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Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
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

R. Hoehndorf, P. N. Schofield, G. V. Gkoutos
2015 Briefings in Bioinformatics  
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

Fumiaki Toyoshima, Adrien Barton, Jean-François Ethier
2020 Joint Ontology Workshops  
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


2003 Biocomputing 2004  
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

O Bodenreider, J A Mitchell, A T McCray
2005 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
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

Olivier Bodenreider, Joyce A. Mitchell, Alexa T. McCray
2003 Pacific Symposium on Biocomputing  
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

Catia Pesquita, Daniel Faria, André O. Falcão, Phillip Lord, Francisco M. Couto, Philip E. Bourne
2009 PLoS Computational Biology  
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

Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson, Fan Meng
2009 BMC Bioinformatics  
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]

Ahmad Aghaebrahimian, Maria Anisimova, Manuel Gil
2022 bioRxiv   pre-print
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

Mark Jensen, Alexander D. Diehl
2017 International Conference on Biomedical Ontology  
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

B. Smith, M. Brochhausen
2010 Methods of Information in Medicine  
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

Federico Boem
2016 Humana.Mente: Journal of Philosophical Studies  
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

R. Hoehndorf, M. Dumontier, G. V. Gkoutos
2012 Briefings in Bioinformatics  
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

L. Jansen, S. Schulz
2013 IMIA Yearbook of Medical Informatics  
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

Tharam Dillon, Elizabeth Chang, Maja Hadzic
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
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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