Abstract
BackgroundBiomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE) systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event.ResultsWe have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events). High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa.ConclusionBy augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative information to be specified as part of the search criteria. This can assist in a number of important tasks, e.g., finding new experimental knowledge to facilitate database curation, enabling textual inference to detect entailments and contradictions, etc. To our knowledge, our scheme is unique within the field with regards to the diversity of meta-knowledge aspects annotated for each event.
Highlights
Biomedical papers contain rich information about entities, facts and events of biological relevance
In response to the issues outlined above, we have developed a new annotation scheme that is tailored to enriching biomedical event corpora with meta-knowledge, in order to facilitate the training of more useful systems in the context of various information extraction (IE) tasks performed on biomedical literature
This is followed by a report on the level of agreement achieved between the annotators in the double-annotated part of the corpus, and an examination of the different kinds of discrepancies that were found within these abstracts
Summary
Biomedical papers contain rich information about entities, facts and events of biological relevance. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE) systems, to facilitate semantic-based searching of documents. Event-based text mining Information extraction (IE) systems facilitate semantic searching by producing classified, structured, templatelike representations of important facts and findings contained within documents, called events. A number of corpora of biomedical texts annotated for events have been produced (e.g., [13,14,15]), on which IE systems in the biomedical domain can be trained
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