Protein MODification
Names
More detailed information about this field from each metasource.
Protein MODification
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
PSI-MOD
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
Protein Modification Ontology
metasource: Biontology / Bioportal
version: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
PSIMOD
metasource: Biontology / Bioportal
version: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
Names
More detailed information about this field from each metasource.
Protein MODification
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
PSI-MOD
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
Protein Modification Ontology
metasource: Biontology / Bioportalversion: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
PSIMOD
metasource: Biontology / Bioportalversion: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
Other names: PSI-MOD, Protein Modification Ontology, PSIMOD
Names
More detailed information about this field from each metasource.
Protein MODification
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
PSI-MOD
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
Protein Modification Ontology
metasource: Biontology / Bioportalversion: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
PSIMOD
metasource: Biontology / Bioportalversion: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
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.
Description
More detailed information about this field from each metasource.
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.
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
metasource: Biontology / Bioportal
version: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
Webpage:
http://www.psidev.info/groups/protein-modificationsWebpage
More detailed information about this field from each metasource.
http://www.psidev.info/groups/protein-modifications
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
http://www.psidev.info/MOD
metasource: Biontology / Bioportalversion: 1.031.6 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/PSIMOD
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The PSI-MOD community standard for representation of protein modification data
PMID: 18688235
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
Publications
More detailed information about this field from each metasource.
The PSI-MOD community standard for representation of protein modification data
PMID: 18688235
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
-
The PSI-MOD community standard for representation of protein modification data
PubMed citations: 82.
82 articles citing: The PSI-MOD community standard for representation of protein modification data
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. PMID:35290070
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology. PMID:35100366
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. PMID:34411258
ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). PMID:33834021
DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PMID:33150092
Global chemical modifications comparison of human plasma proteome from two different age groups. PMID:32929118
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format. PMID:32106352
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. PMID:31363752
Proteomics Standards Initiative Extended FASTA Format. PMID:31081335
DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results. PMID:30523686
iProX: an integrated proteome resource. PMID:30252093
Minimotifs dysfunction is pervasive in neurodegenerative disorders. PMID:30225339
PomBase: The Scientific Resource for Fission Yeast. PMID:29761456
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
ProForma: A Standard Proteoform Notation. PMID:29397739
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets. PMID:28792687
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. PMID:28334105
Tutorial on Protein Ontology Resources. PMID:28150233
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. PMID:27899649
UniProt: the universal protein knowledgebase. PMID:27899622
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Common errors in mass spectrometry-based analysis of post-translational modifications. PMID:26667783
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. PMID:26545397
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
An update on LNCipedia: a database for annotated human lncRNA sequences. PMID:25378313
PomBase 2015: updates to the fission yeast database. PMID:25361970
A standardized framing for reporting protein identifications in mzIdentML 1.2. PMID:25092112
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. PMID:24980485
A controlled vocabulary for pathway entities and events. PMID:24951798
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
MS-viewer: a web-based spectral viewer for proteomics results. PMID:24591702
Canto: an online tool for community literature curation. PMID:24574118
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. PMID:24295440
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
The Reactome pathway knowledgebase. PMID:24243840
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. PMID:23813117
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
From Peptidome to PRIDE: public proteomics data migration at a large scale. PMID:23533138
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. PMID:23517090
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. PMID:23110975
A cell-based approach to the human proteome project. PMID:22976808
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. PMID:22949509
BioJava: an open-source framework for bioinformatics in 2012. PMID:22877863
Post-translational modification of cardiac proteasomes: functional delineation enabled by proteomics. PMID:22523251
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. PMID:22465017
PRIDE: quality control in a proteomics data repository. PMID:22434838
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
ProKinO: an ontology for integrative analysis of protein kinases in cancer. PMID:22194913
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. PMID:22102574
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. PMID:22025670
The Reactome BioMart. PMID:22012987
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
easyDAS: automatic creation of DAS servers. PMID:21244646
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
The Ontology Lookup Service: bigger and better. PMID:20460452
OLS dialog: an open-source front end to the ontology lookup service. PMID:20078892
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
Tags:
Tags
More detailed information about this field from each metasource.
enzymatic reaction
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
protein
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:10 p.m.
Tags
More detailed information about this field from each metasource.
enzymatic reaction
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
protein
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:10 p.m.
Need help integrating and/or managing biomedical data?