I'm looking for a tool (either webservice or downloadable code) which can identify and disambiguate gene mentions in free text. I need the disambiguation to attribute the gene mention to a database ID (any database will do, I can convert between them). I need to annotate genes from multiple species (many are non-human).
I've been using the Whatizit tool from EBI but its having difficulty detecting the organism ... If you want to take a look I've got my analysis code on github.