Hi Jayne,
interesting! Your gist looks like you can use it to find GO terms associated to chemical/gene combinations. So you have nicely modeled your data and queried it. Do you have an actual problem or question :) ?
I use GO and other ontologies a lot and I have similar queries for e.g. microRNAs and genes. For me it often works well to consider the neighborhood of the gene. I added gene-gene interactions (e.g. from KEGG or STRING). Then I do an enrichment analysis with the gene + all neighboring genes instead of simply taking all GO terms associated to the gene. The neighboring genes themselves can give you a hint towards the gene's function. Your gene might be a phosphatase, but the target it phosphorylates could be interesting.
Bio4j is huge but maybe a bit overkill if you are getting started.
Cheers
Martin
Am Sonntag, 13. Juli 2014 um 01:24 schrieb Jayne Ihaka:
> Hi everyone,
>
> Just wondering if this group is still active?
>
> I'm learning how to use Neo4j and Cypher at the moment. I thought I would try combining some results from a synthetic genetic array analysis with data from the Saccharomyces Genome Database and gene ontologies.
>
> I've made my first attempt into a GraphGist and would really appreciate some feedback on it. Finding it a bit of a challenge to clearly articulate why graphs are so useful for this kind of dataset. The link is here (
http://www.neo4j.org/graphgist?e4f4b46237c68cf8ca68).
>
> Has anyone in this group been using data from SGD with Neo4j? If someone can link me to some resources that would be great. I'm currently checking out Bio4j.
>
> Cheers,
>
> Jayne.
>
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