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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  
classifications and ontologies, particularly MeSH and examples in Open Biological and Biomedical Ontologies collection [http://www.obofoundry.org].  ...  We now go on to briefly describe the gene ontology itself, and then to analyse its structure, based on a variety of sources.  ...  Ontological realism Ontologies are representations of domain knowledge, of concepts in a domain, captured in a structured language amenable to computer processing.  ... 
doi:10.1002/asi.23057 fatcat:r7ba7ulm3rgvjbqn6io5jcgnya

Scientific realism and philosophical naturalism in Šmajs' evolutionary ontology

Inéz Melichová, Robert Burgan
2013 Human Affairs  
Šmajs' concept of evolutionary ontology has attracted much attention in recent years especially in Czech and Slovak academic circles, yet it remains, as some of its proponents claim, undervalued in Britain  ...  Even in the Czech Republic and Slovakia, there are, in addition to its strong supporters, several authors who almost a priori reject the concept, pointing to several questionable, contradictory or even  ...  Scientific realism and philosophical naturalism Having introduced Šmajs' evolutionary ontology and its most important concepts (or ideas) in detail, we can now go on to describe the philosophical "background  ... 
doi:10.2478/s13374-013-0149-x fatcat:5c5ag455qnerndlmt5vlufvexy

A realism-based approach to an ontological representation of symbiotic interactions

Matthew Diller, Evan Johnson, Amanda Hicks, William R. Hogan
2020 BMC Medical Informatics and Decision Making  
Results We found one definition of 'symbiosis' in an existing ontology that was consistent with the vast preponderance of scientific usage in biology and ecology.  ...  Conclusion As a result of our efforts here, we have developed a robust representation of symbiotic interactions using a realism-based approach, which fills a gap in existing biomedical ontologies.  ...  Authors' contributions MD helped with reviewing the literature on usage of 'symbiosis' and related terms, helped with the ontology definitions and axioms, conducted the referent tracking analysis, and  ... 
doi:10.1186/s12911-020-01273-0 pmid:33032576 pmcid:PMC7542735 fatcat:ot6ng5xqz5e2tpqwlvj4yaorwq

Epistemology, Theory, and Methodology in Knowledge Organization: Toward a Classification, Metatheory, and Research Framework

Joseph T. Tennis
2008 Knowledge organization  
Information organization is the process of ordering and representing information, which comprises documents and other entities considered information, for example representations of genes in the Gene Ontology  ...  This construct not only accounts for the structures present in regimes of information organization (e.g., classification schemes, bibliographic records, etc.), but also the discourse that surrounds and  ...  For example many of the best minds in philosophy and biology are turning their attention to ontology engineering, and crafting research which appears similar to KO work, but when compared against the classification  ... 
doi:10.5771/0943-7444-2008-2-3-102 fatcat:atmj2yvjj5fznmyn5s4fltiidy

Ontology: Several Theories on the Representation of Knowledge Domains

Maria Luiza de Almeida Campos, Hagar Espanha Gomes
2017 Knowledge organization  
Hagar Espanha Gomes holds a degree in librarianship and documentation from the National Library Foundation, specializing in master's and bibliographic research by the Brazilian Institute of Bibliography  ...  and Documentation, and a MSc in Documentation.  ...  One of the most operative initiatives in the field is the group Gene Ontology Consortium (2015) that gathers several ontologies, including the popular Gene Ontology (GO).  ... 
doi:10.5771/0943-7444-2017-3-178 fatcat:w5efov33pnbm3fytfrlsj2hcdi

Pre-theoretical aspects of Aristotelian definition and classification of animals: The case for common sense

Scott Atran
1985 Studies in History and Philosophy of Science Part A  
Accordingly, in an effort to preserve common sense realism and the Greek conception of ultimate unity, Aristotle sought an explanation of the common sense notion of natural causality for natural kind9'  ...  Exolanatory Structures: Concepts of Explanation in Early Physics and Philosophy (Atlantic Highlands, New Jersey: Humanities, ~1978). p. 95. "Cf. G.  ...  Rather, he aimed to improve our understanding of the uorld as we ordinarily see it, and know it to be -not by refuting 'naive realism', but by simplifying it.  ... 
doi:10.1016/0039-3681(85)90010-x fatcat:6phonsadtrbynihzourefbhic4

Realist Representation of the Medical Practice: an Ontological and Epistemological Analysis

André Queiroz de Andrade, Mauricio Barcellos Almeida
2011 Joint Seminar on Ontology Research in Brazil / International Workshop on Metamodels, Ontologies and Semantic Technologies  
We classified the entities and found several entities that cannot be represented in realist ontologies.  ...  Realist ontologies organize knowledge by strict adherence to philosophical principles, ensuring robustness and coherence.  ...  In the BFO, adopted in the ontological realism stance, we can find structuring divisions made by generic universals called continuants and occurrents.  ... 
dblp:conf/ontobras/AndradeA11 fatcat:yh4nmdnoifae5cx6oa535ypzwe

In defence of classification

John Dupré
2001 Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences  
This perspective fits well with the increasing tendency to reject the search for a monistic basis of classification and embrace a pluralistic and pragmatic account of the species category.  ...  After briefly defending the necessity of this distinction I argue, contrary to the prevailing orthodoxy, that species should be treated as the fundamental units of classification and not, therefore, as  ...  Let me finally say something about the question of realism.  ... 
doi:10.1016/s1369-8486(01)00003-6 fatcat:bnhitnjj3rffvc4eou37i7n5ba

Information Retrieval and Knowledge Organization: A Perspective from the Philosophy of Science

Birger Hjørland
2021 Information  
The classification of documents in KO mostly aims at reflecting the classification of knowledge in the sciences.  ...  No IR technology and no system of knowledge organization can ever be neutral in relation to paradigmatic conflicts, and therefore such philosophical problems represent the basis for the study of IR and  ...  Acknowledgments: The author thanks the three anonymous reviewers for fine reviews, two of which increased the quality of the article.  ... 
doi:10.3390/info12030135 fatcat:vvz7tdbyqjgmra2bz6j4zvg7yq

Towards an Ontology for Representing Malignant Neoplasms

William D. Duncan, Carmelo Gaudioso, Alexander D. Diehl
2017 International Conference on Biomedical Ontology  
In order to conduct effective cancer research, terminologies, classification systems, and ontologies are needed that can integrate these various datasets and provide standards for consistently representing  ...  This ontology is being built using the principles of the OBO Foundry, and makes use of other OBO Foundry ontologies, such as the Ontology for General Medical Sciences, Uberon, and the Cell Ontology.  ...  William Duncan and Carmelo Gaudioso received support from the Clinical Data Network, a Roswell Park Cancer Institute Cancer Center Support Grant shared resource funded by NCI P30CA16056.  ... 
dblp:conf/icbo/DuncanGD17 fatcat:twc5or5h5naaxko43av7tfpxiu

Disease Ontology: a backbone for disease semantic integration

L. M. Schriml, C. Arze, S. Nadendla, Y.-W. W. Chang, M. Mazaitis, V. Felix, G. Feng, W. A. Kibbe
2011 Nucleic Acids Research  
The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease.  ...  The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g.  ...  ACKNOWLEDGEMENTS The authors would like to thank the past and current members of the DO Advisory Board: Michael Ashburner, Judith Blake, Rex Chisholm, Suzanna Lewis, Maryann Martone, Chris Mungall, Alan  ... 
doi:10.1093/nar/gkr972 pmid:22080554 pmcid:PMC3245088 fatcat:cmishce3ejfhrknokmbn7abhqy

IMIA LaMB WG event: 'Biomedical Semantics in the Big Data Era', Workshop at MEDINFO 2015 – São Paulo,Brazil

Roland Cornet, Stephane Meystre, Stefan Schulz, Patrick Ruch, Tomasz Adamusiak, Laszlo Balkanyi, Jianying Hu
2019 Zenodo  
The workshop of IMIA WG 'Language and Meaning in Biomedicine' was held at MEDINFO 2015 – São Paulo,Brazil.  ...  This document set document has (1) all the presentation materials: - Introduction, by Ronald Cornet - From free text to ontology, by Stephane Meystre - Bridging natural and formal languages for representing  ...  Gene function curation of the literature with Gene Ontology (GO) concepts is one particularly time-consuming task in genomics, and the help from bioinformatics is highly requested to keep up with the flow  ... 
doi:10.5281/zenodo.3398964 fatcat:ksn3rajzs5earbjd3kczdvrwdi

Can an Ontologically-Oriented KO Do Without Concepts? [chapter]

Luís Machado, Graça Simões, Claudio Gnoli, Renato Souza
2020 Knowledge Organization at the Interface  
In both systems the use of concepts is considered instrumental, although in the ILC they constitute the intersubjective component of the phenomena whereas in BFO they serve to access the entities of reality  ...  The study aims to compare the ontological approaches of BFO and ILC using a hermeneutic approach.  ...  As an area of study, ontology focuses on how reality is constituted and structured using concepts.  ... 
doi:10.5771/9783956507762-502 fatcat:5vu4ngux2jetblzito6dki7kvy

IMIA WG LaMB event: 'Biomedical Semantics in the Big Data Era', Workshop at MEDINFO 2015 – São Paulo,Brazil

Roland Cornet, Stephane Meystre, Stefan Schulz, Patrick Ruch, Tomasz Adamusiak, Laszlo Balkanyi, Jianying Hu
2019 Zenodo  
The workshop of IMIA WG 'Language and Meaning in Biomedicine' was held at MEDINFO 2015 – São Paulo,Brazil.  ...  This document has all the presentation materials: - Introduction, by Ronald Cornet - From free text to ontology, by Stephane Meystre - Bridging natural and formal languages for representing knowledge and  ...  Gene Ontology concepts such as "MyD88-dependent toll-like receptor signaling pathway" … can be found in no corpora … only in Swiss-Prot !  ... 
doi:10.5281/zenodo.3381015 fatcat:lkccddww7raefbwppmtfzedcgq

A Realist Framework for Ontologies and the Semantic Web

Sanju Mishra, Sonika Malik, N.K. Jain, Sarika Jain
2015 Procedia Computer Science  
The realist approach in Ontology Engineering speaks about representing concepts in reality that science wants to uncover.  ...  The EHCPR specification is quite close to the representation of entities in the real world. The representational units in the EHCPRs ontology map one by one to the realist framework.  ...  Conclusions Key research issues of any research groups are interoperability and information exchange. The proposed scheme uses the concept of EHCPR as a realist framework for ontologies.  ... 
doi:10.1016/j.procs.2015.10.087 fatcat:ysvg5w2kbraf5lflc5bewxyix4
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