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Motivation: The automatic analysis of scientific literature can support authors in writing their manuscripts.Implementation: PaperMaker is a novel IT solution that receives a scientific manuscript via a Web interface, automatically analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It analyses the proper use of acronyms and their definitions, and the use of specialized terminology. It provides Gene Ontology (GO) and Medline Subject Headings (MeSH) categorization of text passages, the retrieval of relevant publications from public scientific literature repositories, and the identification of missing or unused references.Result: The author receives a summary of findings, the manuscript in its corrected form and a digital abstract containing the GO and MeSH annotations in the NLM/PubMed format.Availability: http://www.ebi.ac.uk/Rebholz-srv/PaperMakerContact: rebholz@ebi.ac.uk