STRING Reference Ingest Guide¶

Source Information¶

InfoRes ID: infores:string

Description: STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein–protein interactions hosted by SIB / EMBL / CPR. STRING aggregates evidence from seven channels — genomic neighborhood, gene fusion, phylogenetic co-occurrence, homology, co-expression, experiments, and text mining — plus curated databases, and combines them into a single combined_score per interaction pair. (STITCH, STRING's sister database for protein–chemical interactions, was developed alongside this ingest but split out for a later, properly-scoped effort — preserved on the stitch-ingest branch. See CHANGELOG 2026-05-28.)

Citations: - Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023. Nucleic Acids Res. 2023;51(D1):D638–D646. doi:10.1093/nar/gkac1000

Data Access Locations: - {'STRING downloads': 'https://stringdb-downloads.org/'} - {'STRING main site': 'https://string-db.org/'}

Data Provision Mechanisms: file_download, other, api_endpoint

Data Formats: tsv

Data Versioning and Releases: STRING uses dotted version numbers (currently v12.0). The version is published at https://string-db.org/api/json/version and is embedded in download URLs (e.g. protein.links.v12.0/). get_latest_version() resolves the version dynamically from this endpoint.

Ingest Information¶

Ingest Categories: primary_knowledge_provider

Utility: STRING provides a broad protein–protein interaction graph derived from multiple evidence channels, supplying Translator reasoning with channel-specific "these proteins interact / are coexpressed / are genomic neighbors" signals across human, mouse, and rat.

Scope: Protein–protein interactions for three Translator-target species: human (NCBITaxon:9606), mouse (NCBITaxon:10090), and rat (NCBITaxon:10116). Protein identifiers are kept in their native ENSEMBL form (ENSP / ENSMUSP / ENSRNOP) — no mapping to gene-level identifiers as canonical IDs; NCBIGene equivalents are attached via equivalent_identifiers. Per-channel evidence subscores drive per-channel predicate emission (one edge per high-confidence channel); the aggregate combined_score gates row inclusion. Future iterations may extend to additional species, surface per-channel subscores as edge properties, and add the STITCH protein–chemical layer — see future_considerations below.

Relevant Files¶

Included Content¶

Filtered Content¶

Future Content Considerations¶

edge_content: Add the STITCH protein–chemical layer. Developed alongside this ingest as a stitch_pcl tagged reader but split out for a later, properly-scoped effort — the complete implementation (ChemicalEntity → interacts_with → Protein, CIDm/CIDs → PUBCHEM.COMPOUND parsing, human/mouse/rat) is preserved on the stitch-ingest branch. The reintegration should land mode-of-action predicates from actions.v5.0.tsv (activation, inhibition, binding, catalysis, …) from the start rather than the bare interacts_with form, since no production STITCH KP exists to merely match (confirmed: Automat's STRING-DB graph has no STITCH interaction edges — its only Protein↔ChemicalEntity edges are Ubergraph ontology backbone, primary_knowledge_source: infores:ubergraph). - Relevant files: {taxon}.protein_chemical.links.v5.0.tsv.gz, {taxon}.actions.v5.0.tsv.gz

edge_content: Extend to additional Translator-relevant organisms beyond human/mouse/rat (zebrafish, fly, worm, yeast). The transform accepts arbitrary taxa via the SUPPORTED_TAXA dict in string.py; adding a species is a one-line code change plus a download URL and a reader file entry. Note that non-vertebrate species may use protein ID schemes other than ENSEMBL (e.g. yeast uses ORF names like YAL001C); the parser would accept them but downstream NodeNormalizer coverage should be probed first. - Relevant files: {taxon}.protein.links.full.v12.0.txt.gz

edge_property_content: Surface per-channel subscores as edge properties (not just predicate-driving signals). The channel scores currently drive predicate + KL/AT selection and are then discarded; downstream consumers don't see the actual COEXPRESSION/EXPERIMENTS/TEXTMINING numbers. Attach them as biolink:Attribute instances on each edge, named after the channel. The data is already in the .full file we read; this is a transform-only change. - Relevant files: {taxid}.protein.links.full.v12.0.txt.gz (already ingested)

node_property_content: Ingest protein.aliases.v12.0.txt.gz to populate node name and synonym properties. Currently nodes carry only the ENSEMBL ID as their identifier; biolink validation flags this with INFO-level "missing recommended name" warnings on every node. - Relevant files: 9606.protein.info.v12.0.txt.gz, 9606.protein.aliases.v12.0.txt.gz

Additional Notes: Current scope: STRING protein–protein interactions for human, mouse, and rat. STRING emits 6 per-channel predicates (physically_interacts_with, coexpressed_with, interacts_with, genetic_neighborhood_of, gene_fusion_with, genetically_interacts_with) plus a fallback physically_interacts_with for rows that pass the combined-score gate without any high-confidence channel. knowledge_level / agent_type are derived per row from the dominant evidence channel (ORION-aligned). The predicate-selection rule matches ORION's STRING parser to maintain downstream compatibility with the existing Translator KP ecosystem (Automat STRING-DB, RoboKOP). HOMOLOGY channel is deliberately excluded from predicate emission because STRING's HOMOLOGY score means "inferred via orthologs in another species" not "A is homologous to B." The STITCH protein–chemical sibling ingest was split out for a later effort (preserved on the stitch-ingest branch); see future_considerations and CHANGELOG 2026-05-28. Other growth axes: per-channel subscores as edge properties, additional non-mammalian species, and node names from protein.aliases.

Target Information¶

Target InfoRes ID: infores:string

Edge Types¶

Node Types¶

Provenance Information¶

Contributors: - {'Kenneth Huellas-Bruskiewicz': 'ingest owner, code author'} - {'Richard Bruskiewich': 'data modeling, code co-author'}

Artifacts: - {'Ingest Survey': 'https://docs.google.com/spreadsheets/d/13Q4uJ90UFCXyXZMuhgtm1nREGtIIMsfDEgb4jpkgRIA/edit?gid=0#gid=0'} - {'Ingest Ticket': 'https://github.com/NCATSTranslator/translator-ingests/issues/377'} - {'Monarch STRING reference': 'https://github.com/monarch-initiative/string-ingest/blob/main/src/protein_links.py'} - {'ORION STRING reference': 'https://github.com/RobokopU24/ORION/blob/master/parsers/STRING/src/loadSTRINGDB.py'} - {'Automat STRING-DB knowledge provider (RENCI)': 'https://automat.renci.org/string-db/'}