I developed an algorithm that allows me to get information of crystallized proteins of a particular organism, and more. Among all this information, this algorithm gives me the gene ontology ids for the proteins found. My main target of research is finding potential therapeutic targets based on the action of these proteins, or if they are in some particular importan metabolic pathway. For that I need to make a tree that contain the gene ontology ids and the protein with which its related. This establishes a relationship between the chosen therapeutic target and because of this election, based on the protein action, and that information I will get from the tree of the ontologies. There is a programming tool or something to do this? Thanks to all.
This is a re-submission of the question you posted two days ago. You were given some examples of network programs dealing with GO there, are you in reality looking for help with constructing a gene phylogeny?
I will try to write a better message. I write an algorithm that search information about all the crystallized proteins in PDB and save them. Also save information about GeneBank code, SwissProt code, and saves all. Among all this information, i obtained the gene ontology id for all the proteins. I save them in the following format:
GO:0057896, GO:0002587, GO:0004515 ...
I read different manual of different softwares, and many use the flat format files to work, or the .obo format. Also I read the manuals trying to obtained the format required to work, but i can't. The result that i want is a tree-like image of all my ontologies, in the corresponding levels, and separated in cellular compartment, molecular function and biological process. Something like this [http://respiratory-research.com/content/12/1/63/figure/F4?highres=y]. I tried to used the topGO package of bioconductor and others, but this ones are used for microarray results, and to compare between diferentially expressed genes in diferent conditions. I don't need this, i just need a tree that do a relation of all my ontologies to see in witch celullar compartment are, or to see wath is their molecular function. This will give me the answer to select a potential therapeutic target for the organisms witch i work. I need to find a software or a programming tool that let me do this. Sorry for all the problems, i will be more careful.