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.



How to cite this record FAIRsharing.org: PSI-MOD; Protein MODification; DOI: https://doi.org/10.25504/FAIRsharing.2m4ms9; Last edited: Feb. 22, 2018, 2:02 p.m.; Last accessed: Oct 17 2018 6:34 a.m.


This record is maintained by HUPO PSI  (HUPOPSI)

Record updated: Nov. 17, 2017, 7:32 p.m. by The FAIRsharing Team.

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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

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PSIMOD Ontology Display

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Implementing Databases (5)
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
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites. Additionally, termini are annotated from user submitted lists of termini and inferred from user submitted lists of cleavage sites. As a protein-centric database, TopFIND presents a website for each protein isoform (organized around UniProt accession codes). These websites contain general protein information, such as organism, chromosome location, and proteins sequence. They then list position information such as specific termini evidences, known cleavage sites, sequence features and domains for each protein. In addition, TopFIND shows each protein in the context of the protease web, a network of proteases and their inhibitors, where a protease can cleave of other proteases and their inhibitors thus influencing their activity. All information in TopFIND can be filtered by a powerful filter engine that relies on rich annotation as to the origin of data in TopFIND. TopFIND can also be programmatically queried using the PSICQUIC or XML API. Recently, software tools were developed to enable quick access to TopFIND data for lists of termini obtained by, for example, proteomic termini screens (terminomics). TopFIND Explorer “TopFINDer” reports position specific protein information for protein termini, such as terminus evidences, prime and non-prime sequences, and protein domains affected by cleavage. TopFINDer further reports summary statistics for protein cleavage by known proteases. PathFINDer is a second tool that reports proteolytic paths from a query protease to identified protein substrates thus enabling the differentiation between direct and indirect protease substrates and yielding mechanistic insights into pathways based on existing information.

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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