Senay Kafkas

Learn More
BACKGROUND Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To(More)
We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from(More)
MOTIVATION The identification of protein and gene names (PGNs) from the scientific literature requires semantic resources: Terminological and lexical resources deliver the term candidates into PGN tagging solutions and the gold standard corpora (GSC) train them to identify term parameters and contextual features. Ideally all three resources, i.e. corpora,(More)
Analyzing protein interactions and protein functions is crucial for the analysis of complex biological processes as well as the consequences from aberrant gene products [1]. Protein-Protein Interaction Networks (PPIN) are invaluable means enabling scientists to get a global understanding of interactomes, while analyzing individual protein functions [2].(More)
Publication formats are being sought that facilitate automatic processing and knowledge integration and are better suited to the current pace of research. Here we present an infrastructure for producing and consuming minimal publishable units, nano-publications, directly from a researcher’s electronic notes or manuscripts which allow the integration of(More)
Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles,(More)
BACKGROUND In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating(More)