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The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of integration of the knowledge(More)
BACKGROUND In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named(More)
MOTIVATION Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by reducing the ambiguity inherent to free-text data. Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation,(More)
BACKGROUND The Gene Ontology Annotation (GOA) database http://www.ebi.ac.uk/GOA aims to provide high-quality supplementary GO annotation to proteins in the UniProt Knowledgebase. Like many other biological databases, GOA gathers much of its content from the careful manual curation of literature. However, as both the volume of literature and of proteins(More)
The Gene Regulation Ontology (GRO) is designed as a novel approach to model complex events that are part of the gene regulatory processes. We introduce the design requirements for such a conceptual model and discuss terminological resources suitable to base its construction on. The ontology defines gene regulation events in terms of ontological classes and(More)
BACKGROUND Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or(More)
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO(More)
In recent years, accompanied by lower prices of information and communications technology (ICT) equipment and networks, various items of data gleaned from the real world have come to be accumulated in cloud data centers. There are increasing hopes that analysis of this massive amount of data will provide insight that is valuable to both businesses and(More)
Semantic querying over the biomedical literature has gained popularity, where a semantic representation of biomedical documents is required. Previous BioNLP Shared Tasks exercised semantic event extraction with a small number of pre-defined event concepts. The GRO task of the BioNLP'13-ST imposes the challenge of dealing with over 100 GRO concepts. Its(More)