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STRING: functional protein association networks

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.

This ingest uses a given version (currently, 11.5) of the STRING's .protein.links.detailed..txt.gz files, for a subset of NCBI ID designated species. We filter the input data on the combined_score field (currently with the threshhold recorded in the protein_links.yaml file). The various taxon specific entrez_2_string mapping files are used to map protein subject and concept nodes onto Entrez gene id's.

Special note about Entrez mapping files

A separate Entrez to String identifier mapping file is not available for Rattus norvegicus (Norway rat, NCBI taxon ID 10116) but the mappings are (less conveniently) available inside the aggregated 'all_organisms' entrez_2_string file. See notes in the STRING section of the download.yaml configuration file for (self explanatory) guidance on how to prepare the required mapping file for use in a local running of the digest.

Source File

  • protein1
  • protein2
  • neighborhood
  • fusion
  • cooccurence
  • coexpression
  • experimental
  • database
  • textmining
  • combined_score

Concept Nodes

  • biolink:Gene
  • id (NCBIGene Entrez ID)

Associations

  • biolink:PairwiseGeneToGeneInteraction:
    • id (random uuid)
    • subject (gene.id)
    • predicate (interacts_with)
    • object (gene.id)
    • aggregating_knowledge_source (["infores:monarchinitiative"])
    • primary_knowledge_source (infores:string)

Citation

Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi P. Tsafou, Michael Kuhn, Peer Bork, Lars J. Jensen, Christian von Mering, STRING v10: protein–protein interaction networks, integrated over the tree of life, Nucleic Acids Research, Volume 43, Issue D1, 28 January 2015, Pages D447–D452, https://doi.org/10.1093/nar/gku1003