Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

Abstract

BACKGROUND: A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level. RESULTS: This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context writt..