Sampo Pyysalo

Learn More
The paper presents the design and implementation of the BioNLP’09 Shared Task, and reports the final results with analysis. The shared task consists of three sub-tasks, each of which addresses bio-molecular event extraction at a different level of specificity. The data was developed based on the GENIA event corpus. The shared task was run over 12 weeks,(More)
Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. We present BioInfer (Bio Information Extraction(More)
Automated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In contrast to earlier approaches to PPI extraction, the introduced all-paths graph kernel has the capability to make use of full, general dependency graphs representing the(More)
Cross-linguistically consistent annotation is necessary for sound comparative evaluation and cross-lingual learning experiments. It is also useful for multilingual system development and comparative linguistic studies. Universal Dependencies is an open community effort to create cross-linguistically consistent treebank annotation for many languages within a(More)
We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss(More)
In this paper, we propose a graph kernel based approach for the automated extraction of protein-protein interactions (PPI) from scientific literature. In contrast to earlier approaches to PPI extraction, the introduced alldependency-paths kernel has the capability to consider full, general dependency graphs. We evaluate the proposed method across five(More)
Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate.(More)
The BioNLP Shared Task 2013 is the third edition of the BioNLP Shared Task series that is a community-wide effort to address fine-grained, structural information extraction from biomedical literature. The BioNLP Shared Task 2013 was held from January to April 2013. Six main tasks were proposed. 38 final submissions were received, from 22 teams. The results(More)
The BioNLP Shared Task 2011, an information extraction task held over 6 months up to March 2011, met with community-wide participation, receiving 46 final submissions from 24 teams. Five main tasks and three supporting tasks were arranged, and their results show advances in the state of the art in fine-grained biomedical domain information extraction and(More)