AnnoWiki: a versatile platform for genome annotation
Luca Cozzuto1,2, Antonio Hermoso Pulido1,2 and Jean-François Taly1,2
1Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona
2Universitat Pompeu Fabra (UPF), 08003 Barcelona
DNA sequencing Assembly Annotation
AnnoWiki reads different kind of formats (GFF, BED, FASTA…) for displaying different kind of annotations (genes, transcripts, exons). It is able to deal
with multiple genome or multiple genome versions.
Every annotation and format are described as a PHP object and displayed in the Semantic
Mediawiki within a template. The page can be modified after the data input.
Each annotation is displayed as a page with a number of features. Internal links can be automatically
generated to create a hierarchy between features.
Screenshots from genome browsers can be embedded by using special functions.
AnnoWiki can be mined as any Semantic MediaWiki in a database fashion mode or from API.
The aim of this project is:
• Provide to communities of annotators a central platform for exchanging data
• Support scientists for publishing
• Improve annotations by taking advantage of the comments made by experts
in manual curation
• Embedding JBrowse genome browser
• Expanding the platform for reading different kinds of data
• Streaming of data to third-party webservices
• Transforming the software in a deliverable package
Annotation pages can be manually edited and any necessary correction easily included thanks to embedded forms (which can be used even from tablets or
smartphones). As any wiki, it's also possible to track the collaboration on the different pages.
However, as innovation, we also provide the possibility to define edition role groups for every annotation class and their specific fields
At the end, a modified annotation can be obtained as a new file.
1. Huss, J. W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T. J., Valafar, F., et al. (2008). A gene wiki for
community annotation of gene function. PLoS Biology.
2. Cariaso, M., & Lennon, G. (2012). SNPedia: A wiki supporting personal genome annotation,
interpretationand analysis. Nucleic Acids Research, 40(D1).
3. Sanseverino, W., Hermoso, A., DʼAlessandro, R., Vlasova, A., Andolfo, G., Frusciante, L., Lowy, E., et al.
(2013). PRGdb 2.0: Towards a community-based database model for the analysis of R-genes in plants.
Nucleic Acids Research, 41(D1).
MySQL DB•Parsing the data
•Inserting in the db •Template allows the
selection of fields to show