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

By L. Montecchi-Palazzi, Ronald C. Beavis, P. Binz, R. Chalkley, J. Cottrell, D. Creasy, J. Shofstahl, S. Seymour, J. Garavelli. 2008

148 citations recorded by the source corpus.

Subfields: Molecular Biology

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In Molecular Biology

Citations in the corpus

UniProt: the universal protein knowledgebase (2016, methodology): “Each PTM annotation is associated with a controlled vocabulary established in collaboration with the RESID database (12) and PSI-MOD (13).”
PomBase: a comprehensive online resource for fission yeast (2011, background): “Sequence Ontology DNA features 31 25 650 Protein features 22 919 Gene Ontology Biological process 1861 14 501 Molecular function 1405 9149 Cellular component 543 16 101 Fission yeast phenotype ontology 342 7043 Gene product descriptions 4331 7048 Disease associations 134 378 PSI-MOD(3) protein modif”
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities (2016, methodology): “We then add the PTM information in a specific order based on the position of the modified residue nearest the N terminus, but grouped by type of modification given as a PSI-MOD (8) identifier.”
The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, methodology): “We have mapped Protein Modifications (PMs) in the PDB to the RESID database of PMs (18,19) and the associated Protein Modifications Ontology PSI-MOD (20).”
The Reactome pathway knowledgebase (2013, background): “The underlying chemical similarity between a protein that differs from its canonical form due to a mutation and one that differs due to co- or post-translational modification allows us to maintain compliance with the PSI-MOD standard for annotation of protein modifications (14).”
iProX: an integrated proteome resource (2018, background): “NCBITAXON (NCBI organismal classification) for organismal taxonomy, DOID (Human Disease Ontology) (28) for human disease states, BTO (BRENDA tissue/enzyme source) (29) for tissues, CL (Cell Ontology) (30) for cell types, and PRIDE CV (PRIDE Controlled Vocabulary), PSI-MS CV (MS ontology) (6), MOD (P”
Reactome: a database of reactions, pathways and biological processes (2010, methodology): “In response to user requests, we recently changed the representation of protein modifications in Reactome to the PSI-MOD standard (33).”
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data (2014, background): “For example, every described PTM is associated with a controlled vocabulary established in collaboration with the RESID database (23) and is also linked to the corresponding (24).”