Third-Party Endpoints Used by BioMCP¶

This file is auto-generated from the endpoint registry.

Overview¶

BioMCP connects to 14 external domains across 35 endpoints.

Endpoints by Category¶

Biomedical Literature¶

biorxiv_api¶

URL: https://api.biorxiv.org/details/biorxiv
Description: bioRxiv API for searching biology preprints
Data Types: research_articles
Rate Limit: Not specified
Compliance Notes: Public preprint server, no PII transmitted

europe_pmc¶

URL: https://www.ebi.ac.uk/europepmc/webservices/rest/search
Description: Europe PMC REST API for searching biomedical literature
Data Types: research_articles
Rate Limit: Not specified
Compliance Notes: Public EMBL-EBI service, no PII transmitted

medrxiv_api¶

URL: https://api.biorxiv.org/details/medrxiv
Description: medRxiv API for searching medical preprints
Data Types: research_articles
Rate Limit: Not specified
Compliance Notes: Public preprint server, no PII transmitted

pubtator3_autocomplete¶

URL: https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/
Description: PubTator3 API for entity name autocomplete suggestions
Data Types: gene_annotations
Rate Limit: 20 requests/second
Compliance Notes: Public NIH/NCBI service, no PII transmitted

pubtator3_export¶

URL: https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson
Description: PubTator3 API for fetching full article annotations in BioC-JSON format
Data Types: research_articles
Rate Limit: 20 requests/second
Compliance Notes: Public NIH/NCBI service, no PII transmitted

pubtator3_search¶

URL: https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/
Description: PubTator3 API for searching biomedical literature with entity annotations
Data Types: research_articles
Rate Limit: 20 requests/second
Compliance Notes: Public NIH/NCBI service, no PII transmitted

Clinical Trials¶

clinicaltrials_search¶

URL: https://clinicaltrials.gov/api/v2/studies
Description: ClinicalTrials.gov API v2 for searching clinical trials
Data Types: clinical_trial_data
Rate Limit: 10 requests/second
Compliance Notes: Public NIH service, may contain trial participant criteria

nci_biomarkers¶

URL: https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers
Description: NCI API for biomarkers used in clinical trials
Data Types: clinical_trial_data
Rate Limit: Not specified
Authentication: Optional NCI_API_KEY for increased access
Compliance Notes: Public NCI service, biomarker metadata

nci_diseases¶

URL: https://clinicaltrialsapi.cancer.gov/api/v2/diseases
Description: NCI API for cancer disease vocabulary
Data Types: clinical_trial_data
Rate Limit: Not specified
Authentication: Optional NCI_API_KEY for increased access
Compliance Notes: Public NCI service, disease ontology

nci_interventions¶

URL: https://clinicaltrialsapi.cancer.gov/api/v2/interventions
Description: NCI API for cancer treatment interventions
Data Types: clinical_trial_data
Rate Limit: Not specified
Authentication: Optional NCI_API_KEY for increased access
Compliance Notes: Public NCI service, intervention metadata

nci_organizations¶

URL: https://clinicaltrialsapi.cancer.gov/api/v2/organizations
Description: NCI API for cancer research organizations
Data Types: clinical_trial_data
Rate Limit: Not specified
Authentication: Optional NCI_API_KEY for increased access
Compliance Notes: Public NCI service, organization metadata

nci_trials¶

URL: https://clinicaltrialsapi.cancer.gov/api/v2/trials
Description: NCI Clinical Trials Search API for cancer trials
Data Types: clinical_trial_data
Rate Limit: Not specified
Authentication: Optional NCI_API_KEY for increased access
Compliance Notes: Public NCI service, cancer trial data

Variant Databases¶

ensembl_variation¶

URL: https://rest.ensembl.org/variation/human
Description: Ensembl REST API for human genetic variation data
Data Types: genetic_variants
Rate Limit: 15 requests/second
Compliance Notes: Public EMBL-EBI service, population genetics data

gdc_ssm_occurrences¶

URL: https://api.gdc.cancer.gov/ssm_occurrences
Description: NCI GDC API for mutation occurrences in cancer samples
Data Types: cancer_mutations
Rate Limit: Not specified
Compliance Notes: Public NCI service, aggregate cancer genomics data

gdc_ssms¶

URL: https://api.gdc.cancer.gov/ssms
Description: NCI GDC API for somatic mutations
Data Types: cancer_mutations
Rate Limit: Not specified
Compliance Notes: Public NCI service, aggregate cancer genomics data

mychem_chem¶

URL: https://mychem.info/v1/chem
Description: MyChem.info API for fetching specific drug/chemical details
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, drug/chemical annotation data

mychem_query¶

URL: https://mychem.info/v1/query
Description: MyChem.info API for querying drug/chemical information
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, drug/chemical annotation data

mydisease_disease¶

URL: https://mydisease.info/v1/disease
Description: MyDisease.info API for fetching specific disease details
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, disease ontology data

mydisease_query¶

URL: https://mydisease.info/v1/query
Description: MyDisease.info API for querying disease information
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, disease ontology data

mygene_gene¶

URL: https://mygene.info/v3/gene
Description: MyGene.info API for fetching specific gene details
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, gene annotation data

mygene_query¶

URL: https://mygene.info/v3/query
Description: MyGene.info API for querying gene information
Data Types: gene_annotations
Rate Limit: 10 requests/second
Compliance Notes: Public BioThings service, gene annotation data

myvariant_query¶

URL: https://myvariant.info/v1/query
Description: MyVariant.info API for querying genetic variants
Data Types: genetic_variants
Rate Limit: 1000 requests/hour (anonymous)
Compliance Notes: Public service aggregating variant databases, no patient data

myvariant_variant¶

URL: https://myvariant.info/v1/variant
Description: MyVariant.info API for fetching specific variant details
Data Types: genetic_variants
Rate Limit: 1000 requests/hour (anonymous)
Compliance Notes: Public service aggregating variant databases, no patient data

Cancer Genomics¶

cbioportal_api¶

URL: https://www.cbioportal.org/api
Description: cBioPortal API for cancer genomics data
Data Types: cancer_mutations, clinical_trial_data
Rate Limit: 5 requests/second
Authentication: Optional API token for increased rate limits
Compliance Notes: Public MSKCC/Dana-Farber service, aggregate cancer genomics

cbioportal_cancer_types¶

URL: https://www.cbioportal.org/api/cancer-types
Description: cBioPortal API for cancer type hierarchy
Data Types: cancer_mutations
Rate Limit: 5 requests/second
Compliance Notes: Public MSKCC/Dana-Farber service, cancer type metadata

cbioportal_genes¶

URL: https://www.cbioportal.org/api/genes
Description: cBioPortal API for gene information
Data Types: gene_annotations
Rate Limit: 5 requests/second
Compliance Notes: Public MSKCC/Dana-Farber service, gene metadata

cbioportal_molecular_profiles¶

URL: https://www.cbioportal.org/api/molecular-profiles
Description: cBioPortal API for molecular profiles
Data Types: cancer_mutations
Rate Limit: 5 requests/second
Compliance Notes: Public MSKCC/Dana-Farber service, study metadata

cbioportal_mutations¶

URL: https://www.cbioportal.org/api/mutations
Description: cBioPortal API for mutation data
Data Types: cancer_mutations
Rate Limit: 5 requests/second
Compliance Notes: Public MSKCC/Dana-Farber service, aggregate mutation data

cbioportal_studies¶

URL: https://www.cbioportal.org/api/studies
Description: cBioPortal API for cancer studies
Data Types: clinical_trial_data, cancer_mutations
Rate Limit: 5 requests/second
Compliance Notes: Public MSKCC/Dana-Farber service, study metadata

Regulatory Data¶

fda_drug_shortages¶

URL: https://www.fda.gov/media/169066/download
Description: FDA Drug Shortages database (cached locally)
Data Types: drug_labels
Rate Limit: Cached with 24-hour TTL
Authentication: None required
Compliance Notes: Public FDA service, drug shortage status information

openfda_device_events¶

URL: https://api.fda.gov/device/event.json
Description: FDA MAUDE database for medical device adverse events
Data Types: device_events
Rate Limit: 40 requests/minute (240 with API key)
Authentication: Optional OPENFDA_API_KEY for increased rate limits
Compliance Notes: Public FDA service, device malfunction and adverse event reports

openfda_drug_enforcement¶

URL: https://api.fda.gov/drug/enforcement.json
Description: FDA Enforcement database for drug recall information
Data Types: adverse_events
Rate Limit: 40 requests/minute (240 with API key)
Authentication: Optional OPENFDA_API_KEY for increased rate limits
Compliance Notes: Public FDA service, drug recall and enforcement actions

openfda_drug_events¶

URL: https://api.fda.gov/drug/event.json
Description: FDA Adverse Event Reporting System (FAERS) for drug safety data
Data Types: adverse_events
Rate Limit: 40 requests/minute (240 with API key)
Authentication: Optional OPENFDA_API_KEY for increased rate limits
Compliance Notes: Public FDA service, voluntary adverse event reports, no PII

openfda_drug_labels¶

URL: https://api.fda.gov/drug/label.json
Description: FDA Structured Product Labeling (SPL) for drug prescribing information
Data Types: drug_labels
Rate Limit: 40 requests/minute (240 with API key)
Authentication: Optional OPENFDA_API_KEY for increased rate limits
Compliance Notes: Public FDA service, official drug labeling data

openfda_drugsfda¶

URL: https://api.fda.gov/drug/drugsfda.json
Description: FDA Drugs@FDA database for drug approval information
Data Types: drug_labels
Rate Limit: 40 requests/minute (240 with API key)
Authentication: Optional OPENFDA_API_KEY for increased rate limits
Compliance Notes: Public FDA service, official drug approval records

Domain Summary¶

Domain	Category	Endpoints
api.biorxiv.org	biomedical_literature	2
api.fda.gov	regulatory_data	5
api.gdc.cancer.gov	variant_databases	2
clinicaltrials.gov	clinical_trials	1
clinicaltrialsapi.cancer.gov	clinical_trials	5
mychem.info	variant_databases	2
mydisease.info	variant_databases	2
mygene.info	variant_databases	2
myvariant.info	variant_databases	2
rest.ensembl.org	variant_databases	1
www.cbioportal.org	cancer_genomics	6
www.ebi.ac.uk	biomedical_literature	1
www.fda.gov	regulatory_data	1
www.ncbi.nlm.nih.gov	biomedical_literature	3

Compliance and Privacy¶

All endpoints accessed by BioMCP:

Use publicly available APIs
Do not transmit personally identifiable information (PII)
Access only aggregate or de-identified data
Comply with respective terms of service

Network Control¶

For air-gapped or restricted environments, BioMCP supports:

Offline mode via BIOMCP_OFFLINE=true environment variable
Custom proxy configuration via standard HTTP(S)_PROXY variables
SSL certificate pinning for enhanced security