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  • gene ontology terms second level

    Hi everyone,
    I am working with some proteomes and I did a multipfam2go annotation, so I have a file with multiples Gene Ontology IDs per protein. Now I want to get the 2 level GO-term for each GO-ID. I know there is nothing named second level in gene ontology, but I refer as second level GO-terms to the parent term under the root term for each GO-ID, similar to blast2go 2 level graphs.

    Right now I am able to get the GO-term for each GO-ID (from mysql database) but I don't know how to retrieve the 2 level GO-term. I was reading "Example LEAD queries" from gene ontology web http://wiki.geneontology.org/index.p...stance_to_root but I can't figure out how to do that.

    file format:

    Code:
    #proteinID DomainArchitecture GO-ID GO-ID GO-ID ...
    BBOV_IV005730 PF04811*PF08033*PF04815*PF04810 GO:0003674 GO:0043226 GO:0044446 GO:0006886 GO:0044424 GO:0030117
    One line per protein. DomainArchitecture column refers to the order how Pfam domains are found in the protein.

    Help please!!

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