Guidelines for using ChEBI terms

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Using the major microspecies at pH 7.3

For consistency we prefer to use the ChEBI term representing the major microspecies at pH 7.3. A mapping from ChEBI term IDs to the pH 7.3 form is available from Rhea (chebi_pH7_3_mapping.tsv). A script in the ontology build checks that whenever a mapping is available, only the pH 7.3 form is used within the ontology.

Fixing build failures

To see if a pull request has failed due to the pH 7.3 check, look for output like this:

 ERROR: CHEBI IDs should be mapped to pH 7.3:

The number 7719 indicates the problem ChEBI ID which was used. Go to the mapping file and find the entry for that term:

 7719	166829	computation

The second number is the ChEBI ID to use for the pH 7.3 form.