AmiGO: Prototypes (Archived)

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Summary

Prototypes and information for various additions and permutations of AmiGO

Reference Genome

We wish to provide dynamic visualizations of reference genome target gene annotations. We focus on experimental (IMP, IPI, IGI, IEP, IDA) and ISS evidence codes. The visualization should be able to:

1. Show annotations to a single organism ortholog to a target gene;

2. Show annotations to selected organisms orthologs to a target gene;

3. Show annotations to the full set of orthologs to a target gene.

Currently, reference genome visualization is done as static comparison graphs for all 11 organisms produced from flat files (gene_ontology.obo, gene_association.organism) and using the target genes and orthology calls available as google spreadsheets. The graphs are updated monthly as new targets are added. Ecoli will be added when annotations are available.

The full set of graphs for current targets is available at: http://www.geneontology.org/images/RefGenomeGraphs/ The set includes an html page for each target gene displaying all experimental and ISS annotations for all orthologs.

For example: http://www.geneontology.org/images/RefGenomeGraphs/609309.html

Each page shows GO DAG with annotations color-coded by organism in both fixed (png) and svg formats; a GOSlim organism comparison table; and a table listing full details of all annotations (evidence code, reference).

Ideas, mockups, and software demos for possible Reference Genome Browsers/Visualization.

Clock

SVG and JS

A demonstration possibilities opened by using SVG and JavaScript.

Tree/DAG Browser Test

Early Biaxial and SVG Viewers

These work fairly well on FF (lesser WebKit).

Test Site

An up and down site for various technology tests.