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ORCIDSenay Kafkas
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2020 – today
- 2023
[j15]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): 294 (2023)- [c12]Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf:
Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition. ICBO 2023: 13-24 - [c11]Senay Kafkas, Sumyyah Toonsi, Sakhaa Alsaedi:
Natural Language Processing Tutorial for Biomedical Text Mining. ICBO 2023: 211 - 2022
- [c10]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: 97-102 - 2021
- [j14]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): 2722-2729 (2021) - [j13]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): 17 (2021) - 2020
- [j12]Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf:
Combining lexical and context features for automatic ontology extension. J. Biomed. Semant. 11(1): 1 (2020)
2010 – 2019
- 2019
- [j11]Senay Kafkas, Robert Hoehndorf:
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. Database J. Biol. Databases Curation 2019: baz019 (2019) - [j10]Senay Kafkas, Robert Hoehndorf:
Ontology based mining of pathogen-disease associations from literature. J. Biomed. Semant. 10(1): 15:1-15:5 (2019) - 2018
- [c9]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 - 2017
- [j9]Senay Kafkas, Ian Dunham, Johanna R. McEntyre:
Literature evidence in open targets - a target validation platform. J. Biomed. Semant. 8(1): 20:1-20:9 (2017) - [j8]Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf:
Usage of cell nomenclature in biomedical literature. BMC Bioinform. 18(S-17): 17-24 (2017) - [j7]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): D985-D994 (2017) - 2016
- [c8]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 - 2015
- [j6]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: 1 (2015) - [j5]Senay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo', Andrew Morrison, Johanna R. McEntyre:
Section level search functionality in Europe PMC. J. Biomed. Semant. 6: 7 (2015) - 2013
- [j4]Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno-Yepes, Ian Lewin:
Monitoring named entity recognition: the League Table. J. Biomed. Semant. 4: 19 (2013) - [j3]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: 28 (2013) - [c7]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: 353-367 - [c6]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 - 2012
- [c5]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: 2923-2926 - [c4]Ian Lewin, Senay Kafkas, Dietrich Rebholz-Schuhmann:
Centroids: Gold standards with distributional variation. LREC 2012: 3894-3900 - 2011
- [j2]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): S11 (2011) - [c3]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 - 2010
- [j1]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): P1 (2010) - [c2]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
2000 – 2009
- 2006
- [c1]Senay Kafkas, Zeki Bayram, Huseyin Yaratan:
Implementation Strategies for "Equation Guru" - A User Friendly Intelligent Algebra Tutor. ICEIS (2) 2006: 58-65
Coauthor Index
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