BioMCP

# 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