GO uses external ontologies for the logical definitions of some terms.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. ChEBI is used to describe compounds in GO, as well as in RHEA. Compounds used in GO are the forms present at pH 7.3, the physiological pH under most conditions in most organisms annotated with GO. The pH is not 7.3 in all organelles, organs and organisms, but this was chosen as the most common form of the compounds.
To find which form of a chemical is present at pH7.3, go to www.rhea-db.org and search for the CHEBI ID of the compound you have or for the compound name. Choose one of the reactions and scroll down to "reaction participants"; follow the link to ChEBI to get the compound name and ID.
Missing chemicals should be added to the GO imports file.
Cell Type Ontology