Journal of Biomedical Semantics

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		Research BioUSeR: A semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements María Pérez Catalán, Rafael Berlanga, Ismael Sanz, María José Aramburu Journal of Biomedical Semantics 2013, 4:12 (1 May 2013) Abstract \| Provisional PDF \| PubMed
		Research Using Semantic Web technology to support icd-11 textual definitions authoring Guoqian Jiang, Harold R Solbrig, Christopher G Chute Journal of Biomedical Semantics 2013, 4:11 (21 April 2013) Abstract \| Full text \| PDF \| PubMed
		Research A unified approach for debugging is-a structure and mappings in networked taxonomies Patrick Lambrix, Valentina Ivanova Journal of Biomedical Semantics 2013, 4:10 (31 March 2013) Abstract \| Provisional PDF \| PubMed
		Research Semantic querying of relational data for clinical intelligence: a semantic web services-based approach Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge, Christopher JO Baker Journal of Biomedical Semantics 2013, 4:9 (13 March 2013) Abstract \| Provisional PDF \| PubMed
		Research Building Linked Open Data towards integration of biomedical scientific literature with DBpedia Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa Journal of Biomedical Semantics 2013, 4:8 (13 March 2013) Abstract \| Full text \| PDF \| PubMed
		Software Deploying and sharing U-Compare workflows as web services Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou Journal of Biomedical Semantics 2013, 4:7 (18 February 2013) Abstract \| Provisional PDF \| PubMed
		Review The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido et al. Journal of Biomedical Semantics 2013, 4:6 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This meeting report from the 3rd DBCLS BioHackathon examines how Semantic Web technologies can improve the quality and accessibility of life science research data on the Web.
		Research Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad, Maria Liakata Journal of Biomedical Semantics 2013, 4:5 (26 January 2013) Abstract \| Provisional PDF \| PubMed
		Software MAPI: a software framework for distributed biomedical applications Johan Karlsson, Oswaldo Trelles Journal of Biomedical Semantics 2013, 4:4 (11 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research Pooling annotated corpora for clinical concept extraction Kavishwar B Wagholikar, Manabu Torii, Siddhartha R Jonnalagadda, Hongfang Liu Journal of Biomedical Semantics 2013, 4:3 (8 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pooling annotated corpora does not improve concept extraction, prompting the authors to recommend standardized guidelines to facilitate pooling corpora across institutions.
		Software OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Chris Mungall, Erick Antezana, Alejandro Rodríguez González, Mark D Wilkinson Journal of Biomedical Semantics 2013, 4:2 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Ontology Pre Processor Language (OPPL) combined with the Galaxy framework allows automated ontology manipulations, leading to more advanced biological data analyses.
		Research A common type system for clinical natural language processing Stephen T Wu, Vinod C Kaggal, Dmitriy Dligach, James J Masanz, Pei Chen, Lee Becker, Wendy W Chapman, Guergana K Savova, Hongfang Liu, Christopher G Chute Journal of Biomedical Semantics 2013, 4:1 (3 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He Journal of Biomedical Semantics 2012, 3:18 (20 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses Yu Lin, Yongqun He Journal of Biomedical Semantics 2012, 3:17 (20 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Cited on BioMed Central
		Research Profiling structured product labeling with NDF-RT and RxNorm Qian Zhu, Guoqian Jiang, Christopher G Chute Journal of Biomedical Semantics 2012, 3:16 (20 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Extraction of potential adverse drug events from medical case reports Harsha Gurulingappa, Abdul Mateen‐Rajput, Luca Toldo Journal of Biomedical Semantics 2012, 3:15 (20 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research GalenOWL: Ontology-based drug recommendations discovery Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas, Ioannis Kompatsiaris Journal of Biomedical Semantics 2012, 3:14 (20 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis Cui Tao, Yongqun He, Hannah Yang, Gregory A Poland, Christopher G Chute Journal of Biomedical Semantics 2012, 3:13 (20 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An ontology-based representation of the Vaccine Adverse Event Reporting System (VAERS) allows the analysis of both structured and narrative data, culminating in improved vaccine safety studies.
		Editorial A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012) Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R Abernethy Journal of Biomedical Semantics 2012, 3:12 (18 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Semantically enabling a genome-wide association study database Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes Journal of Biomedical Semantics 2012, 3:9 (17 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Analysing Syntactic Regularities and Irregularities in SNOMED-CT Eleni Mikroyannidi, Robert Stevens, Luigi Iannone, Alan Rector Journal of Biomedical Semantics 2012, 3:8 (17 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The Regularity Inspector of Ontologies (RIO) automatically detects regularities and irregularities in SNOMED-CT, facilitating the quality assurance of semantic resources.
		Software COEUS: “semantic web in a box” for biomedical applications Pedro Lopes, José Luís Oliveira Journal of Biomedical Semantics 2012, 3:11 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute Journal of Biomedical Semantics 2012, 3:10 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Resource Description Framework (RDF) can be employed to enable the analysis of genotype to phenotype associations from clinical data, thereby accurately identifying subjects with specific diseases.
		Research GO2PUB: Querying PubMed with semantic expansion of gene ontology terms Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron Journal of Biomedical Semantics 2012, 3:7 (7 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New web-based tool Go2PUB harnesses Gene Ontology annotations and graph structure to enrich literature retrieval from PubMed queries with gene names, symbols and synonyms.
		Research Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web Soroush Samadian, Bruce McManus, Mark D Wilkinson Journal of Biomedical Semantics 2012, 3:6 (20 July 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A more transparent and reproducible approach to clinical classification is provided by a simple and flexible core data model utilizing both logical reasoning and analytical algorithms to iteratively "lift" clinical data through increasingly complex layers of classification.

	All
		Research BioUSeR: A semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements María Pérez Catalán, Rafael Berlanga, Ismael Sanz, María José Aramburu Journal of Biomedical Semantics 2013, 4:12 (1 May 2013) Abstract \| Provisional PDF \| PubMed
		Research Using Semantic Web technology to support icd-11 textual definitions authoring Guoqian Jiang, Harold R Solbrig, Christopher G Chute Journal of Biomedical Semantics 2013, 4:11 (21 April 2013) Abstract \| Full text \| PDF \| PubMed
		Research A unified approach for debugging is-a structure and mappings in networked taxonomies Patrick Lambrix, Valentina Ivanova Journal of Biomedical Semantics 2013, 4:10 (31 March 2013) Abstract \| Provisional PDF \| PubMed
		Research Semantic querying of relational data for clinical intelligence: a semantic web services-based approach Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge, Christopher JO Baker Journal of Biomedical Semantics 2013, 4:9 (13 March 2013) Abstract \| Provisional PDF \| PubMed
		Research Building Linked Open Data towards integration of biomedical scientific literature with DBpedia Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa Journal of Biomedical Semantics 2013, 4:8 (13 March 2013) Abstract \| Full text \| PDF \| PubMed
		Software Deploying and sharing U-Compare workflows as web services Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou Journal of Biomedical Semantics 2013, 4:7 (18 February 2013) Abstract \| Provisional PDF \| PubMed
		Review The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul JP Bonnal, Brad Chapman, Peter JA Cock, Tore Eriksson, Paul MK Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido et al. Journal of Biomedical Semantics 2013, 4:6 (11 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This meeting report from the 3rd DBCLS BioHackathon examines how Semantic Web technologies can improve the quality and accessibility of life science research data on the Web.
		Research Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad, Maria Liakata Journal of Biomedical Semantics 2013, 4:5 (26 January 2013) Abstract \| Provisional PDF \| PubMed
		Software MAPI: a software framework for distributed biomedical applications Johan Karlsson, Oswaldo Trelles Journal of Biomedical Semantics 2013, 4:4 (11 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research Pooling annotated corpora for clinical concept extraction Kavishwar B Wagholikar, Manabu Torii, Siddhartha R Jonnalagadda, Hongfang Liu Journal of Biomedical Semantics 2013, 4:3 (8 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pooling annotated corpora does not improve concept extraction, prompting the authors to recommend standardized guidelines to facilitate pooling corpora across institutions.
		Software OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Chris Mungall, Erick Antezana, Alejandro Rodríguez González, Mark D Wilkinson Journal of Biomedical Semantics 2013, 4:2 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Ontology Pre Processor Language (OPPL) combined with the Galaxy framework allows automated ontology manipulations, leading to more advanced biological data analyses.
		Research A common type system for clinical natural language processing Stephen T Wu, Vinod C Kaggal, Dmitriy Dligach, James J Masanz, Pei Chen, Lee Becker, Wendy W Chapman, Guergana K Savova, Hongfang Liu, Christopher G Chute Journal of Biomedical Semantics 2013, 4:1 (3 January 2013) Abstract \| Full text \| PDF \| PubMed
		Research Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He Journal of Biomedical Semantics 2012, 3:18 (20 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses Yu Lin, Yongqun He Journal of Biomedical Semantics 2012, 3:17 (20 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Cited on BioMed Central
		Research Profiling structured product labeling with NDF-RT and RxNorm Qian Zhu, Guoqian Jiang, Christopher G Chute Journal of Biomedical Semantics 2012, 3:16 (20 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Extraction of potential adverse drug events from medical case reports Harsha Gurulingappa, Abdul Mateen‐Rajput, Luca Toldo Journal of Biomedical Semantics 2012, 3:15 (20 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research GalenOWL: Ontology-based drug recommendations discovery Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas, Ioannis Kompatsiaris Journal of Biomedical Semantics 2012, 3:14 (20 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis Cui Tao, Yongqun He, Hannah Yang, Gregory A Poland, Christopher G Chute Journal of Biomedical Semantics 2012, 3:13 (20 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An ontology-based representation of the Vaccine Adverse Event Reporting System (VAERS) allows the analysis of both structured and narrative data, culminating in improved vaccine safety studies.
		Editorial A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012) Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R Abernethy Journal of Biomedical Semantics 2012, 3:12 (18 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Semantically enabling a genome-wide association study database Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes Journal of Biomedical Semantics 2012, 3:9 (17 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Analysing Syntactic Regularities and Irregularities in SNOMED-CT Eleni Mikroyannidi, Robert Stevens, Luigi Iannone, Alan Rector Journal of Biomedical Semantics 2012, 3:8 (17 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The Regularity Inspector of Ontologies (RIO) automatically detects regularities and irregularities in SNOMED-CT, facilitating the quality assurance of semantic resources.
		Software COEUS: “semantic web in a box” for biomedical applications Pedro Lopes, José Luís Oliveira Journal of Biomedical Semantics 2012, 3:11 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute Journal of Biomedical Semantics 2012, 3:10 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Resource Description Framework (RDF) can be employed to enable the analysis of genotype to phenotype associations from clinical data, thereby accurately identifying subjects with specific diseases.
		Research GO2PUB: Querying PubMed with semantic expansion of gene ontology terms Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron Journal of Biomedical Semantics 2012, 3:7 (7 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New web-based tool Go2PUB harnesses Gene Ontology annotations and graph structure to enrich literature retrieval from PubMed queries with gene names, symbols and synonyms.
		Research Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web Soroush Samadian, Bruce McManus, Mark D Wilkinson Journal of Biomedical Semantics 2012, 3:6 (20 July 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A more transparent and reproducible approach to clinical classification is provided by a simple and flexible core data model utilizing both logical reasoning and analytical algorithms to iteratively "lift" clinical data through increasingly complex layers of classification.