Is there anyway to load ontologies from the OBO foundry directly into R? For example, I'd like to be able to load one of the Environment Ontology formats (read.obo?) and then run some simple queries like listing all terms assigned under the "fermented food" node. There seems to be alot of different graph classes in ontoTools and other R packages, and lots of ways to query these structures, so I'm not sure where to start. Thanks, Chris -- ------------------- Chris Stubben Los Alamos National Lab BioScience Division MS M888 Los Alamos, NM 87545

I haven't followed this field for a while, but if you can convert your .obo to RDF the Rredland package could be used to import. Rredland currently requires berkeleyDB infrastructure to install... and so we only build source image for linux. if that is a problem let me know, the package could be revised to eliminate this, but there has been limited concern with RDF in this domain thus far. On Tue, Jul 27, 2010 at 3:17 PM, stubben <stubben@lanl.gov> wrote: > Is there anyway to load ontologies from the OBO foundry directly into R? > For example, I'd like to be able to load one of the Environment Ontology > formats (read.obo?) and then run some simple queries like listing all terms > assigned under the "fermented food" node. > > There seems to be alot of different graph classes in ontoTools and other R > packages, and lots of ways to query these structures, so I'm not sure where > to start. > > Thanks, > > Chris > > -- > ------------------- > Chris Stubben > > Los Alamos National Lab > BioScience Division > MS M888 > Los Alamos, NM 87545 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]