Currently the mzML controlled vocabulary file:
http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
Contains terms with a duplicate ID, which is not allowed according to the OBO standard. See the lines:
[Term] id: MS:1002289 name: ProteinProphet def: "A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format." [PMID:14632076] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002289 name: ASAPRatio def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software
This is the only duplicate ID in the file.