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Biomedical ontologies: a functional perspective
2007
Briefings in Bioinformatics
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The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspectiveçdescribing how bio-ontologies can and are being used. ...
Shah is a research scientist at the Stanford Center for Biomedical Informatics group and member of the National Center for Biomedical Ontology. ...
Acknowledgements This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health. ...
doi:10.1093/bib/bbm059
pmid:18077472
fatcat:z3orlk75yzherjf37i3nehqlmm
The role of ontologies in biological and biomedical research: a functional perspective
2015
Briefings in Bioinformatics
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Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. ...
Ontologies are widely used in biological and biomedical research. ...
A functional perspective on ontologies
Classes and relations The principal components of ontologies are classes and relations. ...
doi:10.1093/bib/bbv011
pmid:25863278
pmcid:PMC4652617
fatcat:je3d5kdab5fhnkm3ni3t5xskgq
Functional Parthood: A Dispositional Perspective
2020
Joint Ontology Workshops
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In this paper we sketch out a project to develop a dispositional approach to functional parthood based on a dispositional account of functions and a theory of parthood between dispositions. ...
Functional parthood is relevant to the modeling of material objects and their complex interrelationships. ...
Purpose and methodology In this paper we will outline a "dispositional perspective" on functional parthood. This proposal is motivated by further development of biological and biomedical ontologies. ...
dblp:conf/jowo/ToyoshimaBE20
fatcat:nqxtabdbizdsllitvfga7t46qi
BIOMEDICAL ONTOLOGIES
2003
Biocomputing 2004
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The remaining papers have a somewhat different perspective on biomedical ontologies. ...
A first group of papers investigates foundational issues in biomedical ontology as well as the creation of ontological resources. ...
doi:10.1142/9789812704856_0016
fatcat:d7jq5kpm4fbpnklzbszvuvcgry
Biomedical ontologies
2005
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
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Similarly, a large number of papers presented at the 12 th conference on Intelligent Systems for Molecular Biology (ISMB/ECCB 2004) focused on some aspect of biomedical ontology. ...
In fact, biomedical ontologies play a central role in integrating the information about various model organisms, acquired under different conditions and stored in heterogeneous databases. ...
The remaining papers have a somewhat different perspective on biomedical ontologies. ...
pmid:15759615
pmcid:PMC4300097
fatcat:ctcrtebzr5aqth2lnikub7cgau
Biomedical Ontologies - Session Introduction
2003
Pacific Symposium on Biocomputing
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Existing and yet to be developed biomedical ontologies play a critical role in this effort. ...
Controlled vocabularies define a set of terms to be used for a given purpose (e.g., indexing the literature, annotating gene functions). ...
dblp:conf/psb/BodenreiderMM03
fatcat:4zjirqgg3jhrvdl5otdra2f3kq
Semantic Similarity in Biomedical Ontologies
2009
PLoS Computational Biology
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In recent years, ontologies have become a mainstream topic in biomedical research. ...
Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application ...
of the depth, neither of which is true for existing biomedical ontologies. ...
doi:10.1371/journal.pcbi.1000443
pmid:19649320
pmcid:PMC2712090
fatcat:otsulomg2vgi7oipbu4usf273a
Open Biomedical Ontology-based Medline exploration
2009
BMC Bioinformatics
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trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most ...
It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. It is freely accessible at: ...
From a use case perspective, rather than "the more function the better," it is "the driving principle is the more suitable the better". ...
doi:10.1186/1471-2105-10-s5-s6
pmid:19426463
pmcid:PMC2679406
fatcat:6tlpqsg34zaqbophjqaurnudey
Ontology-Aware Biomedical Relation Extraction
[article]
2022
bioRxiv
pre-print
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We demonstrate that entity type and ontology graph structure provide better representations than simple token-based representations for RE. ...
Motivation: Automatically extracting relationships from biomedical texts among multiple sorts of entities is an essential task in biomedical natural language processing with numerous applications, such ...
From a broad perspective, word embeddings can be of two types, namely static or dynamic. ...
doi:10.1101/2022.03.22.485304
fatcat:p5z2rsfzsnh4pgtenhx47k4fwi
Integrating an Ontology for RDOC with Existing Biomedical Ontologies
2017
International Conference on Biomedical Ontology
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with current biomedical ontologies. ...
We expand our previous analysis of the RDoC matrix and introduce an ontological representation of the Constructs, the RDoC Ontology (RDoCOn), that provides a method for incorporating the RDoC framework ...
and members of the University at Buffalo Department of Biomedical Informatics. ...
dblp:conf/icbo/JensenD17
fatcat:bhx2ue7bczbipbwpiyopa5tmy4
Putting Biomedical Ontologies to Work
2010
Methods of Information in Medicine
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is a prerequisite. ...
Objectives: Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. ...
Ontology). ...
doi:10.3414/me9302
pmid:20135080
pmcid:PMC3116518
fatcat:eg3yrvchenfrfkinglyoxz7rki
Orienteering Tools: Biomedical Research with Ontologies
2016
Humana.Mente: Journal of Philosophical Studies
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Biomedical ontologies are considered a serious innovation for biomedical research and clinical practice. ...
Due to the analysis of some empirical cases I try to elaborate how biomedical ontologies constitute a novelty also from an epistemological point of view. ...
(such as gene function prediction), offering different and unusual perspectives. ...
doaj:2debdd18503a4c1a9f17c8005a9dd99c
fatcat:7g3aidf4lrd2nlrg74uu67ymvu
Evaluation of research in biomedical ontologies
2012
Briefings in Bioinformatics
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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 ...
the objective evaluation and comparison of research results in applied ontology. ...
From the perspective of an ontology user, we then discuss the problem of the 'research question' of biomedical ontology, i.e. what is the 'scientific' problem that research in biomedical ontology addresses ...
doi:10.1093/bib/bbs053
pmid:22962340
pmcid:PMC3888109
fatcat:lyepy5en5vfpzgbq6uaaxr7aiu
Formal Ontologies in Biomedical Knowledge Representation
2013
IMIA Yearbook of Medical Informatics
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Results: We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and ...
Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. ...
Acknowledgements Research for this paper has been supported for both authors by the German Research Agency (DFG) under the auspices of the project Good Ontology Design (GoodOD), JA 1904/2-1, SCHU 2515/ ...
doi:10.1055/s-0038-1638845
fatcat:7v3wlgogcnf5nawigdd5cueddu
Ontology Support for Biomedical Information Resources
2008
2008 21st IEEE International Symposium on Computer-Based Medical Systems
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The importance of ontologies has been recognised within the biomedical domain and work has begun on developing and sharing biomedical ontologies. ...
Ontologies are highly expressive knowledge models and as such increase expressiveness and intelligence of a system. ...
Ontology design is an art in itself; it needs to be done by a number of domain experts and ontology engineers. Different perspectives need to be considered during the ontology design. ...
doi:10.1109/cbms.2008.21
dblp:conf/cbms/DillonCH08
fatcat:rpgo3dhtfva67feujl3tfthb6q
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