I've downloaded GO terms from Phytozome using Biomart. I'd like to know what is the real source of those GO terms and the version of its database if it is possible.
ahahhahahaha I have your same problem, I did my genes anotations with BioMart in Phytozome but now I want to do the GO in Blast2GO because I don't know if Biomart is a realiable tool but the problem is in this database, I can't find a tool to import the gen IDs or GO IDs generated by BioMart, I gonna start doing the hard work: the fasta of my genes and import this for Blast2go. If you find a easier way, please tell me!!
What is/are your species of interest?
C. papaya, is not a model organism :/, I almost finish my analysis and actually I did like to work with Blast2Go, the process is slow, tedious and monotonous but it have good tools and once the GO IDs are obtained you can to use another online database for to organize your information... I think that should to exist some tool for doing easier the work but I didn't find...
I assume this differs for the different species, but the Phytozome staff should be best qualified to answer this question.