New research, ‘Collaborative text-annotation resource for disease-centered relation extraction from biomedical text,’ is the subject of a report. “Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature,” investigators in Granada, Spain report (see also Biomedical Informatics).
“Relation extraction systems cannot be developed without substantial datasets annotated with ground truth for benchmarking and training. The creation of such datasets is hampered by the absence of a resource for launching a distributed annotation effort, as well as by the lack of a standardized annotation schema. We have developed an annotation schema and an annotation tool which can be widely adopted so that the resulting annotated corpora from a multitude of disease studies could be assembled into a unified benchmark dataset. The contribution of this paper is threefold. First, we provide an overview of available benchmark corpora and derive a simple annotation schema for specific binary relation extraction problems such as protein-protein and gene-disease relation extraction. Second, we present BioNotate: an open source annotation resource for the distributed creation of a large corpus,” wrote C. Cano and colleagues, University of Granada.
The researchers concluded: “Third, we present and make available the results of a pilot annotation effort of the autism disease network.”
Cano and colleagues published their study in the Journal of Biomedical Informatics (Collaborative text-annotation resource for disease-centered relation extraction from biomedical text. Journal of Biomedical Informatics, 2009;42(5):967-77).
For additional information, contact C. Cano, University of Granada, Dept. of Computer Science and Artificial Intelligence, 18071 Granada, Spain.