#systems-biology

Protein-protein interaction networks as an API — powered by STRING, the database of known and predicted protein associations that combines evidence from laboratory experiments, curated pathway databases, gene co-expression, genomic context and automated text mining into a single confidence score, across thousands of organisms. Get a protein's top interaction partners (each with the combined confidence score and the seven evidence-channel subscores), the interaction network among any set of proteins as scored edges, and functional enrichment for a gene set — the over-represented GO terms, KEGG pathways, Pfam domains and more, each with its p-value, FDR and member genes. Pass gene symbols (TP53) or STRING/Ensembl ids, for human (default) or any species by NCBI taxon id. It is a cornerstone of systems biology — ideal for network analysis, functional genomics, pathway and bioinformatics tools. A protein-interaction-network resource — distinct from biological pathways (Reactome), curated protein complexes (Complex Portal) and Gene Ontology annotations (QuickGO). Open data from STRING (CC BY 4.0).

api.oanor.com/stringdb-api

BioModels as an API, powered by EMBL-EBI — the world's largest repository of curated, published mathematical models of biological systems. BioModels collects computational models (mostly in SBML, the Systems Biology Markup Language) of metabolism, cell signalling, gene-regulatory networks, the cell cycle, disease processes and physiology, each linked to the peer-reviewed publication it comes from. /v1/search?query=glycolysis searches the repository and returns each matching model's id (such as BIOMD0000000012), name, format, submitter and submission/modification dates. /v1/model?id=BIOMD0000000012 returns a model's metadata — its name and description, the encoding format, the modelling approach (e.g. ordinary differential equation model), the curation status, the publication behind it (title, journal, year, authors) and the model files. Model ids look like BIOMD0000000012 for curated models or MODEL1234567890 for non-curated submissions; get them from the search endpoint. Ideal for systems-biology and computational-modelling tools, reproducible-research and model-reuse workflows, and teaching. Data from EMBL-EBI BioModels (CC0). This is a systems-biology / computational-model repository — distinct from sequence (UniProt, ENA), structure (PDB, AlphaFold), pathway and variant (ClinVar) databases.

api.oanor.com/biomodels-api

The STRING protein–protein interaction database as an API — the curated and predicted network of functional associations between proteins, powered by the official STRING API. Resolve gene or protein names to STRING identifiers with annotations; get a protein's top interaction partners with a combined confidence score and per-channel evidence (experimental, curated databases, co-expression, text-mining, gene fusion, neighbourhood and co-occurrence); build the interaction network among a set of proteins as scored edges; run functional enrichment of a gene set over Gene Ontology, KEGG, Reactome, Pfam, InterPro and more with p-values and false-discovery rates; and score homology between proteins. Covers 12,000+ organisms (default human, NCBI taxon 9606). Ideal for systems-biology and network-biology pipelines, gene-set and pathway analysis, drug-target and disease-gene research, and bioinformatics dashboards.

api.oanor.com/string-api

The Reactome pathway knowledgebase as an API — the open, peer-reviewed database of biological pathways and reactions, powered by the official Reactome ContentService. Search the curated archive of pathways, reactions and molecules; read any entity by its Reactome stable id (a pathway, reaction, complex or protein: name, type, species, compartments, summary and disease flag); list the events (sub-pathways and reactions) contained in a pathway; list the molecules participating in a pathway or reaction with their reference identifiers; get the top-level pathways for any model organism; map a UniProt protein to the pathways it takes part in; and list the supported species. Covers human and 15+ model organisms across metabolism, signal transduction, cell cycle, immune system, disease and more. Ideal for systems-biology and bioinformatics pipelines, pathway-enrichment and drug-target tools, biomedical research apps, teaching resources and life-science chatbots.

api.oanor.com/reactome-api