Genes to human phenotype ontologies

Question

[m_asi]

I am looking for a R package or tool to find human phenotype ontologies (HPO) for a list of genes using semantic methods. I saw one paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115692 where they wrote a R package, namely HPOSim. But I am unable to load it.

Do you know some other R packages like HPOSim or tools? or some has used HPOSim package?

Thanks

Answer 1

[Giovanni M Dall'Olio]

What error do you get when you load HPOSim? If you can't use the package it would be nice of you to write to the authors and ask them to fix it.

In alternative, I used DOSE which allows to do enrichment on Disease Ontology. Not sure how much it is different from HPO.

[m_asi]

I solved the HPOSim problem. But it didn't work for my problem. Is there any package or tool with which I can find genes for disease symptoms?

Thanks

Answer 2

[buske]

It's not quite what you're asking, but you can download known HPO-gene associations computed by the HPO team from their download page (genes_to_phenotype.txt and phenotype_to_genes.txt).