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LINKING BIOMEDICAL INFORMATION THROUGH TEXT MINING: SESSION INTRODUCTION

K. BRETONNEL COHEN, OLIVIER BODENREIDER, LYNETTE HIRSCHMAN
<span title="">2005</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2006 </i> &nbsp;
This session builds on two threads of work that have been well represented at past PSB meetings, namely text mining and ontologies.  ...  Many of the systems discussed in these earlier sessions focused on recognition of biomedical entities and relations in order to provide effective indexing into the literature.  ...  Much of this work was presented at PSB sessions on ontologies in 2003, 2004, and 2005 or the PSB sessions on biomedical language processing listed above.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812701626_0001">doi:10.1142/9789812701626_0001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/idrwqvbmtrgwfbhbkneijgqaui">fatcat:idrwqvbmtrgwfbhbkneijgqaui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161221060228/https://mor.nlm.nih.gov/pubs/pdf/2006-psb-nlp-intro.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e3/6b/e36b3908ffe9b33746fa70e31dc44ad3e1ca5e55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812701626_0001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Ontology for fMRI as a Biomedical Informatics Method

Toshiharu NAKAI, Epifanio BAGARINAO, Yoshio TANAKA, Kayako MATSUO, Daniel RACOCEANU
<span title="">2008</span> <i title="Japanese Society for Magnetic Resonance in Medicine"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bp7c2gl4e5a7vbyzuvm6llfbsi" style="color: black;">Magnetic Resonance in Medical Sciences</a> </i> &nbsp;
Ontological engineering is one of the most challenging topics in biomedical informatics because of its key role in integrating the heterogeneous database used by biomedical information services.  ...  The fMRI ontology of this system will be integrated with established medical ontologies, such as the Uniˆed Medical Language System (UMLS).  ...  Its goal is to create a suite of orthogonal interoperable reference ontologies in the biomedical domain.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2463/mrms.7.141">doi:10.2463/mrms.7.141</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18827457">pmid:18827457</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z4qijfvlqzfojllunm47furzkq">fatcat:z4qijfvlqzfojllunm47furzkq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181031194801/https://www.jstage.jst.go.jp/article/mrms/7/3/7_3_141/_pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/86/76/867625eaa53b1cc076ce59fa8140c358ee794536.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2463/mrms.7.141"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Open Ontology Forge: A Tool for Ontology Creation and Text Annotation Applied to the Biomedical Domain

Ai Kawazoe, Tony Mullen, Koichi Takeuchi, Tuangthong Wattarujeekrit, Nigel Collier
<span title="">2003</span> <i title="Japanese Society for Bioinformatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
Introduction In this paper, we will introduce Open Ontology Forge (OOF), a software tool for ontology creation, terminology annotation, and coreference annotation by experts applied to the biomedical domain  ...  § @ A snapshot of an annotation session using OOF is shown in Figure 1 and Figure 2 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11234/gi1990.14.677">doi:10.11234/gi1990.14.677</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qb52vyti65blfflozilnzfs5le">fatcat:qb52vyti65blfflozilnzfs5le</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160702163241/http://www.jsbi.org/pdfs/journal1/GIW03/GIW03P012.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c0/55/c055e2b777796a83122fea8080d0d24cbcee03b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11234/gi1990.14.677"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy

Ramon Maldonado, Travis R Goodwin, Michael A Skinner, Sanda M Harabagiu
<span title="2018-04-16">2018</span> <i title="American Medical Informatics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g6q27b56yzeupjryv6lby2r2pa" style="color: black;">AMIA Annual Symposium Proceedings</a> </i> &nbsp;
While biomedical ontologies have traditionally been used to guide the identification of concepts or relations in biomedical data, recent advances in deep learning are able to capture high-quality knowledge  ...  Many of the epilepsy-relevant medical concepts from MKE are not yet available in existing biomedical ontologies, but are mentioned in vast collections of epilepsy-related medical records which also imply  ...  Introduction Over the past two decades, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, justified by the steady increase in biological and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29854192">pmid:29854192</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5977726/">pmcid:PMC5977726</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aoxf3j37qjbelnodrjmmqqqavi">fatcat:aoxf3j37qjbelnodrjmmqqqavi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210525184219/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5977726&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/fc/13fc1d33030d8ccc212f044a5f9d91dd99166437.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977726" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Terminology representation guidelines for biomedical ontologies in the semantic web notations

Cui Tao, Jyotishman Pathak, Harold R. Solbrig, Wei-Qi Wei, Christopher G. Chute
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
We identified a set of commonly-used elements in biomedical ontologies and terminologies based on our experience with the Common Terminology Services 2 (CTS2) Specification as well as the Lexical Grid  ...  Terminologies and ontologies are increasingly prevalent in healthcare and biomedicine.  ...  Acknowledgments This research is partially supported by the National Center for Biomedical Ontologies (NCBO) under the NIH Grant #N01-HG04028 and the NSF under Grant #0937060 to the Computing Research  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2012.09.003">doi:10.1016/j.jbi.2012.09.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23026232">pmid:23026232</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3563768/">pmcid:PMC3563768</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dzpfswlv6jcxxdsfd5zrfbtaou">fatcat:dzpfswlv6jcxxdsfd5zrfbtaou</a> </span>
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A Literature Based Approach to Define the Scope of Biomedical Ontologies: A Case Study on a Rehabilitation Therapy Ontology [article]

Mohammad K. Halawani, Rob Forsyth, Phillip Lord
<span title="2017-09-27">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Ontology development requires significant effort from both ontologists and domain experts. Knowledge elicited from domain experts forms the scope of the ontology.  ...  Here, we describe our work toward an alternative approach, bootstrapping the ontology from an initially small corpus of literature that will define the scope of the ontology, expanding this to a set covering  ...  INTRODUCTION Rehabilitation therapies, unlike pharmacologic therapies, are difficult to define precisely both qualitatively and quantitatively (van Heugten et al., 2012) and many approaches have been  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1709.09450v1">arXiv:1709.09450v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tpil3yim7bgtlkw4fxcgqmbc5u">fatcat:tpil3yim7bgtlkw4fxcgqmbc5u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200903203835/https://arxiv.org/pdf/1709.09450v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a7/7d/a77d1912dfd92b2ed6b7e29fe2f3a1a106d74aa1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1709.09450v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Vaccine and Drug Ontology Studies (VDOS 2014)

Cui Tao, Yongqun He, Sivaram Arabandi
<span title="2016-02-25">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugsextending existing clinical terminology  ...  The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs  ...  International Conference on Biomedical Ontology (ICBO 2012).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-015-0039-8">doi:10.1186/s13326-015-0039-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26918107">pmid:26918107</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4766598/">pmcid:PMC4766598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gd466w6vc5bshkt2hq4rut4ili">fatcat:gd466w6vc5bshkt2hq4rut4ili</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010073431/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/277/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMzI2LTAxNS0wMDM5LTgucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/92/df921b7139aaf2d7061f9592d807cd1a6cbd2699.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-015-0039-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766598" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Formal ontology for natural language processing and the integration of biomedical databases

Jonathan Simon, Mariana Dos Santos, James Fielding, Barry Smith
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyf7co46pvdybh6jhdipt5d3im" style="color: black;">International Journal of Medical Informatics</a> </i> &nbsp;
of a philosophically inspired formal ontology will greatly benefit software application ontologies.  ...  To this end LinKBase®, L&C's ontology, which is designed to integrate and reason across various external databases simultaneously,has been submitted to the conceptual demands of IFOMIS's Basic Formal Ontology  ...  Introduction: L&C's LinKBase® and Basic Formal Ontology For millennia, when we have encountered difficulties understanding reality, we have turned to philosophers for solutions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2005.07.015">doi:10.1016/j.ijmedinf.2005.07.015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16153885">pmid:16153885</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4k7oisaty5fpvjpgysehsu6cca">fatcat:4k7oisaty5fpvjpgysehsu6cca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720162705/https://philpapers.org/archive/SIMFOF.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f4/20/f4200cc5323cf496d9314ec925ca53b1bd1542cb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijmedinf.2005.07.015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

SATORI: a system for ontology-guided visual exploration of biomedical data repositories

Fritz Lekschas, Nils Gehlenborg, Janet Kelso
<span title="2017-11-23">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Ontological metadata annotations provide context by semantically relating data sets.  ...  We developed SATORIan integrative search and visual exploration interface for the exploration of biomedical data repositories.  ...  Also, all participants mentioned at the end of the session that SATORI requires some training or introduction. In response, we implemented several stepby-step guides to help first-time users.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx739">doi:10.1093/bioinformatics/btx739</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29186292">pmid:29186292</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6031061/">pmcid:PMC6031061</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eyifgfu75fczdodkxfiinlylf4">fatcat:eyifgfu75fczdodkxfiinlylf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724134536/https://www.biorxiv.org/content/biorxiv/early/2017/10/20/046755.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d6/ca/d6ca0de5a5e1c221f5f8df8f165cd5743e6eb83e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx739"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031061" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories [article]

Fritz Lekschas, Nils Gehlenborg
<span title="2016-04-05">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Ontological metadata annotations provide context by semantically relating data sets.  ...  We developed SATORI--an integrative search and visual exploration interface for the exploration of biomedical data repositories.  ...  Also, all participants mentioned at the end of the session that SATORI requires some training or introduction. In response, we implemented several stepby-step guides to help first-time users.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/046755">doi:10.1101/046755</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2zaqmkydivea7edug4ys727kg4">fatcat:2zaqmkydivea7edug4ys727kg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502082056/https://www.biorxiv.org/content/biorxiv/early/2017/10/20/046755.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/25/25257283451ab91b60b5547fac3305fa19a99f5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/046755"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Towards exergaming commons: composing the exergame ontology for publishing open game data

Giorgos Bamparopoulos, Evdokimos Konstantinidis, Charalampos Bratsas, Panagiotis D. Bamidis
<span title="2016-02-09">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Methods: We have developed an ontology that describes exergames using the Web Ontology Language (OWL); it is available at http://purl.org/net/exergame/ns#.  ...  Results: Exergame components include details for players, game sessions, as well as, data produced during these game-playing sessions.  ...  same URI, in line with repositories of biomedical ontologies such as Ontobee and BioPortal providing an interface for all ontology terms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0046-4">doi:10.1186/s13326-016-0046-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26865947">pmid:26865947</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4748514/">pmcid:PMC4748514</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2rrh3enp4fa6tlyhvipbjcbi5e">fatcat:2rrh3enp4fa6tlyhvipbjcbi5e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922000424/https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-016-0046-4?site=jbiomedsem.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/1b/3f1b9cf50e8d7b67e4eab9573dd4762d0fb71cde.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0046-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748514" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A 2013 workshop: vaccine and drug ontology studies (VDOS 2013)

Cui Tao, Yongqun He, Sivaram Arabandi
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugsextending existing clinical terminology  ...  The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs  ...  International Conference on Biomedical Ontology (ICBO 2012).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-16">doi:10.1186/2041-1480-5-16</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24650607">pmid:24650607</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3994568/">pmcid:PMC3994568</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vrwk2pkgtrct5g4qftjffxbfra">fatcat:vrwk2pkgtrct5g4qftjffxbfra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817222348/https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/2041-1480-5-16?site=jbiomedsem.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/ea/f1eaee8f5d88510a2d4693fba3c48de7a9ba1922.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-16"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994568" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Using an ECG reference ontology for semantic interoperability of ECG data

Bernardo Gonçalves, Giancarlo Guizzardi, José G. Pereira Filho
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
We then argue that a shared anchor, the biomedical reality under scrutiny, can effectively support the semantic integration of these ECG standards into a coherent ECG representation for the sake of a unified  ...  Our hypothesis is tested by means of an integration experiment that uses, on the one hand, an ECG Ontology and, on the other hand, elicited conceptual models of the ECG standards.  ...  Introduction Biomedical data has been ever more available for computing as the use of information systems in Biology and Medicine becomes widespread.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.08.007">doi:10.1016/j.jbi.2010.08.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20800107">pmid:20800107</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k2z6ykdekzexdmi6ugaynjfeue">fatcat:k2z6ykdekzexdmi6ugaynjfeue</a> </span>
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Visualizing the Gene Ontology-Annotated Clusters of Co-expressed Genes: A Two-Design Study

David C. Y. Fung, Seok-Hee Hong, Kai Xu, David Hart
<span title="">2008</span> <i title="IEEE"> 2008 Fifth International Conference BioMedical Visualization: Information Visualization in Medical and Biomedical Informatics </i> &nbsp;
In molecular biology, Gene Ontology (GO) has often been used for annotation and as a data mining dimension.  ...  Introduction In recent years, Gene Ontology (GO) has been used as a proxy for biological function and has increasingly been used for annotation and as a data mining dimension.  ...  The participant was given a trial session to familiarize oneself with the procedure using a synthetic dataset.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/medivis.2008.9">doi:10.1109/medivis.2008.9</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kuxm7zmhlnhkjcdy6matmuos5y">fatcat:kuxm7zmhlnhkjcdy6matmuos5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921232826/http://sydney.edu.au/engineering/it/groups/visual/kaixu/papers/kaixu_IVbm08_GO-Cluster.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/35/bc3554af842e29b7120931da3271826253eedb75.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/medivis.2008.9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

A reusable framework for health counseling dialogue systems based on a behavioral medicine ontology

Timothy W. Bickmore, Daniel Schulman, Candace L. Sidner
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
The model is implemented using an OWL ontology of health behavior change concepts and a public standard task modeling language (ANSI/CEA-2018).  ...  We demonstrate the power of modeling dialogue using an ontology and task model by showing how an exercise promotion system developed in the framework was re-purposed for diet promotion with 98% reuse of  ...  This function is currently used to load parts of the ontology into the runtime dialogue system and to save updated parts of the ontology (User Model) at the completion of a counseling session.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2010.12.006">doi:10.1016/j.jbi.2010.12.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21220044">pmid:21220044</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3063319/">pmcid:PMC3063319</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r5yayu7bbvem3pfntx4l7jbgmi">fatcat:r5yayu7bbvem3pfntx4l7jbgmi</a> </span>
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