Genomics | Bioinformatics
Genome design with the semantic web
Robert Sidney Cox III, Tetsuro Toyoda*
*Corresponding author: Tetsuro Toyoda
Bioinformatics and Systems Engineering Division, RIKEN Institute, Yokohama, Japan
F1000Posters 2012, 3: 46 (poster) [English]
Poster [6.36 MB]
4th International Workshop on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2011, 7 - 9 Dec 2011, 45
Organisms with designer genomes promise to provide fuels, medicines, diagnostics, and food for our civilization. Multiple design choices are informed by biological data, and semantic web technology can empower these choices.
Tools for genome design must be continuously updatable from growing databases, must use standard portable and automatable file formats, must be scalable to the size of entire genomes, and must facilitate queryable alignments of phenotype with sequence data.
To develop a genome design ontology that allows multiple software tools and workflows to share data. This ontology could be linked from current ontologies describing sequence features, genetic components, DNA construction, and phenotype.
Copyright #1: Manmade DNA construct graph was reproduced with kind permission from: Carlson, R. (2009). Nat Biotechnol 27(12), 1091-1094
Copyright #2: Model Gene Function (Figure 1) was reproduced with kind permission from: Chandran, D et al (2009) J Biol Eng, 3:19
Copyright #3: Example: Chimeric protein sensor (Figure 3A) and the promoter library was reproduced with kind permission from: Mukherji, S et al (2009). Nat Rev Genet 10, 859-871
Copyright #4: Transcriptional BioBricks was reproduced with kind permission from: Galdzicki, M et al (2011). PLoS ONE 6,2, e17005
Copyright #5: The process of RNA transcription was reproduced with kind permission from: Eilbeck, K et al (2005). Genome biology 6,5, R44
No relevant competing interests disclosed.
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