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Levels and building blocks—toward a domain granularity framework for the life sciences

Lars Vogt
2019 Journal of Biomedical Semantics  
As a consequence, there is an increasing need for an integrated system of hierarchies of levels of different types of material entities that helps with organizing, structuring and integrating data from  ...  With the emergence of high-throughput technologies, Big Data and eScience, the use of online data repositories and the establishment of new data standards that require data to be computer-parsable become  ...  Author's contributions LV: developed the particular building blocks approach, the different granularity perspectives and their relations with one another, and drafted the manuscript.  ... 
doi:10.1186/s13326-019-0196-2 pmid:30691505 pmcid:PMC6348634 fatcat:ep4u4xjbdjfnxoxv6apyk6oogq

Developing educational software components

J. Roschelle, C. DiGiano, M. Koutlis, A. Repenning, J. Phillips, N. Jackiw, D. Suthers
1999 Computer  
AgentSheets was funded by the National Science Foundation DMI-9761360, RED9253425, REC 9804930, and DARPA CDA 940860. The DARPA CAETI program also funded Belvedere.  ...  E-Slate has been funded by projects IMEL, EC DGXXII, Socrates 25136-CP-1-96-1-GR-ODL; YDEES (EU Support Framework II, Greek Ministry of Industry Energy and Technology, General Secretariat for R&D, Measure  ...  Determining Component Granularity and Connectivity Manolis Koutlis and Jeremy Roschelle How can component developers identify the correct size of component building blocks for a given domain?  ... 
doi:10.1109/2.789751 fatcat:vow5hvzb7fegbg6wnmqq3x5tzq

Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology

Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus, Niall James Haslam
2011 PLoS ONE  
This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology.  ...  The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy.  ...  It goes without saying, however, that we are solely responsible for all the arguments and statements in this paper.  ... 
doi:10.1371/journal.pone.0018794 pmid:21533043 pmcid:PMC3080885 fatcat:jlu25mbyyngrriw33llhkphbtu

BY-COVID - Metadata standards. Documentation on metadata standards for inclusion of resources in data portal

Hennig Hermjakob, Mari Kleemola, Katja Moilanen, Susanna-Assunta Sansone, Allyson Lister, Romain David, Maria Panagiotopoulou, Christian Ohnmann, Jeroen Bellen, Julia Lischke, Nick Juty, Stian Soiland-Reyes
2022 Zenodo  
This work establishes the basis for the further development of the COVID-19 Portal metadata discovery and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as  ...  BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards  ...  level and describes building blocks for a framework for cross-domain metadata interoperability.  ... 
doi:10.5281/zenodo.6885015 fatcat:qvb5qiwezjhtbe625xysoq73qe

A review on E-business Interoperability Frameworks

Reza Rezaei, Thiam Kian Chiew, Sai Peck Lee
2014 Journal of Systems and Software  
This paper describes the existing interoperability frameworks for e-business, and performs a comparative analysis among their findings to determine the similarities and differences in their philosophy  ...  This analysis yields a set of recommendations for any party that is open to the idea of creating or improving an E-business Interoperability Framework.  ...  Acknowledgement This research is funded by the University of Malaya Research Grant (UMRG) RG055-11ICT.  ... 
doi:10.1016/j.jss.2014.02.004 fatcat:ysatsiyfqrfxpmrnpujzyah3bi

Psychological Resilience and Positive Emotional Granularity: Examining the Benefits of Positive Emotions on Coping and Health

Michele M. Tugade, Barbara L. Fredrickson, Lisa Feldman Barrett
2004 Journal of Personality  
We use the broaden-and-build theory of positive emotions (Fredrickson, 1998; as a framework to demonstrate that positive emotions contribute to psychological and physical well-being via more effective  ...  For centuries, folk theory has promoted the idea that positive emotions are good for your health. Accumulating empirical evidence is providing support for this anecdotal wisdom.  ...  Next, we introduce the broaden-and-build theory (Fredrickson, 1998; as a framework to demonstrate the functional utility of positive emotions in health.  ... 
doi:10.1111/j.1467-6494.2004.00294.x pmid:15509280 pmcid:PMC1201429 fatcat:stq52r72mrbhblbzkqg5eh6pk4

Ontologies for the life sciences [chapter]

Steffen Schulze-Kremer, Barry Smith
2005 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics.  ...  A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain.  ...  The degree of abstraction and detail one chooses to adopt in building an ontology of a given domain at a given level of granularity determines the practical quality of the ontology which results, in a  ... 
doi:10.1002/047001153x.g408213 fatcat:slqplkfx2fdcll6tnpwnzzxed4

Ontologies for the Life Sciences [chapter]

2013 Encyclopedia of Systems Biology  
The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics.  ...  A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain.  ...  The degree of abstraction and detail one chooses to adopt in building an ontology of a given domain at a given level of granularity determines the practical quality of the ontology which results, in a  ... 
doi:10.1007/978-1-4419-9863-7_101069 fatcat:vjn5aclbyrdjdio33sbnjsyuv4

Towards Intelligent Context-Aware 6G Security [article]

André N. Barreto, Stefan Köpsell, Arsenia Chorti, Bertram Poettering, Jens Jelitto, Julia Hesse, Jonathan Boole, Konrad Rieck, Marios Kountouris, Dave Singelee, Kumar Ashwinee
2021 arXiv   pre-print
The path towards this vision and some of the challenges along the way are discussed in this contribution.  ...  In this paper we put forward a roadmap towards the realization of a new security paradigm that we articulate as intelligent context-aware security.  ...  System architecture for quantifiable security In this section we propose the architecture of a context-aware security solution and its main building blocks.  ... 
arXiv:2112.09411v1 fatcat:ynadpp5oobh4dpmz7ku2tgaklu

SNAP and SPAN: Towards Dynamic Spatial Ontology

Pierre Grenon, Barry Smith
2004 Spatial Cognition and Computation  
Finally we apply our framework to the domain of geography, culminating in the outline of an ontologically well-founded and comprehensive dynamic geospatial ontology.  ...  light of the interconnections between them. of accounting for spatial reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are two different  ...  Thanks go to the anonymous referees of this journal for insightful comments and to Mike Worboys for his encouragement and support.  ... 
doi:10.1207/s15427633scc0401_5 fatcat:s7csmzanb5cexcqmkqrcjywolm

A context-sensitive conceptual framework for activity modeling

Rahul Deb Das, Stephan Winter
2016 Journal of Spatial Information Science  
Similarly activities at coarser spatial and temporal granularity, e.g., "holidaying in a country," could be recognized in some context or domain.  ...  Three case studies will illustrate how the semantics of the term activity changes based on scale and context. They provide evidence that the framework holds over different domains.  ...  Acknowledgments This research has been supported by a grant from the Australian Research Council, LP120200130.  ... 
doi:10.5311/josis.2016.12.260 fatcat:bdc7uruqgbcvnjljb3xvsarf5i

From a Comprehensive Pool to a Project-Specific List of Key Performance Indicators for Monitoring the Positive Energy Transition of Smart Cities—An Experience-Based Approach

Komninos Angelakoglou, Konstantinos Kourtzanidis, Paraskevi Giourka, Vasilis Apostolopoulos, Nikos Nikolopoulos, Julia Kantorovitch
2020 Smart Cities  
the KPI pool, leading to a ready-to-be-used, project-specific list of 63 KPIs and d) KPIs were sorted and analyzed in different granularity levels to further facilitate the monitoring procedure.  ...  ; Question 2: "Which of those KPIs are the most suitable for assessing the energy transition of smart city projects and PED-related developments?"  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/smartcities3030036 fatcat:pild2jltbzeqfo7qqxsclxmh5m

Towards industrial strength philosophy: how analytical ontology can help medical informatics

Barry Smith, Werner Ceusters
2003 Interdisciplinary Science Reviews  
Medicine is a domain which can sustain classifications reflecting causally relevant distinctions at more than one level of granularity.  ...  Its implementation as a top-level or "backbone" ontology for LinkBase will thus not only provide a more robust framework for the clarification of existing ambiguities and discrepancies in and between ontologies  ... 
doi:10.1179/030801803225010421 fatcat:u6tybiqgezaxznkcs7znkzstzy

Business Object Component Architecture

T. Digre
1998 IEEE Software  
In this context, components embody the semantics of a target problem domain, isolated from the complexities that underlie distributed object technology.  ...  lobal competition and the shift from commodity to short-life-cycle or custom products have created an environment of continuous change.  ...  Semantic primitives Semantic primitives are the building blocks for domain objects. They include, for example, rules and the kinds of relationships between objects.  ... 
doi:10.1109/52.714818 fatcat:ajraxds7jbfalc63ob6to5cwfu

Scientific workflows with the jABC framework

Anna-Lena Lamprecht, Bernhard Steffen, Tiziana Margaria
2016 International Journal on Software Tools for Technology Transfer (STTT)  
The jABC is a framework for process modelling and execution according to the XMDD (eXtreme Model-Driven Design) paradigm, which advocates the rigorous use of user-level models in the software development  ...  We then derive and discuss ongoing further developments and future perspectives for the framework, all with an emphasis on simplicity for end-users through increased domain specificity.  ...  We also thank Alexander Wickert for his assistance in the process modelling courses and for his contributions to the service usage analysis functionality of jABCstats.  ... 
doi:10.1007/s10009-016-0427-0 fatcat:c76uhol7tfbivo7zr7wnz7sixi
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