01

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

  15. Space life sciences strategic plan

    Science.gov (United States)

    Nicogossian, Arnauld E.

    1992-05-01

    Over the last three decades the Life Sciences Program has significantly contributed to NASA's manned and unmanned exploration of space, while acquiring new knowledge in the fields of space biology and medicine. The national and international events which have led to the development and revision of NASA strategy will significantly affect the future of life sciences programs both in scope and pace. This document serves as the basis for synthesizing the options to be pursued during the next decade, based on the decisions, evolution, and guiding principles of the National Space Policy. The strategies detailed in this document are fully supportive of the Life Sciences Advisory Subcommittee's 'A Rationale for the Life Sciences,' and the recent Aerospace Medicine Advisory Committee report entitled 'Strategic Considerations for Support of Humans in Space and Moon/Mars Exploration Missions.' Information contained within this document is intended for internal NASA planning and is subject to policy decisions and direction, and to budgets allocated to NASA's Life Sciences Program.

  16. Space life sciences strategic plan

    Science.gov (United States)

    Nicogossian, Arnauld E.

    1992-01-01

    Over the last three decades the Life Sciences Program has significantly contributed to NASA's manned and unmanned exploration of space, while acquiring new knowledge in the fields of space biology and medicine. The national and international events which have led to the development and revision of NASA strategy will significantly affect the future of life sciences programs both in scope and pace. This document serves as the basis for synthesizing the options to be pursued during the next decade, based on the decisions, evolution, and guiding principles of the National Space Policy. The strategies detailed in this document are fully supportive of the Life Sciences Advisory Subcommittee's 'A Rationale for the Life Sciences,' and the recent Aerospace Medicine Advisory Committee report entitled 'Strategic Considerations for Support of Humans in Space and Moon/Mars Exploration Missions.' Information contained within this document is intended for internal NASA planning and is subject to policy decisions and direction, and to budgets allocated to NASA's Life Sciences Program.

  17. Breathing fresh life into life science education.

    Science.gov (United States)

    Martin, Cyrus

    2014-12-15

    In the US, higher education in the life sciences is being overhauled. There is now a move both to change the way we teach biology students, emphasizing more engaging approaches, and to clearly define what it is a student should know. And for advanced degrees, there is a push to prepare students for a range of possible career paths, not just the tenure track. Cyrus Martin reports.

  18. Back- and fore-grounding ontology: exploring the linkages between critical realism, pragmatism, and methodologies in health & rehabilitation sciences.

    Science.gov (United States)

    DeForge, Ryan; Shaw, Jay

    2012-03-01

    Back- and fore-grounding ontology: exploring the linkages between critical realism, pragmatism, and methodologies in health & rehabilitation sciences As two doctoral candidates in a health and rehabilitation sciences program, we describe in this paper our respective paradigmatic locations along a quite nonlinear ontological-epistemological-axiological-methodological chain. In a turn-taking fashion, we unpack the tenets of critical realism and pragmatism, and then trace the linkages from these paradigmatic locations through to the methodological choices that address a community-based research problem. Beyond serving as an answer to calls for academics in training to demonstrate philosophical-theoretical-methodological integrity and coherence in their scholarship, this paper represents critical realism and its fore-grounding of a deeply stratified ontology in reflexive relation to pragmatism and its back-grounding of ontology. We conclude by considering the merits and challenges of conducting research from within singular versus proliferate paradigmatic perspectives.

  19. Margin based ontology sparse vector learning algorithm and applied in biology science.

    Science.gov (United States)

    Gao, Wei; Qudair Baig, Abdul; Ali, Haidar; Sajjad, Wasim; Reza Farahani, Mohammad

    2017-01-01

    In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented. Finally, the new algorithm is applied to gene ontology and plant ontology to verify its efficiency.

  20. Spacelab Life Sciences 1 results

    Science.gov (United States)

    Seddon, Rhea

    1992-01-01

    Results are presented from the experiments conducted by the first Shuttle/Spacelab mission dedicated entirely to the life sciences, the Spacelab Life Sciences 1, launched on June 5, 1991. The experiments carried out during the 9-day flight included investigations of changes in the human cardiovascular, pulmonary, renal/endocrine, blood, and vestibular systems that were brought about by microgravity. Results were also obtained from the preflight and postflight complementary experiments performed on rats, which assessed the suitability of rodents as animal models for humans. Most results verified, or expanded on, the accepted theories of adaptation to zero gravity.

  1. Ontological metaphors for negative energy in an interdisciplinary context

    Science.gov (United States)

    Dreyfus, Benjamin W.; Geller, Benjamin D.; Gouvea, Julia; Sawtelle, Vashti; Turpen, Chandra; Redish, Edward F.

    2014-12-01

    Teaching about energy in interdisciplinary settings that emphasize coherence among physics, chemistry, and biology leads to a more central role for chemical bond energy. We argue that an interdisciplinary approach to chemical energy leads to modeling chemical bonds in terms of negative energy. While recent work on ontological metaphors for energy has emphasized the affordances of the substance ontology, this ontology is problematic in the context of negative energy. Instead, we apply a dynamic ontologies perspective to argue that blending the substance and location ontologies for energy can be effective in reasoning about negative energy in the context of reasoning about chemical bonds. We present data from an introductory physics for the life sciences course in which both experts and students successfully use this blended ontology. Blending these ontologies is most successful when the substance and location ontologies are combined such that each is strategically utilized in reasoning about particular aspects of energetic processes.

  2. Ontological metaphors for negative energy in an interdisciplinary context

    CERN Document Server

    Dreyfus, Benjamin W; Gouvea, Julia; Sawtelle, Vashti; Turpen, Chandra; Redish, Edward F

    2013-01-01

    Teaching about energy in interdisciplinary settings that emphasize coherence among physics, chemistry, and biology leads to a more central role for chemical bond energy. We argue that an interdisciplinary approach to chemical energy leads to modeling chemical bonds in terms of negative energy. While recent work on ontological metaphors for energy has emphasized the affordances of the substance ontology, this ontology is problematic in the context of negative energy. Instead, we apply a dynamic ontologies perspective to argue that blending the substance and location ontologies for energy can be effective in reasoning about negative energy in the context of reasoning about chemical bonds. We present data from an introductory physics for the life sciences (IPLS) course in which both experts and students successfully use this blended ontology. Blending these ontologies is most successful when the substance and location ontologies are combined such that each is strategically utilized in reasoning about particular ...

  3. Venture Kapital und Life Science

    Science.gov (United States)

    Moss, Sebastian; Beermann, Christian

    Um sich weiter im internationalen Wettbewerb behaupten zu können, müssen deutsche Unternehmen heute in Schlüsseltechnologien wie die Medizintechnik und die Biotechnologie, zusammenfassend unter dem Begriff der Life Sciences bekannt, investieren. Eine führende Wettbewerbsposition erfordert immer die konsequente Weiterentwicklung von Produkten und Lösungen, um Innovationspotenziale in medizinische Verfahren umzusetzen. Die damit unmittelbar verbundenen hohen Ausgaben für Forschung und Entwicklung stellen ein bedeutendes Problem junger Life Science Unternehmen dar. Vor allem die, verglichen mit nicht-medizinischen Branchen, längeren Forschungs- und Entwicklungszyklen in der Frühphase eines Life Science Unternehmens und die längere Dauer bis zur Profitabilität erhöhen das Risiko der Finanzinvestoren. Die Zeitdauer, um ein medizinisches Produkt bis zur Marktreife zu entwickeln und letztlich auf dem Markt anzubieten, kann aufgrund der notwendigen intensiven Forschung nur unscharf geplant werden und erhöht die Unsicherheit über den Zeitpunkt der ersten Einnahmen. Damit verschärfen sich gerade im Life Science Bereich allgemeine Problematiken von Gründungs- und Wachstumsfinanzierungen wie starke Informationsasymmetrien zwischen Gründer und potentiellen Kapitalgebern. Oftmals ist die Entwicklung einer innovativen Technologie abhängig von einzelnen Personen, von deren Wissen und Engagement die Umsetzung und der Erfolg eines gesamten Produktkonzeptes abhängen.

  4. Ontology for vector surveillance and management.

    Science.gov (United States)

    Lozano-Fuentes, Saul; Bandyopadhyay, Aritra; Cowell, Lindsay G; Goldfain, Albert; Eisen, Lars

    2013-01-01

    Ontologies, which are made up by standardized and defined controlled vocabulary terms and their interrelationships, are comprehensive and readily searchable repositories for knowledge in a given domain. The Open Biomedical Ontologies (OBO) Foundry was initiated in 2001 with the aims of becoming an "umbrella" for life-science ontologies and promoting the use of ontology development best practices. A software application (OBO-Edit; *.obo file format) was developed to facilitate ontology development and editing. The OBO Foundry now comprises over 100 ontologies and candidate ontologies, including the NCBI organismal classification ontology (NCBITaxon), the Mosquito Insecticide Resistance Ontology (MIRO), the Infectious Disease Ontology (IDO), the IDOMAL malaria ontology, and ontologies for mosquito gross anatomy and tick gross anatomy. We previously developed a disease data management system for dengue and malaria control programs, which incorporated a set of information trees built upon ontological principles, including a "term tree" to promote the use of standardized terms. In the course of doing so, we realized that there were substantial gaps in existing ontologies with regards to concepts, processes, and, especially, physical entities (e.g., vector species, pathogen species, and vector surveillance and management equipment) in the domain of surveillance and management of vectors and vector-borne pathogens. We therefore produced an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. The Vector Surveillance and Management Ontology (VSMO) includes >2,200 unique terms, of which the vast majority (>80%) were newly generated during the development of this ontology. One core feature of the VSMO is the linkage, through

  5. An Ontology-Based Archive Information Model for the Planetary Science Community

    Science.gov (United States)

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

    2008-01-01

    The Planetary Data System (PDS) information model is a mature but complex model that has been used to capture over 30 years of planetary science data for the PDS archive. As the de-facto information model for the planetary science data archive, it is being adopted by the International Planetary Data Alliance (IPDA) as their archive data standard. However, after seventeen years of evolutionary change the model needs refinement. First a formal specification is needed to explicitly capture the model in a commonly accepted data engineering notation. Second, the core and essential elements of the model need to be identified to help simplify the overall archive process. A team of PDS technical staff members have captured the PDS information model in an ontology modeling tool. Using the resulting knowledge-base, work continues to identify the core elements, identify problems and issues, and then test proposed modifications to the model. The final deliverables of this work will include specifications for the next generation PDS information model and the initial set of IPDA archive data standards. Having the information model captured in an ontology modeling tool also makes the model suitable for use by Semantic Web applications.

  6. An Ontology-Based Archive Information Model for the Planetary Science Community

    Science.gov (United States)

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

    2008-01-01

    The Planetary Data System (PDS) information model is a mature but complex model that has been used to capture over 30 years of planetary science data for the PDS archive. As the de-facto information model for the planetary science data archive, it is being adopted by the International Planetary Data Alliance (IPDA) as their archive data standard. However, after seventeen years of evolutionary change the model needs refinement. First a formal specification is needed to explicitly capture the model in a commonly accepted data engineering notation. Second, the core and essential elements of the model need to be identified to help simplify the overall archive process. A team of PDS technical staff members have captured the PDS information model in an ontology modeling tool. Using the resulting knowledge-base, work continues to identify the core elements, identify problems and issues, and then test proposed modifications to the model. The final deliverables of this work will include specifications for the next generation PDS information model and the initial set of IPDA archive data standards. Having the information model captured in an ontology modeling tool also makes the model suitable for use by Semantic Web applications.

  7. Informal science education: lifelong, life-wide, life-deep.

    Science.gov (United States)

    Sacco, Kalie; Falk, John H; Bell, James

    2014-11-01

    Informal Science Education: Lifelong, Life-Wide, Life-Deep Informal science education cultivates diverse opportunities for lifelong learning outside of formal K-16 classroom settings, from museums to online media, often with the help of practicing scientists.

  8. Datamining with Ontologies.

    Science.gov (United States)

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

    2016-01-01

    The use of ontologies has increased rapidly over the past decade and they now provide a key component of most major databases in biology and biomedicine. Consequently, datamining over these databases benefits from considering the specific structure and content of ontologies, and several methods have been developed to use ontologies in datamining applications. Here, we discuss the principles of ontology structure, and datamining methods that rely on ontologies. The impact of these methods in the biological and biomedical sciences has been profound and is likely to increase as more datasets are becoming available using common, shared ontologies.

  9. The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science.

    Science.gov (United States)

    Klie, Sebastian; Nikoloski, Zoran

    2012-01-01

    Since the introduction of the Gene Ontology (GO), the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis) with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of co-expression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies.

  10. The choice between MapMan and Gene Ontology for automated gene function prediction in plant science

    Directory of Open Access Journals (Sweden)

    Sebastian eKlie

    2012-06-01

    Full Text Available Since the introduction of the Gene Ontology (GO, the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of coexpression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies.

  11. Ontology for Life-Cycle Modeling of Heating, Ventilating, and Air Conditioning (HVAC) Systems: Experimental Applications Using Revit

    Science.gov (United States)

    2012-03-01

    Center, Construction Engineering Research Laboratory (ERDC-CERL) has developed a core life- cycle building information model ( BIM ) based on three...was to promote consistency and quality of content created for Building Information Models ( BIMs ) across various disciplines. The HVAC MVD was...MVD. 15. SUBJECT TERMS building information modeling ( BIM ), ontology, Army facilities, heating, ventilating, and air-conditioning (HVAC) systems

  12. Development and Application of Ontologies in Support of Earth and Space Science Education

    Science.gov (United States)

    Fox, S. P.; Manduca, C. A.; Iverson, E.

    2007-12-01

    Through its work in supporting improved science education the Science Education Resource Center (SERC) has developed and applied a set of Earth and Space Science vocabularies. These controlled vocabularies play a central role in supporting user exploration of our educational materials. The set of over 50 vocabularies run the gamut from small vocabularies with a narrowly targeted use, to broader vocabularies that span multiple disciplines and are applied across multiple projects and collections. Typical specialized vocabularies cover disciplinary themes such as tectonic setting (with terms such as mid-ocean ridge, passive margin, and craton) as well as interdisciplinary work such as geology and human health (with terms such as radionuclides and airborne transport processes). To support project-specific customization of vocabularies while retaining the benefits of cross-project reuse our systems allow for dynamic mapping of terms among multiple vocabularies based on semantic equivalencies. The end result is a weaving of related vocabularies into an ontological network that is exposed as specific vocabularies that employ the natural language of the collections and communities that use them. Our process for vocabulary development is community driven and reflects our experiences in aligning terminology with disciplinary-specific expectations. These experiences include rectifying language differences across disciplines in building a Geoscience Quantitative Skills vocabulary through work with both the Mathematics and Geoscience communities, as well as the iterative development of a vocabulary spanning Earth and Space science through the aggregation of smaller vocabularies, each developed by scientists for use within their own discipline. The vocabularies are exposed as key navigational features in over 100 faceted search interfaces within the web sites of a dozen Earth and Space Science Education projects. Within these faceted search interfaces the terms in the

  13. Realist Ontology and Natural Processes: A Semantic Tool to Analyze the Presentation of the Osmosis Concept in Science Texts

    Science.gov (United States)

    Spinelli Barria, Michele; Morales, Cecilia; Merino, Cristian; Quiroz, Waldo

    2016-01-01

    In this work, we developed an ontological tool, based on the scientific realism of Mario Bunge, for the analysis of the presentation of natural processes in science textbooks. This tool was applied to analyze the presentation of the concept of osmosis in 16 chemistry and biology books at different educational levels. The results showed that more…

  14. Exploring biomedical ontology mappings with graph theory methods.

    Science.gov (United States)

    Kocbek, Simon; Kim, Jin-Dong

    2017-01-01

    In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

  15. Microfluidics and the life sciences.

    Science.gov (United States)

    Becker, Holger; Gärtner, Claudia

    2012-01-01

    The field of microfluidics, often also referred to as "Lab-on-a-Chip" has made significant progress in the last 15 years and is an essential tool in the development of new products and protocols in the life sciences. This article provides a broad overview on the developments on the academic as well as the commercial side. Fabrication technologies for polymer-based devices are presented and a strategy for the development of complex integrated devices is discussed, together with an example on the use of these devices in pathogen detection.

  16. How Peircean semiotic philosophy connects Western science with Eastern emptiness ontology.

    Science.gov (United States)

    Brier, Søren

    2017-08-25

    In recent articles in this journal I have discussed why a traditional physicalist and mechanist, as well as an info-computationalist, view of science cannot fulfil the goal of building a transdisciplinary science across Snow's two cultures. There seems to be no path proceeding from mechanistic physicalism to views that encompass phenomenological theories of experiential consciousness and meaning-based cognition and communication. I have suggested, as an alternative, the Cybersemiotic framework's integration of Peirce's semiotics and Luhmann's autopoietic system theory. The present article considers in greater depth the ontological developments necessary to make this possible. It shows how Peirce avoids materialism and German idealism through his building on a concept of emptiness similar to modern quantum field theory, positing an indeterminist objective chance feeding into an evolutionary philosophy of knowing based on pure mathematics and phenomenology that is itself combined with empirically executed fallibilism. Furthermore, he created a new metaphysics in the form of a philosophical synechist triadic process philosophy. This was integrated into the transcendentalist view of process view of science and spirituality developed from Western Unitarianism by Emerson (agapism), and featuring a metaphysics of emptiness and spontaneity (tychism) that are also essential for the Eastern philosophies of Buddhism and Vedanta. Copyright © 2017. Published by Elsevier Ltd.

  17. Life Sciences Division Spaceflight Hardware

    Science.gov (United States)

    Yost, B.

    1999-01-01

    The Ames Research Center (ARC) is responsible for the development, integration, and operation of non-human life sciences payloads in support of NASA's Gravitational Biology and Ecology (GB&E) program. To help stimulate discussion and interest in the development and application of novel technologies for incorporation within non-human life sciences experiment systems, three hardware system models will be displayed with associated graphics/text explanations. First, an Animal Enclosure Model (AEM) will be shown to communicate the nature and types of constraints physiological researchers must deal with during manned space flight experiments using rodent specimens. Second, a model of the Modular Cultivation System (MCS) under development by ESA will be presented to highlight technologies that may benefit cell-based research, including advanced imaging technologies. Finally, subsystems of the Cell Culture Unit (CCU) in development by ARC will also be shown. A discussion will be provided on candidate technology requirements in the areas of specimen environmental control, biotelemetry, telescience and telerobotics, and in situ analytical techniques and imaging. In addition, an overview of the Center for Gravitational Biology Research facilities will be provided.

  18. Life sciences on the moon

    Science.gov (United States)

    Horneck, G.

    Despite of the fact that the lunar environment lacks essential prerequisites for supporting life, lunar missions offer new and promising opportunities to the life sciences community. Among the disciplines of interest are exobiology, radiation biology, ecology and human physiology. In exobiology, the Moon offers an ideal platform for studies related to the understanding of the principles, leading to the origin, evolution and distribution of life. These include the analysis of lunar samples and meteorites in relatively pristine conditions, radioastronomical search for other planetary systems or Search for Extra-Terrestrial Intelligence (SETI), and studies on the role of radiation in evolutionary processes and on the environmental limits for life. For radiation biology, the Moon provides an unique laboratory with built-in sources for optical as well as ionising radiation to investigate the biological importance of the various components of cosmic and solar radiation. Before establishing a lunar base, precursor missions will provide a characterisation of the radiation field, determination of depth dose distributions in different absorbers, the installation of a solar flare alert system, and a qualification of the biological efficiency of the mixed radiation environment. One of the most challenging projects falls into the domain of ecology with the establishment for the first time of an artificial ecosystem on a celestial body beyond the Earth. From this venture, a better understanding of the dynamics regulating our terrestrial biosphere is expected. It will also serve as a precursor of bioregenerative life support systems for a lunar base. The establishment of a lunar base with eventually long-term human presence will raise various problems in the fields of human physiology and health care, psychology and sociology. Protection guidelines for living in this hostile environment have to be established.

  19. The Next Generation Science Standards and the Life Sciences

    Science.gov (United States)

    Bybee, Rodger W.

    2013-01-01

    Using the life sciences, this article first reviews essential features of the "NRC Framework for K-12 Science Education" that provided a foundation for the new standards. Second, the article describes the important features of life science standards for elementary, middle, and high school levels. Special attention is paid to the teaching…

  20. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

    Ontology or formal ontology? Which word is correct? The aim of this article is to introduce correct terms and explain their basis. Ontology describes a particular area of interest (domain) in a formal way - defines the classes of objects that are in that area, and relationships that may exist between them. Meaning of ontology consists mainly in facilitating communication between people, improve collaboration of software systems and in the improvement of systems engineering. Ontology in all these areas offer the possibility of unification of view, maintaining consistency and unambiguity.

  1. Determination of concept technology - the ontology of the concept as a component of the knowledge development in caring science.

    Science.gov (United States)

    Korhonen, Eila-Sisko; Nordman, Tina; Eriksson, Katie

    2014-12-01

    The purpose of this study is to determine the ontology of the concept of technology from the perspective of caring science. The aim is to increase knowledge of the concept in caring science and to answer the research question concerning what the concept of technology is in caring science. In literature, the concept of technology is used diversely referring it to caring technology, nursing technology, wellbeing technology, information technology, telenursing and technology in care named by a specific device or an area of nursing or medicine. The definition of the concept of technology and its ontology has not been determined from the viewpoint of caring science. Eriksson's model of concept determination provides a method to explore the ontology of the concept. This includes an etymological and semantic analysis as well as a determination of essence and basic category of the concept. The results showed that the concept of technology is multidimensional. It has evolved and altered over the centuries. The origin of the concept formulated from the Greek word 'techne', which has wider ontological dimensions. It is universal, it can be taught and it depends on the substance. Subsequently, the concept was introduced an ethical dimension, and it also developed more to the direction of engineering, mechanics and technical know-how. The semantic analysis revealed synonyms of the concept: art, equipment and knowledge. These introduced concepts such as craft, skill, treatment, engineering, science, study method and way. The nuances of the concept framed its nature. On the one hand, it stands out as practical and advanced, but on the other hand, it is difficult and conventional. The knowledge gained in this study will help to understand the phenomenon of technology in caring science.

  2. The Units Ontology: a tool for integrating units of measurement in science.

    Science.gov (United States)

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

    2012-01-01

    Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. Ontologies are means that facilitate the integration of data and knowledge allowing interoperability and semantic information processing between diverse biomedical resources and domains. Here, we present the Units Ontology (UO), an ontology currently being used in many scientific resources for the standardized description of units of measurements.

  3. Veiled chameleons: Analyzing urban science teachers' epistemological and ontological beliefs on "caring" for urban students' science literacy

    Science.gov (United States)

    Barrett, Channa Nicole

    The present study investigated teachers' epistemological and ontological beliefs and how those beliefs influence "caring" for urban students' science literacy. The grounded theory research involved six teacher participants and 18 student participants and collected the data using the following methods: Teacher and student interviews and six weeks of classroom observations. Using critical race theory (CRT) as a lens, the analysis of the data occurred simultaneously with the data collection. The findings revealed seven categories and 16 themes, which emerged from the analysis on "caring" for students' science literacy. From the CRT model tested in the study, the data illustrated a plethora of evidence relating to the themes colorblindness, interest convergence, and microaggressions. A negative effect of teachers who practiced colorblindness in the classroom revealed an assignment of subordinate positions, meaning the teacher assumed the role of the ultimate-knowledge holder in the classroom and the students assumed an academic co-dependency role in the classroom. Such an environment, allowed the teachers to become epistemically privileged while the students became epistemically oppressed. Implications for teaching suggest that there are different "shades" of caring for students' science literacy and that teachers should acknowledge the vast critical race-gendered epistemologies that students bring into the classroom in an effort to move towards a just epistemic environment.

  4. Life sciences flight experiments microcomputer

    Science.gov (United States)

    Bartram, Peter N.

    1987-01-01

    A promising microcomputer configuration for the Spacelab Life Sciences Lab. Equipment inventory consists of multiple processors. One processor's use is reserved, with additional processors dedicated to real time input and output operations. A simple form of such a configuration, with a processor board for analog to digital conversion and another processor board for digital to analog conversion, was studied. The system used digital parallel data lines between the boards, operating independently of the system bus. Good performance of individual components was demonstrated: the analog to digital converter was at over 10,000 samples per second. The combination of the data transfer between boards with the input or output functions on each board slowed performance, with a maximum throughput of 2800 to 2900 analog samples per second. Any of several techniques, such as use of the system bus for data transfer or the addition of direct memory access hardware to the processor boards, should give significantly improved performance.

  5. Ontologies in biological data visualization.

    Science.gov (United States)

    Carpendale, Sheelagh; Chen, Min; Evanko, Daniel; Gehlenborg, Nils; Gorg, Carsten; Hunter, Larry; Rowland, Francis; Storey, Margaret-Anne; Strobelt, Hendrik

    2014-01-01

    In computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifies a relation between two concepts. Ontological development in biology can serve as a focus to discuss the challenges and possible research directions for ontologies in visualization. The principle challenges are the dynamic and evolving nature of ontologies, the ever-present issue of scale, the diversity and richness of the relationships in ontologies, and the need to better understand the relationship between ontologies and the data analysis tasks scientists wish to support. Research directions include visualizing ontologies; visualizing semantically or ontologically annotated texts, documents, and corpora; automated generation of visualizations using ontologies; and visualizing ontological context to support search. Although this discussion uses issues of ontologies in biological data visualization as a springboard, these topics are of general relevance to visualization.

  6. African Journals Online: Biology & Life Sciences

    African Journals Online (AJOL)

    Items 51 - 71 of 71 ... Nigerian Journal of Genetics .... Africa such as HIV, malaria, tuberculosis, neglected diseases and emerging disease. ... of pure and applied science, natural and life science, medicine, geology, architecture and engineering.

  7. Ayurveda research: Ontological challenges.

    Science.gov (United States)

    Nayak, Jayakrishna

    2012-01-01

    Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the 'ASIIA (A Science Initiative In Ayurveda)' projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed.

  8. Ayurveda research: Ontological challenges

    Directory of Open Access Journals (Sweden)

    Jayakrishna Nayak

    2012-01-01

    Full Text Available Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the ′ASIIA (A Science Initiative In Ayurveda′ projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed.

  9. Semantic Web applications and tools for the life sciences: SWAT4LS 2010.

    Science.gov (United States)

    Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott; Splendiani, Andrea

    2012-01-25

    As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.

  10. 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. However,...

  11. John Greenleaf's life of science.

    Science.gov (United States)

    Watenpaugh, Donald E

    2012-12-01

    This article summarizes the life and career of John E. Greenleaf, PhD. It complements an interview of Dr. Greenleaf sponsored by the American Physiological Society Living History Project found on the American Physiological Society website. Dr. Greenleaf is a "thought leader" and internationally renowned physiologist, with extensive contributions in human systems-level environmental physiology. He avoided self-aggrandizement and believed that deeds rather than words define one's legacy. Viewed another way, however, Greenleaf's words define his deeds: 48% of his 185 articles are first author works, which is an unusually high proportion for a scientist of his stature. He found that writing a thorough and thoughtful discussion section often led to novel ideas that drove future research. Beyond Greenleaf's words are the many students, postdocs, and collaborators lucky enough to have worked with him and thus learn and carry on his ways of science. His core principles included the following: avoid research "fads," embrace diversity, be the first subject in your own research, adhere to rules of fiscal responsibility, and respect administrative forces-but never back down from them when you know you are right. Greenleaf's integrity ensured he was usually right. He thrived on the axiom of many successful scientists: avoid falling in love with hypotheses, so that when unexpected findings appear, they arouse curiosity instead of fear. Dr. Greenleaf's legacy will include the John and Carol Greenleaf Award for prolific environmental and exercise-related publication in the Journal of Applied Physiology.

  12. Science gateways for semantic-web-based life science applications.

    Science.gov (United States)

    Ardizzone, Valeria; Bruno, Riccardo; Calanducci, Antonio; Carrubba, Carla; Fargetta, Marco; Ingrà, Elisa; Inserra, Giuseppina; La Rocca, Giuseppe; Monforte, Salvatore; Pistagna, Fabrizio; Ricceri, Rita; Rotondo, Riccardo; Scardaci, Diego; Barbera, Roberto

    2012-01-01

    In this paper we present the architecture of a framework for building Science Gateways supporting official standards both for user authentication and authorization and for middleware-independent job and data management. Two use cases of the customization of the Science Gateway framework for Semantic-Web-based life science applications are also described.

  13. JPRS Report, Science & Technology, USSR: Life Sciences

    Science.gov (United States)

    2007-11-02

    Melnikov, Laboratory of Bionic Research (Headed by Candidate of Biological Sciences A. A. Kuzmin), Pacific Scientific Research Institute of... architecture have a great deal in common with the arterial systems of whales described earlier. Figures 2, references 14: 6 Russian, 8 Western

  14. JPRS Report - Science & Technology USSR: Life Sciences.

    Science.gov (United States)

    1988-04-22

    conducted in the department of cytophysiology and cellular engineering of the UkSSR Academy of Science Institute of Botany in Kiev. Yuriy Yuryevich... internship under the direct supervision of the institute. 13227 JPRS-ULS-88-008 22 April 1988 Electrical Activity of Human Brain Under Conditions of

  15. Science Teachers' Interpretations of Islamic Culture Related to Science Education versus the Islamic Epistemology and Ontology of Science

    Science.gov (United States)

    Mansour, Nasser

    2010-01-01

    The debate about Islam and science extends to a debate about the relationship between Islam and science education. In this paper, I explore Egyptian teachers' views of the relationship between science and religion within the Islamic context. Teachers' key vision of the relationship between science and religion was that "religion comes first and…

  16. Science Teachers' Interpretations of Islamic Culture Related to Science Education versus the Islamic Epistemology and Ontology of Science

    Science.gov (United States)

    Mansour, Nasser

    2010-01-01

    The debate about Islam and science extends to a debate about the relationship between Islam and science education. In this paper, I explore Egyptian teachers' views of the relationship between science and religion within the Islamic context. Teachers' key vision of the relationship between science and religion was that "religion comes first…

  17. A UML profile for the OBO relation ontology.

    Science.gov (United States)

    Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

    2012-01-01

    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.

  18. JPRS Report Science & Technology USSR: Life Sciences.

    Science.gov (United States)

    1990-07-09

    Traumatology, Orthopedy and Field Surgery (head—professor M. F. Durov) and Chair of VK and LFK (head— docent P. G. Koynosov) of Tyumen Medical...Yu. D., Los, I. P and Popovich, V. M., "Fiziko-matematicheskaya problema deystviya elektro- magnitnykh poley i ionizatsii vozdukha" [The Physico...Article by S. I. Leonovich, docent , and Yu. M. Gain, candidate of medical science, Minsk] [Abstract] An international symposium on lasers in surgery

  19. JPRS Report, Science & Technology USSR: Life Sciences.

    Science.gov (United States)

    1988-07-01

    S. Grigoryan, M. V. Kameneva et ai; DOKLADY AKADEMII NAUK SSSR, No 3, Sep 87] 6 GENETICS Plant Genetics Research in Estonia [O. Priylinn...the hemolysates. Refer- ences 10: 4 Russian, 6 Western. 12126 JPRS-ULS-88-011 1 July 1988 GENETICS Plant Genetics Research in Estonia 18400307...Agriculture"] [Abstract] The department of plant genetics at the Insti- tute of Experimental Biology of the ESSR Academy of Sciences has made a number of

  20. Launching the CUSBEA Article Series in SCIENCE CHINA Life Sciences

    Institute of Scientific and Technical Information of China (English)

    CHANG ZengYi

    2010-01-01

    @@ As a CUSBEA (China-United States Biochemistry Examination and Administration) Program fellow of Class Ⅳ (1985), I am very excited to announce the official launch of the CUSBEA Article Series in SCIENCE CHINA Life Sciences, a journal in which I am currently serving as Executive Vice-Editor-in-Chief.A couple of months ago, I initially proposed this idea to the Editor-in-Chief of SCIENCE CHINA Life Sciences, Professor Wang Da-Cheng and to the Editor General of SCIENCE CHINA Life Sciences, Professor Zhu Zuoyan, both of whom responded very positively.The article contributed by Dr.Luo Liqun [1],CUSBEA fellow of Class Ⅵ (1987) and currently professor in the Department of Biology at Stanford University, as well as Investigator at the Howard Hughes Medical Institute, marks the official beginning of this series.

  1. Geobiology of the Critical Zone: the Hierarchies of Process, Form and Life provide an Integrated Ontology

    Science.gov (United States)

    Cotterill, Fenton P. D.

    2016-04-01

    ways in how ecological fidelity of biodiversity maps on to landforms and their patchy environments, and this interplay has in turn acted to anchor evolutionary signals in the millions of individual species. The antiquity of African landscapes holds exciting opportunities for interdisciplinary explorations seeking mechanistic tests of this interplay between Process, Form and Life. The time is ripe to study African landforms and biota as a coevolving complex. Key words: ontology, hierarchy theory, Individuality Thesis, Ghiselin, geobiology, geoecodynamics

  2. Life sciences: Lawrence Berkeley Laboratory, 1988

    Energy Technology Data Exchange (ETDEWEB)

    1989-07-01

    Life Sciences Research at LBL has both a long history and a new visibility. The physics technologies pioneered in the days of Ernest O. Lawrence found almost immediate application in the medical research conducted by Ernest's brother, John Lawrence. And the tradition of nuclear medicine continues today, largely uninterrupted for more than 50 years. Until recently, though, life sciences research has been a secondary force at the Lawrence Berkeley Laboratory (LBL). Today, a true multi-program laboratory has emerged, in which the life sciences participate as a full partner. The LBL Human Genome Center is a contribution to the growing international effort to map the human genome. Its achievements represent LBL divisions, including Engineering, Materials and Chemical Sciences, and Information and Computing Sciences, along with Cell and Molecular Biology and Chemical Biodynamics. The Advanced Light Source Life Sciences Center will comprise not only beamlines and experimental end stations, but also supporting laboratories and office space for scientists from across the US. This effort reflects a confluence of scientific disciplines --- this time represented by individuals from the life sciences divisions and by engineers and physicists associated with the Advanced Light Source project. And finally, this report itself, the first summarizing the efforts of all four life sciences divisions, suggests a new spirit of cooperation. 30 figs.

  3. Analogical reflection as a source for the science of life: Kant and the possibility of the biological sciences.

    Science.gov (United States)

    Nassar, Dalia

    2016-08-01

    In contrast to the previously widespread view that Kant's work was largely in dialogue with the physical sciences, recent scholarship has highlighted Kant's interest in and contributions to the life sciences. Scholars are now investigating the extent to which Kant appealed to and incorporated insights from the life sciences and considering the ways he may have contributed to a new conception of living beings. The scholarship remains, however, divided in its interest: historians of science are concerned with the content of Kant's claims, and the ways in which they may or may not have contributed to the emerging science of life, while historians of philosophy focus on the systematic justifications for Kant's claims, e.g., the methodological and theoretical underpinnings of Kant's statement that living beings are mechanically inexplicable. My aim in this paper is to bring together these two strands of scholarship into dialogue by showing how Kant's methodological concerns (specifically, his notion of reflective judgment) contributed to his conception of living beings and to the ontological concern with life as a distinctive object of study. I argue that although Kant's explicit statement was that biology could not be a science, his implicit and more fundamental claim was that the study of living beings necessitates a distinctive mode of thought, a mode that is essentially analogical. I consider the implications of this view, and argue that it is by developing a new methodology for grasping organized beings that Kant makes his most important contribution to the new science of life.

  4. Life Sciences in the 21 st Century

    Institute of Scientific and Technical Information of China (English)

    Zou Chenglu (C. L. Tsou)

    2001-01-01

    This article presents a retrospective of the achievements of life sciences in the 20th century and a prospective in the 21 st century.primarily,because of the emergence of molecular biology in the 20th cetury,life sciences have grown up from a descriptive discipline to an exact science.Biology in the 21st century features a unification between analysis and integration,i.e.the unification of analysis and func-tional research.More and more interdisciplinary integration will be based on works of penetrating analyses.Secondly.the deeper understanding of all living phenomena will lead to a unified connition of the essence of life so that general biology in the genuine sese of the term will come into being.finally,basic research on the life sciences will produce an unprecedented influence on all aspects of human life.

  5. JPRS Report, Science & Technology, USSR: Life Sciences

    Science.gov (United States)

    1988-04-15

    Lepidoptera . A toxin isolated from H. hebetor homogenate with a molecular weight of 18,000 daltons possesses analogous biological properties. The...healthy way of life. More than two-thirds of the population is involved in no systematic physical exercise program or in athletics, as much as 30...a consolidated system for evaluating and systematically observing the state of health of the Soviet citizen and the society as a whole. Relying on

  6. JPRS Report, Science & Technology, USSR: Life Sciences.

    Science.gov (United States)

    2007-11-02

    PARAZITARNYYE BOLEZNI, No 3, May-Jun 86) 22 Detection Rate of Virus Hepatitis B Markers in Patients in Hemodialysis Department (V, I. Vasilyeva, A...derivation of valuable products essential to human life. There is not yet, in our opinion, a precise definition of...with a preoccupation with microorganisms and cell cultures. We will, therefore, adhere to a definition that places biotechnology in a division of

  7. An open annotation ontology for science on web 3.0.

    Science.gov (United States)

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

    2011-05-17

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

  8. MATLAB for Engineering and the Life Sciences

    CERN Document Server

    Tranquillo, Joseph

    2011-01-01

    In recent years, the life sciences have embraced simulation as an important tool in biomedical research. Engineers are also using simulation as a powerful step in the design process. In both arenas, Matlab has become the gold standard. It is easy to learn, flexible, and has a large and growing userbase. MATLAB for Engineering and the Life Sciences is a self-guided tour of the basic functionality of MATLAB along with the functions that are most commonly used in biomedical engineering and other life sciences. Although the text is written for undergraduates, graduate students and academics, those

  9. Breathing Life into Engineering: A Lesson Study Life Science Lesson

    Science.gov (United States)

    Lawrence, Maria; Yang, Li-Ling; Briggs, May; Hession, Alicia; Koussa, Anita; Wagoner, Lisa

    2016-01-01

    A fifth grade life science lesson was implemented through a lesson study approach in two fifth grade classrooms. The research lesson was designed by a team of four elementary school teachers with the goal of emphasizing engineering practices consistent with the "Next Generation Science Standards" (NGSS) (Achieve Inc. 2013). The fifth…

  10. Breathing Life into Engineering: A Lesson Study Life Science Lesson

    Science.gov (United States)

    Lawrence, Maria; Yang, Li-Ling; Briggs, May; Hession, Alicia; Koussa, Anita; Wagoner, Lisa

    2016-01-01

    A fifth grade life science lesson was implemented through a lesson study approach in two fifth grade classrooms. The research lesson was designed by a team of four elementary school teachers with the goal of emphasizing engineering practices consistent with the "Next Generation Science Standards" (NGSS) (Achieve Inc. 2013). The fifth…

  11. Launching the CUSBEA Article Series in SCIENCE CHINA Life Sciences

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    As a CUSBEA (China-United States Biochemistry Examination and Administration) Program fellow of Class IV (1985), I am very excited to announce the official launch of the CUSBEA Article Series in SCIENCE CHINA Life

  12. Physical and Life Sciences 2008 Science & Technology Highlights

    Energy Technology Data Exchange (ETDEWEB)

    Correll, D L; Hazi, A U

    2009-05-06

    This document highlights the outstanding research and development activities in the Physical and Life Sciences Directorate that made news in 2008. It also summarizes the awards and recognition received by members of the Directorate in 2008.

  13. McNamara Life Sciences Building

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: General purpose laboratory test building The McNamara Life Sciences building allows scientists to manage and execute the Department of Defense...

  14. Recent CAS Achievements in Life Sciences

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    @@ Recent years have witnessed remarkable progress scored by CAS researchers along with the smooth development of the knowledge innovation program piloted at CAS. The follow-ings are just recent examples of CAS research achievements in life sciences.

  15. More Life-Science Experiments For Spacelab

    Science.gov (United States)

    Savage, P. D., Jr.; Dalton, B.; Hogan, R.; Leon, H.

    1991-01-01

    Report describes experiments done as part of Spacelab Life Sciences 2 mission (SLS-2). Research planned on cardiovascular, vestibular, metabolic, and thermal responses of animals in weightlessness. Expected to shed light on effects of prolonged weightlessness on humans.

  16. More Life-Science Experiments For Spacelab

    Science.gov (United States)

    Savage, P. D., Jr.; Dalton, B.; Hogan, R.; Leon, H.

    1991-01-01

    Report describes experiments done as part of Spacelab Life Sciences 2 mission (SLS-2). Research planned on cardiovascular, vestibular, metabolic, and thermal responses of animals in weightlessness. Expected to shed light on effects of prolonged weightlessness on humans.

  17. «The powerful, non-organic life which grips the world». Vitalism and Ontology in Gilles Deleuze

    Directory of Open Access Journals (Sweden)

    Giulio Piatti

    2017-06-01

    Full Text Available It is well known that Gilles Deleuze is the heir of a complex vitalistic tradition, beginning with Henri Bergson’s Creative Evolution and spanning through an important part of 20th century French philosophy. According to this line of thought, philosophy has to sharpen its vision in order to grasp the irreducible nature of the living. On one hand Deleuze seems to explicitly follow these intuitions, on the other though he strives to find a viable ontological framework for an actual philosophy of life, reaffirming the Nietzschean notion of being as becoming, the Bergsonian virtual coexistence of memory and Scotist univocity of the being. Through such operation, Deleuze actually seems to distance himself from a simply vitalistic approach, and to build instead an original metaphysics that understands life as a powerful inorganic force crossing all levels of reality. The organic, thus, is what traps and diverts (détourne this impersonal and germinal life. Aim of the presentation is to clarify the originality of Deleuze’s vitalistic ontology and point to its ambiguities and debts towards other philosophical traditions. Even if Deleuze apparently overturns his vitalistic roots, it is nevertheless undeniable that the vital domain will engage him throughout all of his work.

  18. Teleology and randomness in the development of natural sciences research: systems, ontology and evolution

    Directory of Open Access Journals (Sweden)

    Paulo Pereira Martins Júnior

    2011-12-01

    Full Text Available This is an investigation on the subject of  Teleology, which has been dealt with all along the history of the human thought with special emphasis to the interval related to the development of scientific theories referring to the study of Nature.  The presentation of the subject starts with the conceptual definitions of Teleology. Following, this subject is revisited all along the historical application of the concept in the development of science. In this respect, the first approach is about teleology in Biology and life sciences, with emphasis on the repercussion over the vitalist conception and natural selection.  Hence, the discussion turns around the dialectic conceptions of teleological systems and random systems. Finally, this paper finishes with a thought about how these themes may be pertinent within the environmental studies whereon physical, biological and human systems are in co-operation, with the various applications of nuances and uses of the teleological concept.

  19. Database Selection in the Life Sciences.

    Science.gov (United States)

    Snow, Bonnie

    1985-01-01

    Focuses on indexing refinements in major life science databases--those specializing in biological/biomedical literature coverage--which influence cross-life searching decisions. Tables included highlight database descriptions, comparisons in coverage, ease of access (indexing of secondary concepts or search modifiers), chemical substance indexing…

  20. Ontologies, methodologies, and new uses of Big Data in the social and cultural sciences

    Directory of Open Access Journals (Sweden)

    Robin Wagner-Pacifici

    2015-12-01

    Full Text Available In our Introduction to the Conceiving the Social with Big Data Special Issue of Big Data & Society , we survey the 18 contributions from scholars in the humanities and social sciences, and highlight several questions and themes that emerge within and across them. These emergent issues reflect the challenges, problems, and promises of working with Big Data to access and assess the social. They include puzzles about the locus and nature of human life, the nature of interpretation, the categorical constructions of individual entities and agents, the nature and relevance of contexts and temporalities, and the determinations of causality. As such, the Introduction reflects on the contributions along a series of binaries that capture the dualities and dynamisms of these themes: Life/Data; Mind/Machine; and Induction/Deduction.

  1. Ontologies, methodologies, and new uses of Big Data in the social and cultural sciences

    Directory of Open Access Journals (Sweden)

    Robin Wagner-Pacifici

    2015-12-01

    Full Text Available In our Introduction to the Conceiving the Social with Big Data Special Issue of Big Data & Society, we survey the 18 contributions from scholars in the humanities and social sciences, and highlight several questions and themes that emerge within and across them. These emergent issues reflect the challenges, problems, and promises of working with Big Data to access and assess the social. They include puzzles about the locus and nature of human life, the nature of interpretation, the categorical constructions of individual entities and agents, the nature and relevance of contexts and temporalities, and the determinations of causality. As such, the Introduction reflects on the contributions along a series of binaries that capture the dualities and dynamisms of these themes: Life/Data; Mind/Machine; and Induction/Deduction.

  2. Physics transforming the life sciences.

    Science.gov (United States)

    Onuchic, José N

    2014-10-08

    Biological physics is clearly becoming one of the leading sciences of the 21st century. This field involves the cross-fertilization of ideas and methods from biology and biochemistry on the one hand and the physics of complex and far from equilibrium systems on the other. Here I want to discuss how biological physics is a new area of physics and not simply applications of known physics to biological problems. I will focus in particular on the new advances in theoretical physics that are already flourishing today. They will become central pieces in the creation of this new frontier of science.

  3. Userscripts for the Life Sciences

    Directory of Open Access Journals (Sweden)

    Guha Rajarshi

    2007-12-01

    Full Text Available Abstract Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in

  4. USSR Space Life Sciences Digest, issue 13

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Teeter, Ronald (Editor); Teeter, Ronald (Editor); Teeter, Ronald (Editor); Teeter, Ronald (Editor)

    1987-01-01

    This is the thirteenth issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 39 papers recently published in Russian-language periodicals and bound collections, two papers delivered at an international life sciences symposium, and three new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Also included is a review of a recent Soviet-French symposium on Space Cytology. Current Soviet Life Sciences titles available in English are cited. The materials included in this issue have been identified as relevant to 31 areas of aerospace medicine and space biology. These areas are: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, cosmonaut training, cytology, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal systems, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, space biology, and space medicine.

  5. Science Education in Second Life

    Science.gov (United States)

    Merchant, Zahira

    2010-01-01

    The purpose of the observational study was to investigate whether spaces in Second Life (SL) displaying interactive scientific exhibits can become potential avenues to promote inquiry in teaching scientific concepts. 42 SL spaces (islands) were selected using inclusion/exclusion criteria out of 155 spaces that were found using three different…

  6. Interdisciplinary reasoning about energy in an introductory physics course for the life sciences

    Science.gov (United States)

    Dreyfus, Benjamin William

    Energy is a unifying concept that cuts across physics, chemistry, and biology. However, students who study all three disciplines can end up with a fragmented understanding of energy. This dissertation sits at the intersection of two active areas of current research: the teaching and learning of energy, and interdisciplinary science education (particularly the intersection of physics and biology). The context for this research is an introductory physics course for undergraduate life sciences majors that is reformed to build stronger interdisciplinary connections between physics, biology, and chemistry. An approach to energy that incorporates chemical bonds and chemical reactions is better equipped to meet the needs of life sciences students than a traditional introductory physics approach that focuses primarily on mechanical energy, and so we present a curricular thread for chemical energy in the physics course. Our first set of case studies examines student reasoning about ATP hydrolysis, a biochemically significant reaction that powers various processes in the cell. We observe students expressing both that an energy input is required to break a chemical bond (which they associate with physics) and that energy is released when the phosphate bond is broken in ATP (which they associate with biology). We use these case studies to articulate a model of interdisciplinary reconciliation: building coherent connections between concepts from different disciplines while understanding each concept in its own disciplinary context and justifying the modeling choices in deciding when to use each disciplinary model. Our second study looks at ontological metaphors for energy: metaphors about what kind of thing energy is. Two ontological metaphors for energy that have previously been documented include energy as a substance and energy as a location. We argue for the use of negative energy in modeling chemical energy in an interdisciplinary context, and for the use of a blended

  7. Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

    Science.gov (United States)

    Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

    2006-01-01

    The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

  8. A comparative analysis of South African Life Sciences and Biology ...

    African Journals Online (AJOL)

    Hennie

    Keywords: Biology textbooks; Life Sciences textbooks; nature of science; school ... reform, this article reports on the analysis of South African Life Sciences and Biology .... molecular studies; structures and control processes; ..... References.

  9. Life sciences space biology project planning

    Science.gov (United States)

    Primeaux, G.; Newkirk, K.; Miller, L.; Lewis, G.; Michaud, R.

    1988-01-01

    The Life Sciences Space Biology (LSSB) research will explore the effect of microgravity on humans, including the physiological, clinical, and sociological implications of space flight and the readaptations upon return to earth. Physiological anomalies from past U.S. space flights will be used in planning the LSSB project.The planning effort integrates science and engineering. Other goals of the LSSB project include the provision of macroscopic view of the earth's biosphere, and the development of spinoff technology for application on earth.

  10. Life sciences and biotechnology in China

    OpenAIRE

    Chen, Zhu; Wang, Hong-Guang; Wen, Zhao-Jun; Wang, Yihuang

    2007-01-01

    Life science and biotechnology have become a top priority in research and development in many countries as the world marches into the new century. China as a developing country with a 1.3 billion population and booming economy is actively meeting the challenge of a new era in this area of research. Owing to support from the government and the scientific community, and reform to improve the infrastructure, recent years have witnessed a rapid progress in some important fields of life science an...

  11. Nonautonomous dynamical systems in the life sciences

    CERN Document Server

    Pötzsche, Christian

    2013-01-01

    Nonautonomous dynamics describes the qualitative behavior of evolutionary differential and difference equations, whose right-hand side is explicitly time dependent. Over recent years, the theory of such systems has developed into a highly active field related to, yet recognizably distinct from that of classical autonomous dynamical systems. This development was motivated by problems of applied mathematics, in particular in the life sciences where genuinely nonautonomous systems abound. The purpose of this monograph is to indicate through selected, representative examples how often nonautonomous systems occur in the life sciences and to outline the new concepts and tools from the theory of nonautonomous dynamical systems that are now available for their investigation.

  12. Space life sciences strategic plan, 1991

    Science.gov (United States)

    1992-01-01

    Over the last three decades the life sciences program has significantly contributed to NASA's manned and unmanned exploration of space, while acquiring new knowledge in the fields of space biology and medicine. The national and international events which have led to the development and revision of NASA strategy will significantly affect the future of life sciences programs both in scope and pace. This document serves as the basis for synthesizing the option to be pursued during the next decade, based on the decisions, evolution, and guiding principles of the National Space Policy.

  13. Life Sciences Division annual report, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Marrone, B.L.; Cram, L.S. (comps.)

    1989-04-01

    This report summarizes the research and development activities of Los Alamos National Laboratory's Life Sciences Division for the calendar year 1988. Technical reports related to the current status of projects are presented in sufficient detail to permit the informed reader to assess their scope and significance. Summaries useful to the casual reader desiring general information have been prepared by the Group Leaders and appear in each group overview. Investigators on the staff of the Life Sciences Division will be pleased to provide further information.

  14. Introductory mathematics for the life sciences

    CERN Document Server

    Phoenix, David

    2002-01-01

    Introductory Mathematics for the Life Sciences offers a straightforward introduction to the mathematical principles needed for studies in the life sciences. Starting with the basics of numbers, fractions, ratios, and percentages, the author explains progressively more sophisticated concepts, from algebra, measurement, and scientific notation through the linear, power, exponential, and logarithmic functions to introductory statistics. Worked examples illustrate concepts, applications, and interpretations, and exercises at the end of each chapter help readers apply and practice the skills they develop. Answers to the exercises are posted at the end of the text.

  15. Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

    Science.gov (United States)

    Christen, Victor; Hartung, Michael; Groß, Anika

    2015-01-01

    A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

  16. Quantum Man: Richard Feynman's Life in Science

    CERN Document Server

    CERN. Geneva

    2011-01-01

    It took a man who was willing to break all the rules to tame a theory that breaks all the rules. This talk will be based on my new book Quantum Man: Richard Feynman's life in science. I will try and present a scientific overview of the contributions of Richard Feynman, as seen through the arc of his fascinating life. From Quantum Mechanics to Antiparticles, from Rio de Janeiro to Los Alamos, a whirlwind tour will provide insights into the character, life and accomplishments of one of the 20th centuries most important scientists, and provide an object lesson in scientific integrity.

  17. Ethical challenges for the life sciences

    NARCIS (Netherlands)

    Korthals, M.J.J.A.A.

    2004-01-01

    In this book we will first discuss broader issues of ethics of the life sciences, which enable us later on to focus on the more specific issues. Therefore, we begin with two contributions on the ethical issues of working in organizations. A fruitful side effect of this start is that it gives a good

  18. Ethical challenges for the life sciences

    NARCIS (Netherlands)

    Korthals, M.J.J.A.A.

    2004-01-01

    In this book we will first discuss broader issues of ethics of the life sciences, which enable us later on to focus on the more specific issues. Therefore, we begin with two contributions on the ethical issues of working in organizations. A fruitful side effect of this start is that it gives a good

  19. 75 Easy Life Science Demonstrations. Teacher Book.

    Science.gov (United States)

    Kardos, Thomas

    This book is a collection of life science classroom demonstrations. Explanations that review key concepts are included. Topics are: stimulus and response; gravitropism; phototropism; living organisms; carbon dioxide; gases emitted by plants; greenhouse effect; stomata; transpiration; leaf skeletons; seed growth; water evaporation in plants; carbon…

  20. Skylab experiments. Volume 4: Life sciences

    Science.gov (United States)

    1973-01-01

    The life sciences experiments conducted during Skylab missions are discussed. The general categories of the experiments are as follows: (1) mineral and hormonal balance, (2) hematology and immunology, (3) cardiovascular status, (4) energy expenditure, (5) neurophysiology, and (7) biology. Each experiment within the general category is further identified with respect to the scientific objectives, equipment used, performance, and data to be obtained.

  1. 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.

  2. USSR Space Life Sciences Digest, issue 1

    Science.gov (United States)

    Hooke, L. R.; Radtke, M.; Rowe, J. E.

    1985-01-01

    The first issue of the bimonthly digest of USSR Space Life Sciences is presented. Abstracts are included for 49 Soviet periodical articles in 19 areas of aerospace medicine and space biology, published in Russian during the first quarter of 1985. Translated introductions and table of contents for nine Russian books on topics related to NASA's life science concerns are presented. Areas covered include: botany, cardiovascular and respiratory systems, cybernetics and biomedical data processing, endocrinology, gastrointestinal system, genetics, group dynamics, habitability and environmental effects, health and medicine, hematology, immunology, life support systems, man machine systems, metabolism, musculoskeletal system, neurophysiology, perception, personnel selection, psychology, radiobiology, reproductive system, and space biology. This issue concentrates on aerospace medicine and space biology.

  3. USSR Space Life Sciences Digest, issue 2

    Science.gov (United States)

    Hooke, L. R. (Editor); Radtke, M. (Editor); Garshnek, V. (Editor); Rowe, J. E. (Editor); Teeter, R. (Editor)

    1985-01-01

    The second issue of the bimonthly digest of USSR Space Life Sciences is presented. Abstracts are included for 39 Soviet periodical articles in 16 areas of aerospace medicine and space biology and published in Russian during the first half of 1985. Selected articles are illustrated with figures from the original. Translated introductions and tables of contents for 14 Russian books on 11 topics related to NASA's life science concerns are presented. Areas covered are: adaptation, biospheric, body fluids, botany, cardiovascular and respiratory systems, cybernetics and biomedical data processing, gastrointestinal system, group dynamics, habitability and environmental effects, health and medical treatment, hematology, immunology, life support systems, metabolism, musculoskeletal system, neurophysiology, psychology, radiobiology, and space biology. Two book reviews translated from Russian are included and lists of additional relevant titles available either in English or in Russian only are appended.

  4. USSR Space Life Sciences Digest, issue 14

    Science.gov (United States)

    Hooke, Lydia Razran; Teeter, Ronald; Radtke, Mike; Rowe, Joseph

    1988-01-01

    This is the fourteenth issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 32 papers recently published in Russian language periodicals and bound collections and of three new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Also included is a review of a recent Soviet conference on Space Biology and Aerospace Medicine. Current Soviet life sciences titles available in English are cited. The materials included in this issue have been identified as relevant to the following areas of aerospace medicine and space biology: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal systems, habitability and environment effects, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, and space biology and medicine.

  5. USSR Space Life Sciences Digest, issue 11

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Radtke, Mike (Editor); Radtke, Mike (Editor); Radtke, Mike (Editor); Radtke, Mike (Editor); Radtke, Mike (Editor)

    1987-01-01

    This is the eleventh issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 54 papers recently published in Russian language periodicals and bound collections and of four new Soviet monographs. Selected abstracts are illustrated. Additional features include the translation of a paper presented in Russian to the United Nations, a review of a book on space ecology, and report of a conference on evaluating human functional capacities and predicting health. Current Soviet Life Sciences titles available in English are cited. The materials included in this issue have been identified as relevant to 30 areas of aerospace medicine and space biology. These areas are: adaptation, aviation physiology, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, cosmonaut training, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal systems, group dynamics, genetics, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, and radiobiology.

  6. USSR Space Life Sciences Digest, issue 3

    Science.gov (United States)

    Hooke, L. R. (Editor); Radtke, M. (Editor); Garshnek, V. (Editor); Rowe, J. E. (Editor); Teeter, R. (Editor)

    1985-01-01

    This is the third issue of NASA's USSR Space Life Sciences Digest. Abstracts are included for 46 Soviet periodical articles in 20 areas of aerospace medicine and space biology and published in Russian during the second third of 1985. Selected articles are illustrated with figures and tables from the original. In addition, translated introductions and tables of contents for seven Russian books on six topics related to NASA's life science concerns are presented. Areas covered are adaptation, biospherics, body fluids, botany, cardiovascular and respiratory systems, endocrinology, exobiology, gravitational biology, habitability and environmental effects, health and medical treatment, immunology, life support systems, metabolism, microbiology, musculoskeletal system; neurophysiology, nutrition, perception, personnel selection, psychology, radiobiology, and space physiology. Two book reviews translated from the Russian are included and lists of additional relevant titles available in English with pertinent ordering information are given.

  7. Library and Information Science's Ontological Position in the Networked Society: Using New Technology to Get Back to an Old Practice

    Science.gov (United States)

    Kåhre, Peter

    2013-01-01

    Introduction: This paper concerns the ontological position of library and informations science in the networked society. The aim of the study is to understand library use and library functions in the age of Internet and artificial intelligent programmed search engines. Theoretical approach: The approach discusses so called sociocognitive tools in…

  8. Benchmarking ontologies: bigger or better?

    Directory of Open Access Journals (Sweden)

    Lixia Yao

    2011-01-01

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

  9. Benchmarking Ontologies: Bigger or Better?

    Science.gov (United States)

    Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A.; Rzhetsky, Andrey

    2011-01-01

    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. PMID:21249231

  10. Benchmarking ontologies: bigger or better?

    Science.gov (United States)

    Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A; Rzhetsky, Andrey

    2011-01-13

    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.

  11. Computational thinking in life science education.

    Directory of Open Access Journals (Sweden)

    Amir Rubinstein

    2014-11-01

    Full Text Available We join the increasing call to take computational education of life science students a step further, beyond teaching mere programming and employing existing software tools. We describe a new course, focusing on enriching the curriculum of life science students with abstract, algorithmic, and logical thinking, and exposing them to the computational "culture." The design, structure, and content of our course are influenced by recent efforts in this area, collaborations with life scientists, and our own instructional experience. Specifically, we suggest that an effective course of this nature should: (1 devote time to explicitly reflect upon computational thinking processes, resisting the temptation to drift to purely practical instruction, (2 focus on discrete notions, rather than on continuous ones, and (3 have basic programming as a prerequisite, so students need not be preoccupied with elementary programming issues. We strongly recommend that the mere use of existing bioinformatics tools and packages should not replace hands-on programming. Yet, we suggest that programming will mostly serve as a means to practice computational thinking processes. This paper deals with the challenges and considerations of such computational education for life science students. It also describes a concrete implementation of the course and encourages its use by others.

  12. Computational thinking in life science education.

    Science.gov (United States)

    Rubinstein, Amir; Chor, Benny

    2014-11-01

    We join the increasing call to take computational education of life science students a step further, beyond teaching mere programming and employing existing software tools. We describe a new course, focusing on enriching the curriculum of life science students with abstract, algorithmic, and logical thinking, and exposing them to the computational "culture." The design, structure, and content of our course are influenced by recent efforts in this area, collaborations with life scientists, and our own instructional experience. Specifically, we suggest that an effective course of this nature should: (1) devote time to explicitly reflect upon computational thinking processes, resisting the temptation to drift to purely practical instruction, (2) focus on discrete notions, rather than on continuous ones, and (3) have basic programming as a prerequisite, so students need not be preoccupied with elementary programming issues. We strongly recommend that the mere use of existing bioinformatics tools and packages should not replace hands-on programming. Yet, we suggest that programming will mostly serve as a means to practice computational thinking processes. This paper deals with the challenges and considerations of such computational education for life science students. It also describes a concrete implementation of the course and encourages its use by others.

  13. The neurological disease ontology.

    Science.gov (United States)

    Jensen, Mark; Cox, Alexander P; Chaudhry, Naveed; Ng, Marcus; Sule, Donat; Duncan, William; Ray, Patrick; Weinstock-Guttman, Bianca; Smith, Barry; Ruttenberg, Alan; Szigeti, Kinga; Diehl, Alexander D

    2013-12-06

    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer's disease, multiple sclerosis, and stroke. ND is implemented in OWL 2 and currently has more than 450 terms that refer to and describe various aspects of neurological diseases. ND directly imports the development version of OGMS, which uses BFO 2. Term development in ND has primarily extended the OGMS terms 'disease', 'diagnosis', 'disease course', and 'disorder'. We have imported and utilize over 700 classes from related ontology efforts including the Foundational Model of Anatomy, Ontology for Biomedical Investigations, and Protein Ontology. ND terms are annotated with ontology metadata such as a label (term name), term editors, textual definition, definition source, curation status, and alternative terms (synonyms). Many terms have logical definitions in addition to these annotations. Current development has focused on the establishment of the upper-level structure of the ND hierarchy, as well as on the representation of Alzheimer's disease, multiple sclerosis, and stroke. The ontology is available as a version-controlled file at http://code.google.com/p/neurological-disease-ontology along with a discussion list and an issue tracker. ND seeks to provide a formal foundation for the representation of clinical and research data

  14. USSR Space Life Sciences Digest, issue 28

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Rowe, Joseph (Editor)

    1990-01-01

    This is the twenty-eighth issue of NASA's Space Life Sciences Digest. It contains abstracts of 60 journal papers or book chapters published in Russian and of 3 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 20 areas of space biology and medicine. These areas include: adaptation, aviation medicine, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, hematology, human performance, immunology, life support systems, mathematical modeling, musculoskeletal system, neurophysiology, personnel selection, psychology, radiobiology, reproductive system, and space medicine.

  15. USSR Space Life Sciences Digest, issue 31

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1990-01-01

    This is the thirty first issue of NASA's Space Life Sciences Digest. It contains abstracts of 55 journal papers or book chapters published in Russian and of 5 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 18 areas of space biology and medicine. These areas include: adaptation, biological rhythms, cardiovascular and respiratory systems, endocrinology, enzymology, genetics, group dynamics, habitability and environmental effects, hematology, life support systems, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, psychology, radiobiology, and space biology and medicine.

  16. USSR Space Life Sciences Digest, issue 30

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Rowe, Joseph (Editor)

    1991-01-01

    This is the thirtieth issue of NASA's Space Life Sciences Digest. It contains abstracts of 47 journal papers or book chapters published in Russian and of three Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 20 areas of space biology and medicine. These areas include: adaptation, biospheric research, cardiovascular and respiratory systems, endocrinology, equipment and instrumentation, gastrointestinal system, group dynamics, habitability and environmental effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, psychology, radiobiology, and space biology and medicine.

  17. USSR Space Life Sciences Digest, issue 4

    Science.gov (United States)

    Hooke, L. R. (Editor); Radtke, M. (Editor); Garshnek, V. (Editor); Teeter, R. (Editor); Rowe, J. E. (Editor)

    1986-01-01

    The fourth issue of NASA's USSR Space Life Science Digest includes abstracts for 42 Soviet periodical articles in 20 areas of aerospace medicine and space biology and published in Russian during the last third of 1985. Selected articles are illustrated with figures and tables from the original. In addition, translated introductions and tables of contents for 17 Russian books on 12 topics related to NASA's life science concerns are presented. Areas covered are: adaptation, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, cytology, developmental biology, endocrinology, exobiology, habitability and environmental effects, health and medical treatment, hematology, histology, human performance, immunology, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, perception, personnel selection, psychology, and radiobiology. Two book reviews translated from the Russian are included and lists of additional relevant titles available in English with pertinent ordering information are given.

  18. "Physics and Life" for Europe's Science Teachers

    Science.gov (United States)

    2003-04-01

    interest in science and current scientific research. The goals of "Physics On Stage 3" [EWST Logo] "Physics on Stage 3" also aims to facilitate the exchange of good practice and innovative ideas among Europe's science teachers and to provide a forum for a broad debate among educators, administrators and policy-makers about the key problems in science education today. Moreover, it will make available the considerable, combined expertise of the EIROforum organisations to the European scientific teaching community, in order to promote the introduction of "fresh" science into the curricula and thus to convey a more realistic image of modern science to the pupils. "Physics on Stage 3" is concerned with basic science and also with the cross-over between different science disciplines - a trend becoming more and more important in today's science, which is not normally reflected in school curricula. A key element of the programme is to give teachers an up-to-date "insiders'" view of what is happening in science and to tell them about new, highly-diverse and interesting career opportunities for their pupils. Theme of the activities The theme of "Physics on Stage" this year is "Physics and Life" , reflecting the decision to broaden the Physics on Stage activities to encompass all the natural sciences. Including other sciences will augment the already successful concept, introducing a mixture of cross-over projects that highlight the multidisciplinary aspects of modern science. Among the many subjects to be presented are radiation, physics and the environment, astrobiology (the search for life beyond earth), complex systems, self-organising systems, sports science, the medical applications of physics, mathematics and epidemiology, etc. The main elements National activities "Physics on Stage 3" has already started and National Steering Committees in 22 countries, composed of eminent science teachers, scientists, administrators and others involved in setting school curricula, are now

  19. Breathing new life into cognitive science

    Directory of Open Access Journals (Sweden)

    Tom Froese

    2011-08-01

    Full Text Available In this article I take an unusual starting point from which to argue for a unified cognitive science, namely a position defined by what is sometimes called the ‘life-mind continuity thesis’. Accordingly, rather than taking a widely accepted starting point for granted and using it in order to propose answers to some well defined questions, I must first establish that the idea of life-mind continuity can amount to a proper starting point at all. To begin with, I therefore assess the conceptual tools which are available to construct a theory of mind on this basis. By drawing on insights from a variety of disciplines, especially from a combination of existential phenomenology and organism-centered biology, I argue that mind can indeed be conceived as rooted in life, but only if we accept at the same time that social interaction plays a constitutive role for our cognitive capacities.

  20. Ontologies for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Agnieszka Leszczynski

    2008-01-01

    Full Text Available The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability.

  1. The environment ontology: contextualising biological and biomedical entities.

    Science.gov (United States)

    Buttigieg, Pier Luigi; Morrison, Norman; Smith, Barry; Mungall, Christopher J; Lewis, Suzanna E

    2013-12-11

    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO's motivation, content, structure, adoption, and governance approach. The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to "obo".

  2. Ontological Forms of Religious Meaning and the Conflict between Science and Religion

    Science.gov (United States)

    Hathcoat, John D.; Habashi, Janette

    2013-01-01

    Epistemological constructions are central considerations in vivisecting an expressed conflict between science and religion. It is argued that the conflict thesis is only meaningful when examined from a specific socio-historical perspective. The dialectical relation between science and religion should therefore be considered at both a macro and…

  3. 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 ...

  4. USSR Space Life Sciences Digest, issue 9

    Science.gov (United States)

    Hooke, Lydia Razran; Radtke, Mike; Teeter, Ronald; Rowe, Joseph E.

    1987-01-01

    This is the ninth issue of NASA's USSR Space Lifes Sciences Digest. It contains abstracts of 46 papers recently published in Russian language periodicals and bound collections and of a new Soviet monograph. Selected abstracts are illustrated with figures and tables from the original. Additional features include reviews of a Russian book on biological rhythms and a description of the papers presented at a conference on space biology and medicine. A special feature describes two paradigms frequently cited in Soviet space life sciences literature. Information about English translations of Soviet materials available to readers is provided. The abstracts included in this issue have been identified as relevant to 28 areas of aerospace medicine and space biology. These areas are: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal system, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, morphology and cytology, musculoskeletal system, nutrition, neurophysiology, operational medicine, perception, personnel selection, psychology, radiobiology, and space biology and medicine.

  5. Brilliant Light in Life and Material Sciences

    CERN Document Server

    Tsakanov, Vasili

    2007-01-01

    The present book contains an excellent overview of the status and highlights of brilliant light facilities and their applications in biology, chemistry, medicine, materials and environmental sciences. Overview papers on diverse fields of research by leading experts are accompanied by the highlights in the near and long-term perspectives of brilliant X-Ray photon beam usage for fundamental and applied research. The book includes advanced topics in the fields of high brightness photon beams, instrumentation, the spectroscopy, microscopy, scattering and imaging experimental techniques and their applications. The book is strongly recommended for students, engineers and scientists in the field of accelerator physics, X-ray optics and instrumentation, life, materials and environmental sciences, bio and nanotechnology.

  6. Life, Science, And Meaning Some Logical Considerations

    Directory of Open Access Journals (Sweden)

    Louis Caruana

    2015-01-01

    Full Text Available Both science and theology involve philosophy. They both involve reasoned argument, evaluation of possible explanations, clarification of concepts, ways of interpreting experience, understanding the present significance of what has gone before us, and other such eminently philosophical tasks. They both involve philosophy especially when they enter into dialogue with each other. In fact, they involve philosophical thinking even when they may not be aware of it. In this paper I will explore a specific area of philosophy that is particularly important as a bridge between theology and science. I am referring to the area of meaning. Questions regarding meaning are fundamental because whatever is said about the nature of life, by scientists, by theologians, or by anyone else, must be expressed in meaningful words. Meaning is like the ground we walk on. It constitutes what we need so as to proceed with our activity. Without solid ground under our feet, we cannot go anywhere.

  7. SPACE LIFE SCIENCE IN 2000-2001

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Chinese scientists studied some of the problems in the field of space life science and achieved success in the area during 2000-2001. Space biological experi ments were carried out in the orbit and the results of ground studies on protein crystallization, space radiation, space motion sickness were introduced in this paper. The influences of simulated weightlessness on the brain-function, the car diovascular, endocrine hormones, immunity, skeletal and muscle systems were presented. In addition, gravity medicine and space environment medicine, as well as countermeasures to space deconditioning, such as the traditional Chinese medicine, were also reported.

  8. USSR Space Life Sciences Digest, issue 32

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Rowe, Joseph (Editor)

    1992-01-01

    This is the thirty-second issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 34 journal or conference papers published in Russian and of 4 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 18 areas of space biology and medicine. These areas include: adaptation, aviation medicine, biological rhythms, biospherics, cardiovascular and respiratory systems, developmental biology, exobiology, habitability and environmental effects, human performance, hematology, mathematical models, metabolism, microbiology, musculoskeletal system, neurophysiology, operational medicine, and reproductive system.

  9. USSR Space Life Sciences Digest, issue 21

    Science.gov (United States)

    Hooke, Lydia Razran; Donaldson, P. Lynn; Garshnek, Victoria; Rowe, Joseph

    1989-01-01

    This is the twenty-first issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 37 papers published in Russian language periodicals or books or presented at conferences and of a Soviet monograph on animal ontogeny in weightlessness. Selected abstracts are illustrated with figures and tables from the original. A book review of a work on adaptation to stress is also included. The abstracts in this issue have been identified as relevant to 25 areas of space biology and medicine. These areas are: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, cytology, developmental biology, endocrinology, enzymology, equipment and instrumentation, exobiology, gravitational biology, habitability and environmental effects, hematology, human performance, life support systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, operational medicine, perception, psychology, and reproductive system.

  10. USSR Space Life Sciences Digest, issue 19

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Donaldson, P. Lynn (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1988-01-01

    This is the 19th issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 47 papers published in Russian language periodicals or presented at conferences and of 5 new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Reports on two conferences, one on adaptation to high altitudes, and one on space and ecology are presented. A book review of a recent work on high altitude physiology is also included. The abstracts in this issue have been identified as relevant to 33 areas of space biology and medicine. These areas are: adaptation, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, cytology, developmental biology, endocrinology, enzymology, biology, group dynamics, habitability and environmental effects, hematology, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, and space biology and medicine.

  11. USSR Space Life Sciences Digest, issue 25

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1990-01-01

    This is the twenty-fifth issue of NASA's Space Life Sciences Digest. It contains abstracts of 42 journal papers or book chapters published in Russian and of 3 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 26 areas of space biology and medicine. These areas include: adaptation, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, exobiology, gravitational biology, habitability and environmental effects, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, psychology, radiobiology, reproductive system, and space biology and medicine.

  12. USSR Space Life Sciences Digest, issue 29

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Rowe, Joseph (Editor)

    1991-01-01

    This is the twenty-ninth issue of NASA's Space Life Sciences Digest. It is a double issue covering two issues of the Soviet Space Biology and Aerospace Medicine Journal. Issue 29 contains abstracts of 60 journal papers or book chapters published in Russian and of three Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. A review of a book on environmental hygiene and a list of papers presented at a Soviet conference on space biology and medicine are also included. The materials in this issue were identified as relevant to 28 areas of space biology and medicine. The areas are: adaptation, aviation medicine, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, digestive system, endocrinology, equipment and instrumentation, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, personnel selection, psychology, radiobiology, reproductive system, space biology and medicine, and the economics of space flight.

  13. USSR Space Life Sciences Digest, Issue 18

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Donaldson, P. Lynn (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1988-01-01

    This is the 18th issue of NASA's USSR Life Sciences Digest. It contains abstracts of 50 papers published in Russian language periodicals or presented at conferences and of 8 new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. A review of a recent Aviation Medicine Handbook is also included. The abstracts in this issue have been identified as relevant to 37 areas of space biology and medicine. These areas are: adaptation, aviation medicine, biological rhythms, biospherics, body fluids, cardiovascular and respiratory systems, cytology, developmental biology, endocrinology, enzymology, equipment and instrumentation, exobiology, gastrointestinal system, genetics, gravitational biology, group dynamics, habitability and environmental effects, hematology, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, reproductive biology, space biology and medicine, and space industrialization.

  14. USSR Space Life Sciences Digest, issue 6

    Science.gov (United States)

    Hooke, L. R. (Editor); Radtke, M. (Editor); Teeter, R. (Editor); Rowe, J. E. (Editor)

    1986-01-01

    This is the sixth issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 54 papers recently published in Russian language periodicals and bound collections and of 10 new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Additional features include a table of Soviet EVAs and information about English translations of Soviet materials available to readers. The topics covered in this issue have been identified as relevant to 26 areas of aerospace medicine and space biology. These areas are adaptation, biospherics, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, exobiology, genetics, habitability and environment effects, health and medical treatment, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism., microbiology, morphology and cytology, musculoskeletal system, neurophysiology, nutrition, perception, personnel selection, psychology, radiobiology, reproductive biology, and space medicine.

  15. USSR Space Life Sciences Digest, issue 7

    Science.gov (United States)

    Hooke, L. R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor)

    1986-01-01

    This is the seventh issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 29 papers recently published in Russian language periodicals and bound collections and of 8 new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Additional features include two interviews with the Soviet Union's cosmonaut physicians and others knowledgable of the Soviet space program. The topics discussed at a Soviet conference on problems in space psychology are summarized. Information about English translations of Soviet materials available to readers is provided. The topics covered in this issue have been identified as relevant to 29 areas of aerospace medicine and space biology. These areas are adaptation, biospherics, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, exobiology, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, morphology and cytology, musculoskeletal system, neurophysiology, nutrition, perception, personnel selection, psychology, radiobiology, and space medicine.

  16. USSR Space Life Sciences Digest, Issue 10

    Science.gov (United States)

    Hooke, Lydia Razran; Radtke, Mike; Teeter, Ronald; Garshnek, Victoria; Rowe, Joseph E.

    1987-01-01

    The USSR Space Life Sciences Digest contains abstracts of 37 papers recently published in Russian language periodicals and bound collections and of five new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Additional features include the translation of a book chapter concerning use of biological rhythms as a basis for cosmonaut selection, excerpts from the diary of a participant in a long-term isolation experiment, and a picture and description of the Mir space station. The abstracts included in this issue were identified as relevant to 25 areas of aerospace medicine and space biology. These areas are adaptation, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, group dynamics, habitability and environmental effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, morphology and cytology, musculosketal system, neurophysiology, nutrition, personnel selection, psychology, and radiobiology.

  17. USSR Space Life Sciences Digest, issue 16

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Teeter, Ronald (Editor); Siegel, Bette (Editor); Donaldson, P. Lynn (Editor); Leveton, Lauren B. (Editor); Rowe, Joseph (Editor)

    1988-01-01

    This is the sixteenth issue of NASA's USSR Life Sciences Digest. It contains abstracts of 57 papers published in Russian language periodicals or presented at conferences and of 2 new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. An additional feature is the review of a book concerned with metabolic response to the stress of space flight. The abstracts included in this issue are relevant to 33 areas of space biology and medicine. These areas are: adaptation, biological rhythms, bionics, biospherics, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, exobiology, gastrointestinal system, genetics, gravitational biology, habitability and environmental effects, hematology, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, reproductive biology, and space biology.

  18. USSR Space Life Sciences Digest, issue 15

    Science.gov (United States)

    Hooke, Lydia Razran (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1988-01-01

    This is the 15th issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 59 papers published in Russian language periodicals or presented at conferences and of two new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. An additional feature is a review of a conference devoted to the physiology of extreme states. The abstracts included in this issue have been identified as relevant to 29 areas of space biology and medicine. These areas are adaptation, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, endocrinology, enzymology, equipment and instrumentation, exobiology, genetics, habitability and environment effects, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception. personnel selection, psychology, radiobiology, reproductive biology, and space biology and medicine.

  19. What are the constituents of matter? an essay concerning the ontological side of science

    CERN Document Server

    Kaufman, Alfred

    2016-01-01

    This essay seeks to understand just what it is that modern science tells us about nature. For the longest time the story told by science appeared to be fully reflective of our common experience: nature was discovered as a collection of reciprocally influencing objects governed by laws which were consistent with that experience. And then, about a hundred years ago, the story suddenly became obscure. Science introduced into nature quantum objects which were supposed to look nothing like anything we had ever seen before and the laws governing them no longer appeared to make much sense to us. Thereafter, what science told us about nature was no longer quite as clear. This shift in the story is conspicuous and bespeaks of an earlier moment in the development of science when the project might have inadvertently taken a step which would eventually make her strange. The essay suggests that the scientific community had in fact made a fateful decision which inevitably led it to the strangeness of quantum mechanics and ...

  20. Life Sciences Space Station planning document: A reference payload for the Life Sciences Research Facility

    Science.gov (United States)

    1986-01-01

    The Space Station, projected for construction in the early 1990s, will be an orbiting, low-gravity, permanently manned facility providing unprecedented opportunities for scientific research. Facilities for Life Sciences research will include a pressurized research laboratory, attached payloads, and platforms which will allow investigators to perform experiments in the crucial areas of Space Medicine, Space Biology, Exobiology, Biospherics and Controlled Ecological Life Support System (CELSS). These studies are designed to determine the consequences of long-term exposure to space conditions, with particular emphasis on assuring the permanent presence of humans in space. The applied and basic research to be performed, using humans, animals, and plants, will increase our understanding of the effects of the space environment on basic life processes. Facilities being planned for remote observations from platforms and attached payloads of biologically important elements and compounds in space and on other planets (Exobiology) will permit exploration of the relationship between the evolution of life and the universe. Space-based, global scale observations of terrestrial biology (Biospherics) will provide data critical for understanding and ultimately managing changes in the Earth's ecosystem. The life sciences community is encouraged to participate in the research potential the Space Station facilities will make possible. This document provides the range and scope of typical life sciences experiments which could be performed within a pressurized laboratory module on Space Station.

  1. Critical Theory and Processual Social Ontology

    Directory of Open Access Journals (Sweden)

    Renault Emmanuel

    2016-03-01

    Full Text Available The purpose of this article is to bridge the gap between critical theory as understood in the Frankfurt school tradition on the one hand, and social ontology understood as a reflection on the ontological presuppositions of social sciences and social theories on the other. What is at stake is the type of social ontology that critical theory needs if it wants to tackle its main social ontological issue: that of social transformation. This paper’s claim is that what is required is neither a substantial social ontology, nor a relational social ontology, but a processual one. The first part of this article elaborates the distinction between substantial, relational and processual social ontologies. The second part analyzes the various ways in which this distinction can be used in social ontological discussions. Finally, the third part focuses on the various possible social ontological approaches to the issue of social transformation.

  2. Engineering Ontologies

    NARCIS (Netherlands)

    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 syst

  3. Speculative Physics: the Ontology of Theory and Experiment in High Energy Particle Physics and Science Fiction

    CERN Document Server

    Lee, Clarissa Ai Ling

    2014-01-01

    The dissertation brings together approaches across the fields of physics, critical theory, literary studies, philosophy of physics, sociology of science, and history of science to synthesize a hybrid approach for instigating more rigorous and intense cross-disciplinary interrogations between the sciences and the humanities. There are two levels of conversations going on in the dissertation; at the first level, the discussion is centered on a critical historiography and philosophical implications of the discovery Higgs boson in relation to its position at the intersection of old (current) and the potential for new possibilities in quantum physics; I then position my findings on the Higgs boson in connection to the double-slit experiment that represents foundational inquiries into quantum physics, to demonstrate the bridge between fundamental physics and high energy particle physics. The conceptualization of the variants of the double-slit experiment informs the aforementioned critical comparisons. At the secon...

  4. Ontology for Life-Cycle Modeling of Electrical Distribution Systems: Application of Model View Definition Attributes

    Science.gov (United States)

    2013-06-01

    Building in- formation exchange (COBie), Building Information Modeling ( BIM ) 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...to develop a life-cycle building model have resulted in the definition of a “core” building information model that contains general information de...develop an information -exchange Model View Definition (MVD) for building electrical systems. The objective of the current work was to document the

  5. Mobile Robot for Life Science Automation

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2013-07-01

    Full Text Available The paper presents a control system for mobile robots in distributed life science laboratories. The system covers all technical aspects of laboratory mobile robotics. In this system: (a to get an accurate and low-cost robot localization, a method using a StarGazer module with a number of ceiling landmarks is utilized; (b to have an expansible communication network, a standard IEEE 802.11g wireless network is adopted and a XML-based command protocol is designed for the communication between the remote side and the robot board side; (c to realize a function of dynamic obstacle measurement and collision avoidance, an artificial potential field method based on a Microsoft Kinect sensor is used; and (d to determine the shortest paths for transportation tasks, a hybrid planning strategy based on a Floyd algorithm and a Genetic Algorithm (GA is proposed. Additionally, to make the traditional GA method suitable for the laboratory robot’s routing, a series of optimized works are also provided in detail. Two experiments show that the proposed system and its control strategy are effective for a complex life science laboratory.

  6. Mobile Robot for Life Science Automation

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2013-07-01

    Full Text Available The paper presents a control system for mobile robots in distributed life science laboratories. The system covers all technical aspects of laboratory mobile robotics. In this system: (a to get an accurate and low-cost robot localization, a method using a StarGazer module with a number of ceiling landmarks is utilized; (b to have an expansible communication network, a standard IEEE 802.11g wireless network is adopted and a XML-based command protocol is designed for the communication between the remote side and the robot board side; (c to realize a function of dynamic obstacle measurement and collision avoidance, an artificial potential field method based on a Microsoft Kinect sensor is used; and (d to determine the shortest paths for transportation tasks, a hybrid planning strategy based on a Floyd algorithm and a Genetic Algorithm (GA is proposed. Additionally, to make the traditional GA method suitable for the laboratory robot's routing, a series of optimized works are also provided in detail. Two experiments show that the proposed system and its control strategy are effective for a complex life science laboratory.

  7. Combined use of semantics and metadata to manage Research Data Life Cycle in Environmental Sciences

    Science.gov (United States)

    Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Pertinez, Esther; Palacio, Aida

    2017-04-01

    The use of metadata to contextualize datasets is quite extended in Earth System Sciences. There are some initiatives and available tools to help data managers to choose the best metadata standard that fit their use cases, like the DCC Metadata Directory (http://www.dcc.ac.uk/resources/metadata-standards). In our use case, we have been gathering physical, chemical and biological data from a water reservoir since 2010. A well metadata definition is crucial not only to contextualize our own data but also to integrate datasets from other sources like satellites or meteorological agencies. That is why we have chosen EML (Ecological Metadata Language), which integrates many different elements to define a dataset, including the project context, instrumentation and parameters definition, and the software used to process, provide quality controls and include the publication details. Those metadata elements can contribute to help both human and machines to understand and process the dataset. However, the use of metadata is not enough to fully support the data life cycle, from the Data Management Plan definition to the Publication and Re-use. To do so, we need to define not only metadata and attributes but also the relationships between them, so semantics are needed. Ontologies, being a knowledge representation, can contribute to define the elements of a research data life cycle, including DMP, datasets, software, etc. They also can define how the different elements are related between them and how they interact. The first advantage of developing an ontology of a knowledge domain is that they provide a common vocabulary hierarchy (i.e. a conceptual schema) that can be used and standardized by all the agents interested in the domain (either humans or machines). This way of using ontologies is one of the basis of the Semantic Web, where ontologies are set to play a key role in establishing a common terminology between agents. To develop an ontology we are using a graphical tool

  8. James Clerk Maxwell: Life and science

    Science.gov (United States)

    Marston, Philip L.

    2016-07-01

    Maxwell's life and science are presented with an account of the progression of Maxwell's research on electromagnetic theory. This is appropriate for the International Year of Light and Light-based Technologies, 2015. Maxwell's own confidence in his 1865 electromagnetic theory of light is examined, along with some of the difficulties he faced and the difficulties faced by some of his followers. Maxwell's interest in radiation pressure and electromagnetic stress is addressed, as well as subsequent developments. Some of Maxwell's other contributions to physics are discussed with an emphasis on the kinetic and molecular theory of gases. Maxwell's theistic perspective on science is illustrated, accompanied by examples of perspectives on Maxwell and his science provided by his peers and accounts of his interactions with those peers. Appendices examine the peer review of Maxwell's 1865 electromagnetic theory paper and the naming of the Maxwell Garnett effective media approximation and provide various supplemental perspectives. From Maxwell's publications and correspondence there is evidence he had a high regard for Michael Faraday. Examples of Maxwell's contributions to electromagnetic terminology are noted.

  9. Spacelab J: Microgravity and life sciences

    Science.gov (United States)

    Spacelab J is a joint venture between NASA and the National Space Development Agency of Japan (NASDA). Using a Spacelab pressurized long module, 43 experiments will be performed in the areas of microgravity and life sciences. These experiments benefit from the microgravity environment available on an orbiting Shuttle. Removed from the effects of gravity, scientists will seek to observe processes and phenomena impossible to study on Earth, to develop new and more uniform mixtures, to study the effects of microgravity and the space environment on living organisms, and to explore the suitability of microgravity for certain types of research. Mission planning and an overview of the experiments to be performed are presented. Orbital research appears to hold many advantages for microgravity science investigations, which on this mission include electronic materials, metals and alloys, glasses and ceramics, fluid dynamics and transport phenomena, and biotechnology. Gravity-induced effects are eliminated in microgravity. This allows the investigations on Spacelab J to help scientists develop a better understanding of how these gravity-induced phenomena affect both processing and products on Earth and to observe subtle phenomena that are masked in gravity. The data and samples from these investigations will not only allow scientists to better understand the materials but also will lead to improvements in the methods used in future experiments. Life sciences research will collect data on human adaptation to the microgravity environment, investigate ways of assisting astronauts to readapt to normal gravity, explore the effects of microgravity and radiation on living organisms, and gather data on the fertilization and development of organisms in the absence of gravity. This research will improve crew comfort and safety on future missions while helping scientists to further understand the human body.

  10. Open Genetic Code: on open source in the life sciences

    NARCIS (Netherlands)

    Deibel, E.

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life

  11. Development and Validation of the Life Sciences Assessment: A Measure of Preschool Children's Conceptions of Basic Life Sciences

    Science.gov (United States)

    Maherally, Uzma Nooreen

    2014-01-01

    The purpose of this study was to develop and validate a science assessment tool termed the Life Sciences Assessment (LSA) in order to assess preschool children's conceptions of basic life sciences. The hypothesis was that the four sub-constructs, each of which can be measured through a series of questions on the LSA, will make a significant…

  12. Nanosystem Characterization Tools in the Life Sciences

    Science.gov (United States)

    Kumar, Challa S. S. R.

    2006-01-01

    This first dedicated, all-encompassing text characterizes nanomaterials intended for biological or physiological environments and biomedical applications, in particular for medicine, healthcare, pharmaceuticals and human wellness. It finally fills the gap for a concise overview of a wide range of different characterization techniques and how to best employ them in the context of nanoscale life science research. It thus serves as a single source of information gathering up the knowledge otherwise spread over many journal articles, and provides an overall picture to members of all the disciplines involved. This handy volume covers all important probing techniques, including nuclear and electron spin resonance, light scattering, infrared and Raman spectroscopy, atomic force microscopy, magnetic resonance, tomography, x-ray techniques, and microbalance measurement of antibody binding. Biochemists, biologists, chemists, materials scientists, and materials engineers as well as all others working in the pharmaceutical and chemical industries or at related research institutions will here a book of great value and importance.

  13. Empowering pharmacoinformatics by linked life science data.

    Science.gov (United States)

    Goldmann, Daria; Zdrazil, Barbara; Digles, Daniela; Ecker, Gerhard F

    2016-11-09

    With the public availability of large data sources such as ChEMBLdb and the Open PHACTS Discovery Platform, retrieval of data sets for certain protein targets of interest with consistent assay conditions is no longer a time consuming process. Especially the use of workflow engines such as KNIME or Pipeline Pilot allows complex queries and enables to simultaneously search for several targets. Data can then directly be used as input to various ligand- and structure-based studies. In this contribution, using in-house projects on P-gp inhibition, transporter selectivity, and TRPV1 modulation we outline how the incorporation of linked life science data in the daily execution of projects allowed to expand our approaches from conventional Hansch analysis to complex, integrated multilayer models.

  14. BIOINFORMATICS FOR UNDERGRADUATES OF LIFE SCIENCE COURSES

    Directory of Open Access Journals (Sweden)

    J.F. De Mesquita

    2007-05-01

    Full Text Available In the recent years, Bioinformatics has emerged as an important research tool. Theability to mine large databases for relevant information has become essential fordifferent life science fields. On the other hand, providing education in bioinformatics toundergraduates is challenging from this multidisciplinary perspective. Therefore, it isimportant to introduced undergraduate students to the available information andcurrent methodologies in Bioinformatics. Here we report the results of a course usinga computer-assisted and problem -based learning model. The syllabus was comprisedof theoretical lectures covering different topics within bioinformatics and practicalactivities. For the latter, we developed a set of step-by-step tutorials based on casestudies. The course was applied to undergraduate students of biological andbiomedical courses. At the end of the course, the students were able to build up astep-by-step tutorial covering a bioinformatics issue.

  15. Empowering pharmacoinformatics by linked life science data

    Science.gov (United States)

    Goldmann, Daria; Zdrazil, Barbara; Digles, Daniela; Ecker, Gerhard F.

    2016-11-01

    With the public availability of large data sources such as ChEMBLdb and the Open PHACTS Discovery Platform, retrieval of data sets for certain protein targets of interest with consistent assay conditions is no longer a time consuming process. Especially the use of workflow engines such as KNIME or Pipeline Pilot allows complex queries and enables to simultaneously search for several targets. Data can then directly be used as input to various ligand- and structure-based studies. In this contribution, using in-house projects on P-gp inhibition, transporter selectivity, and TRPV1 modulation we outline how the incorporation of linked life science data in the daily execution of projects allowed to expand our approaches from conventional Hansch analysis to complex, integrated multilayer models.

  16. Life Sciences Implications of Lunar Surface Operations

    Science.gov (United States)

    Chappell, Steven P.; Norcross, Jason R.; Abercromby, Andrew F.; Gernhardt, Michael L.

    2010-01-01

    The purpose of this report is to document preliminary, predicted, life sciences implications of expected operational concepts for lunar surface extravehicular activity (EVA). Algorithms developed through simulation and testing in lunar analog environments were used to predict crew metabolic rates and ground reaction forces experienced during lunar EVA. Subsequently, the total metabolic energy consumption, the daily bone load stimulus, total oxygen needed, and other variables were calculated and provided to Human Research Program and Exploration Systems Mission Directorate stakeholders. To provide context to the modeling, the report includes an overview of some scenarios that have been considered. Concise descriptions of the analog testing and development of the algorithms are also provided. This document may be updated to remain current with evolving lunar or other planetary surface operations, assumptions and concepts, and to provide additional data and analyses collected during the ongoing analog research program.

  17. Empowering pharmacoinformatics by linked life science data

    Science.gov (United States)

    Goldmann, Daria; Zdrazil, Barbara; Digles, Daniela; Ecker, Gerhard F.

    2017-03-01

    With the public availability of large data sources such as ChEMBLdb and the Open PHACTS Discovery Platform, retrieval of data sets for certain protein targets of interest with consistent assay conditions is no longer a time consuming process. Especially the use of workflow engines such as KNIME or Pipeline Pilot allows complex queries and enables to simultaneously search for several targets. Data can then directly be used as input to various ligand- and structure-based studies. In this contribution, using in-house projects on P-gp inhibition, transporter selectivity, and TRPV1 modulation we outline how the incorporation of linked life science data in the daily execution of projects allowed to expand our approaches from conventional Hansch analysis to complex, integrated multilayer models.

  18. USSR space life sciences digest, issue 27

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Garshnek, Victoria (Editor); Rowe, Joseph (Editor)

    1990-01-01

    This is the twenty-fifth issue of NASA's Space Life Sciences Digest. It contains abstracts of 30 journal papers or book chapters published in Russian and of 2 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 18 areas of space biology and medicine. These areas include: adaptation, aviation medicine, biological rhythms, biospherics, botany, cardiovascular and respiratory systems, endocrinology, enzymology, exobiology, habitability and environmental effects, hematology, immunology, metabolism, musculoskeletal system, neurophysiology, radiobiology, and space medicine. A Soviet book review of a British handbook of aviation medicine and a description of the work of the division on aviation and space medicine of the Moscow Physiological Society are also included.

  19. Life sciences today and tomorrow: emerging biotechnologies.

    Science.gov (United States)

    Williamson, E Diane

    2016-07-03

    The purpose of this review is to survey current, emerging and predicted future biotechnologies which are impacting, or are likely to impact in the future on the life sciences, with a projection for the coming 20 years. This review is intended to discuss current and future technical strategies, and to explore areas of potential growth during the foreseeable future. Information technology approaches have been employed to gather and collate data. Twelve broad categories of biotechnology have been identified which are currently impacting the life sciences and will continue to do so. In some cases, technology areas are being pushed forward by the requirement to deal with contemporary questions such as the need to address the emergence of anti-microbial resistance. In other cases, the biotechnology application is made feasible by advances in allied fields in biophysics (e.g. biosensing) and biochemistry (e.g. bio-imaging). In all cases, the biotechnologies are underpinned by the rapidly advancing fields of information systems, electronic communications and the World Wide Web together with developments in computing power and the capacity to handle extensive biological data. A rationale and narrative is given for the identification of each technology as a growth area. These technologies have been categorized by major applications, and are discussed further. This review highlights: Biotechnology has far-reaching applications which impinge on every aspect of human existence. The applications of biotechnology are currently wide ranging and will become even more diverse in the future. Access to supercomputing facilities and the ability to manipulate large, complex biological datasets, will significantly enhance knowledge and biotechnological development.

  20. BioFed: federated query processing over life sciences linked open data.

    Science.gov (United States)

    Hasnain, Ali; Mehmood, Qaiser; Sana E Zainab, Syeda; Saleem, Muhammad; Warren, Claude; Zehra, Durre; Decker, Stefan; Rebholz-Schuhmann, Dietrich

    2017-03-15

    Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints. Due to the size and complexity of available data, these solutions have to be optimised for efficient retrieval times and for users in life sciences research. Last but not least, over time, the reliability of data resources in terms of access and quality have to be monitored. Our solution (BioFed) federates data over 130 SPARQL endpoints in life sciences and tailors query submission according to the provenance information. BioFed has been evaluated against the state of the art solution FedX and forms an important benchmark for the life science domain. The efficient cataloguing approach of the federated query processing system 'BioFed', the triple pattern wise source selection and the semantic source normalisation forms the core to our solution. It gathers and integrates data from newly identified public endpoints for federated access. Basic provenance information is linked to the retrieved data. Last but not least, BioFed makes use of the latest SPARQL standard (i.e., 1.1) to leverage the full benefits for query federation. The evaluation is based on 10 simple and 10 complex queries, which address data in 10 major and very popular data sources (e.g., Dugbank, Sider). BioFed is a solution for a single-point-of-access for a large number of SPARQL endpoints providing life science data. It facilitates efficient query generation for data access and provides basic provenance information in combination with the retrieved data. BioFed fully supports SPARQL 1.1 and gives access to the

  1. USSR Space Life Sciences Digest, issue 8

    Science.gov (United States)

    Hooke, L. R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor); Teeter, R. (Editor)

    1985-01-01

    This is the eighth issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 48 papers recently published in Russian language periodicals and bound collections and of 10 new Soviet monographs. Selected abstracts are illustrated with figures and tables. Additional features include reviews of two Russian books on radiobiology and a description of the latest meeting of an international working group on remote sensing of the Earth. Information about English translations of Soviet materials available to readers is provided. The topics covered in this issue have been identified as relevant to 33 areas of aerospace medicine and space biology. These areas are: adaptation, biological rhythms, biospherics, body fluids, botany, cardiovascular and respiratory systems, cosmonaut training, cytology, endocrinology, enzymology, equipment and instrumentation, exobiology, gastrointestinal system, genetics, group dynamics, habitability and environment effects, hematology, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, personnel selection, psychology, reproductive biology, and space biology and medicine.

  2. Ontological turns, turnoffs and roundabouts.

    Science.gov (United States)

    Sismondo, Sergio

    2015-06-01

    There has been much talk of an 'ontological turn' in Science and Technology Studies. This commentary explores some recent work on multiple and historical ontologies, especially articles published in this journal, against a background of constructivism. It can be tempting to read an ontological turn as based and promoting a version of perspectivism, but that is inadequate to the scholarly work and opens multiple ontologies to serious criticisms. Instead, we should read our ontological turn or turns as being about multiplicities of practices and the ways in which these practices shape the material world. Ontologies arise out of practices through which people engage with things; the practices are fundamental and the ontologies derivative. The purchase in this move comes from the elucidating power of the verbs that scholars use to analyze relations of practices and objects--which turn out to be specific cases of constructivist verbs. The difference between this ontological turn and constructivist work in Science and Technology Studies appears to be a matter of emphases found useful for different purposes.

  3. Open life science research, open software and the open century

    Institute of Scientific and Technical Information of China (English)

    Youhua Chen

    2015-01-01

    At the age of knowledge explosion and mass scientific information, I highlighted the importance of conducting open science in life and medical researches through the extensive usage of open software and documents. The proposal of conducting open science is to reduce the limited repeatability of researches in life science. I outlined the essential steps for conducting open life science and the necessary standards for creating, reusing and reproducing open materials. Different Creative Commons licenses were presented and compared of their usage scope and restriction. As a conclusion, I argued that open materials should be widely adopted in doing life and medical researches.

  4. Life sciences - On the critical path for missions of exploration

    Science.gov (United States)

    Sulzman, Frank M.; Connors, Mary M.; Gaiser, Karen

    1988-01-01

    Life sciences are important and critical to the safety and success of manned and long-duration space missions. The life science issues covered include gravitational physiology, space radiation, medical care delivery, environmental maintenance, bioregenerative systems, crew and human factors within and outside the spacecraft. The history of the role of life sciences in the space program is traced from the Apollo era, through the Skylab era to the Space Shuttle era. The life science issues of the space station program and manned missions to the moon and Mars are covered.

  5. Ontology Research

    OpenAIRE

    Welty, Christopher

    2003-01-01

    In this issue, I have collected a fairly broad, although by no means exhaustive, sampling of work in the field of ontology research. To define a field is often quite difficult; it is more a collection of people and ideas than it is a specific technology. To represent our field, I present six articles that cover several of the major thrusts of ontology research from the past decade.

  6. Gene function prediction based on the Gene Ontology hierarchical structure.

    Science.gov (United States)

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  7. Generating Application Ontologies from Reference Ontologies

    OpenAIRE

    Shaw, Marianne; Detwiler, Landon T.; Brinkley, James F.; Suciu, Dan

    2008-01-01

    The semantic web provides the possiblity of linking together large numbers of biomedical ontologies. Unfortunately, many of the biomedical ontologies that have been developed are domain-specific and do not share a common structure that will allow them to be easily combined. Reference ontologies provide the necessary ontological framework for linking together these smaller, specialized ontologies.

  8. The Presentation of Science in Everyday Life: The Science Show

    Science.gov (United States)

    Watermeyer, Richard

    2013-01-01

    This paper constitutes a case-study of the "science show" model of public engagement employed by a company of science communicators focused on the popularization of science, technology, engineering and mathematics (STEM) subject disciplines with learner constituencies. It examines the potential of the science show to foster the interest…

  9. Natural products in modern life science.

    Science.gov (United States)

    Bohlin, Lars; Göransson, Ulf; Alsmark, Cecilia; Wedén, Christina; Backlund, Anders

    2010-06-01

    questions in Nature can be of value to increase the attraction for young students in modern life science.

  10. NASDA life science experiment facilities for ISS

    Science.gov (United States)

    Tanigaki, F.; Masuda, D.; Yano, S.; Fujimoto, N.; Kamigaichi, S.

    National Space Development Agency of Japan (NASDA) has been developing various experiment facilities to conduct space biology researches in KIBO (JEM). The Cell Biology Experiment Facility (CBEF) and the Clean Bench (CB) are installed into JEM Life Science Rack. The Biological Experiment Units (BEU) are operated in the CBEF and the CB for many kinds of experiments on cells, tissues, plants, microorganisms, or small animals. It is possible for all researchers to use these facilities under the system of the International Announcement of Opportunity. The CBEF is a CO2 incubator to provide a controlled environment (temperature, humidity, and CO2 concentration), in which a rotating table is equipped to make variable gravity (0-2g) for reference experiments. The containers called "Canisters" can be used to install the BEU in the CBEF. The CBEF supplies power, command, sensor, and video interfaces for the BEU through the utility connectors of Canisters. The BEU is a multiuser system consisting of chambers and control segments. It is operated by pre-set programs and by commands from the ground. NASDA is currently developing three types of the BEU: the Plant Experiment Unit (PEU) for plant life cycle observations and the Cell Experiment Unit (CEU1&2) for cell culture experiments. The PEU has an automated watering system with a water sensor, an LED matrix as a light source, and a CCD camera to observe the plant growth. The CEUs have culture chambers and an automated cultural medium exchange system. Engineering models of the PEU and CEU1 have been accomplished. The preliminary design of CEU2 is in progress. The design of the BEU will be modified to meet science requirements of each experiment. The CB provides a closed aseptic work-space (Operation Chamber) with gloves for experiment operations. Samples and the BEU can be manually handled in the CB. The CB has an air lock (Disinfection Chamber) to prevent contamination, and HEPA filters to make class-100-equivalent clean air

  11. Applying Conceptual Blending to Model Coordinated Use of Multiple Ontological Metaphors

    CERN Document Server

    Dreyfus, Benjamin W; Redish, Edward F

    2014-01-01

    Energy is an abstract science concept, so the ways that we think and talk about energy rely heavily on ontological metaphors: metaphors for what kind of thing energy is. Two commonly used ontological metaphors for energy are energy as a substance and energy as a vertical location. Our previous work has demonstrated that students and experts can productively use both the substance and location ontologies for energy. In this paper, we use Fauconnier and Turner's conceptual blending framework to demonstrate that experts and novices can successfully blend the substance and location ontologies into a coherent mental model in order to reason about energy. Our data come from classroom recordings of a physics professor teaching a physics course for the life sciences, and from an interview with an undergraduate student in that course. We analyze these data using predicate analysis and gesture analysis, looking at verbal utterances, gestures, and the interaction between them. This analysis yields evidence that the spea...

  12. Software Ecosystems for the Life Sciences Application Domains

    NARCIS (Netherlands)

    Tekinerdogan, B.; Scholten, H.

    2015-01-01

    Software ecosystems (SECOs) are gaining importance in and have been applied to different application domains. In this paper we focus on the needs for SECOs for the life science application domains. Similar to other domains the life science application domains also witnesses the emergence and applica

  13. Text mining resources for the life sciences.

    Science.gov (United States)

    Przybyła, Piotr; Shardlow, Matthew; Aubin, Sophie; Bossy, Robert; Eckart de Castilho, Richard; Piperidis, Stelios; McNaught, John; Ananiadou, Sophia

    2016-01-01

    Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable-those that have the crucial ability to share information, enabling smooth integration and reusability. © The Author(s) 2016. Published by Oxford University Press.

  14. Workshop on Life sciences and radiation

    CERN Document Server

    Life Sciences and Radiation : Accomplishments and Future Directions

    2004-01-01

    Scope and ideas of the workshop The workshop which took place at the University of Giessen from Oct. 3 to Oct. 7, 2002 and whose proceedings are collected in this volume started from the idea to convene a number of scientists with the aim to outline their ”visions” for the future of radiation research on the basis of their expertise. As radiation research is a very wide field restrictions were unavoidable. It was decided to concentrate this time mainly on molecular and cellular biology because it was felt that here action is par-ticularly needed. This did not exclude contributions from neighbouring fields as may be seen from the table of contents. It was clearly not planned to have a c- prehensive account of the present scientif fic achievements but the results presented should only serve as a starting point for the discussion of future lines of research, with the emphasis on the ”outreach” to other parts of life sciences. If you are interested in the future ask the young – we attempted, therefore, ...

  15. 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

  16. SUGOI: automated ontology interchangeability

    CSIR Research Space (South Africa)

    Khan, ZC

    2015-04-01

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

  17. 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.

  18. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

    Science.gov (United States)

    2013-01-01

    Background Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses. PMID:23286517

  19. The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

    Science.gov (United States)

    Malone, James; Brown, Andy; Lister, Allyson L; Ison, Jon; Hull, Duncan; Parkinson, Helen; Stevens, Robert

    2014-01-01

    Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs. The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.

  20. Ontology Localization

    OpenAIRE

    2009-01-01

    Nuestra meta principal en esta tesis es proponer una solución para construir una ontología multilingüe, a través de la localización automática de una ontología. La noción de localización viene del área de Desarrollo de Software que hace referencia a la adaptación de un producto de software a un ambiente no nativo. En la Ingeniería Ontológica, la localización de ontologías podría ser considerada como un subtipo de la localización de software en el cual el producto es un modelo compartido de un...

  1. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands.

    Science.gov (United States)

    Eijssen, Lars; Evelo, Chris; Kok, Ruben; Mons, Barend; Hooft, Rob

    2015-01-01

    We describe the Data programme of the Dutch Techcentre for Life Sciences (DTL, www.dtls.nl). DTL is a new national organisation in scientific research that facilitates life scientists with technologies and technological expertise in an era where new projects often are data-intensive, multi-disciplinary, and multi-site. It is run as a lean not-for-profit organisation with research organisations (both academic and industrial) as paying members. The small staff of the organisation undertakes a variety of tasks that are necessary to perform or support modern academic research, but that are not easily undertaken in a purely academic setting. DTL Data takes care of such tasks related to data stewardship, facilitating exchange of knowledge and expertise, and brokering access to e-infrastructure. DTL also represents the Netherlands in ELIXIR, the European infrastructure for life science data. The organisation is still being fine-tuned and this will continue over time, as it is crucial for this kind of organisation to adapt to a constantly changing environment. However, already being underway for several years, our experiences can benefit researchers in other fields or other countries setting up similar initiatives.

  2. The "Next Generation Science Standards" and the Life Sciences

    Science.gov (United States)

    Bybee, Rodger W.

    2013-01-01

    Publication of the "Next Generation Science Standards" will be just short of two decades since publication of the "National Science Education Standards" (NRC 1996). In that time, biology and science education communities have advanced, and the new standards will reflect that progress (NRC 1999, 2007, 2009; Kress and Barrett…

  3. Semantic Web technologies for the big data in life sciences.

    Science.gov (United States)

    Wu, Hongyan; Yamaguchi, Atsuko

    2014-08-01

    The life sciences field is entering an era of big data with the breakthroughs of science and technology. More and more big data-related projects and activities are being performed in the world. Life sciences data generated by new technologies are continuing to grow in not only size but also variety and complexity, with great speed. To ensure that big data has a major influence in the life sciences, comprehensive data analysis across multiple data sources and even across disciplines is indispensable. The increasing volume of data and the heterogeneous, complex varieties of data are two principal issues mainly discussed in life science informatics. The ever-evolving next-generation Web, characterized as the Semantic Web, is an extension of the current Web, aiming to provide information for not only humans but also computers to semantically process large-scale data. The paper presents a survey of big data in life sciences, big data related projects and Semantic Web technologies. The paper introduces the main Semantic Web technologies and their current situation, and provides a detailed analysis of how Semantic Web technologies address the heterogeneous variety of life sciences big data. The paper helps to understand the role of Semantic Web technologies in the big data era and how they provide a promising solution for the big data in life sciences.

  4. Science China Life Sciences in2010:a New Name Marking a New Start%Science China Life Sciences in 2010: a New Name Marking a New Start

    Institute of Scientific and Technical Information of China (English)

    CHANG Zeng-Yi

    2011-01-01

    The year 2010 marks the sixtieth anniversary for the publication of Science in China series journals,and meanwhile the Science in China Series C:Life Sciences took a new name as Science China Life Sciences(SCLS in short).Simultaneously,it has been reformed to make a new start for this journal in its long history.The journal has appeared with a new face to the readers and authors in both the novel publishing style and the highly qualified articles.An extensive review was given to the journal's specific progress in the year 2010 by highlightingsome of the representative publications.%The year 2010 marks the sixtieth anniversary for the publication of Seience in China series journals,and meanwhile the Science in China Series C:Life Sciences took a new name as Science China Life Sciences (SCLS in short).Simultaneously,it has been reformed to make a new start for this journal in its long history.The journal has appeared with a new face to the readers and authors in both the novel publishing style and the highly qualified articles.An extensive review was given to the journal's specific progress in the year 2010 by highlighting some of the representative publications.

  5. Effective Tutorial Ontology Modeling on Organic Rice Farming for Non-Science & Technology Educated Farmers Using Knowledge Engineering

    Science.gov (United States)

    Yanchinda, Jirawit; Chakpitak, Nopasit; Yodmongkol, Pitipong

    2015-01-01

    Knowledge of the appropriate technologies for sustainable development projects has encouraged grass roots development, which has in turn promoted sustainable and successful community development, which a requirement is to share and reuse this knowledge effectively. This research aims to propose a tutorial ontology effectiveness modeling on organic…

  6. Evaluation of Life Sciences and Social Sciences Course Books in Term of Societal Sexuality

    Science.gov (United States)

    Aykac, Necdet

    2012-01-01

    This study aims to evaluate primary school Life Sciences (1st, 2nd, and 3rd grades) and Social Sciences (4th, 5th, and 6th grades) course books in terms of gender discrimination. This study is a descriptive study aiming to evaluate the primary school Life Sciences (1st, 2nd, 3rd grades) and Social Sciences (4th, 5th, and 6th grades) course books…

  7. Infrastructures as Ontological Experiments

    Directory of Open Access Journals (Sweden)

    Casper Bruun Jensen

    2015-11-01

    Full Text Available Ontology has recently gained renewed attention in science and technology studies and anthropology (e.g. Gad, Jensen and Winthereik 2015; Holbraad, Pedersen and Viveiros de Castro 2014; Woolgar and Lezaun 2013. Yet, it has a considerably longer pedigree than these recent debates might lead one to think. Experiments, of course, have long held the attention of sociologists, historians, and philosophers of science (Collins 1985; Gooding 1990; Shapin and Schaffer 1985. And infrastructures have been the focus of sustained inquiry in the sociology and history of technology (Bowker 1994; Hughes 1983. Once these terms are put into conjunction, however, each gets a somewhat different inflection. The following note briefly explores the conceptual purchase of considering infrastructures as ontological experiments.

  8. Japan's patent issues relating to life science therapeutic inventions.

    Science.gov (United States)

    Tessensohn, John A

    2014-09-01

    Japan has made 'innovation in science and technology' as one of its central pillars to ensure high growth in its next stage of economic development and its life sciences market which hosts regenerative medicine was proclaimed to be 'the best market in the world right now.' Although life science therapeutic inventions are patentable subject matter under Japanese patent law, there are nuanced obviousness and enablement challenges under Japanese patent law that can be surmounted in view of some encouraging Japanese court developments in fostering a pro-patent applicant environment in the life sciences therapeutic patent field. Nevertheless, great care must be taken when drafting and prosecuting such patent applications in the world's second most important life sciences therapeutic market.

  9. Cognitive poetics and biocultural (configurations of life, cognition and language. Towards a theory of socially integrated science

    Directory of Open Access Journals (Sweden)

    Juani Guerra

    2013-07-01

    Full Text Available Based on the biocultural dynamics of Greek poiesis and autopoiesis as evolutionary processes of meaning evaluative (configuration, Cognitive Poetics proposes key methodological adjustments, mainly at the philological, ontological and cultural levels. The aim is to improve our understanding of cognitive and conceptual activity and the social foundations of individual language. From its new status as a fundamental metacognitive theory, it searches for a theory of socially integrated sciences from a new alliance as that discerned in current Cognitive Sciences: from Linguistics or Psychology, through Anthropology, Neurophilosophy or Literary Studies, to Neurobiology or Artificial Life Sciences. From a realist turn to a view of cognition as (social action, it provides new unforeseen accounts of the complex dynamics of human understanding processes studying and analyzing all form of texts as active data

  10. Kant on anatomy and the status of the life sciences.

    Science.gov (United States)

    Olson, Michael J

    2016-08-01

    This paper contributes to recent interest in Kant's engagement with the life sciences by focusing on one corner of those sciences that has received comparatively little attention: physical and comparative anatomy. By attending to remarks spread across Kant's writings, we gain some insight into Kant's understanding of the disciplinary limitations but also the methodological sophistication of the study of anatomy and physiology. Insofar as Kant highlights anatomy as a paradigmatic science guided by the principle of teleology in the Critique of the Power of Judgment, a more careful study of Kant's discussions of anatomy promises to illuminate some of the obscurities of that text and of his understanding of the life sciences more generally. In the end, it is argued, Kant's ambivalence with regard to anatomy gives way to a pessimistic conclusion about the possibility that anatomy, natural history, and, by extension, the life sciences more generally might one day become true natural sciences.

  11. Scientific Digital Libraries, Interoperability, and Ontologies

    Science.gov (United States)

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

    2009-01-01

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

  12. Download - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tss (Homo sapiens) (6.5 GB) (reprocessed)pooled_ctss (Mus musculus) (4.5 GB) - 10 Pathway enrichment...rs (160 MB) - 12 Results of de-novo and Motif activity analyses Motifs (6.2 GB) - 13 Sample ontology, GOstat and ontology term enrich...ment Ontology (1.8 MB) - 14 CAGE peaks identified as tru

  13. Ontology Requirements Specification

    OpenAIRE

    Suárez-Figueroa, Mari Carmen; Gómez-Pérez, A.

    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...

  14. Open life science research, open software and the open century

    National Research Council Canada - National Science Library

    Youhua Chen

    2015-01-01

    At the age of knowledge explosion and mass scientific information, I highlighted the importance of conducting open science in life and medical researches through the extensive usage of open software and documents...

  15. License - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base. The license for this database is specified in the Creative Commons Attribut...omy Icon © Database Center for Life Science licensed under CC Attribution 2.1 Japan . The summary of the Creative Commons

  16. USSR Report, Life Sciences Biomedical and Behavioral Sciences

    Science.gov (United States)

    2007-11-02

    academician, Ukrainian SSSR Academy of Sciences, Physicochemical Institute, Ukrainian SSR Academy of Sciences, Odessa [Abstract] Polyacrylamide gel (PAAG...the canned chicken and beef products. For example, it has been demonstrated that one of the common additives in pediatric products, starch ... starch products may react with proteins leading to the formation of polycondensation products and eliminating 20-50% of the free amino acids in the

  17. A study of Corporate Entrepreneurship at ITI LifeSciences

    OpenAIRE

    Middleton, Barry

    2007-01-01

    ITI Life Sciences is a private organisation based in Dundee, Scotland, which was set up in 2003 through Scottish Enterprise (SE), the publicly funded Scottish regional development agency. ITI Life Sciences has grown from a start up phase into a more mature phase of growth, yet the organization has been grappling with a range of corporate issues. It has long been held that in general, entrepreneurial firms display more innovative, risk taking and proactive behaviour than other firms thank...

  18. Opportunities and challenges for the life sciences community.

    Science.gov (United States)

    Kolker, Eugene; Stewart, Elizabeth; Ozdemir, Vural

    2012-03-01

    Twenty-first century life sciences have transformed into data-enabled (also called data-intensive, data-driven, or big data) sciences. They principally depend on data-, computation-, and instrumentation-intensive approaches to seek comprehensive understanding of complex biological processes and systems (e.g., ecosystems, complex diseases, environmental, and health challenges). Federal agencies including the National Science Foundation (NSF) have played and continue to play an exceptional leadership role by innovatively addressing the challenges of data-enabled life sciences. Yet even more is required not only to keep up with the current developments, but also to pro-actively enable future research needs. Straightforward access to data, computing, and analysis resources will enable true democratization of research competitions; thus investigators will compete based on the merits and broader impact of their ideas and approaches rather than on the scale of their institutional resources. This is the Final Report for Data-Intensive Science Workshops DISW1 and DISW2. The first NSF-funded Data Intensive Science Workshop (DISW1, Seattle, WA, September 19-20, 2010) overviewed the status of the data-enabled life sciences and identified their challenges and opportunities. This served as a baseline for the second NSF-funded DIS workshop (DISW2, Washington, DC, May 16-17, 2011). Based on the findings of DISW2 the following overarching recommendation to the NSF was proposed: establish a community alliance to be the voice and framework of the data-enabled life sciences. After this Final Report was finished, Data-Enabled Life Sciences Alliance (DELSA, www.delsall.org ) was formed to become a Digital Commons for the life sciences community.

  19. 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...... of the world view which underlies my current work on product modelling. It contains a justification of my view of concept exemplification, with lines traced back to Kant's work on epistemology....

  20. Bioinformatics: Current Practice and Future Challenges for Life Science Education

    Science.gov (United States)

    Hack, Catherine; Kendall, Gary

    2005-01-01

    It is widely predicted that the application of high-throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in…

  1. Home | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available f use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) com... supports further contribution of each research to life science. Export All Metadata CSV Format JSON Format ...titute of Agrobiological Sciences Junichi Yonemaru QTL Rice The database of Rice QTL information extracted from published research

  2. Thinking Connections: Concept Maps for Life Science. Book B.

    Science.gov (United States)

    Burggraf, Frederick

    The concept maps contained in this book (for grades 7-12) span 35 topics in life science. Topics were chosen using the National Science Education Standards as a guide. The practice exercise in concept mapping is included to give students an idea of what the tasks ahead will be in content rich maps. Two levels of concept maps are included for each…

  3. Categorial Ontology of Complex Systems, Meta-Systems and Levels: The Emergence of Life, Human Consciousness and Society

    Directory of Open Access Journals (Sweden)

    James F. Glazebrook

    2010-06-01

    Full Text Available Relational structures of organisms and the human mind are naturally represented in terms of novel variable topology concepts, non-Abelian categories and Higher Dimensional Algebra{ relatively new concepts that would be defined in
    this tutorial paper. A unifying theme of local-to-global approaches to organismic development, evolution and human consciousness leads to novel patterns of relations that emerge in super- and ultra- complex systems in terms of compositions of local procedures [1]. The claim is defended in this paper that human consciousness is unique and should be viewed as an ultra-complex, global process of processes, at a meta-level not sub{summed by, but compatible with, human brain dynamics [2]-[5]. The emergence of consciousness and its existence
    are considered to be dependent upon an extremely complex structural and functional unit with an asymmetric network topology and connectivities{the human brain. However, the appearance of human consciousness is shown to be critically dependent upon societal co-evolution, elaborate language-symbolic communication and `virtual', higher dimensional, non{commutative processes involving separate space and time perceptions. Theories of the mind are approached from the theory of levels and ultra-complexity viewpoints that throw
    new light on previous semantic models in cognitive science. Anticipatory systems and complex causality at the top levels of reality are discussed in the context of psychology, sociology and ecology. A paradigm shift towards non-commutative, or more generally, non-Abelian theories of highly complex dynamics [6] is suggested to unfold now in physics, mathematics, life and cognitive sciences, thus leading to the realizations of higher dimensional algebras in neurosciences and psychology, as well as in human genomics, bioinformatics and interactomics. The presence of strange attractors in modern society dynamics gives rise to very serious concerns for the future

  4. Student Teachers' Views: What Is an Interesting Life Sciences Curriculum?

    Science.gov (United States)

    de Villiers, Rian

    2011-01-01

    In South Africa, the Grade 12 "classes of 2008 and 2009" were the first to write examinations under the revised Life Sciences (Biology) curriculum which focuses on outcomes-based education (OBE). This paper presents an exploration of what students (as learners) considered to be difficult and interesting in Grades 10-12 Life Sciences…

  5. The ACGT Master Ontology and its applications--towards an ontology-driven cancer research and management system.

    Science.gov (United States)

    Brochhausen, Mathias; Spear, Andrew D; Cocos, Cristian; Weiler, Gabriele; Martín, Luis; Anguita, Alberto; Stenzhorn, Holger; Daskalaki, Evangelia; Schera, Fatima; Schwarz, Ulf; Sfakianakis, Stelios; Kiefer, Stephan; Dörr, Martin; Graf, Norbert; Tsiknakis, Manolis

    2011-02-01

    This paper introduces the objectives, methods and results of ontology development in the EU co-funded project Advancing Clinico-genomic Trials on Cancer-Open Grid Services for Improving Medical Knowledge Discovery (ACGT). While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems, category schemes and reporting methods on the part of different research groups. The goal of the ACGT project is to contribute to the resolution of these problems by developing an ontology-driven, semantic grid services infrastructure that will enable efficient execution of discovery-driven scientific workflows in the context of multi-centric, post-genomic clinical trials. The focus of the present paper is the ACGT Master Ontology (MO). ACGT project researchers undertook a systematic review of existing domain and upper-level ontologies, as well as of existing ontology design software, implementation methods, and end-user interfaces. This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts and clinicians. To date, the results of the ACGT project include (i) the development of a master ontology (the ACGT-MO) based on clearly defined principles of ontology development and evaluation; (ii) the development of a technical infrastructure (the ACGT Platform) that implements the ACGT-MO utilizing independent tools, components and resources that have been developed based on open architectural standards, and which includes an application updating and evolving the ontology efficiently in response to end-user needs; and (iii) the development of an Ontology-based Trial Management Application (ObTiMA) that integrates the ACGT-MO into the design process of clinical trials in order to guarantee automatic semantic

  6. Measuring the evolution of ontology complexity: the gene ontology case study.

    Science.gov (United States)

    Dameron, Olivier; Bettembourg, Charles; Le Meur, Nolwenn

    2013-01-01

    Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches, i.e. biological processes (BP), cellular components (CC) and molecular functions (MF). For each case, we measured complexity by computing metrics related to the size, the nodes connectivity and the hierarchical structure. The number of classes and relations increased monotonously for each branch, with different growth rates. BP and CC had similar connectivity, superior to that of MF. Connectivity increased monotonously for BP, decreased for CC and remained stable for MF, with a marked increase for the three branches in November and December 2012. Hierarchy-related measures showed that CC and MF had similar proportions of leaves, average depths and average heights. BP had a lower proportion of leaves, and a higher average depth and average height. For BP and MF, the late 2012 increase of connectivity resulted in an increase of the average depth and average height and a decrease of the proportion of leaves, indicating that a major enrichment effort of the intermediate-level hierarchy occurred. The variation of the number of classes and relations in an ontology does not provide enough information about the evolution of its complexity. However, connectivity and hierarchy-related metrics revealed different patterns of values as well as of evolution for the three branches of the Gene Ontology. CC was similar to BP in terms of connectivity, and similar to MF in terms of hierarchy. Overall, BP complexity increased, CC was refined with the addition of leaves providing a finer level of annotations but decreasing slightly its complexity, and MF complexity remained stable.

  7. Photons in Natural and Life Sciences An Interdisciplinary Approach

    CERN Document Server

    Lewerenz, Hans-Joachim

    2012-01-01

    The book describes first the principle photon generation processes from nuclear reactions, electron motion and from discrete quantum transitions. It then focuses on the use of photons in various selected fields of modern natural and life sciences. It bridges disciplines such as physics, chemistry, earth- and materials science, proteomics, information technology, photoelectrochemistry, photosynthesis and spintronics. Advanced light sources and their use in natural and life sciences are emphasized and the effects related to the quantum nature of photons (quantum computing, teleportation) are described. The content encompasses among many other examples the role of photons on the origin of life and on homochirality in biology, femtosecond laser slicing, photothermal cancer therapy, the use of gamma rays in materials science, photoelectrochemical surface conditioning, quantum information aspects and photo-spintronics. The book is written for scientists and graduate students from all related disciplines who are int...

  8. Open Genetic Code: on open source in the life sciences.

    Science.gov (United States)

    Deibel, Eric

    2014-01-01

    The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

  9. Life Science Literacy of an Undergraduate Population

    Science.gov (United States)

    Medina, Stephanie R.; Ortlieb, Evan; Metoyer, Sandra

    2014-01-01

    Science content knowledge is a concern for educators in the United States because performance has stagnated for the past decade. Investigators designed this study to determine the current levels of scientific literacy among undergraduate students in a freshman-level biology course (a core requirement for majors and nonmajors), identify factors…

  10. Life science teachers' decision making on sex education

    Science.gov (United States)

    Gill, Puneet Singh

    The desires of young people and especially young bodies are constructed at the intersections of policies that set the parameters of sex education policies, the embodied experiences of students in classrooms, and the way bodies are discussed in the complex language of science. Moreover, more research points to the lack of scientifically and medically accurate information about sex education. Through this research, I hope to extend the discussion about sex education to life science classrooms, where youth can discuss how sex occurs according to scientific concepts and processes. However, science classrooms are caught in a double bind: They maintain positivist methods of teaching science while paying little attention to the nature of science or the nature and function of science that offer explanations of scientific phenomena. In this study, I describe how science teachers made decisions about what to include or not include about sexuality in a life science classroom and the discursive frameworks that shaped these decisions. I also analyzed the ways that these relationships functioned to produce certain truths, or discourses. The current trends in research concerning SSI are pointing to understanding how controversial issues are framed according to personal philosophies, identities, and teaching approaches. If we can understand science teachers' inner aspects as they relate to sexuality education, we can also understand the deep-seeded motivations behind how these specific issues are being taught. In science classrooms where a discussion of the body is part of the curriculum, specific discourses of the body and sex/sexuality are excluded. In this study, I describe how science teachers made decisions about what to include or not include about sexuality in a life science classroom and the discursive practices that shaped these decisions.

  11. USSR Report, Life Sciences Biomedical and Behavioral Sciences.

    Science.gov (United States)

    2007-11-02

    Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow [Abstract] A study was made of the influence of tahyna virus on the...Suppression of Muscle Macrophage Function in Experimental Tahyna Virus Infection (V. V. Vargin, B. F. Semenov; VOPROSY VIRUSOLOGII, No 2, Mar-Apr 83) 14...Tick-Borne Encephalitis Virus Genome DNA-Copies Into Cellular DNA (I. D. Drynov, et al.; VOPROSY VIRUSOLOGII, No 2, Mar-Apr 83) 32 "Strict

  12. USSR Report, Life Sciences Biomedical and Behavioral Sciences

    Science.gov (United States)

    1984-02-10

    Institute of Cytology and Genetics: "Biologists of the Siberian Department, USSR Academy of Sciences Are Working on the Creation of a Reliable Scientific...plan is already being conducted at the Institute of Cytology and Genetics. The synthesis of genes and their transfer from cells of certain organisms...exudative erythema, Stevens Johnson syndrome, chronic aphthous stomatitis, exfoliative cheilitis 30 and certain other disorders of the oral mucosa

  13. JPRS Report, Science and Technology USSR: Life Sciences.

    Science.gov (United States)

    2007-11-02

    lupus erythematosus , atrophic lichen planus, thallium. Signs of thallium poisoning include nausea, mucinous alopecia, scalp traumas) and non...instrument 51 26 25 Transmission of infection from mother to child: total 10 4 6 during pregnancy and par turition 9 3 6 during breast feeding I 1 0...disease and pathologies of pregnancy . Fig- of Microbiology, BSSR Academy of Sciences, Minsk] ures 2; references 18: 16 Russian; 2 Western. [Abstract] A

  14. Scientific Collaboration and Coauthors in Life Science Journal Articles

    Directory of Open Access Journals (Sweden)

    Ya-hsiu Fu

    2002-12-01

    Full Text Available It is common to conduct collaborative research in science and technology. In particular, the development of big science, Internet, and globalization facilitated the scientific collaboration. This study used two databases, Web of Science and Journal Citation Reports as data sources. From the analysis of 320 papers in 16 journals in life sciences, the results showed that there is no significant correlation between the impact factor of journals and the number of authors. Moreover, there is no correlation of authors and the cited times, either. The number of authors and cited times in most papers are under 10 persons and 25 times, respectively.[Article content in Chinese

  15. Scientific report training workshop interdisciplinary life sciences

    NARCIS (Netherlands)

    Rens, E.G.; Merks, R.M.H.; Boas, S.E.M.; Rens, E.G.; Merks, R.M.H.; et al, not CWI

    2014-01-01

    This preprint is the outcome of the “Training Workshop Interdisciplinary Life Sciences”, held in October 2013 in the Lorentz Center, Leiden, The Netherlands. The motivation to organize this event stems from the following considerations: The enormous progress in laboratory techniques and facilities l

  16. Prehistoric Life, Science (Experimental): 5311.15.

    Science.gov (United States)

    Jenks, Lois

    Presented is a survey course of the biological and geological history of the earth which includes: (1) theories of the formation of the earth, (2) theories of the formation of life, (3) geological eras (calendar), (4) fossil formation and fossil fuels, and (5) modern-day research. This course is intended for junior high level and no previous…

  17. The current landscape of pitfalls in Ontologies

    CSIR Research Space (South Africa)

    Keet, CM

    2013-09-01

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

  18. Ontological Surprises

    DEFF Research Database (Denmark)

    Leahu, Lucian

    2016-01-01

    This paper investigates how we might rethink design as the technological crafting of human-machine relations in the context of a machine learning technique called neural networks. It analyzes Google’s Inceptionism project, which uses neural networks for image recognition. The surprising output of...... a hybrid approach where machine learning algorithms are used to identify objects as well as connections between them; finally, it argues for remaining open to ontological surprises in machine learning as they may enable the crafting of different relations with and through technologies....

  19. Gerhard Herzberg an illustrious life in science

    CERN Document Server

    Stoicheff, Boris

    2002-01-01

    Gerhard Herzberg (1904-1999) was one of the greatest scientists of the last century. Born and educated in Germany, he started his research just as the exciting discovery of quantum mechanics began unraveling the mysteries of the microscopic world. Herzberg chose to study spectroscopy, the light emitted and absorbed by atoms and molecules, which has played a central role in the development of modern science.

  20. 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.

  1. Evaluation of research in biomedical ontologies

    Science.gov (United States)

    Dumontier, Michel; Gkoutos, Georgios V.

    2013-01-01

    Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research. PMID:22962340

  2. Evaluation of research in biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gkoutos, Georgios V

    2013-11-01

    Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research.

  3. JPRS Report, Science and Technology USSR: Life Sciences.

    Science.gov (United States)

    1990-07-26

    rusts. In general, the protein percent of the active cultures. The mother cultures of content of the grain is 17.8 percent, and gluten content is...hypertension. A rapid Happened With Students at Harvest"] increase in tolerance develops among addicts, and absti- nence syndrome can develop after as little as...life threw in rather than the pain syndrome typical of opiate addic- another bitter surprise that caused at least as much tion. Diffuse encephalomyelitis

  4. The oblique perspective: philosophical diagnostics of contemporary life sciences research.

    Science.gov (United States)

    Zwart, Hub

    2017-12-01

    This paper indicates how continental philosophy may contribute to a diagnostics of contemporary life sciences research, as part of a "diagnostics of the present" (envisioned by continental thinkers, from Hegel up to Foucault). First, I describe (as a "practicing" philosopher) various options for an oblique (or symptomatic) reading of emerging scientific discourse, bent on uncovering the basic "philosophemes" of science (i.e. the guiding ideas, the basic conceptions of nature, life and technology at work in contemporary life sciences research practices). Subsequently, I outline a number of radical transformations occurring both at the object-pole and at the subject-pole of the current knowledge relationship, namely the technification of the object and the anonymisation or collectivisation of the subject, under the sway of automation, ICT and big machines. Finally, I further elaborate the specificity of the oblique perspective with the help of Lacan's theorem of the four discourses. Philosophical reflections on contemporary life sciences concur neither with a Master's discourse (which aims to strengthen the legitimacy and credibility of canonical sources), nor with university discourse (which aims to establish professional expertise), nor with what Lacan refers to as hysterical discourse (which aims to challenge representatives of the power establishment), but rather with the discourse of the analyst, listening with evenly-poised attention to the scientific files in order to bring to the fore the cupido sciendi (i.e. the will to know, but also to optimise and to control) which both inspires and disrupts contemporary life sciences discourse.

  5. Generating application ontologies from reference ontologies.

    Science.gov (United States)

    Shaw, Marianne; Detwiler, Landon T; Brinkley, James F; Suciu, Dan

    2008-11-06

    The semantic web provides the possiblity of linking together large numbers of biomedical ontologies. Unfortunately, many of the biomedical ontologies that have been developed are domain-specific and do not share a common structure that will allow them to be easily combined. Reference ontologies provide the necessary ontological framework for linking together these smaller, specialized ontologies. We present extensions to the semantic web query language SparQL that will allow researchers to develop application ontologies that are derived from reference ontologies. We have modified the ARQ query processor to support subqueries, recursive subqueries, and Skolem functions for node creation. We demonstrate the utility of these extensions by deriving an application ontology from the Foundational Model of Anatomy.

  6. Improving Group Work Practices in Teaching Life Sciences: Trialogical Learning

    Science.gov (United States)

    Tammeorg, Priit; Mykkänen, Anna; Rantamäki, Tomi; Lakkala, Minna; Muukkonen, Hanni

    2017-08-01

    Trialogical learning, a collaborative and iterative knowledge creation process using real-life artefacts or problems, familiarizes students with working life environments and aims to teach skills required in the professional world. We target one of the major limitation factors for optimal trialogical learning in university settings, inefficient group work. We propose a course design combining effective group working practices with trialogical learning principles in life sciences. We assess the usability of our design in (a) a case study on crop science education and (b) a questionnaire for university teachers in life science fields. Our approach was considered useful and supportive of the learning process by all the participants in the case study: the students, the stakeholders and the facilitator. Correspondingly, a group of university teachers expressed that the trialogical approach and the involvement of stakeholders could promote efficient learning. In our case in life sciences, we identified the key issues in facilitating effective group work to be the design of meaningful tasks and the allowance of sufficient time to take action based on formative feedback. Even though trialogical courses can be time consuming, the experience of applying knowledge in real-life cases justifies using the approach, particularly for students just about to enter their professional careers.

  7. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  8. Richard Feynman a life in science

    CERN Document Server

    Gribbin, John

    1998-01-01

    This text is a portrayal of one of the greatest scientists of the late 20th-century, which also provides a picture of the significant physics of the period. It combines personal anecdotes, writings and recollections with narrative. Richard Feynman's career included: war-time work on the atomic bomb at Los Alamos; a theory of quantum mechanics for which he won the Nobel prize; and major contributions to the sciences of gravity, nuclear physics and particle theory. In 1986, he was able to show that the Challenger disaster was due to the effect of cold on the booster rocket rubber sealings.

  9. When Cognitive Sciences Meet Real Life

    DEFF Research Database (Denmark)

    Smith, Viktor; Selsøe Sørensen, Henrik; Nissilä, Niina

    2012-01-01

    with his/her existing knowledge, expectations and buying motivations. A cross-disciplinary Danish research project provides a new, shared frame of reference for food manufacturers, authorities, and consumer organisations for assessing in-store food-to-consumer communication from a fairness perspective......Consumers in general pay little attention to food labels. The study of expert-to-layperson communication related to food labels integrates many aspects of what cognitive sciences are about: Knowledge modelling and knowledge transfer, termhood and precision as well as fuzziness, interaction between...

  10. Bringing Climate Change into the Life Science Classroom: Essentials, Impacts on Life, and Addressing Misconceptions

    Science.gov (United States)

    Hawkins, Amy J.; Stark, Louisa A.

    2016-01-01

    Climate change is at the forefront of our cultural conversation about science, influencing everything from presidential debates to Leonardo DiCaprio's 2016 Oscar acceptance speech. The topic is becoming increasingly socially and scientifically relevant but is no closer to being resolved. Most high school students take a life science course but…

  11. Case for Building Informal Ontology of a Subject Matter at School Level Science Education with Community Collaboration

    Science.gov (United States)

    Datt, Sachin

    2015-01-01

    School science textbooks are an amalgamation of concepts collected from different fields of Science like Physics, Chemistry and Biology. The actual number of concepts in the different domains of science are enormous. Educationists have to make a decision of choosing some concept that they think are necessary for students to know at a certain age.…

  12. Geo-Information (Lake Data Service Based on Ontology

    Directory of Open Access Journals (Sweden)

    Long-hua He

    2007-12-01

    Full Text Available Recently ontology research has received much attention in geo-information science and the concept of ontology is very important for spatial information concept modeling and data sharing, classification of geographical classes. More importantly, it enriches the semantic theory of spatial information. Geo-information services and geo-information interpretation and extraction are the two main applications of geo-ontology. Ontologies have great application potential for geo-information service.

  13. [Relationship between science, politics, religion and daily life].

    Science.gov (United States)

    Slaus, Ivo; Kurjak, Asim

    2002-01-01

    The relationship between science, politics and religion is discussed, with special reference to the effect of scientific discoveries on the improvement of the quality of everyday life. It is concluded that the results of scientific research lead to prosperity of man and nations. However, the society appears to insufficiently use these advantages which can be partly the result of failing to recognize the connection between basic science and products that re-define everyday life. On the other hand, problems might originate from the aversion towards the risks as well as from short-term planning.

  14. Surface enhanced raman spectroscopy analytical, biophysical and life science applications

    CERN Document Server

    Schlücker, Sebastian

    2013-01-01

    Covering everything from the basic theoretical and practical knowledge to new exciting developments in the field with a focus on analytical and life science applications, this monograph shows how to apply surface-enhanced Raman scattering (SERS) for solving real world problems. From the contents: * Theory and practice of SERS * Analytical applications * SERS combined with other analytical techniques * Biophysical applications * Life science applications including various microscopies Aimed at analytical, surface and medicinal chemists, spectroscopists, biophysicists and materials scientists. Includes a Foreword by the renowned Raman spectroscopist Professor Wolfgang Kiefer, the former Editor-in-Chief of the Journal of Raman Spectroscopy.

  15. International Conference for Innovation in Biomedical Engineering and Life Sciences

    CERN Document Server

    Usman, Juliana; Mohktar, Mas; Ahmad, Mohd

    2016-01-01

    This volumes presents the proceedings of ICIBEL 2015, organized by the Centre for Innovation in Medical Engineering (CIME) under Innovative Technology Research Cluster, University of Malaya. It was held in Kuala Lumpur, Malaysia, from 6-8 December 2015. The ICIBEL 2015 conference promotes the latest researches and developments related to the integration of the Engineering technology in medical fields and life sciences. This includes the latest innovations, research trends and concerns, challenges and adopted solution in the field of medical engineering and life sciences. .

  16. Applying ontological realism to medically unexplained syndromes.

    Science.gov (United States)

    Doing-Harris, Kristina; Meystre, Stephane M; Samore, Matthew; Ceusters, Werner

    2013-01-01

    The past decade has witnessed an increased interest in what are called "medically unexplained syndromes" (MUS). We address the question of whether structuring the domain knowledge for MUS can be achieved by applying the principles of Ontological Realism in light of criticisms about their usefulness in areas where science has not yet led to insights univocally endorsed by the relevant communities. We analyzed whether the different perspectives held by MUS researchers can be represented without taking any particular stance and whether existing ontologies based on Ontological Realism can be further built upon. We did not find refutation of the applicability of the principles. We found the Ontology of General Medical Science and Information Artifact Ontology to provide useful frameworks for analyzing certain MUS controversies, although leaving other questions open.

  17. Practical theology as life science: Fides Quaerens Vivendi and its connection to Hebrew thinking (Hālak

    Directory of Open Access Journals (Sweden)

    Daniël J. Louw

    2017-02-01

    Full Text Available The term practical theology is complex and, due to many different religious and cultural settings, a many layered concept. During the past 40 years the paradigm in theory formation for an academic and disciplinary approach to practical theology shifted from the clerical and ecclesial paradigm of ministerial actions to experiences of faith with the emphasis on an empirical based epistemology. Rather than a deductive approach, the shift is towards a more inductive approach within the methodological framework of phenomenology. Currently, in the international discourse on theory formation, there is a tendency towards a hermeneutical approach with the focus on the networking, relational dynamics of civil society Thus, the attempt to describe practical theology as a kind of ‘life science’ (the concern for the mundane and existential reality of everyday life – Alltagsreligion. Within the context of African spiritualties, with its emphasis on the communal dynamics of vital, human relationships, the focus on lifestyles becomes vital. In light of an ontology of life (l’energie spirituelle – Henri Bergson, the notion of fides quaerens vivendi [faith seeking lifestyles] is researched. With reference to the theory of complexification and chaosmos as well as the impact thereof on different theories in life sciences, the connection between sapientia and the vivid praxis of God is critically explored. The focus of this article is on the question: What is the impact of an ontology of life on both praxis thinking and theological reflection? Instead of the Cartesian framework of causative definitions, the notion of the ‘infinition of God’ is proposed within the praxis of Hebrew, wisdom thinking.

  18. CSEO - the Cigarette Smoke Exposure Ontology

    National Research Council Canada - National Science Library

    Younesi, Erfan; Ansari, Sam; Guendel, Michaela; Ahmadi, Shiva; Coggins, Chris; Hoeng, Julia; Hofmann-Apitius, Martin; Peitsch, Manuel C

    2014-01-01

    ...) is composed of 20091 concepts. The ontology in its current form is able to capture a wide range of cigarette smoke exposure concepts within the knowledge domain of exposure science with a reasonable sensitivity and specificity...

  19. Space life sciences perspectives for Space Station Freedom

    Science.gov (United States)

    Young, Laurence R.

    1992-01-01

    It is now generally acknowledged that the life science discipline will be the primary beneficiary of Space Station Freedom. The unique facility will permit advances in understanding the consequences of long duration exposure to weightlessness and evaluation of the effectiveness of countermeasures. It will also provide an unprecedented opportunity for basic gravitational biology, on plants and animals as well as human subjects. The major advantages of SSF are the long duration exposure and the availability of sufficient crew to serve as subjects and operators. In order to fully benefit from the SSF, life sciences will need both sufficient crew time and communication abilities. Unlike many physical science experiments, the life science investigations are largely exploratory, and frequently bring unexpected results and opportunities for study of newly discovered phenomena. They are typically crew-time intensive, and require a high degree of specialized training to be able to react in real time to various unexpected problems or potentially exciting findings. Because of the long duration tours and the large number of experiments, it will be more difficult than with Spacelab to maintain astronaut proficiency on all experiments. This places more of a burden on adequate communication and data links to the ground, and suggests the use of AI expert system technology to assist in astronaut management of the experiment. Typical life science experiments, including those flown on Spacelab Life Sciences 1, will be described from the point of view of the demands on the astronaut. A new expert system, 'PI in a Box,' will be introduced for SLS-2, and its applicability to other SSF experiments discussed. (This paper consists on an abstract and ten viewgraphs.)

  20. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

  1. Simple Ontology Format (SOFT)

    Energy Technology Data Exchange (ETDEWEB)

    2011-10-01

    Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

  2. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  3. The LAILAPS search engine: relevance ranking in life science databases.

    Science.gov (United States)

    Lange, Matthias; Spies, Karl; Bargsten, Joachim; Haberhauer, Gregor; Klapperstück, Matthias; Leps, Michael; Weinel, Christian; Wünschiers, Röbbe; Weissbach, Mandy; Stein, Jens; Scholz, Uwe

    2010-01-15

    Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. With a set of features, extracted from each database hit in combination with user relevance preferences, a neural network predicts user specific relevance scores. Using expert knowledge as training data for a predefined neural network or using users own relevance training sets, a reliable relevance ranking of database hits has been implemented. In this paper, we present the LAILAPS system, the concepts, benchmarks and use cases. LAILAPS is public available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  4. Introduction to Life Science (Introduccion a la Ciencia Biologica).

    Science.gov (United States)

    Barnhard, Diana; And Others

    These materials were developed to meet an expressed need for bilingual materials for a secondary school Life Science Course. Eight units were prepared. These include the following topics: (1) Introduction to the Scientific Method; (2) The Microscope; (3) The Cell; (4) Single-celled Protists, Plants, and Animals; (5) Multicellular Living Things;…

  5. Introduction to Life Science (Introduccion a la Ciencia Biologica).

    Science.gov (United States)

    Barnhard, Diana; And Others

    These materials were developed to meet an expressed need for bilingual materials for a secondary school Life Science Course. Eight units were prepared. These include the following topics: (1) Introduction to the Scientific Method; (2) The Microscope; (3) The Cell; (4) Single-celled Protists, Plants, and Animals; (5) Multicellular Living Things;…

  6. Improving Reuse in Software Development for the Life Sciences

    Science.gov (United States)

    Iannotti, Nicholas V.

    2013-01-01

    The last several years have seen unprecedented advancements in the application of technology to the life sciences, particularly in the area of data generation. Novel scientific insights are now often driven primarily by software development supporting new multidisciplinary and increasingly multifaceted data analysis. However, despite the…

  7. Politics and the life sciences: an unfinished revolution.

    Science.gov (United States)

    Johnson, Gary R

    2011-01-01

    Politics and the life sciences--also referred to as biopolitics--is a field of study that seeks to advance knowledge of politics and promote better policymaking through multidisciplinary analysis that draws on the life sciences. While the intellectual origins of the field may be traced at least into the 1960s, a broadly organized movement appeared only with the founding of the Association for Politics and the Life Sciences (APLS) in 1980 and the establishment of its journal, Politics and the Life Sciences ( PLS ), in 1982. This essay--contributed by a past journal editor and association executive director--concludes a celebration of the association's thirtieth anniversary. It reviews the founding of the field and the association, as well as the contributions of the founders. It also discusses the nature of the empirical work that will advance the field, makes recommendations regarding the identity and future of the association, and assesses the status of the revolution of which the association is a part. It argues that there is progress to celebrate, but that this revolution--the last of three great scientific revolutions--is still in its early stages. The revolution is well-started, but remains unfinished.

  8. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  9. Introductory Life Science Mathematics and Quantitative Neuroscience Courses

    Science.gov (United States)

    Duffus, Dwight; Olifer, Andrei

    2010-01-01

    We describe two sets of courses designed to enhance the mathematical, statistical, and computational training of life science undergraduates at Emory College. The first course is an introductory sequence in differential and integral calculus, modeling with differential equations, probability, and inferential statistics. The second is an…

  10. Life Science Professional Societies Expand Undergraduate Education Efforts

    Science.gov (United States)

    Matyas, Marsha Lakes; Ruedi, Elizabeth A.; Engen, Katie; Chang, Amy L.

    2017-01-01

    The "Vision and Change in Undergraduate Biology Education" reports cite the critical role of professional societies in undergraduate life science education and, since 2008, have called for the increased involvement of professional societies in support of undergraduate education. Our study explored the level of support being provided by…

  11. Sustainable Infrastructures for Life Science Communication: Workshop Summary

    Science.gov (United States)

    Brown, Elizabeth Stallman; Yeung, Laurence; Sawyer, Keegan

    2014-01-01

    Advances in the life sciences--from the human genome to biotechnology to personalized medicine and sustainable communities--have profound implications for the well-being of society and the natural world. Improved public understanding of such scientific advances has the potential to benefit both individuals and society through enhanced quality of…

  12. Collaborating in Life Science Research Groups: The Question of Authorship

    Science.gov (United States)

    Muller, Ruth

    2012-01-01

    This qualitative study explores how life science postdocs' perceptions of contemporary academic career rationales influence how they relate to collaboration within research groups. One consequential dimension of these perceptions is the high value assigned to publications. For career progress, postdocs consider producing publications and…

  13. Improving Reuse in Software Development for the Life Sciences

    Science.gov (United States)

    Iannotti, Nicholas V.

    2013-01-01

    The last several years have seen unprecedented advancements in the application of technology to the life sciences, particularly in the area of data generation. Novel scientific insights are now often driven primarily by software development supporting new multidisciplinary and increasingly multifaceted data analysis. However, despite the…

  14. 76 FR 17621 - Biotech Life Science Trade Mission to China

    Science.gov (United States)

    2011-03-30

    ... releases to general and trade media, direct mail, notices by industry trade associations and other... International Trade Administration Biotech Life Science Trade Mission to China AGENCY: International Trade... Commerce, International Trade Administration, U.S. and Foreign Commercial Service (CS) is organizing a...

  15. Photoelectron microscopy in the life sciences: Imaging neuron networks

    Energy Technology Data Exchange (ETDEWEB)

    Mercanti, D. (Istituto di Neurobiologia del CNR, Viale Marx 15, 00100 Roma (Italy)); De Stasio, G. (ISM-CNR, Via E. Fermi 38, 00044 Frascati, Roma (Italy)); Ciotti, M.T. (Istituto di Neurobiologia del CNR, Viale Marx 15, 00100 Roma (Italy)); Capasso, C.; Ng, W.; Ray-Chaudhuri, A.K.; Liang, S.H.; Cole, R.K.; Guo, Z.Y.; Wallace, J. (Department of Physics, University of Wisconsin, Madison, WI (USA) Electrical and Computer Engineering, University of Wisconsin, Madison, WI (USA)); Margaritondo, G. (Institut de Physique Appliquee, Ecole Polytechnique Federale de Lausanne, Ecublens (Switzerland)); Cerrina, F. (Departments of Physics, University of Wisconsin, Madison, WI (USA) Electrical and Computer Engineering, University of Wisconsin, Madison, WI (USA)); Underwood, J.; Perera, R.; Kortright, J. (Center for X-ray Optics, Lawrence Berkeley Laboratory, Berkeley, CA 94720 (USA))

    1991-05-01

    Photoemission techniques like electron spectroscopy for chemical analysis are the leading electronic probes in materials science---but their impact in the life sciences has been minimal. A critical problem is that the lateral resolution in ordinary photoemission does not exceed a few tenths of a millimeter. This space-averaged probe is nearly useless for most of the fundamental problems in biophysics and biochemistry, which deal with microstructures in the submicron range or smaller. This limit is being overcome with photoemission microscopes, such as our scanning instrument MAXIMUM. The first scanning photoelectron micrographs of a cellular system with submicron resolution are presented. Minute details of neuron networks are imaged on MAXIMUM, thereby opening the way to novel applications of photoemission in the life sciences. The details include individual neurons, axons, dendrites, and synapses, and composite large-area scanning micrographs were routinely produced with a lateral resolution of 0.5 {mu}m.

  16. Fish Ontology framework for taxonomy-based fish recognition

    Science.gov (United States)

    Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

    2017-01-01

    Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

  17. Life sciences research on the space station: An introduction

    Science.gov (United States)

    1985-01-01

    The Space Station will provide an orbiting, low gravity, permanently manned facility for scientific research, starting in the 1990s. The facilities for life sciences research are being designed to allow scientific investigators to perform research in Space Medicine and Space Biology, to study the consequences of long-term exposure to space conditions, and to allow for the permanent presence of humans in space. This research, using humans, animals, and plants, will provide an understanding of the effects of the space environment on the basic processes of life. In addition, facilities are being planned for remote observations to study biologically important elements and compounds in space and on other planets (exobiology), and Earth observations to study global ecology. The life sciences community is encouraged to plan for participation in scientific research that will be made possible by the Space Station research facility.

  18. 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.

  19. 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

  20. Ontology and Epistemology in Management Research: An Islamic Perspective

    Directory of Open Access Journals (Sweden)

    Naail Mohammed KAMIL

    2011-09-01

    Full Text Available From the Western value system, two kinds of ontological and epistemological standpoints are characterized in Management and Social Sciences research;realist ontology and subjectivist ontology or objectivist epistemology and subjectivist epistemology. The kind of ontology and epistemology a researcher commits to has inherent effects towards the researcher’s way of contributing new knowledge. This short communication attempts to contribute new knowledge to the literature of philosophical standpoints in management research by discussing the ontological and epistemological stances with respect to Islam. It was shown that the Islamic viewpoint of ontology and epistemology is in the middle side between realist – subjectivist ontology and between objectivist – subjectivist epistemology. This stance of Islam on ontology andepistemology as elaborated in the Qur’an and the tradition of the Prophet Muhammad (peace be upon him increases the resilience with which knowledge is contributed in a holistic manner regardless of social, cultural or political backgrounds.

  1. Miguel De Unamuno: A Science And A Religion For Life

    Directory of Open Access Journals (Sweden)

    Alicia Villar Ezcurra

    2016-02-01

    Full Text Available Miguel de Unamuno´s science reflections are defined in different debates which must be distinguished. His stance about science is much more complex than it is believed when his thinking is summarized in the following sentence: ¨let them invent!». This manuscript presents Unamuno´s evolution (from 1984 to 1906 and analyzes some texts in which he appreciated science positively. Finally, some of the Unamuno´s thoughts that he planified to develop in his work ¨Religion and Science¨ (around 1902 are emphasized. Hence, Don Miguel defends the need to develop our intellectual and spiritual dimension to be able to have a more plenty life.

  2. Research on Life Science and Life Support Engineering Problems of Manned Deep Space Exploration Mission

    Science.gov (United States)

    Qi, Bin; Guo, Linli; Zhang, Zhixian

    2016-07-01

    Space life science and life support engineering are prominent problems in manned deep space exploration mission. Some typical problems are discussed in this paper, including long-term life support problem, physiological effect and defense of varying extraterrestrial environment. The causes of these problems are developed for these problems. To solve these problems, research on space life science and space medical-engineering should be conducted. In the aspect of space life science, the study of space gravity biology should focus on character of physiological effect in long term zero gravity, co-regulation of physiological systems, impact on stem cells in space, etc. The study of space radiation biology should focus on target effect and non-target effect of radiation, carcinogenicity of radiation, spread of radiation damage in life system, etc. The study of basic biology of space life support system should focus on theoretical basis and simulating mode of constructing the life support system, filtration and combination of species, regulation and optimization method of life support system, etc. In the aspect of space medical-engineering, the study of bio-regenerative life support technology should focus on plants cultivation technology, animal-protein production technology, waste treatment technology, etc. The study of varying gravity defense technology should focus on biological and medical measures to defend varying gravity effect, generation and evaluation of artificial gravity, etc. The study of extraterrestrial environment defense technology should focus on risk evaluation of radiation, monitoring and defending of radiation, compound prevention and removal technology of dust, etc. At last, a case of manned lunar base is analyzed, in which the effective schemes of life support system, defense of varying gravity, defense of extraterrestrial environment are advanced respectively. The points in this paper can be used as references for intensive study on key

  3. Small Science: Infants and Toddlers Experiencing Science in Everyday Family Life

    Science.gov (United States)

    Sikder, Shukla; Fleer, Marilyn

    2015-06-01

    Vygotsky (1987) stated that the restructured form of everyday concepts learned at home and in the community interact with scientific concepts introduced in formal school settings, leading to a higher level of scientific thinking for school-aged children. But, what does this mean for the scientific learning of infants and toddlers? What kinds of science learning are afforded at home during this early period of life? The study reported in this paper sought to investigate the scientific development of infants-toddlers (10 to 36 months) growing up in Bangladeshi families living in Australia and Singapore. Four families were studied over 2 years. Digital video observations were made of everyday family life and analysed using Vygotsky's theoretical framework of everyday concepts and scientific concepts (51 h of digital observations). While there are many possibilities for developing scientific concepts in infants-toddlers' everyday life, our study found four categories of what we have called small science: multiple possibilities for science; discrete science; embedded science and counter intuitive science. The findings of this study contribute to the almost non-existent literature into infants and toddlers' scientific development and advance new understandings of early childhood science education.

  4. International Space Station Research and Facilities for Life Sciences

    Science.gov (United States)

    Robinson, Julie A.; Ruttley, Tara M.

    2009-01-01

    Assembly of the International Space Station is nearing completion in fall of 2010. Although assembly has been the primary objective of its first 11 years of operation, early science returns from the ISS have been growing at a steady pace. Laboratory facilities outfitting has increased dramatically 2008-2009 with the European Space Agency s Columbus and Japanese Aerospace Exploration Agency s Kibo scientific laboratories joining NASA s Destiny laboratory in orbit. In May 2009, the ISS Program met a major milestone with an increase in crew size from 3 to 6 crewmembers, thus greatly increasing the time available to perform on-orbit research. NASA will launch its remaining research facilities to occupy all 3 laboratories in fall 2009 and winter 2010. To date, early utilization of the US Operating Segment of the ISS has fielded nearly 200 experiments for hundreds of ground-based investigators supporting international and US partner research. With a specific focus on life sciences research, this paper will summarize the science accomplishments from early research aboard the ISS- both applied human research for exploration, and research on the effects of microgravity on life. We will also look ahead to the full capabilities for life sciences research when assembly of ISS is complete in 2010.

  5. The space life sciences strategy for the 21st century.

    Science.gov (United States)

    Nicogossian, A E; Gaiser, K K

    1992-06-01

    In the past, space life sciences has focused on gaining an understanding of physiological tolerance to spaceflight, but, for the last 10 years, the focus has evolved to include issues relevant to extended duration missions. In the 21st century, NASA's long-term strategy for the exploration of the solar system will combine the assurance of human health and performance for long periods in space with investigations aimed at searching for traces of life on other planets and acquiring fundamental scientific knowledge of life processes. Implementation of this strategy will involve a variety of disciplines including radiation health, life support, human factors, space physiology and countermeasures, medical care, environmental health, and exobiology. It will use both ground-based and flight research opportunities such as those found in current on-going programs, on Spacelab and unmanned biosatellite flights, and during Space Station Freedom missions.

  6. Social science in a stem cell laboratory: what happened when social and life sciences met.

    Science.gov (United States)

    Stacey, Glyn; Stephens, Neil

    2012-01-01

    We describe the experience of conducting intensive social science research at the UK Stem Cell Bank from the viewpoint of both the person conducting the social science research and the Director of the Bank. We detail the initial misunderstandings and concerns held by both and the problems these caused. Then we describe how the relationship developed as the project progressed and shared benefits became apparent. Finally, while acknowledging potential areas of tension between the life and social sciences, we suggest further interaction between the disciplines would prove beneficial for both and speculate as to how this may be achieved. In the discussion we identify a set of learning points from our experience and definitions of social science terminology that may help to inform future engagements between life and social scientists.

  7. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Science.gov (United States)

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  8. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    Directory of Open Access Journals (Sweden)

    Janna Hastings

    Full Text Available Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA.

  9. [Alumni of medical sciences and their life satisfaction].

    Science.gov (United States)

    Rockenbauch, K; Meister, U; Schmutzer, G; Alfermann, D

    2006-03-01

    Medical doctors are especially burdened with psychological and social aspects of their occupation. These circumstances may lead to low life satisfaction and substance abusing behaviour and burn out symptoms are probable. In this paper we investigate, if alumni of medical sciences show lower life satisfaction compared to their peers. If so, we want to know, which factors influence this result. This survey is based on n = 671 alumni of medicine in seven German universities. The life satisfaction of alumni differs significantly from the peer sample. Outstanding are the highly significant and powerful differences to the scale "leisure". It was evident by an iterative regression that the variables "extreme input at work", "instrumentality/masculinity", "effort-reward imbalance", "expressivity/femininity" as well as "career self-efficacy-expectation", clarify 43 % of the variance in the group of alumni working by the time of enquiry. The results point out, that already alumni of medical science are in the "circle of burn-out". Their life satisfaction is more affected, if the workload is perceived high and the perceived benefits are low. Individual as well as external aspects influence life satisfaction and can be a starting-point for prevention.

  10. Applying Conceptual Blending to Model Coordinated Use of Multiple Ontological Metaphors

    Science.gov (United States)

    Dreyfus, Benjamin W.; Gupta, Ayush; Redish, Edward F.

    2015-04-01

    Energy is an abstract science concept, so the ways that we think and talk about energy rely heavily on ontological metaphors: metaphors for what kind of thing energy is. Two commonly used ontological metaphors for energy are energy as a substance and energy as a vertical location. Our previous work has demonstrated that students and experts can productively use both the substance and location ontologies for energy. In this paper, we use Fauconnier and Turner's conceptual blending framework to demonstrate that experts and novices can successfully blend the substance and location ontologies into a coherent mental model in order to reason about energy. Our data come from classroom recordings of a physics professor teaching a physics course for the life sciences, and from an interview with an undergraduate student in that course. We analyze these data using predicate analysis and gesture analysis, looking at verbal utterances, gestures, and the interaction between them. This analysis yields evidence that the speakers are blending the substance and location ontologies into a single blended mental space.

  11. Knowledge sharing in public-private partnerships in life science: An open science perspective

    OpenAIRE

    Sánchez Jiménez, Óscar David; Aibar Puentes, Eduard

    2016-01-01

    Resultados preliminares sobre la adopción de prácticas de ciencia abierta en partenariados público-privados en Ciencias de la Vida. Resultats preliminars sobre l'adopció de pràctiques de ciència oberta a partenariats publico-privats en Ciències de la Vida. Preliminary results on the adoption of open science practices in public-private partnerships in Life Sciences.

  12. 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...

  13. Advancing palliative and end-of-life science in cardiorespiratory populations: The contributions of nursing science.

    Science.gov (United States)

    Grady, Patricia A

    Nursing science has a critical role to inform practice, promote health, and improve the lives of individuals across the lifespan who face the challenges of advanced cardiorespiratory disease. Since 1997, the National Institute of Nursing Research (NINR) has focused attention on the importance of palliative and end-of-life care for advanced heart failure and advanced pulmonary disease through the publication of multiple funding opportunity announcements and by supporting a cadre of nurse scientists that will continue to address new priorities and future directions for advancing palliative and end-of-life science in cardiorespiratory populations. Published by Elsevier Inc.

  14. The foundational ontology library ROMULUS

    CSIR Research Space (South Africa)

    Khan, ZC

    2013-09-01

    Full Text Available A purpose of a foundational ontology is to solve interoperability issues among domain ontologies and they are used for ontology- driven conceptual data modelling. Multiple foundational ontologies have been developed in recent years, and most of them...

  15. Life Sciences Data Archives (LSDA) in the Post-Shuttle Era

    Science.gov (United States)

    Fitts, Mary A.; Johnson-Throop, Kathy; Havelka, Jacque; Thomas, Diedre

    2010-01-01

    for something they do, and learn how to do it better as they interact regularly. LSDA works with the HRP community of practice to ensure that we are preserving the relevant research and data they need in the LSDA repository. An evidence-based approach to risk management is required in space life sciences. Evidence changes over time. LSDA has a pilot project with Collexis, a new type of Web-based search engine. Collexis differentiates itself from full-text search engines by making use of thesauri for information retrieval. The high-quality search is based on semantics that have been defined in a life sciences ontology. Additionally, Collexis' matching technology is unique, allowing discovery of partially matching dicuments. Users do not have to construct a complicated (Boolean) search query, but can simply enter a free text search without the risk of getting "no results". Collexis may address these issues by virtue of its retrieval and discovery capabilities across multiple repositories.

  16. A Practical Guide to Photoacoustic Tomography in the Life Sciences

    Science.gov (United States)

    Wang, Lihong V.; Yao, Junjie

    2016-01-01

    The life sciences can benefit greatly from imaging technologies that connect microscopic discoveries with macroscopic observations. Photoacoustic tomography (PAT), a highly sensitive modality for imaging rich optical absorption contrast over a wide range of spatial scales at high speed, is uniquely positioned for this need. In PAT, endogenous contrast reveals tissue’s anatomical, functional, metabolic, and histologic properties, and exogenous contrast provides molecular and cellular specificity. The spatial scale of PAT covers organelles, cells, tissues, organs, and small-animal organisms. Consequently, PAT is complementary to other imaging modalities in contrast mechanism, penetration, spatial resolution, and temporal resolution. We review the fundamentals of PAT and provide practical guidelines to the broad life science community for matching PAT systems with research needs. We also summarize the most promising biomedical applications of PAT, discuss related challenges, and envision its potential to lead to further breakthroughs. PMID:27467726

  17. Kierkegaard and psychology as the science of the "multifarious life".

    Science.gov (United States)

    Klempe, Sven Hroar

    2013-09-01

    The aim of this paper is to demonstrate the actuality of some considerations around psychology made by the Danish philosopher Søren Kierkegaard (1813-1855). According to him psychology is about the "multifarious" life, which is a term that pinpoints the challenges psychology still have when it comes to including changes and genetic perspectives on its understanding of actual living. Yet Kierkegaard discusses psychology in relationship to metaphysics, which is an almost forgotten perspective. His understanding opens up for narrowing the definition of psychology down to the science of subjectivity, which at the same time elevates psychology to being the only science that focuses on the actual human life. Yet Kierkegaard's most important contribution to psychology is to maintain a radical distinction between subjectivity and objectivity, and in this respect the psychology of today is challenged.

  18. Knowledge-Based Systems in Biomedicine and Computational Life Science

    CERN Document Server

    Jain, Lakhmi

    2013-01-01

    This book presents a sample of research on knowledge-based systems in biomedicine and computational life science. The contributions include: ·         personalized stress diagnosis system ·         image analysis system for breast cancer diagnosis ·         analysis of neuronal cell images ·         structure prediction of protein ·         relationship between two mental disorders ·         detection of cardiac abnormalities ·         holistic medicine based treatment ·         analysis of life-science data  

  19. Life Sciences Division and Center for Human Genome Studies 1994

    Energy Technology Data Exchange (ETDEWEB)

    Cram, L.S.; Stafford, C. [comp.

    1995-09-01

    This report summarizes the research and development activities of the Los Alamos National Laboratory`s Life Sciences Division and the biological aspects of the Center for Human Genome Studies for the calendar year 1994. The technical portion of the report is divided into two parts, (1) selected research highlights and (2) research projects and accomplishments. The research highlights provide a more detailed description of a select set of projects. A technical description of all projects is presented in sufficient detail so that the informed reader will be able to assess the scope and significance of each project. Summaries useful to the casual reader desiring general information have been prepared by the group leaders and appear in each group overview. Investigators on the staff of the Life Sciences Division will be pleased to provide further information.

  20. Venture Capital Investment in the Life Sciences in Switzerland.

    Science.gov (United States)

    Hosang, Markus

    2014-12-01

    Innovation is one of the main driving factors for continuous and healthy economic growth and welfare. Switzerland as a resource-poor country is particularly dependent on innovation, and the life sciences, which comprise biotechnologies, (bio)pharmaceuticals, medical technologies and diagnostics, are one of the key areas of innovative strength of Switzerland. Venture capital financing and venture capitalists (frequently called 'VCs') and investors in public equities have played and still play a pivotal role in financing the Swiss biotechnology industry. In the following some general features of venture capital investment in life sciences as well as some opportunities and challenges which venture capital investors in Switzerland are facing are highlighted. In addition certain means to counteract these challenges including the 'Zukunftsfonds Schweiz' are discussed.

  1. European Bioinformatics Institute: Research Infrastructure needed for Life Science

    CERN Document Server

    CERN. Geneva

    2015-01-01

    The life science community is an ever increasing source of data from increasing diverse range of instruments and sources. EMBL-EBI has a remit to store and exploit this data, collected and made available openly across the world, for the benefit of the whole research community. The research infrastructure needed to support the big data analysis around this mission encompasses high performance networks, high-throughput computing, and a range of cloud and storage solutions - and will be described in the presentation.

  2. Microfluidics: an enabling technology for the life sciences

    OpenAIRE

    Zengerle, Roland; Koltay, P.; Ducrée, Jens

    2004-01-01

    During the last year we have investigated existing and future markets, products and technologies for microfluidics in the life sciences. Within this paper we present some of the findings and discuss a major trend identified within this project: the development of microfluidic platforms for flexible design of application specific integrated microfluidic systems. We discuss two platforms in detail which are currently under development in our lab: microfluidics on a rotating CD ("Lab-CD") as wel...

  3. Reconstruction of biological networks based on life science data integration

    OpenAIRE

    Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

    2010-01-01

    For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and V...

  4. Hiroshima University Research and Technology Guide 2012 Version : Life Science

    OpenAIRE

    Center for Collaborative Research & Community Cooperation,

    2012-01-01

    I Life ScienceDevelopment of Treatment Strategy for Hepatocellular Carcinoma to Improve the Long Term Prognosis / Hiroshi AIKATA...2Development of Revolutional Apatite-implant Complex with Simultaneous Bone Augmentation and Osseointegration / Yasumasa AKAGAWA...3How Do Patients with Alzheimer’s Disease Experience Memory Impairments? / Sawako ARAI...4Development of New Therapies for Chronic Viral Hepatitis Using Human Hepatocyte Chimeric Mice / Kazuaki CHAYAMA...5Identification of High Risk Pa...

  5. Hiroshima University Research and Technology Guide 2012 Version : Life Science

    OpenAIRE

    Center for Collaborative Research & Community Cooperation,

    2012-01-01

    I Life ScienceDevelopment of Treatment Strategy for Hepatocellular Carcinoma to Improve the Long Term Prognosis / Hiroshi AIKATA...2Development of Revolutional Apatite-implant Complex with Simultaneous Bone Augmentation and Osseointegration / Yasumasa AKAGAWA...3How Do Patients with Alzheimer’s Disease Experience Memory Impairments? / Sawako ARAI...4Development of New Therapies for Chronic Viral Hepatitis Using Human Hepatocyte Chimeric Mice / Kazuaki CHAYAMA...5Identification of High Risk Pa...

  6. Life Sciences Research and Development Opportunities During Suborbital Space Flight

    Science.gov (United States)

    Davis, Jeffrey R.

    2010-01-01

    Suborbital space platforms provide a unique opportunity for Space Life Sciences in the next few years. The opportunities include: physiological characterization of the first few minutes of space flight; evaluation of a wide-variety of medical conditions during periods of hyper and hypo-gravity through physiological monitoring; and evaluation of new biomedical and environmental health technologies under hyper and hypo-gravity conditions

  7. Digest of Russian Space Life Sciences, issue 33

    Science.gov (United States)

    Stone, Lydia Razran (Editor); Teeter, Ronald (Editor); Rowe, Joseph (Editor)

    1993-01-01

    This is the thirty-third issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 55 papers published in Russian journals. The abstracts in this issue have been identified as relevant to the following areas of space biology and medicine: biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, equipment and instrumentation, gastrointestinal system, genetics, hematology, human performance, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, psychology, radiobiology, and reproductive system.

  8. Improving life sciences information retrieval using semantic web technology.

    Science.gov (United States)

    Quan, Dennis

    2007-05-01

    The ability to retrieve relevant information is at the heart of every aspect of research and development in the life sciences industry. Information is often distributed across multiple systems and recorded in a way that makes it difficult to piece together the complete picture. Differences in data formats, naming schemes and network protocols amongst information sources, both public and private, must be overcome, and user interfaces not only need to be able to tap into these diverse information sources but must also assist users in filtering out extraneous information and highlighting the key relationships hidden within an aggregated set of information. The Semantic Web community has made great strides in proposing solutions to these problems, and many efforts are underway to apply Semantic Web techniques to the problem of information retrieval in the life sciences space. This article gives an overview of the principles underlying a Semantic Web-enabled information retrieval system: creating a unified abstraction for knowledge using the RDF semantic network model; designing semantic lenses that extract contextually relevant subsets of information; and assembling semantic lenses into powerful information displays. Furthermore, concrete examples of how these principles can be applied to life science problems including a scenario involving a drug discovery dashboard prototype called BioDash are provided.

  9. NASA space life sciences research and education support program

    Science.gov (United States)

    Jones, Terri K.

    1995-01-01

    USRA's Division of Space Life Sciences (DSLS) was established in 1983 as the Division of Space Biomedicine to facilitate participation of the university community in biomedical research programs at the NASA Johnson Space Center (JSC). The DSLS is currently housed in the Center for Advanced Space Studies (CASS), sharing quarters with the Division of Educational Programs and the Lunar and Planetary Institute. The DSLS provides visiting scientists for the Johnson Space Center; organizes conferences, workshops, meetings, and seminars; and, through subcontracts with outside institutions, supports NASA-related research at more than 25 such entities. The DSLS has considerable experience providing visiting scientists, experts, and consultants to work in concert with NASA Life Sciences researchers to define research missions and goals and to perform a wide variety of research administration and program management tasks. The basic objectives of this contract have been to stimulate, encourage, and assist research and education in the NASA life sciences. Scientists and experts from a number of academic and research institutions in this country and abroad have been recruited to support NASA's need to find a solution to human physiological problems associated with living and working in space and on extraterrestrial bodies in the solar system.

  10. Data life cycle: a perspective from the Information Science

    Directory of Open Access Journals (Sweden)

    Ricardo César Gonçalves Sant’Ana

    2016-08-01

    Full Text Available Introduction: Access and use of data as a key factor has been extended to several areas of knowledge of today's society. It’s necessary to develop a new perspective that presents phases and factors involved in these processes, providing an initial analysis structure, allowing the efforts, skills and actions organization related to the data life cycle. Purpose: This article is a proposal for a new look at the data life cycle, that assumes, as a central element, the data itself, supporting itself on the concepts and contributions that Information Science can provide, without giving up the reflections on the role of other key areas such as Computer Science. Methodology: The methodological procedures consisted of bibliographic research and content analysis to describe the phases and factors related to the Data Life Cycle, developing reflections and considerations from context already consolidated in the development of systems that can corroborate the idea of centrality of data. Results: The results describe the phases of: collect, storage, recovery and discard, permeated by transverse factors: privacy, integration, quality, copyright, dissemination and preservation, composing a Data Life Cycle. Conclusions: The current context of the availability of large volumes of data, with great variety and at speeds that provide access in real time, setting the so-called Big Data that requires new concerns about access and use processes of data. The Information Science may offer a new approach, now centered in the data, and contribute to the optimization of Data Life Cycle as a whole, extending bridges between users and the data they need.

  11. Emerging Tensions at the Interface of Artificial Intelligence, IPRs & Competition Law in the Health & Life Sciences

    DEFF Research Database (Denmark)

    Minssen, Timo

    This presentation: • describes the interface between Big Data, IPRs & competition law in the life sciences. • highlights selected life-science areas, where tensions and potential clashes are crystallizing. • discusses how these tensions could be addressed...

  12. Crafting a science life: Learning from twentieth century women

    Science.gov (United States)

    Lenz, Michele Ann

    This study examined how women in the field of science craft a science life. Within a historical and cultural framework, the study analyzed the autobiographies, biographies, and other written works of five noted women scientists who lived during the time period of 1878 through 1992. The women scientists chosen for the study were Lise Meitner, Florence Seibert, Barbara McClintock, Rita Levi-Montalcini, and Rosalind Franklin. Together they represented the three major science disciplines of biology, chemistry and physics. I attempted to make sense of my own science life using the stories of the women scientists as a framework. Situating my experiences within the context of the lives of the women scientists allowed me to use a phenomenological approach to discern commonalities within their lives and my own. The results indicated that the women scientists and myself encountered multiple obstacles in terms of access and equity. However, it was also indicated that all of the women in the study developed a variety of techniques, including resistance and accommodation, in order to navigate these obstacles while still being able to pursue their chosen career path. These women did, however, make great sacrifices that cost them personally, emotionally, financially, and even in terms of their career advancement. Their success was closely tied to their ability to forge their own path, to create their own way of living, and to accept themselves as nonconformists.

  13. Application of Ontologies for Big Earth Data

    Science.gov (United States)

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

    2014-12-01

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

  14. Science, culture and the search for life on other worlds

    CERN Document Server

    Traphagan, John W

    2016-01-01

    This book explores humanity’s thoughts and ideas about extraterrestrial life, paying close attention to the ways science and culture interact with one another to create a context of imagination and discovery related to life on other worlds. Despite the recent explosion in our knowledge of other planets and the seeming era of discovery in which we live, to date we have found no concrete evidence that we are not alone. Our thinking about life on other worlds has been and remains the product of a combination of scientific investigation and human imagination shaped by cultural values--particularly values of exploration and discovery connected to American society. The rapid growth in our awareness of other worlds makes this a crucial moment to think about and assess the influence of cultural values on the scientific search for extraterrestrial life. Here the author considers the junction of science and culture with a focus on two main themes: (1) the underlying assumptions, many of which are tacitly based upon c...

  15. Towards ontology-driven navigation of the lipid bibliosphere.

    Science.gov (United States)

    Baker, Christopher Jo; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Low, Hong-Sang; Wenk, Markus R

    2008-01-01

    The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer. We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations. As scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining

  16. 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.

  17. Beyond integrating social sciences: Reflecting on the place of life sciences in empirical bioethics methodologies.

    Science.gov (United States)

    Mertz, Marcel; Schildmann, Jan

    2017-07-21

    Empirical bioethics is commonly understood as integrating empirical research with normative-ethical research in order to address an ethical issue. Methodological analyses in empirical bioethics mainly focus on the integration of socio-empirical sciences (e.g. sociology or psychology) and normative ethics. But while there are numerous multidisciplinary research projects combining life sciences and normative ethics, there is few explicit methodological reflection on how to integrate both fields, or about the goals and rationales of such interdisciplinary cooperation. In this paper we will review some drivers for the tendency of empirical bioethics methodologies to focus on the collaboration of normative ethics with particularly social sciences. Subsequently, we argue that the ends of empirical bioethics, not the empirical methods, are decisive for the question of which empirical disciplines can contribute to empirical bioethics in a meaningful way. Using already existing types of research integration as a springboard, five possible types of research which encompass life sciences and normative analysis will illustrate how such cooperation can be conceptualized from a methodological perspective within empirical bioethics. We will conclude with a reflection on the limitations and challenges of empirical bioethics research that integrates life sciences.

  18. Science at the supermarket: multiplication, personalization and consumption of science in everyday life.

    Science.gov (United States)

    Tateo, Luca

    2014-06-01

    Which is the kind science's psychological guidance upon everyday life? I will try to discuss some issues about the role that techno-scientific knowledge plays in sense-making and decision making about practical questions of life. This relation of both love and hate, antagonism and connivance is inscribable in a wider debate between a trend of science to intervene in fields that are traditionally prerogative of political, religious or ethical choices, and, on the other side, the position of those who aim at stemming "technocracy" and governing these processes. I argue that multiplication, personalization and consumption are the characteristics of the relationship between science, technology and society in the age of "multiculturalism" and "multi-scientism". This makes more difficult but intriguing the study and understanding of the processes through which scientific knowledge is socialized. Science topics, like biotech, climate change, etc. are today an unavoidable reference frame. It is not possible to not know them and to attach them to the most disparate questions. Like in the case of Moscovici's "Freud for all seasons", the fact itself that the members of a group or a society believe in science as a reference point for others, roots its social representation and the belief that it can solve everyday life problems.

  19. Inspiring the Next Generation in Space Life Sciences

    Science.gov (United States)

    Hayes, Judith

    2010-01-01

    Competitive summer internships in space life sciences at NASA are awarded to college students every summer. Each student is aligned with a NASA mentor and project that match his or her skills and interests, working on individual projects in ongoing research activities. The interns consist of undergraduate, graduate, and medical students in various majors and disciplines from across the United States. To augment their internship experience, students participate in the Space Life Sciences Summer Institute (SLSSI). The purpose of the Institute is to offer a unique learning environment that focuses on the current biomedical issues associated with human spaceflight; providing an introduction of the paradigms, problems, and technologies of modern spaceflight cast within the framework of life sciences. The Institute faculty includes NASA scientists, physicians, flight controllers, engineers, managers, and astronauts; and fosters a multi-disciplinary science approach to learning with a particular emphasis on stimulating experimental creativity and innovation within an operational environment. This program brings together scientists and students to discuss cutting-edge solutions to problems in space physiology, environmental health, and medicine; and provides a familiarization of the various aspects of space physiology and environments. In addition to the lecture series, behind-the-scenes tours are offered that include the Neutral Buoyancy Laboratory, Mission Control Center, space vehicle training mockups, and a hands-on demonstration of the Space Shuttle Advanced Crew Escape Suit. While the SLSSI is managed and operated at the Johnson Space Center in Texas, student interns from the other NASA centers (Glenn and Ames Research Centers, in Ohio and California) also participate through webcast distance learning capabilities.

  20. Life Science Start-up Activities at the Universities of Applied Sciences (UAS).

    Science.gov (United States)

    Huber, Gerda

    2014-12-01

    The universities of applied sciences (UAS) provide several values for the society and economy of a country. Besides education of high level professionals, transfer of knowledge from research to applications in industry or as new start-up companies is an important task. This is done in different ways in the various disciplines. In Life Sciences, a key industry branch in Switzerland, innovation is a competitive success factor and research findings from UAS/Life Sciences contribute to the valorization of new technologies to products, services and to business performance. In order to foster awareness for the innovation need of industry, UAS install processes and support for transfer of research and technology results to marketable applications. Furthermore they may facilitate contacts of researchers and students with entrepreneurs in order to animate start-up founding as a true alternative to being employed. Access to coaching and entrepreneurial training completes the essential basis.

  1. Promoting Prospective Elementary Teachers' Learning to Use Formative Assessment for Life Science Instruction

    Science.gov (United States)

    Sabel, Jaime L.; Forbes, Cory T.; Zangori, Laura

    2015-01-01

    To support elementary students' learning of core, standards-based life science concepts highlighted in the "Next Generation Science Standards," prospective elementary teachers should develop an understanding of life science concepts and learn to apply their content knowledge in instructional practice to craft elementary science learning…

  2. Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

    Science.gov (United States)

    Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

    2011-07-01

    Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

  3. 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

  4. A methodology for creating ontologies for engineering design

    DEFF Research Database (Denmark)

    Ahmed, Saeema; Kim, Sanghee; Wallace, Ken

    2005-01-01

    This paper describes a methodology for developing ontologies for engineering design. The methodology combines a number of methods from social science and computer science, together with taxonomies developed in the field of engineering design. A case study is used throughout the paper focusing upon...... the use of an ontology for searching, indexing and retrieving of engineering knowledge. An ontology for indexing design knowledge can assist the users to formulate their queries when searching for engineering design knowledge. The root concepts of the ontology were elicited from engineering designers...

  5. Engineering and simulation of life sciences Spacelab experiments.

    Science.gov (United States)

    Johnston, R S; Bush, W H; Rummel, J A; Alexander, W C

    1979-10-01

    The third in a series of Spacelab Mission Development tests was conducted at the Johnson (correction of Johnston) Space Center as a part of the development of Life Sciences experiments for the Space Shuttle era. The latest test was a joint effort of the Ames Research and Johnson Space Centers and utilized animals and men for study. The basic objective of this test was to evaluate the operational concepts planned for the Space Shuttle life science payloads program. A three-man crew (Mission Specialist and two Payload Specialists) conducted 26 experiments and 12 operational tests, which were selected for this 7-day mission simulation. The crew lived on board a simulated Orbiter/Spacelab mockup 24 hr a day. The Orbiter section contained the mid deck crew quarters area, complete with sleeping, galley and waste management provisions. The Spacelab was identical in geometry to the European Space Agency Spacelab design, complete with removable rack sections and stowage provisions. Communications between the crewmen and support personnel were configured and controlled as currently planned for operational shuttle flights. For this test a Science Operations Remote Center was manned at the Ames Research Center and was managed by simulated Mission Control and Payload Operation Control Centers at the Johnson Space Center. This paper presents the test objectives, description of the facilities and test program, and the results of this test.

  6. Ontology-guided data preparation for discovering genotype-phenotype relationships.

    Science.gov (United States)

    Coulet, Adrien; Smaïl-Tabbone, Malika; Benlian, Pascale; Napoli, Amedeo; Devignes, Marie-Dominique

    2008-04-25

    Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles in knowledge discovery in life science providing semantics to data and to extracted units, by taking advantage of the progress of Semantic Web technologies concerning the understanding and availability of tools for knowledge representation, extraction, and reasoning. This paper presents a method that exploits bio-ontologies for guiding data selection within the preparation step of the KDD process. We propose three scenarios in which domain knowledge and ontology elements such as subsumption, properties, class descriptions, are taken into account for data selection, before the data mining step. Each of these scenarios is illustrated within a case-study relative to the search of genotype-phenotype relationships in a familial hypercholesterolemia dataset. The guiding of data selection based on domain knowledge is analysed and shows a direct influence on the volume and significance of the data mining results. The method proposed in this paper is an efficient alternative to numerical methods for data selection based on domain knowledge. In turn, the results of this study may be reused in ontology modelling and data integration.

  7. Physical sciences and engineering advances in life sciences and oncology a WTEC global assessment

    CERN Document Server

    Fletcher, Daniel; Gerecht, Sharon; Levine, Ross; Mallick, Parag; McCarty, Owen; Munn, Lance; Reinhart-King, Cynthia

    2016-01-01

    This book presents an Assessment of Physical Sciences and Engineering Advances in Life Sciences and Oncology (APHELION) by a panel of experts. It covers the status and trends of applying physical sciences and engineering principles to oncology research in leading laboratories and organizations in Europe and Asia. The book elaborates on the six topics identified by the panel that have the greatest potential to advance understanding and treatment of cancer, each covered by a chapter in the book. The study was sponsored by the National Cancer Institute (NCI) at the National Institute of Health (NIH), the National Science Foundation (NSF) and the National Institute of Biomedical Imaging and Bioengineering at the NIH in the US under a cooperative agreement with the World Technology Evaluation Center (WTEC).

  8. 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.

  9. Arnold Sommerfeld science, life and turbulent times : 1868-1951

    CERN Document Server

    Eckert, Michael

    2013-01-01

    Arnold Sommerfeld (1868-1951) belongs with Max Planck (1858-1947), Albert Einstein (1879-1955) and Niels Bohr (1885-1962) among the founders of modern theoretical physics, a science that developed into a budding discipline during his lifetime. Sommerfeld witnessed many of the most dramatic scientific, cultural and political events of this era. His correspondence with his family offers a vivid testament to the challenges and joys of a life in science. This biography attempts to reconstruct Sommerfeld’s life and work not only from the perspective of his achievements in theoretical physics but also with the goal of portraying the career of a scientist within the social and political environment in which it evolved. It is based to a large extent on Sommerfeld’s voluminous correspondence, which sheds light both on his private and scientific life. Furthermore, it provides an authentic view on the circumstances that shaped Sommerfeld’s career in different places – Königsberg, Göttingen, Clausthal, Aachen, ...

  10. 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 d...... classification systems and meta data taxonomies, should be based on ontologies.......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...

  11. Vision and change in introductory physics for the life sciences

    CERN Document Server

    Mochrie, S G J

    2015-01-01

    Since 2010, the Yale physics department has offered a novel calculus-based introductory physics for the life science (IPLS) sequence, that re-imagines the IPLS syllabus to include a selection of biologically and medically relevant topics, that are highly meaningful to its audience of biological science and premedical undergraduates. The first semester, in particular, differs considerably from traditional first-semester introductory physics. Here, we highlight the novel aspects of Yale's first-semester course, and describe student feedback about the course, including a comparison between how students evaluate the course and how they evaluate courses with a traditional syllabus, and how students' perceptions of the relevance of physics to biology and medicine are affected by having taken the course.

  12. The why of things: causality in science, medicine, and life

    CERN Document Server

    Rabins, Peter V.

    2013-01-01

    Why was there a meltdown at the Fukushima power plant? Why do some people get cancer and not others? Why is global warming happening? Why does one person get depressed in the face of life's vicissitudes while another finds resilience? Questions like these -- questions of causality -- form the basis of modern scientific inquiry, posing profound intellectual and methodological challenges for researchers in the physical, natural, biomedical, and social sciences. In this groundbreaking book, noted psychiatrist and author Peter Rabins offers a conceptual framework for analyzing daunting questions of causality. Navigating a lively intellectual voyage between the shoals of strict reductionism and relativism, Rabins maps a three-facet model of causality and applies it to a variety of questions in science, medicine, economics, and more. Throughout this book, Rabins situates his argument within relevant scientific contexts, such as quantum mechanics, cybernetics, chaos theory, and epigenetics. A renowned communicator o...

  13. [From human genome to man-made life: J. Craig Venter leads the life sciences].

    Science.gov (United States)

    Sun, Mingwei; Li, Yin; Gao, George F

    2010-06-01

    For the first time ever, the scientists of J. Craig Venter team have created actual self-replicating synthetic life. The research was just published in the Journal of Science on May 20, 2010. Although this news immediately brings the worry about the possible potential threat to biosecurity and biosafety as well as the ethical disputes, it yet indicates that mankind have made a new step forward in synthetic biology. In the time of post-genome era, we believe the advancement of synthetic biology that might affect or change the future life of human being will be widely used in energy, environment, materials, medication and many other fields.

  14. Exploration of very high spatial resolution data for vegetation mapping using cartographic ontologies: Identifying life forms to mapping formations

    Science.gov (United States)

    Rodriguez-Gallegos, Hugo Benigno

    Vegetation mapping is often considered the process of identifying landscape patterns of individuals or clusters of species or life forms (LF). At the landscape scale, the larger pattern represented by individuals or clusters represents the conceptualization of "vegetation mapping" and can be used as a building block to describe an ecosystem. To represent these building blocks or LF a "common entity (CE)" concept is introduced to represent the components of Formations as described by the National Vegetation Classification (NVC) system. The NVC has established protocols to consistently represent plant communities and promote coordinated management, particularly across jurisdictional boundaries. However, it is not a universal standard and the methods of producing detailed maps of vegetation CE from very high spatial resolution (VHR) remote sensing data are important research questions. This research addressed how best to understand and represent plant cover in arid regions, the most effective methods of mapping vegetation cover using high spatial resolution data, how to assess the accuracy of these maps, and their value in establishing more standardized mapping protocols across ecosystems. Utilizing VHR products from the IKONOS and QuickBird sensors the study focused on the Coronado National Memorial and Chiricahua National Monument in Arizona and Los Ajos and Pinacate - Grand Desierto Biosphere Reserves in Mexico. Individual CE were semi-automatically mapped incorporating spectral, textural and geostatistical variables. The results were evaluated across sensors, study sites, and input variables. In addition, multiple methods of acquiring field data for accuracy assessment were evaluated and then an evaluation was made of a semi-automatic determination of Formation based on CE. The results of the study suggest consistency across study sites using the IKONOS data. A comparison between VHR products from the same place is feasible but sensor spectral differences may

  15. Introduction to statistical data analysis for the life sciences

    CERN Document Server

    Ekstrom, Claus Thorn

    2014-01-01

    This text provides a computational toolbox that enables students to analyze real datasets and gain the confidence and skills to undertake more sophisticated analyses. Although accessible with any statistical software, the text encourages a reliance on R. For those new to R, an introduction to the software is available in an appendix. The book also includes end-of-chapter exercises as well as an entire chapter of case exercises that help students apply their knowledge to larger datasets and learn more about approaches specific to the life sciences.

  16. Professional Networks in the Life Sciences: Linking the Linked

    Directory of Open Access Journals (Sweden)

    Thomas S. Deisboeck

    2010-08-01

    Full Text Available The world wide web has furthered the emergence of a multitude of online expert communities. Continued progress on many of the remaining complex scientific questions requires a wide ranging expertise spectrum with access to a variety of distinct data types. Moving beyond peer-to-peer to community-to-community interaction is therefore one of the biggest challenges for global interdisciplinary Life Sciences research, including that of cancer. Cross-domain data query, access, and retrieval will be important innovation areas to enable and facilitate this interaction in the coming years.

  17. Life sciences research in space: The requirement for animal models

    Science.gov (United States)

    Fuller, C. A.; Philips, R. W.; Ballard, R. W.

    1987-01-01

    Use of animals in NASA space programs is reviewed. Animals are needed because life science experimentation frequently requires long-term controlled exposure to environments, statistical validation, invasive instrumentation or biological tissue sampling, tissue destruction, exposure to dangerous or unknown agents, or sacrifice of the subject. The availability and use of human subjects inflight is complicated by the multiple needs and demands upon crew time. Because only living organisms can sense, integrate and respond to the environment around them, the sole use of tissue culture and computer models is insufficient for understanding the influence of the space environment on intact organisms. Equipment for spaceborne experiments with animals is described.

  18. Spatial Health and Life Sciences Business Ecosystems: Research Frame

    Directory of Open Access Journals (Sweden)

    Jukka Majava

    2014-12-01

    Full Text Available Industry competition is moving from the company-level towards business ecosystems, where organizations must develop mutually beneficial relationships with each other. This paper studies business ecosystem phenomena, focusing especially on the spatial (geographical context within the health and life sciences industry. In addition, business ecosystem evolution and change dynamics are addressed. This study is literature-based; the findings and analysis provide a research frame for forthcoming empirical studies. Despite increasing attention, business ecosystem literature is still relatively immature, and previous studies have mostly focused on software and the information technology (it industries. Hence, this paper provides new insights into the business ecosystem concept in a novel context.

  19. 08301 Final Report -- Group Testing in the Life Sciences

    OpenAIRE

    2008-01-01

    Group testing AKA smart-pooling is a general strategy for minimizing the number of tests necessary for identifying positives among a large collection of items. It has the potential to efficiently identify and correct for experimental errors (false–positives and false–negatives). It can be used whenever tests can detect the presence of a positive in a group (or pool) of items, provided that positives are rare. Group testing has numerous applications in the life sciences, such as physical ma...

  20. At the dawn of a new revolution in life sciences

    Institute of Scientific and Technical Information of China (English)

    Frantiek; Baluka; Guenther; Witzany

    2013-01-01

    In a recently published article Sydney Brenner argued that the most relevant scientific revolution in biology at his time was the breakthrough of the role of "information" in biology.The fundamental concept that integrates this new biological "information" with matter and energy is the universal Turing machine and von Neumann’s self-reproducing machines.In this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce themselves.Additionally current knowledge on the roles of noncoding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.

  1. Progress Report of Space Life Science in China

    Institute of Scientific and Technical Information of China (English)

    CHEN Shanguang; LI Yinghui

    2008-01-01

    In the past two years, space life sciences research in China is characterized by a tendency toward integration of scientific and engineering resources in preparing and implementing advanced space programs. In the field of operational medicine, we carried out an international cooperated Head-Down Bed Rest (HDBR) experiment and investigated the effects of Chinese herbs compounds on astronaut's physiological functions. The effect of microgravity and its mechanisms were further studied from the level of physiology and biology. At the same time, state-level platform for ground and space experiment was established.

  2. Darwin and the origin of life: public versus private science.

    Science.gov (United States)

    Strick, James E

    2009-12-01

    In the first twenty years after the publication of Darwin's On the Origin of Species, an intense debate took place within the ranks of Darwin's supporters over exactly what his theory implied about the means by which the original living organism formed on Earth. Many supporters of evolutionary science also supported the doctrine of spontaneous generation: life forming from nonliving material not just once but many times up to the present day. Darwin was ambivalent on this topic. He feared its explosive potential to drive away liberal-minded Christians who might otherwise be supporters. His ambivalent wording created still more confusion, both among friends and foes, about what Darwin actually believed about the origin of life. A famous lecture by Thomas H. Huxley in 1870 set forth what later became the 'party line' Darwinian position on the subject.

  3. Philosophical Approaches towards Sciences of Life in Early Cybernetics

    Science.gov (United States)

    Montagnini, Leone

    2008-07-01

    The article focuses on the different conceptual and philosophical approaches towards the sciences of life operating in the backstage of Early Cybernetics. After a short reconstruction of the main steps characterizing the origins of Cybernetics, from 1940 until 1948, the paper examines the complementary conceptual views between Norbert Wiener and John von Neumann, as a "fuzzy thinking" versus a "logical thinking", and the marked difference between the "methodological individualism" shared by both of them versus the "methodological collectivism" of most of the numerous scientists of life and society attending the Macy Conferences on Cybernetics. The main thesis sustained here is that these different approaches, quite invisible to the participants, were different, maybe even opposite, but they could provoke clashes, as well as cooperate in a synergic way.

  4. Large-scale networks in engineering and life sciences

    CERN Document Server

    Findeisen, Rolf; Flockerzi, Dietrich; Reichl, Udo; Sundmacher, Kai

    2014-01-01

    This edited volume provides insights into and tools for the modeling, analysis, optimization, and control of large-scale networks in the life sciences and in engineering. Large-scale systems are often the result of networked interactions between a large number of subsystems, and their analysis and control are becoming increasingly important. The chapters of this book present the basic concepts and theoretical foundations of network theory and discuss its applications in different scientific areas such as biochemical reactions, chemical production processes, systems biology, electrical circuits, and mobile agents. The aim is to identify common concepts, to understand the underlying mathematical ideas, and to inspire discussions across the borders of the various disciplines.  The book originates from the interdisciplinary summer school “Large Scale Networks in Engineering and Life Sciences” hosted by the International Max Planck Research School Magdeburg, September 26-30, 2011, and will therefore be of int...

  5. Factors in life science textbooks that may deter girls' interest in science

    Science.gov (United States)

    Potter, Ellen F.; Rosser, Sue V.

    In order to examine factors that may deter girls' interest in science, five seventh-grade life science textbooks were analyzed for sexism in language, images, and curricular content, and for features of activities that have been found to be useful for motivating girls. Although overt sexism was not apparent, subtle forms of sexism in the selection of language, images, and curricular content were found. Activities had some features useful to girls, but other features were seldom included. Teachers may wish to use differences that were found among texts as one basis for text selection.

  6. Students' Ontological Security and Agency in Science Education—An Example from Reasoning about the Use of Gene Technology

    Science.gov (United States)

    Lindahl, Mats Gunnar; Linder, Cedric

    2013-09-01

    This paper reports on a study of how students' reasoning about socioscientific issues is framed by three dynamics: societal structures, agency and how trust and security issues are handled. Examples from gene technology were used as the forum for interviews with 13 Swedish high-school students (year 11, age 17-18). A grid based on modalities from the societal structures described by Giddens was used to structure the analysis. The results illustrate how the participating students used both modalities for 'Legitimation' and 'Domination' to justify positions that accept or reject new technology. The analysis also showed how norms and knowledge can be used to justify opposing positions in relation to building trust in science and technology, or in democratic decisions expected to favour personal norms. Here, students accepted or rejected the authority of experts based on perceptions of the knowledge base that the authority was seen to be anchored in. Difficulty in discerning between material risks (reduced safety) and immaterial risks (loss of norms) was also found. These outcomes are used to draw attention to the educational challenges associated with students' using knowledge claims (Domination) to support norms (Legitimation) and how this is related to the development of a sense of agency in terms of sharing norms with experts or with laymen.

  7. Premenstrual syndrome and life quality in Turkish health science students.

    Science.gov (United States)

    İşik, Hatice; Ergöl, Şule; Aynioğlu, Öner; Şahbaz, Ahmet; Kuzu, Ayşe; Uzun, Müge

    2016-04-19

    The purpose of the present study was to investigate the incidence of PMS, risk factors affecting PMS symptoms, and life quality in health science students. A total of 608 volunteer female students studying at the health campus of a state university in Turkey were included in the study. The participants were asked to fill out questionnaires on sociodemographic data, PMS symptoms, and SF-36 life quality tests. The overall frequency of PMS among participants was 84.5%. The average PMS and general health SF scores were 118.34 ± 37.3 and 20.03 ± 3.72, respectively. Students who had irregular breakfast, drank ≥2 cups of coffee/day, and consumed alcohol or fast food had higher PMS scores. Irregular menstruation and family history increased PMS scores and decreased life quality (P students significantly decreased as the severity of PMS increased (P consumption and irregular breakfasts, and coffee and alcohol consumption increased PMS risk significantly. In order to improve their life quality, students should be informed about the symptoms, risk factors, and management options of PMS.

  8. Data List | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available with appropriate ontology terms. The listed observation data are correspond to original observation data one...base 3986 10.18908/lsdba.nbdc01509-004 Combination of phenotype observation and gene modification found by l...(defined in PO) Quality in PATO Quality (defined in PATO) Num of observation data The number of entries wher

  9. The Proteasix Ontology.

    Science.gov (United States)

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

    2016-06-04

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

  10. The MMI Device Ontology: Enabling Sensor Integration

    Science.gov (United States)

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

    2010-12-01

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

  11. S3QL: A distributed domain specific language for controlled semantic integration of life sciences data

    Directory of Open Access Journals (Sweden)

    de Lencastre Hermínia

    2011-07-01

    Full Text Available Abstract Background The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control. We have previously described the Simple Sloppy Semantic Database (S3DB as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL, to operate on its underlying core model and facilitate management of Linked Data. Results Reflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA and molecular epidemiology of infectious diseases. Conclusions S3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms.

  12. 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.)

  13. Life Science Professional Societies Expand Undergraduate Education Efforts

    Science.gov (United States)

    Matyas, Marsha Lakes; Ruedi, Elizabeth A.; Engen, Katie; Chang, Amy L.

    2017-01-01

    The Vision and Change in Undergraduate Biology Education reports cite the critical role of professional societies in undergraduate life science education and, since 2008, have called for the increased involvement of professional societies in support of undergraduate education. Our study explored the level of support being provided by societies for undergraduate education and documented changes in support during the Vision and Change era. Society representatives responded to a survey on programs, awards, meetings, membership, teaching resources, publications, staffing, finances, evaluation, and collaborations that address undergraduate faculty and students. A longitudinal comparison group of societies responded to surveys in both 2008 and 2014. Results indicate that life science professional societies are extensively engaged in undergraduate education in their fields, setting standards for their discipline, providing vetted education resources, engaging students in both research and education, and enhancing professional development and recognition/status for educators. Societies are devoting funding and staff to these efforts and engaging volunteer leadership. Longitudinal comparison group responses indicate there have been significant and quantifiable expansions of undergraduate efforts in many areas since 2008. These indicators can serve as a baseline for defining, aligning, and measuring how professional societies can promote sustainable, evidence-based support of undergraduate education initiatives. PMID:28130272

  14. Hybrid cloud and cluster computing paradigms for life science applications.

    Science.gov (United States)

    Qiu, Judy; Ekanayake, Jaliya; Gunarathne, Thilina; Choi, Jong Youl; Bae, Seung-Hee; Li, Hui; Zhang, Bingjing; Wu, Tak-Lon; Ruan, Yang; Ekanayake, Saliya; Hughes, Adam; Fox, Geoffrey

    2010-12-21

    Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.

  15. Design concepts for the Centrifuge Facility Life Sciences Glovebox

    Science.gov (United States)

    Sun, Sidney C.; Horkachuck, Michael J.; Mckeown, Kellie A.

    1989-01-01

    The Life Sciences Glovebox will provide the bioisolated environment to support on-orbit operations involving non-human live specimens and samples for human life sceinces experiments. It will be part of the Centrifuge Facility, in which animal and plant specimens are housed in bioisolated Habitat modules and transported to the Glovebox as part of the experiment protocols supported by the crew. At the Glovebox, up to two crew members and two habitat modules must be accommodated to provide flexibility and support optimal operations. This paper will present several innovative design concepts that attempt to satisfy the basic Glovebox requirements. These concepts were evaluated for ergonomics and ease of operations using computer modeling and full-scale mockups. The more promising ideas were presented to scientists and astronauts for their evaluation. Their comments, and the results from other evaluations are presented. Based on the evaluations, the authors recommend designs and features that will help optimize crew performance and facilitate science accommodations, and specify problem areas that require further study.

  16. Life Science Research In Space: The Spacelab Era

    Science.gov (United States)

    Farrell, R. M.; Cramer, D. B.; Reid, D. H.

    1982-02-01

    This manuscript summarizes the events leading to the first Spacelab mission dedicated exclusively to life sciences experimentation. This mission is currently planned for a Space Shuttle flight in the 1984-1985 time frame. Following publication of a NASA Announce ment of Opportunity in 1978, approximately 400 proposals were received from researchers in universities, government laboratories, and industrial firms both in the U. S. and abroad. In 1979, 87 candidate experiments were selected for definition studies to identify the detailed resources which would need to be accommodated by the Spacelab. These proposals addressed problems encountered in man's previous space flight experience, such as space motion sickness, cardiovascular deconditioning, muscle wasting, calcium loss and a reduction in red cell mass. Additionally, experiments were selected in areas of bioengineering, behavior and performance, Plant physiology, and cell biology. Animal species (rodents and small primates) to be investigated will be housed in a specially-developed animal holding facility which will provide all life support requirements for the animals. Human subjects will consist of a Mission Specialist Astronaut and up to four Payload Specialists. Plant species will be housed in Plant Growth Units. A general purpose work station and biological containment facility will provide the working area for much of the in-space experimentation. A comprehensive array of flight qualified laboratory equipment will be made available by NASA to Principal Investigators for in-flight use by the Payload Specialists. This equipment includes microscopes, biotelemetry systems, cameras, centrifuges, refrigerators, and similar equipment. All of this equipment has been designed for use in weightlessness. The process to develop a primary payload of about 20 experiments is now underway for Spacelab mission number four, the first dedicated life sciences flight. Under the overall guidance of NASA Headquarters

  17. The International Space Station human life sciences experiment implementation process

    Science.gov (United States)

    Miller, L. J.; Haven, C. P.; McCollum, S. G.; Lee, A. M.; Kamman, M. R.; Baumann, D. K.; Anderson, M. E.; Buderer, M. C.

    2001-01-01

    The selection, definition, and development phases of a Life Sciences flight research experiment has been consistent throughout the past decade. The implementation process, however, has changed significantly within the past two years. This change is driven primarily by the shift from highly integrated, dedicated research missions on platforms with well defined processes to self contained experiments with stand alone operations on platforms which are being concurrently designed. For experiments manifested on the International Space Station (ISS) and/or on short duration missions, the more modular, streamlined, and independent the individual experiment is, the more likely it is to be successfully implemented before the ISS assembly is completed. During the assembly phase of the ISS, science operations are lower in priority than the construction of the station. After the station has been completed, it is expected that more resources will be available to perform research. The complexity of implementing investigations increases with the logistics needed to perform the experiment. Examples of logistics issues include- hardware unique to the experiment; large up and down mass and volume needs; access to crew and hardware during the ascent or descent phases; maintenance of hardware and supplies with a limited shelf life,- baseline data collection schedules with lengthy sessions or sessions close to the launch or landing; onboard stowage availability, particularly cold stowage; and extensive training where highly proficient skills must be maintained. As the ISS processes become better defined, experiment implementation will meet new challenges due to distributed management, on-orbit resource sharing, and adjustments to crew availability pre- and post-increment. c 2001. Elsevier Science Ltd. All rights reserved.

  18. Ninth Graders' Learning Interests, Life Experiences and Attitudes towards Science & Technology

    Science.gov (United States)

    Chang, Shu-Nu; Yeung, Yau-Yuen; Cheng, May Hung

    2009-01-01

    Students' learning interests and attitudes toward science have both been studied for decades. However, the connection between them with students' life experiences about science and technology has not been addressed much. The purpose of this study is to investigate students' learning interests and life experiences about science and technology, and…

  19. Phenomenology and the life sciences: Clarifications and complementarities.

    Science.gov (United States)

    Sheets-Johnstone, Maxine

    2015-12-01

    This paper first clarifies phenomenology in ways essential to demonstrating its basic concern with Nature and its recognition of individual and cultural differences as well as commonalities. It furthermore clarifies phenomenological methodology in ways essential to understanding the methodology itself, its purpose, and its consequences. These clarifications show how phenomenology, by hewing to the dynamic realities of life itself and experiences of life itself, counters reductive thinking and "embodiments" of one kind and another. On the basis of these clarifications, the paper then turns to detailing conceptual complementarities between phenomenology and the life sciences, particularly highlighting studies in coordination dynamics. In doing so, it brings to light fundamental relationships such as those between mind and motion and between intrinsic dynamics and primal animation. It furthermore highlights the common concern with origins in both phenomenology and evolutionary biology: the history of how what is present is related to its inception in the past and to its transformations from past to present. Copyright © 2015. Published by Elsevier Ltd.

  20. A Comparative Analysis of South African Life Sciences and Biology Textbooks for Inclusion of the Nature of Science

    Science.gov (United States)

    Ramnarain, Umesh; Padayachee, Keshni

    2015-01-01

    This study reports on the analysis of South African Life Sciences and Biology textbooks for the inclusion of the nature of science using a conceptual framework developed by Chiappetta, Fillman and Sethna (1991). In particular, we investigated the differences between the representation of the nature of science in Biology textbooks that were written…

  1. Of Responsible Research--Exploring the Science-Society Dialogue in Undergraduate Training within the Life Sciences

    Science.gov (United States)

    Almeida, Maria Strecht; Quintanilha, Alexandre

    2017-01-01

    We explore the integration of societal issues in undergraduate training within the life sciences. Skills in thinking about science, scientific knowledge production and the place of science in society are crucial in the context of the idea of responsible research and innovation. This idea became institutionalized and it is currently well-present in…

  2. Primer on Ontologies.

    Science.gov (United States)

    Hastings, Janna

    2017-01-01

    As molecular biology has increasingly become a data-intensive discipline, ontologies have emerged as an essential computational tool to assist in the organisation, description and analysis of data. Ontologies describe and classify the entities of interest in a scientific domain in a computationally accessible fashion such that algorithms and tools can be developed around them. The technology that underlies ontologies has its roots in logic-based artificial intelligence, allowing for sophisticated automated inference and error detection. This chapter presents a general introduction to modern computational ontologies as they are used in biology.

  3. Kuhn's Ontological Relativism.

    Science.gov (United States)

    Sankey, Howard

    2000-01-01

    Discusses Kuhn's model of scientific theory change. Documents Kuhn's move away from conceptual relativism and rational relativism. Provides an analysis of his present ontological form of relativism. (CCM)

  4. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  5. Toward an Ecosystem for Innovation in a Newly Industrialized Economy: Singapore and the Life Sciences

    Science.gov (United States)

    Wong, Poh-Kam

    2006-01-01

    In the late 1990s the Singapore government embarked on a set of far-reaching strategies intended to develop the city-state into one of the major life science R&D and industrial clusters in Asia. Besides efforts to attract leading overseas life science companies to establish operations in Singapore, the government has developed new life science…

  6. Challenges and Opportunities for Education about Dual Use Issues in the Life Sciences

    Science.gov (United States)

    National Academies Press, 2011

    2011-01-01

    The Challenges and Opportunities for Education About Dual Use Issues in the Life Sciences workshop was held to engage the life sciences community on the particular security issues related to research with dual use potential. More than 60 participants from almost 30 countries took part and included practicing life scientists, bioethics and…

  7. 国际图书情报领域本体研究的知识图谱分析*%Knowledge Mapping Analysis of International Ontology Research in the Field of Library and Information Science

    Institute of Scientific and Technical Information of China (English)

    洪海娟; 池晓波; 万跃华

    2013-01-01

    To reveal the theoretical evolution in the late two decades, research hotspots and research fronts of international ontology re-search in the field of library and information science, 728 papers published between 1990 and 2012 are retrieved from Web of Science with the topic search of ontology in library and information science. Using knowledge visualization tool CiteSpaceII, documents are visualized through a number of co-citation maps, which filtered the critical node documents in the evolution of ontology research. The functions of keywords clustering and burst terms detecting are used to analyze the research hotspots and research fronts.%  为梳理20年来国际图书情报领域本体研究的理论演进路径,揭示研究热点和研究前沿,将1990-2012年ISI Web of Science数据库收录的图书情报领域本体研究728篇文献数据作为研究对象,应用CiteSpaceII知识可视化软件绘制文献共被引网络图谱,分析国际图书情报领域本体研究理论演进过程中的关键节点文献,并利用关键词聚类和膨胀词探测功能分析研究热点与研究前沿。

  8. A Case for Embedded Natural Logic for Ontological Knowledge Bases

    DEFF Research Database (Denmark)

    Andreasen, Troels; Nilsson, Jørgen Fischer

    2014-01-01

    We argue in favour of adopting a form of natural logic for ontology-structured knowledge bases as an alternative to description logic and rule based languages. Natural logic is a form of logic resembling natural language assertions, unlike description logic. This is essential e.g. in life science...... negation in description logic. We embed the natural logic in DATALOG clauses which is to take care of the computational inference in connection with querying.......We argue in favour of adopting a form of natural logic for ontology-structured knowledge bases as an alternative to description logic and rule based languages. Natural logic is a form of logic resembling natural language assertions, unlike description logic. This is essential e.g. in life sciences......, where the large and evolving knowledge specifications should be directly accessible to domain experts. Moreover, natural logic comes with intuitive inference rules. The considered version of natural logic leans toward the closed world assumption (CWA) unlike the open world assumption with classical...

  9. Paul Scherrer Institute Scientific Report 1998. Volume II: Life Sciences

    Energy Technology Data Exchange (ETDEWEB)

    Gschwend, Beatrice; Jaussi, Rolf [eds.

    1999-09-01

    The Department of Life Sciences, is aiming to perform high quality research in biosciences focused primarily on oncology and in close interaction with the technical facilities at PSI e.g. proton therapy, SINQ, SLS, and the national and international bioscience community. Within this department, the Division of Radiation Protection and Radioactive Waste Treatment is responsible for the radiological safety of the personnel, the installations and the environment at PSI, and it is charged with dismantling obsolete nuclear installations at PSI. The principal research and development activities of this division concern novel methods for neutron dosimetry, and the study of presence and pathways of natural and man made radioactivity in humans and in the environment. (author) figs., tabs., refs.

  10. First-principles quantum chemistry in the life sciences.

    Science.gov (United States)

    van Mourik, Tanja

    2004-12-15

    The area of computational quantum chemistry, which applies the principles of quantum mechanics to molecular and condensed systems, has developed drastically over the last decades, due to both increased computer power and the efficient implementation of quantum chemical methods in readily available computer programs. Because of this, accurate computational techniques can now be applied to much larger systems than before, bringing the area of biochemistry within the scope of electronic-structure quantum chemical methods. The rapid pace of progress of quantum chemistry makes it a very exciting research field; calculations that are too computationally expensive today may be feasible in a few months' time! This article reviews the current application of 'first-principles' quantum chemistry in biochemical and life sciences research, and discusses its future potential. The current capability of first-principles quantum chemistry is illustrated in a brief examination of computational studies on neurotransmitters, helical peptides, and DNA complexes.

  11. Life Sciences Division and Center for Human Genome Studies

    Energy Technology Data Exchange (ETDEWEB)

    Spitzmiller, D.; Bradbury, M.; Cram, S. (comps.)

    1992-05-01

    This report summarizes the research and development activities of Los Alamos National Laboratories Life Sciences Division and biological aspects of the Center for Human Genome Studies for the calendar year 1991. Selected research highlights include: yeast artificial chromosome libraries from flow sorted human chromosomes 16 and 21; distances between the antigen binding sites of three murine antibody subclasses measured using neutron and x-ray scattering; NFCR 10th anniversary highlights; kinase-mediated differences found in the cell cycle regulation of normal and transformed cells; and detecting mutations that cause Gaucher's disease by denaturing gradient gel electrophoresis. Project descriptions include: genomic structure and regulation, molecular structure, cytometry, cell growth and differentiation, radiation biology and carcinogenesis, and pulmonary biology.

  12. 5th International Conference on Optics Within Life Sciences

    CERN Document Server

    Papazoglou, Theodore; Kalpouzos, Costas

    2000-01-01

    Following to previous OWLS conferences devoted to widespread applications of optics in life sciences, this 5th OWLS Conference focuses on recent achievements in applying lasers and optics in biomedicine and the preservation of our cultural heritage. Particular attention is paid to laser diagnostics in medicine, interaction of laser radiation with biological tissue, aspects of the preservation of cultural heritage, and the development of new systems for these studies. The contributors to this volume cover international research activities in the following areas: Laser-tissue interactions and tissue optics - photon migration in tissue; Medical sensors - fiber optics; Clinical use of lasers (dermatology, ENT, cardiology, etc.); Laser-based techniques in art conservation (cleaning, diagnostics, analytical applications); Imaging techniques and lasers in archaeology; Laser technologies in contemporary art (holography, marking, etc.); and New laser and opto-electronic systems for biomedical and art-related studies.

  13. The International Space Station human life sciences experiment implementation process.

    Science.gov (United States)

    Miller, L J; Haven, C P; McCollum, S G; Lee, A M; Kamman, M R; Baumann, D K; Anderson, M E; Buderer, M C

    2001-01-01

    The selection, definition, and development phases of a Life Sciences flight research experiment has been consistent throughout the past decade. The implementation process, however, has changed significantly within the past two years. This change is driven primarily by the shift from highly integrated, dedicated research missions on platforms with well defined processes to self contained experiments with stand alone operations on platforms which are being concurrently designed. For experiments manifested on the International Space Station (ISS) and/or on short duration missions, the more modular, streamlined, and independent the individual experiment is, the more likely it is to be successfully implemented before the ISS assembly is completed. During the assembly phase of the ISS, science operations are lower in priority than the construction of the station. After the station has been completed, it is expected that more resources will be available to perform research. The complexity of implementing investigations increases with the logistics needed to perform the experiment. Examples of logistics issues include- hardware unique to the experiment; large up and down mass and volume needs; access to crew and hardware during the ascent or descent phases; maintenance of hardware and supplies with a limited shelf life,- baseline data collection schedules with lengthy sessions or sessions close to the launch or landing; onboard stowage availability, particularly cold stowage; and extensive training where highly proficient skills must be maintained. As the ISS processes become better defined, experiment implementation will meet new challenges due to distributed management, on-orbit resource sharing, and adjustments to crew availability pre- and post-increment.

  14. The international space station human life sciences experiment implementation process

    Science.gov (United States)

    Miller, LadonnaJ.; Haven, CynthiaP.; McCollum, SuzanneG.; Lee, AngeleneM.; Kamman, MichelleR.; Baumann, DavidK.; Anderson, MarkE.; Buderer, MelvinC.

    2001-08-01

    The selection, definition, and development phases of a Life Sciences flight research experiment has been consistent throughout the past decade. The implementation process, however, has changed significantly within the past two years. This change is driven primarily by the shift from highly integrated, dedicated research missions on platforms with well defined processes to self contained experiments with stand alone operations on platforms which are being concurrently designed. For experiments manifested on the International Space Station (ISS) and / or on short duration missions, the more modular, streamlined, and independent the individual experiment is, the more likely it is to be successfully implemented before the ISS assembly is completed. During the assembly phase of the ISS, science operations are lower in priority than the construction of the station. After the station has been completed, it is expected that more resources will be available to perform research. The complexity of implementing investigations increases with the logistics needed to perform the experiment. Examples of logistics issues include: hardware unique to the experiment; large up and down mass and volume needs; access to crew and hardware during the ascent or descent phases; maintenance of hardware and supplies with a limited shelf life; baseline data collection schedules with lengthy sessions or sessions close to the launch or landing; onboard stowage availability, particularly cold stowage; and extensive training where highly proficient skills must be maintained. As the ISS processes become better defined, experiment implementation will meet new challenges due to distributed management, on-orbit resource sharing, and adjustments to crew availability pre- and post-increment.

  15. Chemical energy in an introductory physics course for the life sciences

    OpenAIRE

    2013-01-01

    Energy is a complex idea that cuts across scientific disciplines. For life science students, an approach to energy that incorporates chemical bonds and chemical reactions is better equipped to meet the needs of life sciences students than a traditional introductory physics approach that focuses primarily on mechanical energy. We present a curricular sequence, or thread, designed to build up students' understanding of chemical energy in an introductory physics course for the life sciences. Thi...

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

    KAUST Repository

    Gkoutos, Georgios V.

    2015-07-28

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

  17. Meghnad Saha his life in science and politics

    CERN Document Server

    Naik, Pramod V

    2017-01-01

    This biography is a short yet comprehensive overview of the life of Meghnad Saha, the mastermind behind the frequently used Saha equations and a strong contributor to the foundation of science in India. The author explores the lesser known details behind the man who played a major role in building scientific institutions in India, developed the breakthrough theory of thermal ionization, and whose fervor about India’s rapid progress in science and technology, along with concern for uplifting his countrymen and optimizing resources, led him to eventually enter politics and identify the mismanagement of many programs of national importance to Parliament. This book is free of most academic technicalities, so that the reader with general scientific knowledge can read and understand it easily. One interested only in Saha’s contribution to physics can pick up just that part and read it. Conversely, the average reader may skip the technical chapters, and read the book without loss of continuity or generality to s...

  18. The uses of radiotracers in the life sciences

    Science.gov (United States)

    Ruth, Thomas J.

    2009-01-01

    Radionuclides have been used to follow physical, chemical and biological processes almost from the time of their discovery. Probably the application with the biggest impact has been in the medical field where radionuclides have been incorporated into biologically active molecules and used to diagnose a wide variety of diseases and to treat many disorders. Other uses in the life sciences, in general, are related to using a radioactive isotope as marker for an existing species such as nitrogen-13 in plant studies or copper-67 to track copper catalysts in phytoplankton. This review describes in general terms these uses as well as providing the reader with the background related to the physical properties of radioactive decay, the concepts associated with the production of radionuclides using reactors or accelerators and the fundamentals of imaging radioactivity. The advances in imaging technology in recent years has had a profound impact on the use of radionuclides in positron emission tomography and the coupling of other imaging modalities to provide very precise insights into human disease. The variety of uses for radiotracers in science is almost boundless dependent only upon ones imagination.

  19. Environmental control and life support systems analysis for a Space Station life sciences animal experiment

    Science.gov (United States)

    So, Kenneth T.; Hall, John B., Jr.; Thompson, Clifford D.

    1987-01-01

    NASA's Langley and Goddard facilities have evaluated the effects of animal science experiments on the Space Station's Environmental Control and Life Support System (ECLSS) by means of computer-aided analysis, assuming an animal colony consisting of 96 rodents and eight squirrel monkeys. Thirteen ECLSS options were established for the reclamation of metabolic oxygen and waste water. Minimum cost and weight impacts on the ECLSS are found to accrue to the system's operation in off-nominal mode, using electrochemical CO2 removal and a static feed electrolyzer for O2 generation.

  20. The Development of Ontology from Multiple Databases

    Science.gov (United States)

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

    2017-08-01

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

  1. 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…

  2. 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…

  3. 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…

  4. 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…

  5. Database Description - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nnovation Program / Omics Science Center Journal Search: Creator Name: Hideya Kawaji Creator Affiliation: RI...tion / Center for Life Science Technologies / Omics Science Center Journal Search...: Creator Name: Takeya Kasukawa Creator Affiliation: RIKEN Center for Life Science Technologies Journal Sear... VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. Journal: Nature. 2014 Mar 27...k P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A. Journal

  6. Convergence facilitating transdisciplinary integration of life sciences, physical sciences, engineering, and beyond

    CERN Document Server

    2014-01-01

    Convergence of the life sciences with fields including physical, chemical, mathematical, computational, engineering, and social sciences is a key strategy to tackle complex challenges and achieve new and innovative solutions. However, institutions face a lack of guidance on how to establish effective programs, what challenges they are likely to encounter, and what strategies other organizations have used to address the issues that arise. This advice is needed to harness the excitement generated by the concept of convergence and channel it into the policies, structures, and networks that will enable it to realize its goals. Convergence investigates examples of organizations that have established mechanisms to support convergent research. This report discusses details of current programs, how organizations have chosen to measure success, and what has worked and not worked in varied settings. The report summarizes the lessons learned and provides organizations with strategies to tackle practical needs and imple...

  7. Turning to ontology in STS? Turning to STS through ‘ontology’?

    NARCIS (Netherlands)

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

    2013-01-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  9. Improvements to cardiovascular gene ontology.

    Science.gov (United States)

    Lovering, Ruth C; Dimmer, Emily C; Talmud, Philippa J

    2009-07-01

    Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism. Although one might initially wonder what relevance a 'controlled vocabulary' might have for cardiovascular science, such a resource is proving highly useful for researchers investigating complex cardiovascular disease phenotypes as well as those interpreting results from high-throughput methodologies. GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets. In this way, the GO data provides a very effective way of linking biological knowledge with the analysis of the large datasets of post-genomics research. Consequently, users of high-throughput methodologies such as expression arrays or proteomics will be the main beneficiaries of such annotation sets. However, as GO annotations increase in quality and quantity, groups using small-scale approaches will gradually begin to benefit too. For example, genome wide association scans for coronary heart disease are identifying novel genes, with previously unknown connections to cardiovascular processes, and the comprehensive annotation of these novel genes might provide clues to their cardiovascular link. At least 4000 genes, to date, have been implicated in cardiovascular processes and an initiative is underway to focus on annotating these genes for the benefit of the cardiovascular community. In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.

  10. 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...

  11. Ames Life Science Data Archive: Translational Rodent Research at Ames

    Science.gov (United States)

    Wood, Alan E.; French, Alison J.; Ngaotheppitak, Ratana; Leung, Dorothy M.; Vargas, Roxana S.; Maese, Chris; Stewart, Helen

    2014-01-01

    The Life Science Data Archive (LSDA) office at Ames is responsible for collecting, curating, distributing and maintaining information pertaining to animal and plant experiments conducted in low earth orbit aboard various space vehicles from 1965 to present. The LSDA will soon be archiving data and tissues samples collected on the next generation of commercial vehicles; e.g., SpaceX & Cygnus Commercial Cargo Craft. To date over 375 rodent flight experiments with translational application have been archived by the Ames LSDA office. This knowledge base of fundamental research can be used to understand mechanisms that affect higher organisms in microgravity and help define additional research whose results could lead the way to closing gaps identified by the Human Research Program (HRP). This poster will highlight Ames contribution to the existing knowledge base and how the LSDA can be a resource to help answer the questions surrounding human health in long duration space exploration. In addition, it will illustrate how this body of knowledge was utilized to further our understanding of how space flight affects the human system and the ability to develop countermeasures that negate the deleterious effects of space flight. The Ames Life Sciences Data Archive (ALSDA) includes current descriptions of over 700 experiments conducted aboard the Shuttle, International Space Station (ISS), NASA/MIR, Bion/Cosmos, Gemini, Biosatellites, Apollo, Skylab, Russian Foton, and ground bed rest studies. Research areas cover Behavior and Performance, Bone and Calcium Physiology, Cardiovascular Physiology, Cell and Molecular Biology, Chronobiology, Developmental Biology, Endocrinology, Environmental Monitoring, Gastrointestinal Physiology, Hematology, Immunology, Life Support System, Metabolism and Nutrition, Microbiology, Muscle Physiology, Neurophysiology, Pharmacology, Plant Biology, Pulmonary Physiology, Radiation Biology, Renal, Fluid and Electrolyte Physiology, and Toxicology. These

  12. Evaluation of an international doctoral educational program in space life sciences: The Helmholtz Space Life Sciences Research School (SpaceLife) in Germany

    Science.gov (United States)

    Hellweg, C. E.; Spitta, L. F.; Kopp, K.; Schmitz, C.; Reitz, G.; Gerzer, R.

    2016-01-01

    Training young researchers in the field of space life sciences is essential to vitalize the future of spaceflight. In 2009, the DLR Institute of Aerospace Medicine established the Helmholtz Space Life Sciences Research School (SpaceLife) in cooperation with several universities, starting with 22 doctoral candidates. SpaceLife offered an intensive three-year training program for early-stage researchers from different fields (biology, biomedicine, biomedical engineering, physics, sports, nutrition, plant and space sciences). The candidates passed a multistep selection procedure with a written application, a self-presentation to a selection committee, and an interview with the prospective supervisors. The selected candidates from Germany as well as from abroad attended a curriculum taught in English. An overview of space life sciences was given in a workshop with introductory lectures on space radiation biology and dosimetry, space physiology, gravitational biology and astrobiology. The yearly Doctoral Students' Workshops were also interdisciplinary. During the first Doctoral Students' Workshop, every candidate presented his/her research topic including hypothesis and methods to be applied. The progress report was due after ∼1.5 years and a final report after ∼3 years. The candidates specialized in their subfield in advanced lectures, Journal Clubs, practical trainings, lab exchanges and elective courses. The students attended at least one transferable skills course per year, starting with a Research Skills Development course in the first year, a presentation and writing skills course in the second year, and a career and leadership course in the third year. The whole program encompassed 303 h and was complemented by active conference participation. In this paper, the six years' experience with this program is summarized in order to guide other institutions in establishment of structured Ph.D. programs in this field. The curriculum including elective courses is

  13. 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 ...

  14. Database Description - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available name - DOI - Creator Creator Name: Hiromasa Ono Creator Affiliation: Database Center for Life Science Journ...ese; pronunciation symbol is [toɯgoɯ]) that is one of the services in the Database Center for Life Science (...e to be used all over the world. License CC BY Detail Background and funding Name: MEXT Integrated Database Project Life...Bioinformatics.(2011/7/29) External Links: Original website information Database maintenance site Database Center for Life

  15. Future opportunities and future trends for e-infrastructures and life sciences: going beyond grid to enable life science data analysis

    Directory of Open Access Journals (Sweden)

    Fotis ePsomopoulos

    2015-06-01

    Full Text Available With the increasingly rapid growth of data in Life Sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. In the context of the European Grid Infrastructure Community Forum 2014 (Helsinki, 19–23 May 2014, a workshop was held aimed at understanding the state of the art of Grid/Cloud computing in EU research as viewed from within the field of Life Sciences. The workshop brought together Life Science researchers and infrastructure providers from around Europe and facilitated networking between them within the context of EGI. The first part of the workshop included talks from key infrastructures and projects within the Life Sciences community. This was complemented by technical talks that established the key aspects present in major research approaches. Finally, the discussion phase provided significant insights into the road ahead with proposals for possible collaborations and suggestions for future actions.

  16. 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

  17. Discourse in science communities: Issues of language, authority, and gender in a life sciences laboratory

    Science.gov (United States)

    Conefrey, Theresa Catherine

    Government-sponsored and private research initiatives continue to document the underrepresentation of women in the sciences. Despite policy initiatives, women's attrition rates each stage of their scientific careers remain higher than those of their male colleagues. In order to improve retention rates more information is needed about why many drop out or do not succeed as well as they could. While broad sociological studies and statistical surveys offer a valuable overview of institutional practices, in-depth qualitative analyses are needed to complement these large-scale studies. This present study goes behind statistical generalizations about the situation of women in science to explore the actual experience of scientific socialization and professionalization. Beginning with one reason often cited by women who have dropped out of science: "a bad lab experience," I explore through detailed observation in a naturalistic setting what this phrase might actually mean. Using ethnographic and discourse analytic methods, I present a detailed analysis of the discourse patterns in a life sciences laboratory group at a large research university. I show how language accomplishes the work of indexing and constituting social constraints, of maintaining or undermining the hierarchical power dynamics of the laboratory, of shaping members' presentation of self, and of modeling social and professional skills required to "do science." Despite the widespread conviction among scientists that "the mind has no sex," my study details how gender marks many routine interactions in the lab, including an emphasis on competition, a reinforcement of sex-role stereotypes, and a conversational style that is in several respects more compatible with men's than women's forms of talk.

  18. Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a Biomedical Ethics Ontology

    OpenAIRE

    Koepsell, David; Arp, Robert; Fostel, Jennifer; Smith, Barry

    2009-01-01

    Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology (BMEO) would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigat...

  19. 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

  20. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

    NARCIS (Netherlands)

    Katayama, T.; Wilkinson, M.D.; Aoki-Kinoshita, K.F.; Prins, J.C.P.

    2014-01-01

    The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities

  1. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

    NARCIS (Netherlands)

    Katayama, T.; Wilkinson, M.D.; Aoki-Kinoshita, K.F.; Prins, J.C.P.

    2014-01-01

    The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities

  2. Paul Scherrer Institute Scientific Report 1999. Volume II: Life Sciences

    Energy Technology Data Exchange (ETDEWEB)

    Jaussi, Rolf; Gschwend, Beatrice [eds.

    2000-07-01

    The existing activities of the Department of Life Sciences have grown out of the specific know how and the unique experimental possibilities available at PSI. Primarily, these have been and are complex facilities for using particle beams (protons, neutrons) on the one hand and know how in the production, handling and chemistry of radionuclides on the other. The common theme of the department has thus been the study and use of various types of radiation in therapy and diagnostics of human disease and in particular of cancer. The four units active in this area are: The major activity in the Radiation Medicine unit is Proton Therapy, which aims to further develop and optimise the world-wide unique spot scanning facility for irradiating malignant tumours with minimal damage to surrounding healthy tissues, including the established OPTIS program for the treatment of eye tumours. The Centre for Radiopharmaceutical Science represents a joint activity of PSI with the Swiss Federal Institute of Technology (ETHZ) and the University of Zurich. Its major goals are the development of novel tumour targeted radioconjugates for cancer diagnosis and therapy and the production and evaluation of new PET (positron emission tomography) radiotracers for various applications in neuro physiology and drug development. The Institute of Medical Radiobiology analyses questions of the molecular biology of DNA repair. It is a joint activity of PSI and the University of Zurich. The Structural Biology unit is currently being established. A strong in-house research activity in macromolecular crystallography will complement the more user-oriented protein crystallography beam line, which is being built at the Swiss Light Source (SLS). In particular, tumour targeting by molecular vehicles and DNA repair are areas where structural information can provide important insights. Progress in 1999 in these topical areas is described in this report. A list of scientific publications in 1999 is also provided.

  3. Paul Scherrer Institute Scientific Report 2000. Volume II: Life Sciences

    Energy Technology Data Exchange (ETDEWEB)

    Jaussi, Rolf; Gschwend, Beatrice [eds.

    2001-07-01

    The existing activities of the Department of Life Sciences have grown out of the specific know-how and the unique experimental possibilities available at PSI. Primarily, these have been and are complex facilities for using particle beams (protons, neutrons) on the one hand and know-how in the production, handling and chemistry of radionuclides on the other. The common theme of the department has thus been the study and use of various types of radiation in therapy and diagnostics of human disease and in particular of cancer. The four units active in this area are: The major activity in the Radiation Medicine unit is Proton Therapy, which aims to further develop and optimise the world-wide unique spot scanning facility for irradiating malignant tumours with minimal damage to surrounding healthy tissues, including the established OPTIS program for the treatment of eye tumours. The Centre for Radiopharmaceutical Science represents a joint activity of PSI with the Swiss Federal Institute of Technology (ETHZ) and the University of Zurich. Its major goals are the development of novel tumour targeted radioconjugates for cancer diagnosis and therapy and the production and evaluation of new PET (positron emission tomography) radiotracers for various applications in neuro physiology and drug development. The Institute of Medical Radiobiology analyses questions of the molecular biology of DNA repair. It is a joint activity of PSI and the University of Zurich. The newly established Structural Biology group is still in the build-up phase. A strong in-house research activity in macromolecular crystallography will complement the more user-oriented protein crystallography beam line, which is being built at the Swiss Light Source (SLS). In particular, tumour targeting by molecular vehicles and DNA repair are areas where structural information can provide important insights. Progress in 2000 in these topical areas is described in this report. A list of scientific publications in 2000

  4. Modelling the cybersecurity environment using morphological ontology design engineering

    CSIR Research Space (South Africa)

    Jansen van Vuuren, JC

    2015-03-01

    Full Text Available ). This methodology is based on the combination of three different research methods, i.e. design science, general morphological analysis, and ontology based representation. General morphological analysis offers a solution for extracting meaningful information from...

  5. [ ] 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.

  6. Perspectives on ontology learning

    CERN Document Server

    Lehmann, J

    2014-01-01

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

  7. The sexual and ontology

    Directory of Open Access Journals (Sweden)

    Zupančič Alenka

    2014-01-01

    Full Text Available This paper explores some of the crucial ontological implications of the psychoanalytic theory of sexuality in its Freudo-Lacanian orientation. As irreducible to different sexual practices and contents, the concept of sexuality obtains conceptual weight that makes it particularly relevant for philosophical ontological thinking. Starting from the hypothesis that something about sexuality is constitutively unconscious - that is to say, existing only in the form of the unconscious - the paper points at the singular short-circuit of the epistemological and ontological level which is at work in psychoanalytic theory, and which cannot be neglected in philosophical examination of the relation between knowledge and being.

  8. 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.

  9. Changing Lives: The Baltimore City Community College Life Sciences Partnership with the University of Maryland, Baltimore

    Science.gov (United States)

    Carroll, Vanessa G.; Harris-Bondima, Michelle; Norris, Kathleen Kennedy; Williams, Carolane

    2010-01-01

    Baltimore City Community College (BCCC) leveraged heightened student interest and enrollment in the sciences and allied health with Maryland's world-leading biotechnology industry to build a community college life sciences learning and research center right on the University of Maryland, Baltimore's downtown BioPark campus. The BCCC Life Sciences…

  10. Spacelab Life Sciences (SLS) echocardiograph in mockup rack in JSC's Bldg 36

    Science.gov (United States)

    1987-01-01

    Spacelab Life Sciences (SLS) life sciences laboratory equipment (LSLE) echocardiograph is documented in the JSC Bioengineering and Test Support Facility Bldg 36. Displayed on the echocardiograph monitor is a heart image. The echocardiograph equipment is located in Rack 6 and will be used in conjunction with Experiment No. 294 Cardiovascular Adaptation to Zero Gravity during the STS-40 SLS-1 mission.

  11. Changing Lives: The Baltimore City Community College Life Sciences Partnership with the University of Maryland, Baltimore

    Science.gov (United States)

    Carroll, Vanessa G.; Harris-Bondima, Michelle; Norris, Kathleen Kennedy; Williams, Carolane

    2010-01-01

    Baltimore City Community College (BCCC) leveraged heightened student interest and enrollment in the sciences and allied health with Maryland's world-leading biotechnology industry to build a community college life sciences learning and research center right on the University of Maryland, Baltimore's downtown BioPark campus. The BCCC Life Sciences…

  12. Computer Literacy for Life Sciences: Helping the Digital-Era Biology Undergraduates Face Today's Research

    Science.gov (United States)

    Smolinski, Tomasz G.

    2010-01-01

    Computer literacy plays a critical role in today's life sciences research. Without the ability to use computers to efficiently manipulate and analyze large amounts of data resulting from biological experiments and simulations, many of the pressing questions in the life sciences could not be answered. Today's undergraduates, despite the ubiquity of…

  13. Possibilities, Intentions and Threats: Dual Use in the Life Sciences Reconsidered

    NARCIS (Netherlands)

    Van der Bruggen, K.

    2011-01-01

    Due to the terrorist attacks of 9/11 and the anthrax letters of a few weeks later, the concept of dual use has spread widely in the life sciences during the past decade. This article is aimed at a clarification of the dual use concept and its scope of application for the life sciences. Such a clarif

  14. Longitudinal effects of college type and selectivity on degrees conferred upon undergraduate females in physical science, life science, math and computer science, and social science

    Science.gov (United States)

    Stevens, Stacy Mckimm

    There has been much research to suggest that a single-sex college experience for female undergraduate students can increase self-confidence and leadership ability during the college years and beyond. The results of previous studies also suggest that these students achieve in the workforce and enter graduate school at higher rates than their female peers graduating from coeducational institutions. However, some researchers have questioned these findings, suggesting that it is the selectivity level of the colleges rather than the comprised gender of the students that causes these differences. The purpose of this study was to justify the continuation of single-sex educational opportunities for females at the post-secondary level by examining the effects that college selectivity, college type, and time have on the rate of undergraduate females pursuing majors in non-traditional fields. The study examined the percentage of physical science, life science, math and computer science, and social science degrees conferred upon females graduating from women's colleges from 1985-2001, as compared to those at comparable coeducational colleges. Sampling for this study consisted of 42 liberal arts women's (n = 21) and coeducational (n = 21) colleges. Variables included the type of college, the selectivity level of the college, and the effect of time on the percentage of female graduates. Doubly multivariate repeated measures analysis of variance testing revealed significant main effects for college selectivity on social science graduates, and time on both life science and math and computer science graduates. Significant interaction was also found between the college type and time on social science graduates, as well as the college type, selectivity level, and time on math and computer science graduates. Implications of the results and suggestions for further research are discussed.

  15. Towards automated biomedical ontology harmonization.

    Science.gov (United States)

    Uribe, Gustavo A; Lopez, Diego M; Blobel, Bernd

    2014-01-01

    The use of biomedical ontologies is increasing, especially in the context of health systems interoperability. Ontologies are key pieces to understand the semantics of information exchanged. However, given the diversity of biomedical ontologies, it is essential to develop tools that support harmonization processes amongst them. Several algorithms and tools are proposed by computer scientist for partially supporting ontology harmonization. However, these tools face several problems, especially in the biomedical domain where ontologies are large and complex. In the harmonization process, matching is a basic task. This paper explains the different ontology harmonization processes, analyzes existing matching tools, and proposes a prototype of an ontology harmonization service. The results demonstrate that there are many open issues in the field of biomedical ontology harmonization, such as: overcoming structural discrepancies between ontologies; the lack of semantic algorithms to automate the process; the low matching efficiency of existing algorithms; and the use of domain and top level ontologies in the matching process.

  16. Influence of an Intensive, Field-Based Life Science Course on Preservice Teachers' Self-Efficacy for Environmental Science Teaching

    Science.gov (United States)

    Trauth-Nare, Amy

    2015-01-01

    Personal and professional experiences influence teachers' perceptions of their ability to implement environmental science curricula and to positively impact students' learning. The purpose of this study was twofold: to determine what influence, if any, an intensive field-based life science course and service learning had on preservice teachers'…

  17. Assessing the Life Science Knowledge of Students and Teachers Represented by the K-8 National Science Standards

    Science.gov (United States)

    Sadler, Philip M.; Coyle, Harold; Cook Smith, Nancy; Miller, Jaimie; Mintzes, Joel; Tanner, Kimberly; Murray, John

    2013-01-01

    We report on the development of an item test bank and associated instruments based on the National Research Council (NRC) K-8 life sciences content standards. Utilizing hundreds of studies in the science education research literature on student misconceptions, we constructed 476 unique multiple-choice items that measure the degree to which test…

  18. Influence of an Intensive, Field-Based Life Science Course on Preservice Teachers' Self-Efficacy for Environmental Science Teaching

    Science.gov (United States)

    Trauth-Nare, Amy

    2015-01-01

    Personal and professional experiences influence teachers' perceptions of their ability to implement environmental science curricula and to positively impact students' learning. The purpose of this study was twofold: to determine what influence, if any, an intensive field-based life science course and service learning had on preservice teachers'…

  19. Translating complex science into life-course health promoting strategies.

    Science.gov (United States)

    Buttriss, Judith L

    2011-02-01

    These days, we are bombarded with nutrition information from diverse sources and of varying quality. There has been a dramatic increase in communication channels, including more television channels with airtime to fill, and the emergence of the Internet and 'new media' such as social networking sites. Part of this culture is to deliver ever changing and novel angles. The background 'noise' that this creates can make delivery of evidence-based advice about healthy eating that generally carries less novelty value, a huge challenge. This paper illustrates ways in which complex scientific information can be translated into meaningful health promoting strategies that can be applied across the life course. The examples used are nutrition in the context of healthy ageing, communicating the concept of energy density in the context of satiety, healthy hydration, health effects of probiotics and resources for use by teachers in the classroom. This selection of examples demonstrates the processes adopted at the British Nutrition Foundation to identify the evidence base for a particular topic and then to communicate this information to various target audiences. The British Nutrition Foundation's approach typically starts with preparation of a detailed review of the evidence, often with the involvement of external expertise, followed by peer review. For much of this work conventional science communication routes are used, but use is also made of the Internet and various forms of new media.

  20. Analysis of debris from Spacelab Space Life Sciences-1

    Science.gov (United States)

    Caruso, S. V.; Rodgers, E. B.; Huff, T. L.

    1992-07-01

    Airborne microbiological and particulate contamination generated aboard Spacelab modules is a potential safety hazard. In order to shed light on the characteristics of these contaminants, microbial and chemical/particulate analyses were performed on debris vacuumed from cabin and avionics air filters in the Space Life Sciences-1 (SLS-1) module of the Space Transportation System 40 (STS-40) mission 1 month after landing. The debris was sorted into categories (e.g., metal, nonmetal, hair/fur, synthetic fibers, food particles, insect fragments, etc.). Elemental analysis of particles was done by energy dispersive analysis of x rays (metals) and Fourier transform infrared spectroscopy (nonmetals). Scanning electron micrographs were done of most particles. Microbiological samples were grown on R2A culture medium and identified. Clothing fibers dominated the debris by volume. Other particles, all attributed to the crew, resulted from abrasions and impacts during missions operations (e.g., paint chips, plastic, electronic scraps and clothing fibers). All bacterial species identified are commonly found in the atmosphere or on the human body. Bacillus sp. was the most frequently seen bacterium. One of the bacterial species, Enterobacter agglomerans, could cause illness in crew members with depressed immune systems.

  1. The first dedicated life sciences mission - Spacelab 4

    Science.gov (United States)

    Cramer, D. R.; Reid, D. H.; Klein, H. P.

    1983-01-01

    The details of the payload and the experiments in Spacelab 4, the first Spacelab mission dedicated entirely to the life sciences, are discussed. The payload of Spacelab 4, carried in the bay of the Shuttle Orbiter, consists of 25 tentatively selected investigations combined into a comprehensive integrated exploration of the effects of acute weightlessness on living systems. The payload contains complementary designs in the human and animal investigations in order to validate animal models of human physiology in weightlessness. Animals used as experimental subjects will include squirrel monkeys, laboratory rats, several species of plants, and frog eggs. The main scientific objectives of the investigations include the study of the acute cephalic fluid shift, cardiovascular adaptation to weightlessness, including postflight reductions in orthostatic tolerance and exercise capacity, and changes in vestibular function, including space motion sickness, associated with weightlessness. Other scientific objective include the study of red cell mass reduction, negative nitrogen balance, altered calcium metabolism, suppressed in vitro lymphocyte reactivity, gravitropism and photropism in plants, and fertilization and early development in frog eggs.

  2. Multi-copter application to life sciences in partial gravity.

    Science.gov (United States)

    Hasegawa, Katsuya; Kumei, Yasuhiro; Atomi, Yoriko

    Although parabolic flight is a well-defined experimental platform to simulate microgravity conditions, it has not been used extensively for pure scientific purposes due to many limitations in accessibility and reproducibility as well as the high cost. To overcome this problem, we have developed a brand-new low-gravity simulation system that is operated by a radio-controlled multi-copter. The outline of the new multi-copter is, 1) dimension and weight:Width 800mm,5kg, 2) low-gravity generation: 1/6 ~1G for 5 seconds, 3) payloads: up to 30 kg, 4) measurable instrument: G-sensor, 5) observational instruments: high speed camera, high-definition camera, zoom camera, video recorder, 6) data collection: analog data 128ch memory. We can conduct the experiments 10 times a day without any cost, and get an enough number of samples for statistical analysis. The newly developed multi-copter system enables physical, chemical, and basic life sciences with graded levels of low gravities as an experimental parameter.

  3. Advanced Biotelemetry Systems for Space Life Sciences: PH Telemetry

    Science.gov (United States)

    Hines, John W.; Somps, Chris; Ricks, Robert; Kim, Lynn; Connolly, John P. (Technical Monitor)

    1995-01-01

    The SENSORS 2000! (S2K!) program at NASA's Ames Research Center is currently developing a biotelemetry system for monitoring pH and temperature in unrestrained subjects. This activity is part of a broader scope effort to provide an Advanced Biotelemetry System (ABTS) for use in future space life sciences research. Many anticipated research endeavors will require biomedical and biochemical sensors and related instrumentation to make continuous inflight measurements in a variable-gravity environment. Since crew time is limited, automated data acquisition, data processing, data storage, and subject health monitoring are required. An automated biochemical and physiological data acquisition system based on non invasive or implantable biotelemetry technology will meet these requirements. The ABTS will ultimately acquire a variety of physiological measurands including temperature, biopotentials (e.g. ECG, EEG, EMG, EOG), blood pressure, flow and dimensions, as well as chemical and biological parameters including pH. Development activities are planned in evolutionary, leveraged steps. Near-term activities include 1) development of a dual channel pH/temperature telemetry system, and 2) development of a low bandwidth, 4-channel telemetry system, that measures temperature, heart rate, pressure, and pH. This abstract describes the pH/temperature telemeter.

  4. Toward a general ontology for digital forensic disciplines.

    Science.gov (United States)

    Karie, Nickson M; Venter, Hein S

    2014-09-01

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

  5. 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...... 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...... and relations into taxonomies. As an epistemological foundation for the concepts formalisation, The Suggested Upper Merged Ontology (SUMO) proposed by IEEE, was reused. As the result of the previously described process, the ontology content has been categorised into six main subcategories divided between...

  6. Mechanisms in biomedical ontology

    National Research Council Canada - National Science Library

    Röhl, Johannes

    2012-01-01

    .... Taking some hints from an "ontology of devices" I suggest as a general approach for this task the introduction of functional kinds and functional parts by which the particular relations between a mechanism and its components can be captured.

  7. APPENDIX AND BIBLIOGRAPHY TO BE USED WITH LIFE AND EARTH SCIENCE GUIDES.

    Science.gov (United States)

    MAHLER, FRED

    CONTAINED IN THIS TEACHER'S GUIDE FOR LIFE AND EARTH SCIENCES ARE BIBLIOGRAPHIES, DEMONSTRATIONS, AND EXPERIMENTS. BOOKS ARE LISTED FOR JUNIOR HIGH SCHOOL SCIENCE WHICH COVER A WIDE RANGE OF SUBJECTS, INCLUDING NATURE STUDY, BIOLOGY, CHEMISTRY, AND PHYSICS AS WELL AS MORE HIGHLY SPECIALIZED FIELDS OF THE PHYSICAL SCIENCES. TEXTBOOKS LISTED INCLUDE…

  8. Manufacturing ontology through templates

    Directory of Open Access Journals (Sweden)

    Diciuc Vlad

    2017-01-01

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

  9. Ontology alignment with OLA

    OpenAIRE

    Euzenat, Jérôme; Loup, David; Touzani, Mohamed; Valtchev, Petko

    2004-01-01

    euzenat2004d; International audience; Using ontologies is the standard way to achieve interoperability of heterogeneous systems within the Semantic web. However, as the ontologies underlying two systems are not necessarily compatible, they may in turn need to be aligned. Similarity-based approaches to alignment seems to be both powerful and flexible enough to match the expressive power of languages like OWL. We present an alignment tool that follows the similarity-based paradigm, called OLA. ...

  10. 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.

  11. My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

    Science.gov (United States)

    Rabattu, Pierre-Yves; Massé, Benoit; Ulliana, Federico; Rousset, Marie-Christine; Rohmer, Damien; Léon, Jean-Claude; Palombi, Olivier

    2015-01-01

    Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human

  12. Life satisfaction, health, self-evaluation and sexuality in current university students of sport sciences, education and natural sciences

    Directory of Open Access Journals (Sweden)

    Martin Sigmund

    2014-12-01

    Full Text Available Background: Lifestyle and health of an individual are influenced by many factors; a significant factor is life satisfaction. Life satisfaction is understood as a multidimensional construct closely related to the area of personal wellbeing and quality of life. Life satisfaction in university students represents one of the determinants of good health, high motivation for studying, work productivity, satisfactory interpersonal relationships and overall healthy lifestyle. Objective: The main objective of the present study is to identify and compare the level of overall life satisfaction and selected components of health, self-evaluation and sexuality in current university students with respect to their study specialization. Methods: The study included a total of 522 students from Palacký University. These were students from the Faculty of Physical Culture (n = 118, Faculty of Education (n = 218 and Faculty of Science (n = 186. In terms of age, the study focused on young adults aged 19 to 26. To assess the current level of life satisfaction, the research study used a standardized psychodiagnostic tool - Life Satisfaction Questionnaire (LSQ. The used diagnostic methods are fully standardized and contain domestic normative values. Statistical result processing was conducted using the Statistica programme v10.0. Results: The highest level of overall life satisfaction was revealed in university students of sport sciences. In comparison with the students of education and students of natural sciences the difference is significant. Satisfaction with health among the students of sport sciences is significantly higher than in the students of education (p ≤ .001; d = 0.53 and the students of natural sciences (p ≤ .05; d = 0.38. Similar results were found in the area of satisfaction with own person and self-evaluation, where the values of the students of sport sciences were significantly higher compared with the students of education (p

  13. Applications of ontology design patterns in biomedical ontologies.

    Science.gov (United States)

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

    2012-01-01

    Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP prevalence or effectiveness thus far. In this work, we determine the use and applicability of ODPs in a case study of biomedical ontologies. We encoded ontology design patterns from two ODP catalogs. We then searched for these patterns in a set of eight ontologies. We found five patterns of the 69 patterns. Two of the eight ontologies contained these patterns. While ontology design patterns provide a vehicle for capturing formally reoccurring models and best practices in ontology design, we show that today their use in a case study of widely used biomedical ontologies is limited.

  14. Applications of Ontology Design Patterns in Biomedical Ontologies

    Science.gov (United States)

    Mortensen, Jonathan M.; Horridge, Matthew; Musen, Mark A.; Noy, Natalya F.

    2012-01-01

    Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP prevalence or effectiveness thus far. In this work, we determine the use and applicability of ODPs in a case study of biomedical ontologies. We encoded ontology design patterns from two ODP catalogs. We then searched for these patterns in a set of eight ontologies. We found five patterns of the 69 patterns. Two of the eight ontologies contained these patterns. While ontology design patterns provide a vehicle for capturing formally reoccurring models and best practices in ontology design, we show that today their use in a case study of widely used biomedical ontologies is limited. PMID:23304337

  15. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

    This paper describes a frame-based integration of the three GO subontologies, the Chemicals of Biological Interest ontology (ChEBI), and the Cell Type Ontology (CTO) in which relationships between elements of the ontologies are modeled in a way that better captures the relational semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions of the form (subject, relationship, object) by identifying patterns in GO terms, mapping these patterns and subpatterns to relationships, matching concepts to these patterns and subpatterns, and integrating these assertions into the ontologies. Using this methodology, a large number of reliable assertions linking previously unlinked OBO terms using a wide variety of specific, hierarchically arranged relationships were created: A predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid; a further 429 assertions (corresponding to 6% of the matching terms) were manually created, resulting in an initial set of 4,497 assertions. Furthermore, this methodology programmatically integrates assertions into a base ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels. Such an integration is absent from previous compositional efforts, and we argue its necessity for the creation of coherent biological ontologies when linking previously unlinked terms. PMID:17011833

  16. Database Description - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ation: National Institute of Crop Science, National Agriculture and Food Research Organization Journal Searc...titute of Crop Science, National Agriculture and Food Research Organization Setsuko Komatsu E-mail: Database

  17. The Ontology of the Gene Ontology

    Science.gov (United States)

    Smith, Barry; Williams, Jennifer; Steffen, Schulze-Kremer

    2003-01-01

    The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. PMID:14728245

  18. Life sciences flight hardware development for the International Space Station

    Science.gov (United States)

    Kern, V. D.; Bhattacharya, S.; Bowman, R. N.; Donovan, F. M.; Elland, C.; Fahlen, T. F.; Girten, B.; Kirven-Brooks, M.; Lagel, K.; Meeker, G. B.; Santos, O.

    During the construction phase of the International Space Station (ISS), early flight opportunities have been identified (including designated Utilization Flights, UF) on which early science experiments may be performed. The focus of NASA's and other agencies' biological studies on the early flight opportunities is cell and molecular biology; with UF-1 scheduled to fly in fall 2001, followed by flights 8A and UF-3. Specific hardware is being developed to verify design concepts, e.g., the Avian Development Facility for incubation of small eggs and the Biomass Production System for plant cultivation. Other hardware concepts will utilize those early research opportunities onboard the ISS, e.g., an Incubator for sample cultivation, the European Modular Cultivation System for research with small plant systems, an Insect Habitat for support of insect species. Following the first Utilization Flights, additional equipment will be transported to the ISS to expand research opportunities and capabilities, e.g., a Cell Culture Unit, the Advanced Animal Habitat for rodents, an Aquatic Facility to support small fish and aquatic specimens, a Plant Research Unit for plant cultivation, and a specialized Egg Incubator for developmental biology studies. Host systems (Figure 1A, B), e.g., a 2.5 m Centrifuge Rotor (g-levels from 0.01-g to 2-g) for direct comparisons between μg and selectable g levels, the Life Sciences Glove☐ for contained manipulations, and Habitat Holding Racks (Figure 1B) will provide electrical power, communication links, and cooling to the habitats. Habitats will provide food, water, light, air and waste management as well as humidity and temperature control for a variety of research organisms. Operators on Earth and the crew on the ISS will be able to send commands to the laboratory equipment to monitor and control the environmental and experimental parameters inside specific habitats. Common laboratory equipment such as microscopes, cryo freezers, radiation

  19. 基于Web of Science的本体和社会化标签关联研究的进展分析%Current Status of Association Study on Ontology and Social Tag Based on Web of Science

    Institute of Scientific and Technical Information of China (English)

    窦永香; 王帮金; 方倩

    2014-01-01

    社会化标签兴起后,其与本体的关联研究越来越受到国内外研究者的关注。基于Web of Science的检索数据,使用CiteSpace软件,从作者及国家、共被引文献及突现词等角度对本体与社会化标签关联研究的现状进行可视化分析。从研究人员及国家来看,研究人员的合作程度较高,但是团体间的合作较少,另外,美国、德国、中国和澳大利亚的研究较多,且研究较早;从研究热点的发展来看,本体和社会化标签的关联研究由其与知识共享、与语义网及元数据的研究转变而来。在2008年后产生了多个研究热点,其中研究得最多的是用户生成内容、标签本体和标签推荐。%With the widespread use of social tag,the association study on ontology and social tag has increasingly become a hot concern. In this paper, a visual analysis of the development status of this study is shown by using the CiteSpace from different aspects of the authors and their countries, co-cited references and burst terms based on the data from Web of Science. In the aspect of the researchers and their countries, the cooperation level between researchers is high, while a low level of cooperation is seen between the groups;USA, Germany, China and Australia started the related research from an early period and have accumulated a lot of related researches. In the aspect of the development of research hotspots, the association study on ontology and social tag evolved from the researches about ontology, social tag and knowledge sharing, semantic and metadata. Many hotspots emerged after 2008,and the first three research hotspots are user generated content,tag ontology and tag recommendation.

  20. Bioclipse 2: A scriptable integration platform for the life sciences

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2009-12-01

    Full Text Available Abstract Background Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. Results Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments. Conclusion Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research. Bioclipse 2 is released under the Eclipse Public License (EPL, a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code

  1. Nanocrystalline diamond--an excellent platform for life science applications.

    Science.gov (United States)

    Kloss, Frank R; Najam-Ul-Haq, Muhammed; Rainer, Matthias; Gassner, Robert; Lepperdinger, Günter; Huck, Christian W; Bonn, Günther; Klauser, Frederik; Liu, Xianjie; Memmel, Norbert; Bertel, Erminald; Garrido, Jose A; Steinmüller-Nethl, Doris

    2007-12-01

    Nanocrystalline diamond (NCD) has recently been successfully utilized in a variety of life science applications. NCD films are favorable and salubrious substrates for cells during cultivation. Therefore NCD has also been employed in tissue engineering strategies. NCD as reported in this contribution was grown by means of a modified hot-filament chemical vapor deposition technique, which results in less than 3% sp2-hybridization and yields grain sizes of 5-20 nm. After production the NCD surface was rather hydrophobic, however it could be efficiently refined to exhibit more hydrophilic properties. Changing of the surface structure was found to be an efficient means to influence growth and differentiation capacity of a variety of cells. The particular needs for any given cell type has to be proven empirically. Yet flexible features of NCD appear to be superior to plastic surfaces which can be hardly changed in quality. Besides its molecular properties, crystal structural peculiarities of NCD appear to influence cell growth as well. In our attempt to facilitate, highly specialized applications in biomedicine, we recently discovered that growth factors can be tightly bound to NCD by mere physisorption. Hence, combination of surface functionalization together with further options to coat NCD with any kind of three-dimensional structure opens up new avenues for many more applications. In fact, high through-put protein profiling of early disease stages may become possible from serum samples, because proteins bound to NCD can now be efficiently analyzed by MALDI/TOF-MS. Given these results, it is to be presumed that the physical properties and effective electrochemical characteristics of NCD will allow tailoring devices suitable for many more diagnostic as well as therapeutic applications.

  2. Missing the (question) mark? What is a turn to ontology?

    Science.gov (United States)

    Woolgar, Steve; Lezaun, Javier

    2015-06-01

    Our introductory essay in this journal's 2013 Special Issue on the 'turn to ontology' examined the shift from epistemology to ontology in science and technology studies and explored the implications of the notion of enactment. Three responses to that Special Issue argue that (I) there is no fundamental qualitative difference between the ontological turn and social constructivism, (2) we need to be wary of overly generic use of the term 'ontology' and (3) the language of 'turns' imposes constraints on the richness and diversity of science and technology studies. In this brief reply, we show how each of those critiques varies in its commitment to circumspection about making objective determinations of reality and to resisting reification. We illustrate our point by considering overlapping discussions in anthropology. This brings out the crucial difference between the science and technology studies slogan 'it could be otherwise' and the multinaturalist motto 'it actually is otherwise'.

  3. The late Husserl’s project of science of the life-world

    Directory of Open Access Journals (Sweden)

    Layla Siavoshi

    2016-08-01

    Full Text Available The purpose of this article is to representthe obvious understanding of the challenging concept of a science of the life-world in The Crisis of European Sciences and Transcendental Phenomenology and meaning of this project by Husserl. Hereof, first is very important to perpend distinction and yet relationship between the objective science and the life-world then it seems inevitable to reflect on steps to this transcendental science including epochs of the objective science, epochs ofa science of the life-world and transcendental reduction. Here, the main focus lays onthe possibility of a science of the life-world project with tow attitude a reflective and a non-reflective. In the first attitude be accomplished the universal structures of the life-world in format of anontologyofthe life-world and in the second attitude be discovered on Husserl's transcendental turn on the life-world and its manner-of-givenness the transcendental solidarity between the world and the world consciousness.

  4. Origins of life science teachers' beliefs underlying curriculum reform in Texas

    Science.gov (United States)

    Crawley, Frank E.; Salyer, Barbara A.

    This study explores the beliefs about reform of life science teachers in central Texas who were retained to teach Coordinated Thematic Science I. In particular, we were interested in identifying the beliefs that serve as the foundation for the grade 7 life science teachers' intentions to introduce physical science activities in the life science classes they teach. To accomplish this purpose, we selected four teachers, using purposeful sampling procedures. We also adapted an empirical model for investigating rational decisionmaking, the Theory of Planned Behavior, for use in an interview format. Two additional data sources were used to triangulate our findings set out in seven assertions developed from the 52 pages of transcribed interviews. Our results call attention to the need for all three levels of education - state, district, and school - to cooperate in implementing science curriculum reform in Texas.

  5. Swiss Life Sciences - a science communication project for both schools and the wider public led by the foundation Science et Cité.

    Science.gov (United States)

    Röthlisberger, Michael

    2012-01-01

    The foundation Science et Cité was founded 1998 with the aim to inform the wider Swiss public about current scientific topics and to generate a dialogue between science and society. Initiated as an independent foundation by the former State Secretary for Science and Research, Dr. Charles Kleiber, Science et Cité is now attached to the Swiss Academies of Arts and Sciences as a competence center for dialogue with the public. Due to its branches in all language regions of the country, the foundation is ideally suited to initiate and implement communication projects on a nationwide scale. These projects are subdivided into three categories: i) science communication for children/adolescents, ii) establishing a dialogue between science and the wider public, and iii) conducting the role of a national center of competence and networking in science communication. Swiss Life Sciences is a project that fits into all of these categories: a year-round program for schools is complemented with an annual event for the wider public. With the involvement of most of the major Swiss universities, the Swiss National Science Foundation, the foundation Gen Suisse and many other partners, Swiss Life Sciences also sets an example of national networking within the science communication community.

  6. 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.

  7. Plant phenotype - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available of organs, tissues, development stages. The vocabulary is defined in Plant Ontology(PO). Qualities: Characte...ristics, attributes of entities. The vocabulary is defined in Phenotype Ontology(PATO). Data file File name:

  8. NASA - selected life science experiments for the first NASA/ESA Spacelab flight 1980

    Science.gov (United States)

    Larson, C. A.

    1977-01-01

    Spacelab 1 will carry 17 NASA-sponsored research projects. Seven of these investigations will concern the life sciences. Because of NASA's interest in space motion sickness, two vestibular studies will be conducted. Two other experiments will be concerned with the effects of spaceflight on the hematologic system. The fifth life science study will involve nutations in plant organs. The sixth investigation will examine the effects of the Spacelab environment on circadian rhythms in microorganisms. Finally, cosmic radiation inside the Spacelab will be mapped. These seven life science experiments represent both basic and applied areas of research.

  9. NASA - selected life science experiments for the first NASA/ESA Spacelab flight 1980

    Science.gov (United States)

    Larson, C. A.

    1977-01-01

    Spacelab 1 will carry 17 NASA-sponsored research projects. Seven of these investigations will concern the life sciences. Because of NASA's interest in space motion sickness, two vestibular studies will be conducted. Two other experiments will be concerned with the effects of spaceflight on the hematologic system. The fifth life science study will involve nutations in plant organs. The sixth investigation will examine the effects of the Spacelab environment on circadian rhythms in microorganisms. Finally, cosmic radiation inside the Spacelab will be mapped. These seven life science experiments represent both basic and applied areas of research.

  10. ICP-MS and elemental tags for the life sciences

    Energy Technology Data Exchange (ETDEWEB)

    Giesen, Charlotte

    2012-08-07

    Inductively coupled plasma mass spectrometry (ICP-MS) has been applied for the analysis of biomolecules due to its high sensitivity, wide linear dynamic range, and multielement capabilities. However, outside the elemental MS community the potential of this technique, e.g. for life sciences applications, is not yet fully exploited. Thus, the development of ICP-MS-based (immuno) assays for a wide range of medical (cancer diagnostics, cisplatin toxicity studies), biochemical (DNA microarray, single cell analysis), and environmental (analysis of comestible goods) applications was accomplished by utilization of chemical labels. Laser ablation (LA)-ICP-MS was employed for the direct analysis of solid samples like microarrays and thin tissue sections. An immunoassay was developed for ochratoxin A (OTA) determination in wine, and ICP-MS detection was compared to conventional photometry by gold nanoparticle tagging and horseradish peroxidase, respectively. Detection limits of the assay were optimized to 0.003 {mu}g L{sup -1}, and the quantification range was 0.01-1 {mu}g L{sup -1} for both methods. For LA-ICP-MS-based DNA microarray detection, gold nanoparticle tags were specifically introduced via a streptavidin-biotin linkage. In immunohistochemistry (IHC), up to 20 tumor markers are routinely evaluated for one patient and thus, a common analysis results in a series of time consuming staining procedures. Hence, LA-ICP-MS was elaborated as a detection tool for a novel, multiplexed IHC analysis of tissue sections. Different lanthanides were employed for the simultaneous detection of up to three tumor markers (Her 2, CK 7, and MUC 1) in a breast cancer tissue. Additionally, iodine was employed as a labeling reagent, and a new LA-ICP-MS method for single cell and cell nucleus imaging was developed at 4 {mu}m laser spot size. Iodine was also applied as a new internal standard for tissue samples. Moreover, Pt-protein complexes separated by an optimized 1D and 2D gel

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

    Directory of Open Access Journals (Sweden)

    Andrey Rzhetsky

    2011-09-01

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

  12. War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

    Science.gov (United States)

    Rzhetsky, Andrey; Evans, James A.

    2011-01-01

    The use of structured knowledge representations—ontologies and terminologies—has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies. PMID:21980276

  13. Database Description - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available of Advanced Industrial Science and Technology (AIST) Journal Search: Creator Name...: Motonori Ota Creator Affiliation: Graduate School of Information Sciences, Nagoya University Journal Searc...rai, Kengo Kinoshita, Tamotsu Noguchi, Motonori Ota Journal: Nucleic Acids Research, 2011, Vol. 39, External

  14. Stopping to Squell the "Rhosus": Bringing Science Vocabulary to Life

    Science.gov (United States)

    Shore, Rebecca

    2015-01-01

    A research study conducted in an urban district middle school setting applies cognitive science principles to science vocabulary. Within the context of a personal story told by the lead investigator, the results of the study are shared and suggest that more active, engaging strategies with complex core curriculum may improve retention and…

  15. Educational challenges of molecular life science: Characteristics and implications for education and research.

    Science.gov (United States)

    Tibell, Lena A E; Rundgren, Carl-Johan

    2010-01-01

    Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life-often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from "pure sciences," such as math, chemistry, and physics, through "applied sciences," such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences.

  16. Alien To Me? Science in Search for Life Beyond Earth and Perceptions of Alien Life in Popular Culture

    Science.gov (United States)

    Capova, K. A.

    2013-09-01

    The paper will introduce an original piece of research that is devoted to the socio-cultural aspects of scientifi c search for life in outer space and it draws from doctoral research in anthropology of science. In this piece of research the extraterrestrial life hypothesis is conceptualized as a significant part of the general world-view, constantly shaped by the work and discoveries of science. The paper presents data from qualitative ethnographic fieldwork conducted in the UK as well as uses quantitative data from public from the USA, UK and other countries.

  17. Ontology Based Access Control

    Directory of Open Access Journals (Sweden)

    Özgü CAN

    2010-02-01

    Full Text Available As computer technologies become pervasive, the need for access control mechanisms grow. The purpose of an access control is to limit the operations that a computer system user can perform. Thus, access control ensures to prevent an activity which can lead to a security breach. For the success of Semantic Web, that allows machines to share and reuse the information by using formal semantics for machines to communicate with other machines, access control mechanisms are needed. Access control mechanism indicates certain constraints which must be achieved by the user before performing an operation to provide a secure Semantic Web. In this work, unlike traditional access control mechanisms, an "Ontology Based Access Control" mechanism has been developed by using Semantic Web based policies. In this mechanism, ontologies are used to model the access control knowledge and domain knowledge is used to create policy ontologies.

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

    Directory of Open Access Journals (Sweden)

    Nicola Mulder

    2016-06-01

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

  19. From darwin to the census of marine life: marine biology as big science.

    Science.gov (United States)

    Vermeulen, Niki

    2013-01-01

    With the development of the Human Genome Project, a heated debate emerged on biology becoming 'big science'. However, biology already has a long tradition of collaboration, as natural historians were part of the first collective scientific efforts: exploring the variety of life on earth. Such mappings of life still continue today, and if field biology is gradually becoming an important subject of studies into big science, research into life in the world's oceans is not taken into account yet. This paper therefore explores marine biology as big science, presenting the historical development of marine research towards the international 'Census of Marine Life' (CoML) making an inventory of life in the world's oceans. Discussing various aspects of collaboration--including size, internationalisation, research practice, technological developments, application, and public communication--I will ask if CoML still resembles traditional collaborations to collect life. While showing both continuity and change, I will argue that marine biology is a form of natural history: a specific way of working together in biology that has transformed substantially in interaction with recent developments in the life sciences and society. As a result, the paper does not only give an overview of transformations towards large scale research in marine biology, but also shines a new light on big biology, suggesting new ways to deepen the understanding of collaboration in the life sciences by distinguishing between different 'collective ways of knowing'.

  20. From darwin to the census of marine life: marine biology as big science.

    Directory of Open Access Journals (Sweden)

    Niki Vermeulen

    Full Text Available With the development of the Human Genome Project, a heated debate emerged on biology becoming 'big science'. However, biology already has a long tradition of collaboration, as natural historians were part of the first collective scientific efforts: exploring the variety of life on earth. Such mappings of life still continue today, and if field biology is gradually becoming an important subject of studies into big science, research into life in the world's oceans is not taken into account yet. This paper therefore explores marine biology as big science, presenting the historical development of marine research towards the international 'Census of Marine Life' (CoML making an inventory of life in the world's oceans. Discussing various aspects of collaboration--including size, internationalisation, research practice, technological developments, application, and public communication--I will ask if CoML still resembles traditional collaborations to collect life. While showing both continuity and change, I will argue that marine biology is a form of natural history: a specific way of working together in biology that has transformed substantially in interaction with recent developments in the life sciences and society. As a result, the paper does not only give an overview of transformations towards large scale research in marine biology, but also shines a new light on big biology, suggesting new ways to deepen the understanding of collaboration in the life sciences by distinguishing between different 'collective ways of knowing'.