Senay Kafkas

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 14

Top Topics

Gene Prediction

Medical Literature

Top Venues

J. Biomed. Semant.

Publications

Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition. ICBO (2023)
Senay Kafkas, Sumyyah Toonsi, Sakhaa Alsaedi
Natural Language Processing Tutorial for Biomedical Text Mining. ICBO (2023)
Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. BMC Bioinform. 24 (1) (2023)
Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf
Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase. SWAT4HCLS (2022)
Wang Liu-Wei, Senay Kafkas, Jun Chen, Nicholas J. Dimonaco, Jesper Tegnér, Robert Hoehndorf
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. Bioinform. 37 (17) (2021)
Senay Kafkas, Sara Althubaiti, Georgios V. Gkoutos, Robert Hoehndorf, Paul N. Schofield
Linking common human diseases to their phenotypes; development of a resource for human phenomics. J. Biomed. Semant. 12 (1) (2021)
Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf
Combining lexical and context features for automatic ontology extension. J. Biomed. Semant. 11 (1) (2020)
Senay Kafkas, Robert Hoehndorf
Ontology based mining of pathogen-disease associations from literature. J. Biomed. Semant. 10 (1) (2019)
Senay Kafkas, Robert Hoehndorf
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database J. Biol. Databases Curation 2019 (2019)
Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. SWAT4LS (2018)
Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf
Usage of cell nomenclature in biomedical literature. BMC Bioinform. 18 (S-17) (2017)
Senay Kafkas, Ian Dunham, Johanna R. McEntyre
Literature evidence in open targets - a target validation platform. J. Biomed. Semant. 8 (1) (2017)
Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45 (Database-Issue) (2017)
Senay Kafkas, Ian Dunham, Helen E. Parkinson, Johanna R. McEntyre
Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation. ICBO/BioCreative (2016)
Senay Kafkas, Jee-Hyub Kim, Xingjun Pi, Johanna R. McEntyre
Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles. J. Biomed. Semant. 6 (2015)
Senay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo', Andrew Morrison, Johanna R. McEntyre
Section level search functionality in Europe PMC. J. Biomed. Semant. 6 (2015)
Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. 4 (2013)
Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno-Yepes, Ian Lewin
Monitoring named entity recognition: the League Table. J. Biomed. Semant. 4 (2013)
Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Quoc-Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn, Jan A. Kors
Multilingual Semantic Resources and Parallel Corpora in the Biomedical Domain: the CLEF-ER Challenge. CLEF (Working Notes) (2013)
Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Quoc-Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn, Jan A. Kors
Entity Recognition in Parallel Multi-lingual Biomedical Corpora: The CLEF-ER Laboratory Overview. CLEF (2013)
Senay Kafkas, Ian Lewin, David Milward, Erik M. van Mulligen, Jan A. Kors, Udo Hahn, Dietrich Rebholz-Schuhmann
CALBC: Releasing the Final Corpora. LREC (2012)
Ian Lewin, Senay Kafkas, Dietrich Rebholz-Schuhmann
Centroids: Gold standards with distributional variation. LREC (2012)
Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J. Biomed. Semant. 2 (S-5) (2011)
Amanda Clare, Samuel Croset, Christoph Grabmüller, Senay Kafkas, Maria Liakata, Anika Oellrich, Dietrich Rebholz-Schuhmann
Exploring the Generation and Integration of Publishable Scientific Facts Using the Concept of Nano-publications. SePublica (2011)
Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn
Assessment of NER solutions against the first and second CALBC silver standard corpus. Semantic Mining in Biomedicine (2010)
Senay Kafkas, Ekrem Varoglu, Dietrich Rebholz-Schuhmann, Bahar Taneri
Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach. BMC Bioinform. 11 (S-5) (2010)
Senay Kafkas, Zeki Bayram, Huseyin Yaratan
Implementation Strategies for "Equation Guru" - A User Friendly Intelligent Algebra Tutor. ICEIS (2) (2006)