Senay Kafkas

According to our database, Senay Kafkas authored at least 26 papers between 2006 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes.

Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf

BMC Bioinform., December, 2023

Exploring the Use of Ontology Components for Distantly-Supervised Disease and Phenotype Named Entity Recognition.

Sumyyah Toonsi, Senay Kafkas, Robert Hoehndorf

Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Brasília, Brazil, August 28, 2023

Natural Language Processing Tutorial for Biomedical Text Mining.

Senay Kafkas, Sumyyah Toonsi, Sakhaa Alsaedi

Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023), Brasília, Brazil, August 28, 2023

2022

Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase.

Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf

Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

2021

Linking common human diseases to their phenotypes; development of a resource for human phenomics.

Senay Kafkas, Sara Althubaiti, Georgios V. Gkoutos, Robert Hoehndorf, Paul N. Schofield

J. Biomed. Semant., 2021

DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes.

Wang Liu-Wei, Senay Kafkas, Jun Chen, Nicholas J. Dimonaco, Jesper Tegnér, Robert Hoehndorf

Bioinform., 2021

2020

Combining lexical and context features for automatic ontology extension.

Sara Althubaiti, Senay Kafkas, Marwa Abdelhakim, Robert Hoehndorf

J. Biomed. Semant., 2020

2019

Ontology based mining of pathogen-disease associations from literature.

Senay Kafkas, Robert Hoehndorf

J. Biomed. Semant., 2019

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction.

Senay Kafkas, Robert Hoehndorf

Database J. Biol. Databases Curation, 2019

2018

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings.

Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf

Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

2017

Open Targets: a platform for therapeutic target identification and validation.

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

Nucleic Acids Res., 2017

Usage of cell nomenclature in biomedical literature.

Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf

BMC Bioinform., 2017

Literature evidence in open targets - a target validation platform.

Senay Kafkas, Ian Dunham, Johanna R. McEntyre

J. Biomed. Semant., 2017

2016

Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation.

Senay Kafkas, Ian Dunham, Helen E. Parkinson, Johanna R. McEntyre

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015

Section level search functionality in Europe PMC.

Senay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo', Andrew Morrison, Johanna R. McEntyre

J. Biomed. Semant., 2015

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

Senay Kafkas, Jee-Hyub Kim, Xingjun Pi, Johanna R. McEntyre

J. Biomed. Semant., 2015

2013

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin

J. Biomed. Semant., 2013

Monitoring named entity recognition: the League Table.

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Jimeno-Yepes, Ian Lewin

J. Biomed. Semant., 2013

Multilingual Semantic Resources and Parallel Corpora in the Biomedical Domain: the CLEF-ER Challenge.

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

Proceedings of the Working Notes for CLEF 2013 Conference , 2013

Entity Recognition in Parallel Multi-lingual Biomedical Corpora: The CLEF-ER Laboratory Overview.

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

Proceedings of the Information Access Evaluation. Multilinguality, Multimodality, and Visualization, 2013

2012

Centroids: Gold standards with distributional variation.

Ian Lewin, Senay Kafkas, Dietrich Rebholz-Schuhmann

Proceedings of the Eighth International Conference on Language Resources and Evaluation, 2012

CALBC: Releasing the Final Corpora.

Senay Kafkas, Ian Lewin, David Milward, Erik M. van Mulligen, Jan A. Kors, Udo Hahn, Dietrich Rebholz-Schuhmann

Proceedings of the Eighth International Conference on Language Resources and Evaluation, 2012

2011

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

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

J. Biomed. Semant., 2011

Exploring the Generation and Integration of Publishable Scientific Facts Using the Concept of Nano-publications.

Amanda Clare, Samuel Croset, Christoph Grabmüller, Senay Kafkas, Maria Liakata, Anika Oellrich, Dietrich Rebholz-Schuhmann

Proceedings of the 1st Workshop on Semantic Publishing 2011, 2011

2010

Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach.

Senay Kafkas, Ekrem Varoglu, Dietrich Rebholz-Schuhmann, Bahar Taneri

BMC Bioinform., 2010

2006

Implementation Strategies for "Equation Guru" - A User Friendly Intelligent Algebra Tutor.

Senay Kafkas, Zeki Bayram, Huseyin Yaratan

Proceedings of the ICEIS 2006, 2006