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Analyzing PSI/MSI controlled vocabularies according to ontology best practices

Daniel Schober, ... and Steffen Neumann (submitted).


Besides a plethora of formal ontologies, the requirement for simple data annotation has led to an increased use of so called controlled vocabularies (CV) in multiple omics communities. We analyze two of those CVs from an ontological viewpoint, highlight typical modelling errors and propose more adequate solutions. Found errors are discussed in the light of different good and bad practice collections, namely the OBO Foundry naming conventions and the OOPS ontology pitfall framework.

Supplementary Material

Downloadable here.

Contact & Questions

For comments and questions please contact

dschober at ipb-halle dot de


We like to thank the Cosmos and PSI working groups. DS and SN were funded through the EU 7FP project COSMOS grant EC312941. GM is funded by ‘ProteomeXchange’ (, EU FP7 grant number 260558). ME is funded by the Protein Unit for Research in Europe (