Am I missing something, specificity does not appear to be captured in the GOMO XML output though present in the HTML

[Anne Deslattes Mays]

Hello,

I've just used GOMO after running AME on sequences against the ATtRACT motif database.  Very useful HTML output, now I want to parse the results, when I downloaded the XML gzipped results it does not appear to include the specificity information, or all of the information one sees in the HTML pages.  Is this correct?

[CharlesEGrant]

The specificity is in the XML file, but only implicitly. In the XML file, each GO term has attributes "nabove" and "nbelow", where "nabove" is the number of parent GO terms between the term in question and the root term, and "nbelow" is the number of GO terms that have the term in question as a parent. The specificity is just

specificity = (nabove / (nabove + nbelow)) * (100)