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Ontologies in Amine Platform: Structures and Processes [chapter]

Adil Kabbaj, Karim Bouzouba, Khalid El Hachimi, Nabil Ourdani
2006 Lecture Notes in Computer Science  
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

Charlie Mayor, Lyn Robinson
2014 Journal of the Association for Information Science and Technology  
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  
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

Ted Goranson, Beth Cardier, Keith Devlin
2015 Progress in Biophysics and Molecular Biology  
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

Michael W. Caldwell
1997 Nature  
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

Daniel L Cook, Jose L V Mejino, Cornelius Rosse
2004 Studies in Health Technology and Informatics  
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

Peter J. Boettke, Christopher J. Coyne, John Davis, Francesco Guala, Alain Marciano, Jochen Runde, Margaret Schabas
2006 Economic Journal  
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

Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot (+62 others)
2015 PLoS Biology  
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

Barry Smith, David M. Mark
2001 International Journal of Geographical Information Science  
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]

David Mark, Barry Smith
2006 Classics from IJGIS  
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

Yorick Wilks, Christopher Brewster
2007 Foundations and Trends® in Web Science  
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

David Rousseau, Julie Billingham, Javier Calvo-Amodio
2018 Systems  
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

Emanuele Bottazzi, Carola Catenacci, Aldo Gangemi, Jos Lehmann
2006 Cognitive Systems Research  
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

Marsonet Michele
2021 Academicus : International Scientific Journal  
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

Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek, Paolo Romano
2014 BMC Bioinformatics  
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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