BioModels Systems Biology Models Scraper

Scrape curated mathematical models of biological systems from the EBI BioModels repository — the reference database for reproducible, quantitative models in systems biology. Get SBML file metadata, curation status, modelling approach, and full publication details (title, journal, year, authors, link, synopsis) in one clean dataset. No API key required.

Pricing: pay-as-you-go, roughly ~$0.5 per 1,000 models in platform usage. BioModels content is released under CC0 (public domain).

What it does

Two modes:

• search — query BioModels by keyword (e.g. glycolysis, circadian, apoptosis). Each matching model is enriched with its full detail record.
• models — fetch explicit model IDs directly (e.g. BIOMD0000000012, MODEL1234567890).

Input

Field	Type	Description
mode	select	search (keyword query) or models (explicit IDs). Default search.
queries	array	Keywords to search for. Prefilled ["glycolysis","circadian","apoptosis"]. Used in search mode.
modelIds	array	Explicit BioModels IDs. Used in models mode.
maxItems	integer	Max models to scrape. Default 200, max 3000.

Example input

{
  "mode": "search",
  "queries": ["glycolysis", "circadian"],
  "maxItems": 100
}

Output

One record per model:

{
  "type": "model",
  "model_id": "BIOMD0000000012",
  "name": "Elowitz2000 - Repressilator",
  "description": "This model describes the deterministic version of the repressilator system.",
  "format": "SBML",
  "curation_status": "CURATED",
  "modelling_approach": "ordinary differential equation model",
  "submitter": "Nicolas Le Novere",
  "submission_id": "MODEL6615351360",
  "publication_title": "A synthetic oscillatory network of transcriptional regulators.",
  "publication_journal": "Nature",
  "publication_year": 2000,
  "publication_authors": ["M B Elowitz", "S Leibler"],
  "publication_link": "http://identifiers.org/pubmed/10659856",
  "publication_synopsis": "Networks of interacting biomolecules carry out many essential functions...",
  "main_file": "BIOMD0000000012_url.xml",
  "main_file_size": 43901,
  "additional_file_count": 15,
  "last_modified": "2024-08-21T18:29:21+00:00",
  "download_url": "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012",
  "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000012",
  "source": "biomodels",
  "scraped_at": "2026-08-11T00:00:00+00:00"
}

Download the raw SBML from download_url for direct simulation.

Use cases

• Systems biology — bulk-collect curated ODE/stochastic models for a pathway or topic.
• Model reuse — find and reuse existing SBML models instead of rebuilding from scratch.
• Quantitative biology teaching — assemble worked example models with their source papers.
• Reproducibility — track curation status, provenance, and publication links for reproducible research.

Related actors

• Reactome Pathways Scraper
• KEGG Scraper
• STRING Interactions Scraper
• UniProt Scraper

Notes

Data is served by the public BioModels REST API (no key). Please be considerate with request volume. BioModels content is CC0-licensed.