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BioNotes – A Sequence Annotation System

One of the most important tasks of genome projects is the interpretation of experimental data in order to derive biological knowledge from the data. To achieve this goal, researchers typically search external data sources, execute analysis programs on the sequences, analyze previous annotations and add new annotations to register their interpretation of the data. This abstract presents the annotation system BioNotes, stressing the advantages it brings to the life science researchers. The BioNotes system stores in a data warehouse annotations manually created by the researchers, annotations automatically generated by analysis programs, annotations imported from external data sources and hyperlinks to annotations stored in external data sources. The system offers tools to search the annotations stored, to navigate through hyperlinks to annotations stored in external data sources, to locate annotations by “drilling down” the data pertaining to a genome (such as chromosomes, contigs, reads, ORFs, among others), to visualize the sequences and their characteristics using reports, graphics and figures. BioNotes also tabulates annotations assigned by different data sources or different analysis programs to the same sequence. This feature helps users compare the annotations and make their conclusion. For example, the user may run BLAST to compare a new sequence against various data sources to detect similar sequences, and then work with the functional annotations of the similar sequences to help him annotate the new sequence. The system is especially useful to annotate genome data with incomplete sequencing. While a genome project is in progress, sequencing of the genome will generate new reads, creating new versions of the data. Hence, BioNotes offers tools to help users transfer manual annotations from older to newer versions of the data, as otherwise it would be very discouraging to annotate data from on-going sequencing projects. The system maintains versions of the annotations. BioNotes has workflow-like facilities to control the execution of analysis programs and to specify which programs generate annotations stored in the data warehouse. The BioNotes project is flexible and the system can be used to annotate sequences from complete genome project and from EST projects. It is currently used by the Department of Biochemistry and Molecular Biology, Federal University of Rio de Janeiro, to annotate EST sequences of Rhodnius prolixus, and by RioGene Consortium, to annotate the complete genome of the bacteria Gluconacetobacter diazotrophicus. The implementation uses the infrastructure of the BioAXS system, is written in Java for portability, and offers a distributed access to the annotations using a user-friendly web interface implemented with JSP technology. The tool runs on top of a relational database management system which stores XML documents and supports Xpath queries. The system is under development at the Pontifical Catholic University of Rio de Janeiro.