Su Lab project proposal accepted to Biohackathon 2016 in Tsuruoka, Yamagata, Japan
To create a model organism database web application, using Wikidata as the backend, that the microbial research community can use to load an organism and view its taxonomic information as well as genome, gene and functional annotations all in one place. It will be simple interface with 4 frames/boxes of content (e.g. Taxonomy, Genome Browser, Gene, Gene Product), and a search box for each window. The 4 domain windows include:
- Organism Info (i.e. basic taxonomy information/identifiers, gram -/+, microbiome/host association, disease/drug associations etc…)
- Genome Browser (Apollo Genome browser to view genome annotations)
- Gene Info (i.e. basic gene information/annotations/identifiers) and
- Gene Product Info (i.e. basic gene product information/identifiers/functional annotations etc…).
In addition to viewing data, the user will have the ability to write evidence based claims to Wikidata for each domain of data in the interface. A user could add a regulatory annotation to a gene, a functional annotation to a protein, a disease caused by an organism, or small-RNA annotation to the genome.
The application will provide a means for a domain expert to be able to access the knowledge stored in Wikidata, and contribute their own knowledge to the graph with write-back functionality. This would allow scientists in different fields, in different parts of the world to collaborate, and provide a much needed structured centralized model organism database for the microbiology community,with potential to expand to all organisms.
–Tim Putman and Sebastian Burgstaller-Muelbacher