standards > terminology artifact > DOI:10.25504/FAIRsharing.2m4ms9


ready Protein MODification

Abbreviation: PSI-MOD


General Information
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.

Homepage http://www.psidev.info/groups/protein-modifications

Countries that developed this resource Canada , Switzerland , United Kingdom , United States

Created in 2007

Taxonomic range

Subjects 




How to cite this record FAIRsharing.org: PSI-MOD; Protein MODification; DOI: https://doi.org/10.25504/FAIRsharing.2m4ms9; Last edited: March 11, 2019, 11:23 a.m.; Last accessed: Apr 17 2021 3 p.m.

Publication for citation  The PSI-MOD community standard for representation of protein modification data. Montecchi-Palazzi L,Beavis R,Binz PA,Chalkley RJ,Cottrell J,Creasy D,Shofstahl J,Seymour SL,Garavelli JS; Nat Biotechnol ; 2008; 10.1038/nbt0808-864;


This record is maintained by HUPO PSI  (HUPOPSI)

Record updated: March 11, 2019, 11:21 a.m. by The FAIRsharing Team.

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In Collections
FAIRDOM Community Standards
HUPO Proteomics Standards Initiative


Support

General

support email Pierre-Alain Binz
Mailing List PSI-MOD Mailing List
online documentation PSI-MOD Changelist

Additional Information

Contact John S Garavelli

External Links

Bioportal http://bioportal.bioontology.org/ontologies/PSIMOD
OBO http://obofoundry.org/ontology/mod.html

Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Download (OWL) http://purl.obolibrary.org/obo/mod.owl

Data Access

browse http://www.ebi.ac.uk/ols/ontologies/mod
search https://www.ebi.ac.uk/ols/ontologies/mod



Publications

The PSI-MOD community standard for representation of protein modification data.

Montecchi-Palazzi L,Beavis R,Binz PA,Chalkley RJ,Cottrell J,Creasy D,Shofstahl J,Seymour SL,Garavelli JS
Nat Biotechnol 2008

View Paper (PubMed) View Publication

PSIMOD Ontology Display

View in BioPortal.


Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.



Related Standards

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Related Databases (6)
Minimotif Miner 3.0
A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.
PomBase
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
Termini-Oriented Protein Function INferred Database
The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
Complex Portal
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download.

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