Protein Modification Ontology

Last uploaded: June 12, 2026

Details

Acronym	PSIMOD
Visibility	Public
Description	PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.
Status	Production
Format	OBO
Groups	Proteomics Standards Initiative OBO Foundry

Contact	Sylvie Ricard Blum ([email protected]) Pierre Alain Binz ([email protected])
Creation date	June 12, 2026
Deprecated	false See more...
Homepage	http://www.psidev.info/MOD See more...
Notes	Annotation note 09 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references. See more... PSI-MOD version: 1.033.0 See more... Annotation note 07 - The synonym cross-reference "MOD:old name" has been replaced by "MOD:alternate name". See more... RESID release: 75.00 See more... Annotation note 08 - The DeltaMass listings for free amino acids have been removed. Most Unimod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter. See more... PSI-MOD version: 1.032.1 See more... Annotation note 01 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235. See more... Annotation note 04 - The elemental formulas are in strict alphabetical order, not in CAS ("C" and "H" first) order. Isotope numbers are in parentheses before the element symbol, and an element should not occur in a formula both with and without an isotope number. In difference formulas, counts can be zero or negative. See more... PSI-MOD version: 1.032.4 See more... PSI-MOD version: 1.032.2 See more... Annotation note 10 - GNOme is the Glycan Naming and Subsumption Ontology (https://gnome.glyomics.org/), an ontology for the support of glycomics. PSI-MOD does not have all possible glycans in its entries, just the ones that are noted to be on proteins and have been requested for addition. GNOme uses GlyTouCan (http://glytoucan.org/) to provide stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). See more... Annotation note 06 - For cross-link modifications, the number following "Cross-link" in the comment record indicates the number of amino acid residues that appear in the origin record, used to check the difference formula and masses. This usage differs from RESID, where the cross-link number indicates the maximum number of peptide chains that can be cross-linked. See more... Annotation note 02 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var". See more... Annotation note 03 - When an entry in the Unimod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the Unimod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term". See more... Annotation note 05 - In entries with an isotope indicator in the formula, average masses are meaningless and are assigned the value equal to the monoisotopic mass, but rounded to a lower precision; monoisotopic masses are calculated by using the masses for the indicated isotopes and the most common isotopes for other elements without isotope indicators in the formulas. See more... ISO-8601 date: 2022-06-13 12:12Z See more...
Object creation date property	http://purl.org/dc/elements/1.1/created http://purl.org/dc/elements/1.1/created
Object modification date property	http://purl.org/dc/elements/1.1/modified http://purl.org/dc/elements/1.1/modified
Preferred namespace prefix	PSI-MOD See more...
Submission date	June 12, 2026
Syntax	http://purl.obolibrary.org/obo/oboformat/spec.html http://purl.obolibrary.org/obo/oboformat/spec.html
Version IRI	http://purl.obolibrary.org/obo/mod/1.036.0/mod.owl http://purl.obolibrary.org/obo/mod/1.036.0/mod.owl
Version information	1.031.6 See more...
uri	http://purl.obolibrary.org/obo/mod.owl http://purl.obolibrary.org/obo/mod.owl

Version	Released	Uploaded	Downloads
1.031.6 (Parsed, Indexed, Metrics, Annotator)	06/12/2026	06/12/2026	OBO \| CSV \| RDF/XML \| Diff
1.031.6 (Archived)	06/02/2026	06/02/2026	OBO \| Diff
1.031.6 (Archived)	04/17/2026	04/17/2026	OBO \| Diff
1.031.6 (Archived)	11/21/2025	11/21/2025	OBO \| Diff
1.031.6 (Archived)	11/17/2025	11/17/2025	OBO \| Diff
1.031.6 (Archived)	11/04/2025	11/04/2025	OBO \| Diff
1.031.6 (Archived)	06/14/2022	06/14/2022	OBO \| Diff
1.031.4 (Archived)	05/13/2022	05/13/2022	OBO \| Diff
1.031.4 (Archived)	02/21/2022	02/21/2022	OBO \| Diff
1.031.3 (Archived)	02/20/2022	02/20/2022	OBO \| Diff
1.013.0 (Archived)	03/10/2021	03/10/2021	OBO \| Diff
1.013.0 (Archived)	02/12/2021	02/12/2021	OBO \| Diff
1.013.0 (Archived)	02/01/2021	02/01/2021	OBO \| Diff
1.013.0 (Archived)	01/11/2021	01/11/2021	OBO \| Diff
1.013.0 (Archived)	12/04/2020	12/04/2020	OBO \| Diff
1.013.0 (Archived)	12/03/2020	12/03/2020	OBO \| Diff
1.013.0 (Archived)	11/30/2020	11/30/2020	OBO \| Diff
1.013.0 (Archived)	11/24/2020	11/24/2020	OBO \| Diff
1.013.0 (Archived)	10/20/2020	10/20/2020	OBO \| Diff
1.013.0 (Archived)	10/05/2020	10/05/2020	OBO \| Diff
1.013.0 (Archived)	07/22/2020	07/22/2020	OBO \| Diff
1.013.0 (Archived)	06/25/2020	06/25/2020	OBO \| Diff
1.013.0 (Archived)	06/18/2020	06/18/2020	OBO \| Diff
1.013.0 (Archived)	05/08/2020	05/08/2020	OBO \| Diff
1.013.0 (Archived)	04/20/2020	04/20/2020	OBO \| Diff
1.013.0 (Archived)	04/09/2020	04/09/2020	OBO \| Diff
1.013.0 (Archived)	02/22/2020	02/22/2020	OBO \| Diff
1.013.0 (Archived)	01/29/2018	03/01/2018	OBO \| Diff
1.013.0 (Archived)	05/30/2014	06/17/2014	OBO \| Diff
1.317 (Archived)	11/27/2007	11/27/2007	OBO
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Classes	2,116
Individuals	0
Properties	4
Maximum depth	9
Maximum number of children	118
Average number of children	6
Classes with a single child	104
Classes with more than 25 children	29
Classes with no definition	0

No projects using PSIMOD