The Naming of Things

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The systematic renaming process

Reactome, the pathway database, often needs to represent a protein in several different forms, perhaps the initial translated form and fragments of this following processing, or after many different kinds of post-translational modification. In response to this need, we have developed a systematic nomenclature for the names of peptides.

Gene symbol core

We use HGNC gene symbols as the 'core' of the name. These are identified from UniProt.

Peptide coordinates suffix

We often represent several peptides that are derived from the same translated protein, all sharing a common UniProt external reference. To generate unique names for these we add the start and end coordinates of the peptide as a suffix to the gene symbol. The coordinates of the Reactome peptide are compared with UniProt's 'Chain' feature; in UniProt this feature is part of an annotation group called Molecular Features. This feature is used because it represents the 'default' peptide; this usage is consistent with our use of Uniprot IDs as our primary external peptide reference. If the start and end coordinates of the Reactome peptide agree with the Uniprot Chain feature, the coordinates are not added to the gene symbol. If either coordinate is not the same as the Chain feature, both Reactome coordinates are added as a gene symbol suffix. When the true peptide start or end coordinates are unknown, the '?' symbol is used. This combination of gene symbol plus coordinates is usually sufficient to generate a unique name.

Post-translational modification (PTM) prefixes

PTMs are shown as prefixes to the gene symbol.

Exemptions

Some Reactome peptides are exempt from systematic renaming. Peptides exempted from renaming are named in a style that is similar to the systematic style, so far as possible.

Find out more

Reactome is an open-source, open access, manually curated and peer-reviewed pathway database.

You can read a full explanation of the peptide renaming process ion the Reactome Wiki.