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Ontologies in Amine Platform: Structures and Processes
[chapter]
2006
Lecture Notes in Computer Science
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A resolution of this conflict is proposed, where Ontology is considered as a special case of CK (i.e. a formal CK). ...
By this "rehabilitation" of Ontology to "CK Base", we extend "by the way" the meaning and scope of Ontology to include "CK-based Ontology". ...
They have developed also "Domain-specific Ontologies" like "Ontology for Physics", "Ontology for Biology", "Ontology for Medicine", "Ontology for Math", etc. as well as "Ultra-domain-specific Ontologies ...
doi:10.1007/11787181_22
fatcat:thulxdf2tvgebh72hmkb5e3xhm
Ontological realism and classification: Structures and concepts in the Gene Ontology
2014
Journal of the Association for Information Science and Technology
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The Gene Ontology (hereafter GO) is such a formal vocabulary, which is used for the indexing of gene products from any species. ...
It has been widely used in molecular biology research for more than a decade; the PubMed database had more than 5,000 references to the GO, and its applications, at the beginning of 2013, and the initial ...
The OBO Foundry and its members adhere to a set of principles for ontology development (OBO Foundry 2011), grounded in the framework of Basic Formal Ontology (BFO) which offers an extended philosophical ...
doi:10.1002/asi.23057
fatcat:r7ba7ulm3rgvjbqn6io5jcgnya
Old companions who learn new tricks
1997
Nature
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Topics covered include basic ontology (the nature of events, properties and things), the interpretation of the probability calculus and the nature of truth and evidence. ...
The biologist J. H. Woodger is remembered for his attempts to make biology live up to this ideal. ...
doi:10.1038/38435
fatcat:qitec3n2fjhe3iir5nn6hmunya
Pragmatic phenomenological types
2015
Progress in Biophysics and Molecular Biology
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The intent is to further practical tools that can be used in the clinical context. An example proposes a formal type system that would support this kind of reasoning, including in machines. ...
We approach a well-known problem: how to relate component physical processes in biological systems to governing imperatives in multiple system levels. ...
Acknowledgements This paper has been greatly improved by suggestions from anonymous reviewers plus input from the editors and other associates. ...
doi:10.1016/j.pbiomolbio.2015.07.006
pmid:26196088
fatcat:grmeumnxwbbwvkqmqvohyofbta
Fins, legs, fins
1997
Nature
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Topics covered include basic ontology (the nature of events, properties and things), the interpretation of the probability calculus and the nature of truth and evidence. ...
The biologist J. H. Woodger is remembered for his attempts to make biology live up to this ideal. ...
doi:10.1038/38438
fatcat:oaihxf6hzbbtje6c7vncpetkwu
Evolution of a Foundational Model of Physiology: symbolic representation for functional bioinformatics
2004
Studies in Health Technology and Informatics
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We describe the need for a Foundational Model of Physiology (FMP) as a reference ontology for "functional bioinformatics". ...
The FMP will serve as a symbolic representation of biological functions initially pertaining to human physiology and ultimately extensible to other species. ...
This work was supported in part by grant GM064433 from the National Institute of General Medical Sciences of the NIH. ...
pmid:15360830
fatcat:sji2syxncnaz5imxwy7lfnh5p4
Where Economics and Philosophy Meet: Review of the Elgar Companion to Economics and Philosophy with Responses from the Authors
2006
Economic Journal
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In the philosophy of science ontology has arguably always been a key area of research, under the guise of ÔThe foundations of . . .Õ (physics, biology, chemistry etc.). ...
Research, the Laboratory for Ontology in Turin, the Institute for Formal Ontology and Medical Information Science in Saarland). ...
doi:10.1111/j.1468-0297.2006.01101.x
fatcat:jr22x5pznrfindapjznwcrxiri
Finding Our Way through Phenotypes
2015
PLoS Biology
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Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. ...
The lack of a community-wide, consensusbased, human-and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck ...
For epidemiological studies, environment may refer to features in the physical proximity, such as to a nuclear plant, or relate to prior personal behavior, such as a history of smoking. ...
doi:10.1371/journal.pbio.1002033
pmid:25562316
pmcid:PMC4285398
fatcat:5reifkvhcnh53ab6cv44ewlrba
Geographical categories: an ontological investigation
2001
International Journal of Geographical Information Science
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The data suggest, rather, a special role in determining the subject-matter of scienti c geography for the concept of what can be portrayed on a map. ...
The results yield an ontology of geographical categories-a catalogue of the prime geospatial concepts and categories shared in common by human subjects independently of their exposure to scienti c geography ...
We also wish to thank the student subjects and their instructors for participating in the study. ...
doi:10.1080/13658810110061199
fatcat:rilnuwhh3bb4lcfkpujllnhgqa
Geographical Categories
[chapter]
2006
Classics from IJGIS
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The data suggest, rather, a special role in determining the subject-matter of scienti c geography for the concept of what can be portrayed on a map. ...
The results yield an ontology of geographical categories-a catalogue of the prime geospatial concepts and categories shared in common by human subjects independently of their exposure to scienti c geography ...
We also wish to thank the student subjects and their instructors for participating in the study. ...
doi:10.1201/9781420006377.ch19
fatcat:ohksxzemwrbahlmddfymkinx3a
Natural Language Processing as a Foundation of the Semantic Web
2007
Foundations and Trends® in Web Science
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Acknowledgments CB would like to thank José Iria for help in discussing and formulating the Abraxas model, and Ziqi Zhang for undertaking parts of the implementation and evaluation. ...
Our thanks also to Kieron O'Hara and Wendy Hall for comments, discussion and aid with editing. ...
Ontological Basics: A Reminder Before proceeding to the core of the paper, let us just remind ourselves again of the basic vocabulary for stating the problem: the initial issue in structuring an ontology ...
doi:10.1561/1800000002
fatcat:n2xfw3qdhverrokidb2globwyq
Systemic Semantics: A Systems Approach to Building Ontologies and Concept Maps
2018
Systems
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To this end, this paper lays the groundwork for a community effort to develop an 'Ontology of Systemology'. ...
The outcome of this paper is therefore twofold: We show the value in applying a systems perspective to ontology development in any discipline, and we provide a starting outline for an Ontology of Systemology ...
Acknowledgments: We would like to thank the two anonymous reviewers of this paper for their helpful comments, which have greatly aided us in improving the structure and clarity of this paper. ...
doi:10.3390/systems6030032
fatcat:f5n5rmfb6vd6jea7anrimo4ujy
From collective intentionality to intentional collectives: An ontological perspective
2006
Cognitive Systems Research
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Moreover, and less trivially, it involves a multiplicity of non- a formal-ontological account of the notion of collection in terms of what defined in section
agentive physical entities and a number ...
In our ontology, this formally amounts to have at least physical, individual agents (like human beings); cf. ...
doi:10.1016/j.cogsys.2005.11.009
fatcat:vqao5i72ibbixjuvyow2toe36a
Language and Idealism
2021
Academicus : International Scientific Journal
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Within this field, the techniques of contemporary formal logic are exalted because they allow us to build artificial languages which - at least theoretically - eliminate the ambiguities of everyday speech ...
In the philosophical inquiry adopted by logical empiricists, analysis of scientific language becomes something similar to a metaphysical endeavor which is meant to establish the bounds of sense, and this ...
Our standard for appraising basic changes of conceptual scheme must be, not a realistic standard of correspondence to reality, but a pragmatic standard (on this theme see Duhem). ...
doi:10.7336/academicus.2021.23.10
fatcat:uoqgwnybhzh3fd7hiuw44bp36i
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
2014
BMC Bioinformatics
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Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. ...
Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. ...
to unicellular, animal, and plant science", a EU FP7 ...
doi:10.1186/1471-2105-15-s1-s2
pmid:24564249
pmcid:PMC4015876
fatcat:xv4pyzwxtnfnjhquglv4j4lpna
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