Recapping gene-disease mining (via Twitter)

Gene Wiki Plus extensions

Storified by Andrew Su · Mon, May 07 2012 14:03:56

The uber-hacker Pierre posted a great blog post about using getting gene-disease mappings from the the Human Disease Ontology project.  I replied that our GeneWikiPlus effort was also generally focused on the same problem:
New blog post: Using the Disease ontology (DO) to map the genes involved in a category of disease. My notebook: http://bit.ly/INGQ57Pierre Lindenbaum
@yokofakun Nice… FYI, we also created http://genewikiplus.org to map gene-disease (and -SNP) links based on Gene Wiki + SNPedia #inpressAndrew Su
Chris Evelo subsequently followed up with an idea to adapt GeneWikiPlus to the Micronutrient Genomics Project:
@andrewsu any chance you can create "group of genes" -> genes -> SNP relationships for micronutrient relations on genewikiplus?Chris Evelo
@Chris_Evelo I think so? more details on what you’re thinking esp what you mean by "micronutrient relations"? perhaps easier by email…Andrew Su
@andrewsu Might be interesting to tweet as well. Is is about the Micronutrient Genomics Project (MGP) see: http://bit.ly/IWkAZJChris Evelo
MGP a.o. collects lists of genes and pathways about micronutrient metabolism and physiological role. Pathways at: http://bit.ly/IWlsNXChris Evelo
An example MGP genelist (iron) can be found here: http://bit.ly/IWlHsd but actually many genes are in micronutrient Gene Ontology classesChris Evelo
Would be great to automatically get those lists add SNPs and SNP function.Chris Evelo
Unfortunately, I promptly dropped the ball.  I’m picking that ball up now, resuming the discussion via Twitter

Incidentally, Pierre followed up his gene-disease mining effort with another implementation using the GeneWikiPlus SPARQL endpoint that the UniProt team put together:

Gene Wiki SPARQL endpoint http://ff.im/V9UEfBenjamin Good
New blog post: Mapping the genes involved in a category of disease: the GeneWikiPlus + SPARQL way.: http://bit.ly/IzxPyfPierre Lindenbaum
As usual, Pierre amazes with his hackery. 

I get a bit defensive that GeneWikiPlus isn’t yet “complete”, thinking we need to do more importing.  Ben rightly points out that it would be even better to get everyone to join the Linked Data world.

.@yokofakun works his magic again http://bit.ly/IzxPyf; GW+ clearly needs to import DO annotations for one-stop shoppingAndrew Su
@andrewsu of course if the DO gene Rif data was also shared as LInked Data, @yokofakun could produce that shop w/ one more import statementBenjamin Good


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