PHI-Canto v1509
Community curation
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Curating Protein Modifications

A protein modification is any covalent modification or other change that alters the measured molecular mass of a peptide or protein amino acid residue.

Canto uses the PSI-MOD ontology for protein modification annotations.

When you choose "Protein modification", you go to an ontology term search page that works the same way as those for GO and phenotype terms: start typing a term, and matching suggestions will appear.

You may find it helpful to search for a broad term (e.g. phosphorylated, methylated, lysine), especially if you have trouble finding a specific term.

After you choose a term from the autocomplete list, you will go to a page that shows the term definition and any more specific terms in the ontology. You can thus refine your search iteratively before making your final selection (examples of more specific terms are: O-phospho-L-serine, monomethylated L-lysine). Also see the hints below, which should help you search for, and recognize, the terms you need. Please read the definition carefully to ensure that it fits your results accurately and completely.

When you have decided which term to use, click "Proceed" on the term page. On the next page, select the applicable evidence from the pulldown, then "Proceed" again. On the final page, you can add a comment; for example, if you have any details that don't fit the available annotation extensions, you can put them in the "message to curators" box (which you see when you submit your curation session).

Gene products may be annotated with multiple protein modification terms.

Hints for finding useful modification terms

Because PSI-MOD contains a number of very specific terms that may not be familiar to all Canto users, PomBase curators have assembled a list of common modifications and the best PSI-MOD terms to use for them.

Annotation extensions

You can add annotation extensions to provide additional specificity for protein modification annotations. (See the PomBase documentation for more information on annotation extensions.) After you have selected an ontology term and evidence, the Canto interface will display any available extension types. Click the link to choose an extension type and bring up a pop-up in which you specify the required details for the extension. For example, an annotation to "O-phospho-L-threonine" can have any of these extensions:

Modification annotation extension options

Several annotation extension types are allowed for protein modifications, falling into a few categories:

In all cases, the actual relation name used by the database will appear when you have finished the annotation plus extensions.

You can add one of each type, but if you add them at the same time they will be interpreted as going together to form a compound annotation in which all of the parts apply at once. To create independent annotations (i.e. where one or another may apply, but not necessarily all at once), finish the annotation with one extension (or set of extensions), and then use the "Copy and edit" feature to create another annotation where you can edit the extension(s).

When you edit or duplicate an annotation, extensions can also be added, amended or deleted. An "Edit" button in the pop-up launches the annotation extension addition steps.

button to edit annotation extensions

To change an existing extension, first delete it and then add a new one. Editing interface ("protein mislocalized to nucleus" example from FYPO):

Annotation extension editing interface