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Journal of Biomedical Semantics

ISSN: 2041--1480
Publisher: BioMed Central


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A common type system for clinical natural language processing

Author(s): Wu Stephen T | Kaggal Vinod C | Dligach Dmitriy | Masanz James J | Chen Pei | Becker Lee | Chapman Wendy W | Savova Guergana K | Liu Hongfang | Chute Christopher G
Volume: 4
Issue: 1
Year: 2013
MAPI: a software framework for distributed biomedical applications

Author(s): Karlsson Johan | Trelles Oswaldo
Volume: 4
Issue: 1
Year: 2013
Finding biomedical categories in Medline®

Author(s): Yeganova Lana | Kim Won | Comeau Donald C | Wilbur W John
Volume: 3
Issue: Suppl 3
Year: 2012
Unsupervised grammar induction of clinical report sublanguage

Author(s): Kate Rohit J
Volume: 3
Issue: Suppl 3
Year: 2012
Literature mining of protein-residue associations with graph rules learned through distant supervision

Author(s): Ravikumar KE | Liu Haibin | Cohn Judith D | Wall Michael E | Verspoor Karin
Volume: 3
Issue: Suppl 3
Year: 2012
Thematic clustering of text documents using an EM-based approach

Author(s): Kim Sun | Wilbur W
Volume: 3
Issue: Suppl 3
Year: 2012
Ranking relations between diseases, drugs and genes for a curation task

Author(s): Clematide Simon | Rinaldi Fabio
Volume: 3
Issue: Suppl 3
Year: 2012
Topics in machine learning for biomedical literature analysis and text retrieval

Author(s): Islamaj Doğan Rezarta | Yeganova Lana
Volume: 3
Issue: Suppl 3
Year: 2012
Continuation-like semantics for modeling structural process anomalies

Author(s): Grewe Niels
Volume: 3
Issue: Suppl 2
Year: 2012
Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology

Author(s): Oellrich Anika | Gkoutos Georgios V | Hoehndorf Robert | Rebholz-Schuhmann Dietrich
Volume: 3
Issue: Suppl 2
Year: 2012
Mechanisms in biomedical ontology

Author(s): Röhl Johannes
Volume: 3
Issue: Suppl 2
Year: 2012
Towards an ontological representation of morbidity and mortality in Description Logics

Author(s): Santana Filipe | Freitas Fred | Fernandes Roberta | Medeiros Zulma | Schober Daniel
Volume: 3
Issue: Suppl 2
Year: 2012
Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology

Author(s): Seddig-Raufie Djamila | Jansen Ludger | Schober Daniel | Boeker Martin | Grewe Niels | Schulz Stefan
Volume: 3
Issue: Suppl 2
Year: 2012
Open biomedical pluralism: formalising knowledge about breast cancer phenotypes

Author(s): Sojic Aleksandra | Kutz Oliver
Volume: 3
Issue: Suppl 2
Year: 2012
OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

Author(s): Schober Daniel | Tudose Ilinca | Svatek Vojtech | Boeker Martin
Volume: 3
Issue: Suppl 2
Year: 2012
Towards improving phenotype representation in OWL

Author(s): Loebe Frank | Stumpf Frank | Hoehndorf Robert | Herre Heinrich
Volume: 3
Issue: Suppl 2
Year: 2012
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

Author(s): Gkoutos Georgios V | Hoehndorf Robert
Volume: 3
Issue: Suppl 2
Year: 2012
Linking genes to diseases with a SNPedia-Gene Wiki mashup

Author(s): Good Benjamin M | Clarke Erik L | Loguercio Salvatore | Su Andrew I
Volume: 3
Issue: Suppl 1
Year: 2012
OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

Author(s): Tcheremenskaia Olga | Benigni Romualdo | Nikolova Ivelina | Jeliazkova Nina | Escher Sylvia E | Batke Monika | Baier Thomas | Poroikov Vladimir | Lagunin Alexey | Rautenberg Micha | Hardy Barry
Volume: 3
Issue: Suppl 1
Year: 2012
Open semantic annotation of scientific publications using DOMEO

Author(s): Ciccarese Paolo | Ocana Marco | Clark Tim
Volume: 3
Issue: Suppl 1
Year: 2012
Annotation analysis for testing drug safety signals using unstructured clinical notes

Author(s): LePendu Paea | Iyer Srinivasan V | Fairon Cédrick | Shah Nigam H
Volume: 3
Issue: Suppl 1
Year: 2012
Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Author(s): Soldatova Larisa N | Sansone Susanna-Assunta | Dumontier Michel | Shah Nigam H
Volume: 3
Issue: Suppl 1
Year: 2012
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL

Author(s): Jupp Simon | Stevens Robert | Hoehndorf Robert
Volume: 3
Issue: Suppl 1
Year: 2012
A Maximum-Entropy approach for accurate document annotation in the biomedical domain

Author(s): Tsatsaronis George | Macari Natalia | Torge Sunna | Dietze Heiko | Schroeder Michael
Volume: 3
Issue: Suppl 1
Year: 2012
Profiling structured product labeling with NDF-RT and RxNorm

Author(s): Zhu Qian | Jiang Guoqian | Chute Christopher G
Volume: 3
Issue: 1
Year: 2012
Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

Author(s): Pathak Jyotishman | Kiefer Richard C | Bielinski Suzette J | Chute Christopher G
Volume: 3
Issue: 1
Year: 2012
GalenOWL: Ontology-based drug recommendations discovery

Author(s): Doulaverakis Charalampos | Nikolaidis George | Kleontas Athanasios | Kompatsiaris Ioannis
Volume: 3
Issue: 1
Year: 2012
COEUS: “semantic web in a box” for biomedical applications

Author(s): Lopes Pedro | Oliveira José Luís
Volume: 3
Issue: 1
Year: 2012
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

Author(s): Parikh Priti P | Zheng Jie | Logan-Klumpler Flora | Stoeckert Christian J | Louis Christos | Topalis Pantelis | Protasio Anna V | Sheth Amit P | Carrington Mark | Berriman Matthew | Sahoo Satya S
Volume: 3
Issue: 1
Year: 2012
Towards the creation of a flexible classification scheme for voluntarily reported transfusion and laboratory safety events

Author(s): Whitehurst Julie M | Schroder John | Leonard Dave | Horvath Monica M | Cozart Heidi | Ferranti Jeffrey
Volume: 3
Issue: 1
Year: 2012
Semantically enabling a genome-wide association study database

Author(s): Beck Tim | Free Robert C | Thorisson Gudmundur A | Brookes Anthony J
Volume: 3
Issue: 1
Year: 2012
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)

Author(s): He Yongqun | Toldo Luca | Burns Gully | Tao Cui | Abernethy Darrell R
Volume: 3
Issue: 1
Year: 2012
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis

Author(s): Tao Cui | He Yongqun | Yang Hannah | Poland Gregory A | Chute Christopher G
Volume: 3
Issue: 1
Year: 2012
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

Author(s): Liu Haibin | Christiansen Tom | Baumgartner William A | Verspoor Karin
Volume: 3
Issue: 1
Year: 2012
Discovering opinion leaders for medical topics using news articles

Author(s): Jonnalagadda Siddhartha | Peeler Ryan | Topham Philip
Volume: 3
Issue: 1
Year: 2012
OMG U got flu? Analysis of shared health messages for bio-surveillance

Author(s): Collier Nigel | Son Nguyen | Nguyen Ngoc
Volume: 2
Issue: Suppl 5
Year: 2011
Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora

Author(s): Vincze Veronika | Szarvas György | Móra György | Ohta Tomoko | Farkas Richárd
Volume: 2
Issue: Suppl 5
Year: 2011
Coreference based event-argument relation extraction on biomedical text

Author(s): Yoshikawa Katsumasa | Riedel Sebastian | Hirao Tsutomu | Asahara Masayuki | Matsumoto Yuji
Volume: 2
Issue: Suppl 5
Year: 2011
Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

Author(s): Kim Jung-jae | Rebholz-Schuhmann Dietrich
Volume: 2
Issue: Suppl 5
Year: 2011
Event extraction for DNA methylation

Author(s): Ohta Tomoko | Pyysalo Sampo | Miwa Makoto | Tsujii Jun’ichi
Volume: 2
Issue: Suppl 5
Year: 2011
Towards mature use of semantic resources for biomedical analyses

Author(s): Rebholz-Schuhmann D | Rinaldi F | Pyysalo S | Collier N | Hahn U
Volume: 2
Issue: Suppl 5
Year: 2011
Towards cross-lingual alerting for bursty epidemic events

Author(s): Collier Nigel
Volume: 2
Issue: Suppl 5
Year: 2011
Automatic extraction of semantic relations between medical entities: a rule based approach

Author(s): Ben Abacha Asma | Zweigenbaum Pierre
Volume: 2
Issue: Suppl 5
Year: 2011
Ontology design patterns to disambiguate relations between genes and gene products in GENIA

Author(s): Hoehndorf Robert | Ngonga Ngomo Axel-Cyrille | Pyysalo Sampo | Ohta Tomoko | Oellrich Anika | Rebholz-Schuhmann Dietrich
Volume: 2
Issue: Suppl 5
Year: 2011
An analysis of gene/protein associations at PubMed scale

Author(s): Pyysalo Sampo | Ohta Tomoko | Tsujii Jun’ichi
Volume: 2
Issue: Suppl 5
Year: 2011
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Author(s): Rebholz-Schuhmann Dietrich | Yepes Antonio | Li Chen | Kafkas Senay | Lewin Ian | Kang Ning | Corbett Peter | Milward David | Buyko Ekaterina | Beisswanger Elena | Hornbostel Kerstin | Kouznetsov Alexandre | Witte René | Laurila Jonas B | Baker Christopher JO | Kuo Cheng-Ju | Clematide Simone | Rinaldi Fabio | Farkas Richárd | Móra György | Hara Kazuo | Furlong Laura I | Rautschka Michael | Neves Mariana | Pascual-Montano Alberto | Wei Qi | Collier Nigel | Chowdhury Md | Lavelli Alberto | Berlanga Rafael | Morante Roser | Van Asch Vincent | Daelemans Walter | Marina José | van Mulligen Erik | Kors Jan | Hahn Udo
Volume: 2
Issue: Suppl 5
Year: 2011
Anatomy ontologies and potential users: bridging the gap

Author(s): Travillian Ravensara S | Adamusiak Tomasz | Burdett Tony | Gruenberger Michael | Hancock John | Mallon Ann-Marie | Malone James | Schofield Paul | Parkinson Helen
Volume: 2
Issue: Suppl 4
Year: 2011
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