The AnnoTrack software system (Kokocinski et al. 2010) was developed as part of the GENCODE collaboration to facilitate the processing and tracking of the HAVANA annotation and the heterogeneous sources of information used in the genome annotation. It integrates data from distributed sources via DAS (Distributed Annotation System) servers set up by the GENCODE partners following a defined format (http://www.gencodegenes.org/gencodedasformats.html), a direct database connection to Ensembl, and flat file adaptors. The system highlights conflicts and facilitates the quick identification, prioritization, and resolution of problems during the process of genome annotation. Using controlled terms for the solutions chosen by the manual annotators when resolving conflicts allows a retrospective assessment in order to improve the analysis methods or external data sources. More than 4000 issues have been resolved this way in the last year. AnnoTrack also helps to track the progress of the overall HAVANA annotation and to inform external scientists about current issues about the genes they might be working with. The interface can be accessed at http://annotrack.sanger.ac.uk/human.
