Journal: J. Biomedical Semantics

Volume 8, Issue 1

0 -- 0Patryk Burek, Frank Loebe, Heinrich Herre. Towards refactoring the Molecular Function Ontology with a UML profile for function modeling
0 -- 0Yannis Papanikolaou, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos, Ioannis P. Vlahavas. Large-scale online semantic indexing of biomedical articles via an ensemble of multi-label classification models
0 -- 0Olga L. Giraldo, Alexander García Castro, Federico López, Óscar Corcho. Using semantics for representing experimental protocols
0 -- 0Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay. SAFE: SPARQL Federation over RDF Data Cubes with Access Control
0 -- 0Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz. Ontological interpretation of biomedical database content
0 -- 0Dongliang Xu, Jingchang Pan, BaiLing Wang. Multiple kernels learning-based biological entity relationship extraction method
0 -- 0David Osumi-Sutherland, Melanie Courtot, James P. Balhoff, Christopher J. Mungall. Dead simple OWL design patterns
0 -- 0Jingcheng Du, Jun Xu 0007, Hsing-yi Song, Xiangyu Liu, Cui Tao. Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets
0 -- 0Marco Basaldella, Lenz Furrer, Carlo Tasso, Fabio Rinaldi. Entity recognition in the biomedical domain using a hybrid approach
0 -- 0Louise Deléger, Leonardo Campillos, Anne-Laure Ligozat, Aurélie Névéol. Design of an extensive information representation scheme for clinical narratives
0 -- 0William R. Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos, Chris Delcher. Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request
0 -- 0Milos Jovanovik, Dimitar Trajanov. Consolidating drug data on a global scale using Linked Data
0 -- 0Jelena Jovanovic, Ebrahim Bagheri. Semantic annotation in biomedicine: the current landscape
0 -- 0Maryam Khordad, Robert E. Mercer. Identifying genotype-phenotype relationships in biomedical text
0 -- 0Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe. Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques
0 -- 0Junguk Hur, Arzucan Özgür, Yongqun He. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks
0 -- 0Vincent Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux, Christine Froidevaux, Vincent Fromion. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes
0 -- 0Jisoo Park, Benjamin J. Hescott, Donna K. Slonim. Towards a more molecular taxonomy of disease
0 -- 0Senay Kafkas, Ian Dunham, Johanna R. McEntyre. Literature evidence in open targets - a target validation platform
0 -- 0Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis, Martin Boeker. Analysis and visualization of disease courses in a semantically-enabled cancer registry
0 -- 0Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney, Mark A. Musen. An ontology-driven tool for structured data acquisition using Web forms
0 -- 0Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet. Discovering associations between adverse drug events using pattern structures and ontologies
0 -- 0Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md. Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay. Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data
0 -- 0Behrouz Bokharaeian, Alberto Díaz Esteban, Nasrin Taghizadeh, Hamidreza Chitsaz, Ramyar Chavoshinejad. SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature
0 -- 0Marija Djokic-Petrovic, Vladimir M. Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J. Wild. PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets
0 -- 0Marcos Martínez Romero, Clement Jonquet, Martin J. O'Connor, John Graybeal, Alejandro Pazos, Mark A. Musen. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation
0 -- 0Hua Min, Hedyeh Mobahi, Katherine Irvin, Sanja Avramovic, Janusz Wojtusiak. Predicting activities of daily living for cancer patients using an ontology-guided machine learning methodology
0 -- 0Zlatan Dragisic, Valentina Ivanova, Huanyu Li 0001, Patrick Lambrix. Experiences from the anatomy track in the ontology alignment evaluation initiative
0 -- 0Maxat Kulmanov, Robert Hoehndorf. Evaluating the effect of annotation size on measures of semantic similarity
0 -- 0Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude N. Warren Jr., Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann. BioFed: federated query processing over life sciences linked open data
0 -- 0Freddy Priyatna, Raúl Alonso-Calvo, Sergio Paraiso-Medina, Óscar Corcho. Querying clinical data in HL7 RIM based relational model with morph-RDB
0 -- 0Adrien Barton, Jean-François Ethier, Régis Duvauferrier, Anita Burgun. An ontological analysis of medical Bayesian indicators of performance
0 -- 0Mark E. Sharp. Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources
0 -- 0Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute, Guoqian Jiang. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies
0 -- 0Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian Bologa, Tudor I. Oprea, Stephan C. Schürer. Drug target ontology to classify and integrate drug discovery data
0 -- 0James G. Mork, Alan R. Aronson, Dina Demner-Fushman. 12 years on - Is the NLM medical text indexer still useful and relevant?
0 -- 0Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye, Adrien Coulet. Learning from biomedical linked data to suggest valid pharmacogenes
0 -- 0Samuel Lampa, Egon L. Willighagen, Pekka Kohonen, Ali King, Denny Vrandecic, Roland Grafstrom, Ola Spjuth. RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
0 -- 0Ferdinand Dhombres, Paul Maurice, Stéphanie Friszer, Lucie Guilbaud, Nathalie Lelong, Babak Khoshnood, Jean Charlet, Nicolas Perrot, Eric Jauniaux, Davor Jurkovic, Jean-Marie Jouannic. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy
0 -- 0Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Dominik Stegemann, Frank Portheine, Heinrich Herre. Ontology-based specification, identification and analysis of perioperative risks
0 -- 0Aleksandra Gruca, Marek Sikora. Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets
0 -- 0Vianney Jouhet, Fleur Mougin, Bérénice Bréchat, Frantz Thiessard. Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus
0 -- 0Muhammad Amith, Cui Tao. Modulated evaluation metrics for drug-based ontologies
0 -- 0Isabel Segura-Bedmar, Paloma Martínez. Simplifying drug package leaflets written in Spanish by using word embedding
0 -- 0Yuqing Mao, Zhiyong Lu. MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank
0 -- 0Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone, Arild Waaler. Matching disease and phenotype ontologies in the ontology alignment evaluation initiative
0 -- 0Hugo Leroux, Alejandro Metke-Jimenez, Michael John Lawley. Towards achieving semantic interoperability of clinical study data with FHIR
0 -- 0Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz. Ontological interpretation of biomedical database content
0 -- 0Aisha Blfgeh, Jennifer D. Warrender, Catharien M. U. Hilkens, Phillip Lord. A document-centric approach for developing the tolAPC ontology
0 -- 0Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Integrating phenotype ontologies with PhenomeNET
0 -- 0Richard D. Boyce, Erica A. Voss, Vojtech Huser, Lee Evans, Christian G. Reich, Jon D. Duke, Nicholas P. Tatonetti, Tal Lorberbaum, Michel Dumontier, Manfred Hauben, Magnus Wallberg, Lili Peng, Sara Dempster, Yongqun He, Anthony G. Sena, Vassilis Koutkias, Pantelis Natsiavas, Patrick B. Ryan. Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data
0 -- 0Claudia Mazo, Liliana Salazar, Óscar Corcho, María P. Trujillo, Enrique Alegre. A histological ontology of the human cardiovascular system