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Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology
Yu Lin, Zuoshuang Xiang, Yongqun He Journal of Biomedical Semantics 2011, 2:9 (31 October 2011)
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Editor’s summary
The first reported bacterial infectious disease ontology, that provides a brucellosis knowledge-base and supports brucellosis data integration and automated reasoning.
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The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Mark D Wilkinson, Benjamin Vandervalk, Luke McCarthy Journal of Biomedical Semantics 2011, 2:8 (24 October 2011)
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Identifying and relating biological concepts in the Catalogue of Life
Andrew C Jones, Richard J White, Ewen R Orme Journal of Biomedical Semantics 2011, 2:7 (17 October 2011)
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Editor’s summary
The challenge of managing the variability of species names can be addressed with globally unique Life Science Identifiers (LSIDs) to map species names to abstract concepts, which should assist in data integration and interoperability in biomedicine.
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GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution
Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm Journal of Biomedical Semantics 2011, 2:6 (13 September 2011)
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Disjunctive shared information between ontology concepts: application to Gene Ontology
Francisco M Couto, Mário J Silva Journal of Biomedical Semantics 2011, 2:5 (31 August 2011)
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The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul JP Bonnal, José M Fernández, Takatomo Fujisawa, Paul MK Gordon, Naohisa Goto, Syed Haider, Todd Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R Kinjo, Fumikazu Konishi, Yulia Kovarskaya Journal of Biomedical Semantics 2011, 2:4 (2 August 2011)
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Editor’s summary
The challenges discussed during the second DBCLS BioHackathon, from data providers, middleware providers, interface designers and end-users perspective.
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A shortest-path graph kernel for estimating gene product semantic similarity
Marco A Alvarez, Xiaojun Qi, Changhui Yan Journal of Biomedical Semantics 2011, 2:3 (29 July 2011)
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Semantic validation of the use of SNOMED CT in HL7 clinical documents
Stijn Heymans, Matthew McKennirey, Joshua Phillips Journal of Biomedical Semantics 2011, 2:2 (15 July 2011)
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Protein interaction sentence detection using multiple semantic kernels
Tamara Polajnar, Theodoros Damoulas, Mark Girolami Journal of Biomedical Semantics 2011, 2:1 (14 May 2011)
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Foundations for a realist ontology of mental disease
Werner Ceusters, Barry Smith Journal of Biomedical Semantics 2010, 1:10 (9 December 2010)
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Simple tricks for improving pattern-based information extraction from the biomedical literature
Quang Nguyen, Domonkos Tikk, Ulf Leser Journal of Biomedical Semantics 2010, 1:9 (24 September 2010)
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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho Journal of Biomedical Semantics 2010, 1:8 (21 August 2010)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Enriching a primary health care version of ICD-10 using SNOMED CT mapping
Mikael Nyström, Anna Vikström, Gunnar H Nilsson, Hans Åhlfeldt, Håkan Örman Journal of Biomedical Semantics 2010, 1:7 (17 June 2010)
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De-identifying Swedish clinical text - refinement of a gold standard and experiments with Conditional random fields
Hercules Dalianis, Sumithra Velupillai Journal of Biomedical Semantics 2010, 1:6 (12 April 2010)
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Rewriting and suppressing UMLS terms for improved biomedical term identification
Kristina M Hettne, Erik M van Mulligen, Martijn J Schuemie, Bob JA Schijvenaars, Jan A Kors Journal of Biomedical Semantics 2010, 1:5 (31 March 2010)
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Applying the functional abnormality ontology pattern to anatomical functions
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso Journal of Biomedical Semantics 2010, 1:4 (31 March 2010)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
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Analysis of syntactic and semantic features for fine-grained event-spatial understanding in outbreak news reports
Hutchatai Chanlekha, Nigel Collier Journal of Biomedical Semantics 2010, 1:3 (31 March 2010)
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What's unusual in online disease outbreak news?
Nigel Collier Journal of Biomedical Semantics 2010, 1:2 (31 March 2010)
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Biomedical Semantics: the Hub for Biomedical Research 2.0
Dietrich Rebholz-Schuhmann, Goran Nenadic Journal of Biomedical Semantics 2010, 1:1 (31 March 2010)
Full text | PDF | PubMed | Cited on BioMed Central
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