Text Mining Tools

  • eGIFT: identifies terms and documents that are relevant to a gene and its products
  • RLIMS-P: a rule-based text-mining program specifically designed to extract protein phosphorylation information on protein kinase, substrate and phosphorylation sites from the abstracts
  • eFIP: presents ranked abstracts mentioning impact of protein phosphorylation

Protein Ontology (PRO)

PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes).

Relevant PTM Resources

  • PhosphoSitePlus: a comprehensive PTM resource covering phosphorylation, acetylation, methylation, ubiquitination and O-glycosylation data manually curated from literature and integrated from other data sources, primarily on human and mouse
  • PHOSIDA: providing phosphorylation sites information for model organisms such as human, yeast, and E. coli (but no plant species), and some acelylation sites and N-glycosylation sites
  • Phospho.ELM: a manually-curated database of experimentally verified phosphorylation sites in animal proteins
  • PhosphoPep: including phosphorylation site data from human, yeast, C. elegans and D. melanogaster
  • Phosphorylation site database: for prokaryotic organisms
  • PhosPhAt: an Arabidopsis thaliana phosphorylation site database identified by mass spectrometry in large scale experiments
  • P3DB: with the largest collection of plant phosphorylation data
  • O-GlycBase: of O- and C-glycosylated proteins
  • UbiProt of ubiquitylated proteins, mainly in human and yeast
  • SCUD: for the ubiquitination system in yeast with enzymes and substrates
  • PlantsUPS of plants Ubiquitin Proteasome System
  • Arabidopsis myristoylation data sets: stored at TAIR
The enzyme databases: