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Journal of Biomedical Semantics

ISSN Print: 2041-1480

ISSN Online:

Website: http://www.jbiomedsem.com

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A common type system for clinical natural language processing

Wu Stephen T,Kaggal Vinod C,Dligach Dmitriy,Masanz James J

MAPI: a software framework for distributed biomedical applications

Karlsson Johan,Trelles Oswaldo

Discovering opinion leaders for medical topics using news articles

Siddhartha Jonnalagadda, Ryan Peeler, Philip Topham

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

Haibin Liu, Tom Christiansen, William A Baumgartner, Karin Verspoor

An ontology-based exploration of the concepts and relationships in the activities and participation component of the international classification of functioning, disability and health

Vincenzo Della Mea, Andrea Simoncello

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

Priti P Parikh, Jie Zheng, Flora Logan-Klumper, Christian J Stoeckert, Christos Louis, Pantelis Topalis, Anna V Protasio, Amit P Sheth, Mark Carrington, Matthew Berriman, Satya S Sahoo

Towards the creation of a flexible classification scheme for voluntarily reported transfusion and laboratory safety events

Julie M Whitehurst, John Schroder, Dave Leonard, Monica M Horvath, Heidi Cozart, Jeffrey Ferranti

Thematic clustering of text documents using an EM-based approach

Kim Sun,Wilbur W

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis

Tao Cui,He Yongqun,Yang Hannah,Poland Gregory A

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)

He Yongqun,Toldo Luca,Burns Gully,Tao Cui

COEUS: “semantic web in a box” for biomedical applications

Lopes Pedro,Oliveira José Luís

Unsupervised grammar induction of clinical report sublanguage

Kate Rohit J

Literature mining of protein-residue associations with graph rules learned through distant supervision

Ravikumar KE,Liu Haibin,Cohn Judith D,Wall Michael E

Topics in machine learning for biomedical literature analysis and text retrieval

Islamaj Do？an Rezarta,Yeganova Lana

GalenOWL: Ontology-based drug recommendations discovery

Doulaverakis Charalampos,Nikolaidis George,Kleontas Athanasios,Kompatsiaris Ioannis

Finding biomedical categories in Medline

Yeganova Lana,Kim Won,Comeau Donald C,Wilbur W John

Semantically enabling a genome-wide association study database

Beck Tim,Free Robert C,Thorisson Gudmundur A,Brookes Anthony J

Ranking relations between diseases, drugs and genes for a curation task

Clematide Simon,Rinaldi Fabio

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

Pathak Jyotishman,Kiefer Richard C,Bielinski Suzette J,Chute Christopher G

Profiling structured product labeling with NDF-RT and RxNorm

Zhu Qian,Jiang Guoqian,Chute Christopher G

Towards improving phenotype representation in OWL

Loebe Frank,Stumpf Frank,Hoehndorf Robert,Herre Heinrich

Towards valid and reusable reference alignments — ten basic quality checks for ontology alignments and their application to three different reference data sets

Beisswanger Elena,Hahn Udo

Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology

Yu Lin, Zuoshuang Xiang, Yongqun He

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Mark D Wilkinson, Benjamin Vandervalk, Luke McCarthy

Identifying and relating biological concepts in the Catalogue of Life

Andrew C Jones, Richard J White, Ewen R Orme

GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm

Disjunctive shared information between ontology concepts: application to Gene Ontology

Francisco M Couto, Mário J Silva

A shortest-path graph kernel for estimating gene product semantic similarity

Marco A Alvarez, Xiaojun Qi, Changhui Yan

Semantic validation of the use of SNOMED CT in HL7 clinical documents

Stijn Heymans, Matthew McKennirey, Joshua Phillips

Protein interaction sentence detection using multiple semantic kernels

Tamara Polajnar, Theodoros Damoulas, Mark Girolami

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

Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora

Vincze Veronika,Szarvas Gy？rgy,Móra Gy？rgy,Ohta Tomoko

OMG U got flu? Analysis of shared health messages for bio-surveillance

Collier Nigel,Son Nguyen,Nguyen Ngoc

Automatic extraction of semantic relations between medical entities: a rule based approach

Ben Abacha Asma,Zweigenbaum Pierre

An analysis of gene/protein associations at PubMed scale

Pyysalo Sampo,Ohta Tomoko,Tsujii Jun’ichi

Predicting speculation: a simple disambiguation approach to hedge detection in biomedical literature

Velldal Erik

Towards mature use of semantic resources for biomedical analyses

Rebholz-Schuhmann D,Rinaldi F,Pyysalo S,Collier N

Biomedical semantics in the Semantic Web

Splendiani Andrea,Burger Albert,Paschke Adrian,Romano Paolo

Coreference based event-argument relation extraction on biomedical text

Yoshikawa Katsumasa,Riedel Sebastian,Hirao Tsutomu,Asahara Masayuki

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

Hoehndorf Robert,Ngonga Ngomo Axel-Cyrille,Pyysalo Sampo,Ohta Tomoko

Towards cross-lingual alerting for bursty epidemic events

Collier Nigel

MedEval — A Swedish medical test collection with doctors and patients user groups

Heppin Karin

Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

Kim Jung-jae,Rebholz-Schuhmann Dietrich

Event extraction for DNA methylation

Ohta Tomoko,Pyysalo Sampo,Miwa Makoto,Tsujii Jun’ichi

Anatomy ontologies and potential users: bridging the gap

Travillian Ravensara S,Adamusiak Tomasz,Burdett Tony,Gruenberger Michael

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Rebholz-Schuhmann Dietrich,Yepes Antonio,Li Chen,Kafkas Senay

Enriching a primary health care version of ICD-10 using SNOMED CT mapping

Mikael Nystr？m, Anna Vikstr？m, Gunnar H Nilsson, Hans ？hlfeldt, H？kan ？rman

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

Biomedical Semantics: the Hub for Biomedical Research 2.0

Dietrich Rebholz-Schuhmann, Goran Nenadic

Applying the functional abnormality ontology pattern to anatomical functions

Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso

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