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RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized… (More)
BackgroundWe report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles.… (More)
In biomedical information extraction (IE), a central problem is the disambiguation of ambiguous names for domain specific entities, such as proteins, genes, etc. One important dimension of ambiguity… (More)
BackgroundDetermining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go… (More)
In the rest of this paper, we first give some background on the context in which the system used in the MUC-7 NE task was developed. We then outline its internal structure, concentrating on the rule… (More)
Attempto Controlled English (ACE) is a knowledge representation language with an English syntax. Thus ACE can be used by anyone, even without being familiar with formal notations. The Attempto… (More)
Describes the ExtrAns answer-extraction system which uses logical forms and lexical relations for semantic representation, to delve into and leverage the meaning of sentences, phrases, and words.
We present a Question Answering system for technical domains which makes an intelligent use of paraphrases to increase the likelihood of finding the answer to the user's question. The system… (More)
In this paper we describe current efforts aimed at adapting an existing Question Answering system to a new document set, namely research papers in the genomics domain. The system has been originally… (More)
Discovering the interactions between genes and proteins is seen as one of the core tasks in molecular biology. The quantity of research results in this area is growing at such a rate that it is very… (More)