IntAct Reference Ingest Guide¶

Source Information¶

InfoRes ID: infores:intact

Description: IntAct is a curated, open data resource of molecular interactions hosted by EMBL-EBI. It stores experimentally determined molecular interactions, primarily protein–protein interactions, derived from literature curation and direct user submissions. IntAct uses detailed controlled vocabularies (e.g., PSI-MI) to describe experimental details such as interaction type, detection method, and participant roles, enabling consistent representation and downstream reuse of fine-grained interaction evidence.

Citations: - del-Toro N, Duesbury M, Koch M, et al. The IntAct molecular interaction database in 2022. Nucleic Acids Res. 2022;50(D1):D648–D653 - {'Hermjakob H, Montecchi-Palazzi L, Bader G, et al. IntAct': 'an open source molecular interaction database. Nucleic Acids Res. 2004;32(Database issue):D452–D455.'}

Terms of Use: IntAct is a fully open-source, open-data resource whose materials are freely available to anyone. All IntAct data—including PSI-MI XML, MI-JSON, MITAB files, and data accessed through the website or web services—are licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license, which allows users to use, reproduce, share, and adapt the data as long as appropriate credit is given. All IntAct software, including the Curator Tool, derived websites and services, SQL and graph database dumps, and branding materials, are provided under the Apache License 2.0, a permissive open-source license that allows reuse and modification with standard notice requirements. IntAct collects minimal personal data (author names and corresponding emails) solely for data traceability, and its curation activities follow EBI’s long-term data preservation policies. The licensing policy is described here: https://www.ebi.ac.uk/intact/about#license_privacy

Data Access Locations: - {'IntAct main site': 'https://www.ebi.ac.uk/intact/'} - {'IntAct Download / FTP or bulk access': 'https://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.zip'}

Data Provision Mechanisms: file_download, web_interface, web_service_api

Data Formats: PSI-MI TAB (MITAB), PSI-MI XML

Data Versioning and Releases: IntAct is released in regular monthly updates: https://www.ebi.ac.uk/legacy-intact/downloads. Each release is identified by a release number and associated with a release date. The ingest documented here is based on IntAct Release 251 - September 2025; last modified on August 28, 2025 and downloaded on November 16, 2025, using psimitab 2.7 format from: https://ftp.ebi.ac.uk/pub/databases/intact/current. See the IntAct FTP page about the release and contents of the FTP directory: https://www.ebi.ac.uk/intact/download/ftp.

Ingest Information¶

Ingest Categories: Primary Knowledge Provider

Utility: IntAct is a key curated source of experimentally supported molecular interactions, particularly protein–protein interactions, which are critical for many NCATS Translator use cases including pathway and network-based reasoning, target discovery, mechanism-of-action hypotheses, and evaluation of biological plausibility for drug–disease or gene–disease connections. It provides detailed interaction-level metadata (e.g., detection method, interaction type, source database, publications) that supports evidence tracking and assessment of interaction quality and context.

Scope: IntAct ingest focuses on experimentally determined molecular interactions where at least one participant can be normalized to a Biolink-compatible protein or small molecule identifier, with an emphasis on human protein–protein interactions. All interaction records with valid PSI-MI interaction types and detection methods are considered within scope. The ingest is designed to preserve interaction evidence metadata (detection method, interaction type, source database, publications) while providing a Biolink-compliant edge representation.

Relevant Files¶

Included Content¶

Filtered Content¶

Future Content Considerations¶

edge_content: Consider expanding beyond human-only interactions to include selected non-human organisms (e.g., key model organisms) where this adds substantial value for mechanistic or translational reasoning, while still maintaining manageable graph size. - Relevant files: intact.txt

edge_content: Consider importing the long tail of records with additional interaction types not taken in first iteration. - Relevant files: intact.txt

edge_property_content: Longer term, consider creating ExperimentalStudyResult objects to capture metadata for each experiment that supports an edge (e.g. interactor roles, host organism, stoichiometries, features, parameters, experiment-associated publications etc). - Relevant files: intact.txt

Additional Notes: Exploratory data analysis (EDA) of the IntAct MITAB dataset revealed 59 unique PSI-MI interaction types across the full resource, of which 41 appear in the human-only subset for this ingest. A similar 'long tail' distribution was observed for detection methods and source databases, with a small number of highly frequent, widely used terms (e.g., association, physical association, self interaction) and many low-frequency or highly specific terms. Based on these findings, the ingest strategy retains all positive human–human interactions and preserves all observed interaction types, detection methods, and source database annotations (without removing rare terms), while constraining biological scope to human-only records. Negative interactions were excluded for this version of the ingest, as they are not currently used in Translator molecular interaction reasoning or Biolink predicate mapping.

Target Information¶

Target InfoRes ID: infores:intact

Edge Types¶

Node Types¶

Provenance Information¶

Contributors: - {'Shilpa Sundar': 'ingest owner, code author'} - {'Matthew Brush': 'data modeling, domain expertise'}

Artifacts: - {'Ingest Survey': 'https://docs.google.com/spreadsheets/d/1sgiHZ_d_o7FWDxhfaP72BVg0FPCNJ7Vx9N6IBuEzHbs/edit?gid=0#gid=0'} - {'Causal Mechanism Mappings': 'https://docs.google.com/spreadsheets/d/1DeAE04O1mz3R9s3dCZpG2hQp9hwif5WjdkUMsBci-u8/edit?gid=1886396936#gid=1886396936'} - {'IntAct EDA Summary': 'https://docs.google.com/spreadsheets/d/1-WF7veY_UXXRogq8f7uRMpgYgiv6lJdx/edit?gid=2068335761#gid=2068335761'} - {'Ingest Ticket': None}