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.
Protein Links
This ingest uses a given version (currently, 11.5) of the STRING'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
Biolink classes and properties captured
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