knowledgebase-mcp
projectother official build verified scannedBioContextAI Knowledgebase MCP server for biomedical agentic AI
run it
on your own machines, one way per deploy method# once, as root:
docker build -t mcp-local/knowledgebase:92518edf337196d4b4d445dc828dd957bf35d39c https://github.com/biocontext-ai/knowledgebase-mcp.git#92518edf337196d4b4d445dc828dd957bf35d39c
#!/usr/bin/env bash
# knowledgebase (io.github.biocontext-ai/knowledgebase-mcp), recipe docker (worker, verified 2026-10-17 on v, run r-20261017T191820Z-1633f4f8b0fd).
# Generated by Hub for toolset "my-agent"; started by mcp-my-agent-knowledgebase.service.
set -euo pipefail
export HOST=127.0.0.1 PORT=8101
exec docker run --rm --name mcp-my-agent-knowledgebase -p 127.0.0.1:${PORT}:8000 --env-file /etc/mcp/my-agent.env mcp-local/knowledgebase:92518edf337196d4b4d445dc828dd957bf35d39c
[Unit]
Description=MCP server knowledgebase (toolset my-agent), generated by Hub
After=network-online.target docker.service
Wants=network-online.target
[Service]
Type=simple
User=mcp
Group=mcp
SupplementaryGroups=docker
EnvironmentFile=/etc/mcp/my-agent.env
Environment=HOME=/var/lib/mcp/knowledgebase
WorkingDirectory=/var/lib/mcp/knowledgebase
ExecStart=/opt/mcp/my-agent/bin/knowledgebase.sh
Restart=on-failure
RestartSec=5
NoNewPrivileges=true
ProtectSystem=strict
ProtectHome=true
PrivateTmp=true
ReadWritePaths=/var/lib/mcp/knowledgebase
[Install]
WantedBy=multi-user.target
docker build -t knowledgebase https://github.com/biocontext-ai/knowledgebase-mcp.git#92518edf337196d4b4d445dc828dd957bf35d39c docker run --rm -p 127.0.0.1:8101:8000 knowledgebase
# Generated by Hub for toolset "my-agent" (2026-10-17T20:37:03+00:00).
# Each package server runs behind a stdio->HTTP bridge and listens on localhost only.
# cp .env.example .env # fill the ${VAR}s
# docker compose up -d && bash smoke.sh
# Remote servers are not here: clients reach them directly (see clients/).
name: mcp-my-agent
services:
knowledgebase:
build:
context: https://github.com/biocontext-ai/knowledgebase-mcp.git#92518edf337196d4b4d445dc828dd957bf35d39c
ports:
- 127.0.0.1:8101:8000
restart: unless-stopped
x-note: 'CHANGE_ME: built from the repository''s Dockerfile, assuming it serves streamable HTTP at
:8000/mcp. Nothing has run this yet; the worker replaces it with a tested recipe.'
volumes:
npm-cache: {}
uv-cache: {}
# Generated by Hub for toolset "my-agent" (2026-10-17T20:37:03+00:00).
# kubectl create namespace mcp
# kubectl -n mcp create secret generic mcp-credentials --from-env-file=.env
# kubectl apply -f kubernetes.yaml
# Services are cluster-internal: <name>.mcp.svc.cluster.local:8000/mcp. Put an ingress
# with auth in front before exposing any of them.
apiVersion: v1
kind: Namespace
metadata:
name: mcp
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: knowledgebase
namespace: mcp
labels: &id001
app: knowledgebase
spec:
replicas: 1
selector:
matchLabels: *id001
template:
metadata:
labels: *id001
spec:
containers:
- name: knowledgebase
image: CHANGE_ME
ports:
- containerPort: 8000
name: http
env: []
---
apiVersion: v1
kind: Service
metadata:
name: knowledgebase
namespace: mcp
spec:
selector:
app: knowledgebase
ports:
- port: 8000
targetPort: http
name: http
# Generated by Hub for toolset "my-agent" (2026-10-17T20:37:03+00:00).
# Credentials come from the Secret 'mcp-credentials' (kubectl create secret generic ... --from-env-file=.env).
# Each server under `servers` is one Deployment + Service; the keys after it configure
# upstream charts a worker verified.
servers:
knowledgebase:
enabled: true
replicas: 1
port: 8000
path: /mcp
container:
name: knowledgebase
image: CHANGE_ME
ports:
- containerPort: 8000
name: http
env: []
# helm install my-agent helm/my-agent -n mcp
Scanned github.com/biocontext-ai/knowledgebase-mcp at 92518edf3371 with [email protected][email protected] on 2026-10-17 before the build: 22 dependencies, 110 known vulnerabilities (5 critical, 56 high, 42 medium, 5 low, 2 unknown), nothing in the code that looks malicious.
in the cloud
one click: the provider's deploy form opens filled in, in your own account- koyeb
-
Koyeb builds the repository's Dockerfile from branch main, not commit 92518edf3371, the one the worker scanned and built (it takes branches only); change the branch in the form if the default one has another name.
Clients connect to the service's https://…koyeb.app address plus /mcp.
- cloud run
-
Cloud Shell clones the repository, builds its Dockerfile and deploys it to Cloud Run.
knowledgebase: Cloud Shell clones the default branch, not the commit the worker scanned and built (it takes branches only).
Cloud Run sends requests to $PORT (8080); the recipe expects :8000, so the server has to read PORT, or set the container port on the service afterwards.
connect to it
copy what your client needs{
"mcpServers": {
"knowledgebase": {
"command": "CHANGE_ME",
"args": []
}
}
}
#!/usr/bin/env bash # Registers every server with Claude Code (run once; `claude mcp list` to check). set -euo pipefail set -a; [ -f .env ] && source .env; set +a claude mcp add knowledgebase -- CHANGE_ME
{
"mcpServers": {
"knowledgebase": {
"command": "CHANGE_ME",
"args": []
}
}
}
{
"servers": {
"knowledgebase": {
"type": "stdio",
"command": "CHANGE_ME",
"args": []
}
}
}
name: my-agent target: local servers: - hub: io.github.biocontext-ai/knowledgebase-mcp
- no tested recipe for target 'local' yet: build it from https://github.com/biocontext-ai/knowledgebase-mcp by hand, or wait for the worker
tools · 49
bc_count_drugs_by_fieldCount unique values in a field across FDA-approved drugs. Useful for statistical analysis. Returns: dict: Results array with term and count for each unique value or error message.Count unique values in a field across FDA-approved drugs. Useful for statistical analysis. Returns: dict: Results array with term and count for each unique value or error message.
pin 1cc40e6581873d52c43fc19d9b7896b9d4c68890c7b9561a0cbf6dd21f20d24fbc_get_alphafold_info_by_protein_symbolQuery AlphaFold database using protein name. First converts protein symbol to UniProt ID, then fetches structure predictions. Returns: dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.Query AlphaFold database using protein name. First converts protein symbol to UniProt ID, then fetches structure predictions. Returns: dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.
pin c9bd6e7e06d5cefdb237206185532b10c63219ead4ddd2cb7fef428ef8d39509bc_get_antibody_informationGet detailed antibody information by ID. Retrieves catalog number, vendor, clonality, epitope, applications, and more. Returns: dict: Antibody details including abId, catalog numbers, vendor, clonality, epitope, applications, target species, isotype, citations or error message.Get detailed antibody information by ID. Retrieves catalog number, vendor, clonality, epitope, applications, and more. Returns: dict: Antibody details including abId, catalog numbers, vendor, clonality, epitope, applications, target species, isotype, citations or error message.
pin 6ce91b54b64dc1f6e4105f12a5b6e68c151ee14ded5345ced7ee2f582a7c12aabc_get_antibody_listSearch Antibody Registry for antibodies. Returns catalog numbers, vendors, clonality, applications, and metadata. Returns: dict: Search results containing list of antibodies with catalog numbers, vendors, clonality, applications, metadata or error message.Search Antibody Registry for antibodies. Returns catalog numbers, vendors, clonality, applications, and metadata. Returns: dict: Search results containing list of antibodies with catalog numbers, vendors, clonality, applications, metadata or error message.
pin db765cb524de3a3437d179102103633289913f7ecf635c2ac1bc5d064075a4e9bc_get_available_ontologiesQuery OLS for all available ontologies with their metadata. Use this first to discover available ontologies. Returns: dict: Ontologies list with id, name, description, prefix, homepage, number of terms, status or error message.Query OLS for all available ontologies with their metadata. Use this first to discover available ontologies. Returns: dict: Ontologies list with id, name, description, prefix, homepage, number of terms, status or error message.
pin 1800a4b00c53f829b9566e81c4f7dc8e3e3340119c1c83c51acd0289a9a0ce01bc_get_available_pharmacologic_classesGet available pharmacologic classes from FDA database. Call this first to see available options. Returns: dict: Class type, field, available_classes array with term/count, total_found or error message.Get available pharmacologic classes from FDA database. Call this first to see available options. Returns: dict: Class type, field, available_classes array with term/count, total_found or error message.
pin 53eedea5db890604c2d0d7c63b0910850a16c1e01c1c2b2ba03378e52da177ccbc_get_biorxiv_preprint_detailsGet detailed preprint metadata by DOI. Retrieves title, authors, abstract, date, version, category, license, and publication status. Returns: dict: Preprint metadata including doi, title, authors, abstract, date, version, category, license, publication status or error message.Get detailed preprint metadata by DOI. Retrieves title, authors, abstract, date, version, category, license, and publication status. Returns: dict: Preprint metadata including doi, title, authors, abstract, date, version, category, license, publication status or error message.
pin a2ddcb7e967bd2a73863132be2678a133b305a3ec8cc39d1e8ec80a172bb5a41bc_get_cell_ontology_termsSearch OLS for Cell Ontology (CL) terms using a controlled vocabulary for cell types. Returns: dict: Cell ontology terms with cl_terms array containing id, label, definition, synonyms or error message.Search OLS for Cell Ontology (CL) terms using a controlled vocabulary for cell types. Returns: dict: Cell ontology terms with cl_terms array containing id, label, definition, synonyms or error message.
pin 4a1c72419726df210a31b513eb529932b45eade82f0f08ccfc639afd899a37d0bc_get_chebi_terms_by_chemicalSearch OLS for ChEBI (Chemical Entities of Biological Interest) terms for a chemical or drug name. Returns: dict: ChEBI terms with chebi_terms array containing id, label, description, synonyms or error message.Search OLS for ChEBI (Chemical Entities of Biological Interest) terms for a chemical or drug name. Returns: dict: ChEBI terms with chebi_terms array containing id, label, description, synonyms or error message.
pin cf7837262642324c75eac714b4473afb5197f67075f582b03dd64a3cff5ab84ebc_get_drug_by_application_numberGet detailed information about an FDA-approved drug by application number. Format: NDA/ANDA/BLA followed by 6 digits. Returns: dict: FDA drug results with application details, products, sponsor information or error message.Get detailed information about an FDA-approved drug by application number. Format: NDA/ANDA/BLA followed by 6 digits. Returns: dict: FDA drug results with application details, products, sponsor information or error message.
pin 8378d9c5c8cac3271da4a99c7471dc04172cea542c1de5fd117b55ee192f2eedbc_get_drug_label_infoGet comprehensive drug labeling information from FDA. Includes active ingredients, dosage forms, administration routes. Returns: dict: Drug label results with indications, warnings, dosage, active ingredients or error message.Get comprehensive drug labeling information from FDA. Includes active ingredients, dosage forms, administration routes. Returns: dict: Drug label results with indications, warnings, dosage, active ingredients or error message.
pin 3f62191dd841a46aa3a7318b254b0466967f51627870e2452e69d50315c41bb0bc_get_drug_statisticsGet general statistics about the FDA Drugs@FDA database. Includes top sponsors, dosage forms, routes, marketing status. Returns: dict: Top sponsors, dosage_forms, administration_routes, marketing_statuses with counts or error message.Get general statistics about the FDA Drugs@FDA database. Includes top sponsors, dosage forms, routes, marketing status. Returns: dict: Top sponsors, dosage_forms, administration_routes, marketing_statuses with counts or error message.
pin b2e274062c58f3af2c6b2607a8ee5229838ac4c84e2b9cab04e3869992f6d99bbc_get_efo_id_by_disease_nameSearch OLS for EFO/Mondo/HP IDs related to a disease name. Use this to get EFO IDs for Open Targets queries. Returns: dict: EFO IDs with efo_ids array containing id, label, description or error message.Search OLS for EFO/Mondo/HP IDs related to a disease name. Use this to get EFO IDs for Open Targets queries. Returns: dict: EFO IDs with efo_ids array containing id, label, description or error message.
pin 552e1d87c9eb9711eacba2649e8b775fcec33c4be48313bb639c18c0d212bccebc_get_ensembl_id_from_gene_symbolGet Ensembl gene ID from gene symbol. Returns the stable Ensembl ID (ENSG*) for the given gene symbol and species. Returns: dict: Ensembl gene ID in format {'ensembl_id': 'ENSG...'} or error message.Get Ensembl gene ID from gene symbol. Returns the stable Ensembl ID (ENSG*) for the given gene symbol and species. Returns: dict: Ensembl gene ID in format {'ensembl_id': 'ENSG...'} or error message.
pin 7e8c200f020e57149178b9843629870eadef08079acd3a4e54a6a16d85b29f2bbc_get_europepmc_articlesSearch Europe PMC articles by query, title, abstract, or author. Combine search terms with 'and'/'or' logic. Returns: dict: Search results with resultList containing articles (title, authors, abstract, journal, PMC/DOI IDs) or error message.Search Europe PMC articles by query, title, abstract, or author. Combine search terms with 'and'/'or' logic. Returns: dict: Search results with resultList containing articles (title, authors, abstract, journal, PMC/DOI IDs) or error message.
pin 8b2980a448bf547a47aefd2cb17d77bb8fef4effee010ded1079799dd03c19ccbc_get_europepmc_fulltextGet full-text XML for a PMC ID. Returns the complete article XML for processing and analysis. Returns: dict: Full-text XML content in format {'fulltext_xml': '...'} or error message.Get full-text XML for a PMC ID. Returns the complete article XML for processing and analysis. Returns: dict: Full-text XML content in format {'fulltext_xml': '...'} or error message.
pin 84346940102b4fbad0a93971b55958ed73e8e88a95415247f0fb0b860d2f222bbc_get_generic_equivalentsFind generic equivalents for a brand name drug. Searches ANDA entries with matching active ingredients. Returns: dict: Brand drug info, generic_equivalents array, total_generics_found count or error message.Find generic equivalents for a brand name drug. Searches ANDA entries with matching active ingredients. Returns: dict: Brand drug info, generic_equivalents array, total_generics_found count or error message.
pin e1c88c0b366137aa4f776f9ee57804a139f0751cda18e222872a71efd72cb665bc_get_go_terms_by_geneSearch OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies. Returns: dict: GO terms with go_terms array containing id, label, description, type or error message.Search OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies. Returns: dict: GO terms with go_terms array containing id, label, description, type or error message.
pin 0e86c7f3b96266ab8c8f390eff92150c732a3c2a5383fd411f3f355dfaa51ad8bc_get_human_protein_atlas_infoRetrieve Human Protein Atlas information including expression, localization, and pathology data. Provide either gene_id or gene_symbol. Returns: dict: Protein atlas data with tissue_expression, subcellular_location, pathology, antibodies, RNA/protein levels or error message.Retrieve Human Protein Atlas information including expression, localization, and pathology data. Provide either gene_id or gene_symbol. Returns: dict: Protein atlas data with tissue_expression, subcellular_location, pathology, antibodies, RNA/protein levels or error message.
pin bb41badffbb861b3254e64435527934e22ed23fe4701ce2c2ad6a12e8f3a294fbc_get_interpro_entryGet InterPro entry details (family, domain, or functional site). Returns metadata from member databases like PFAM, PROSITE. Returns: dict: Entry metadata including name, type, description, member databases, optionally interactions/pathways/cross-references or error message.Get InterPro entry details (family, domain, or functional site). Returns metadata from member databases like PFAM, PROSITE. Returns: dict: Entry metadata including name, type, description, member databases, optionally interactions/pathways/cross-references or error message.
pin 99af6c6f5b20a4e6fe26601b76e758c4cc9d0c34358c4d301a516723b3971d56bc_get_open_targets_graphql_schemaRetrieve the Open Targets GraphQL schema for query construction. Returns: dict: Schema string in format {'schema': '...'} containing GraphQL type definitions or error message.Retrieve the Open Targets GraphQL schema for query construction. Returns: dict: Schema string in format {'schema': '...'} containing GraphQL type definitions or error message.
pin 91ff778528ffcc7b285f2caf1b7205a0ec6561f7f2657ff6b552c3ec4ae09e49bc_get_open_targets_query_examplesRetrieve example GraphQL queries for the Open Targets API. Examples demonstrate common use cases. Returns: dict: Example queries mapped by category (informationForTarget, drugsForTarget, associatedDiseases, etc.) with GraphQL query strings.Retrieve example GraphQL queries for the Open Targets API. Examples demonstrate common use cases. Returns: dict: Example queries mapped by category (informationForTarget, drugsForTarget, associatedDiseases, etc.) with GraphQL query strings.
pin 997dbb5daf928b9cc1cca4520986c577d5bc0becb460a135b01445005cf46b71bc_get_panglaodb_marker_genesRetrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol. Returns: dict: Markers array with gene symbols, cell types, organs, sensitivity/specificity scores or error message.Retrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol. Returns: dict: Markers array with gene symbols, cell types, organs, sensitivity/specificity scores or error message.
pin ac75cd694a75eb9df50615bc0a0be15c87bb17e6316f5eac117ea68cd3cc991dbc_get_panglaodb_optionsRetrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types. Returns: dict: Lists of unique organ and cell_type values available in PanglaoDB dataset or error message.Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types. Returns: dict: Lists of unique organ and cell_type values available in PanglaoDB dataset or error message.
pin 0be888b77a879307bec6bd331d068c03d6235033beec66b3c56f60f7b4021dc7bc_get_pride_projectRetrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details. Returns: dict: Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details. Returns: dict: Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.
pin 2455371e3ec50d2e2b2334367a67424ba739e03f0f9eac6c4462422a7356f857bc_get_protein_domainsGet protein domain architecture and InterPro matches. Returns all InterPro domains, functional sites, and domain architecture. Returns: dict: Protein metadata with interpro_matches array, interpro_match_count, domain_architecture, optionally structure data or error message.Get protein domain architecture and InterPro matches. Returns all InterPro domains, functional sites, and domain architecture. Returns: dict: Protein metadata with interpro_matches array, interpro_match_count, domain_architecture, optionally structure data or error message.
pin f7d72a41487a64a0a76fcbf96c87fda5760d4d0785f683fc8b07ff1bc14ffdd7bc_get_reactome_info_by_identifierQuery the Reactome API identifier endpoint. Use this endpoint to retrieve pathways associated with a given identifier. Always provide the species parameter to ensure the correct protein is returned. Args: identifier (str): The identifier of the element to be retrieved base_url (str): Base URL for the Reactome API interactors (bool): Include interactors species (str or list): List of species to filter the result (accepts taxonomy ids, species names and dbId) page_size (int): Pathways per page page (int): Page number sort_by (str): Field to sort results by (e.g., "ENTITIES_PVALUE", "ENTITIES_FDR") order (str): Sort order ("ASC" or "DESC") resource (str): Resource to filter by (TOTAL includes all molecule types) p_value (float): P-value threshold (only pathways with p-value <= threshold will be returned) include_disease (bool): Set to False to exclude disease pathways min_entities (int): Minimum number of contained entities per pathway max_entities (int): Maximum number of contained entities per pathway importable_only (bool): Filter to only include importable resources timeout (int): Request timeout in seconds Returns: dict: API response data or error informationQuery the Reactome API identifier endpoint. Use this endpoint to retrieve pathways associated with a given identifier. Always provide the species parameter to ensure the correct protein is returned. Args: identifier (str): The identifier of the element to be retrieved base_url (str): Base URL for the Reactome API interactors (bool): Include interactors species (str or list): List of species to filter the result (accepts taxonomy ids, species names and dbId) page_size (int): Pathways per page page (int): Page number sort_by (str): Field to sort results by (e.g., "ENTITIES_PVALUE", "ENTITIES_FDR") order (str): Sort order ("ASC" or "DESC") resource (str): Resource to filter by (TOTAL includes all molecule types) p_value (float): P-value threshold (only pathways with p-value <= threshold will be returned) include_disease (bool): Set to False to exclude disease pathways min_entities (int): Minimum number of contained entities per pathway max_entities (int): Maximum number of contained entities per pathway importable_only (bool): Filter to only include importable resources timeout (int): Request timeout in seconds Returns: dict: API response data or error information
pin 0821a1f75fbe675ea74ed3d916bbb426fb9e7067b9773f2250dad0c6c43cdf57bc_get_recent_biorxiv_preprintsSearch bioRxiv/medRxiv preprints by date range or recent count. Specify one search method: date range, days, or recent_count. Returns: dict: Search results with server, search_params, total_returned, papers list (each with title, authors, abstract, metadata), pagination info or error message.Search bioRxiv/medRxiv preprints by date range or recent count. Specify one search method: date range, days, or recent_count. Returns: dict: Search results with server, search_params, total_returned, papers list (each with title, authors, abstract, metadata), pagination info or error message.
pin 31160014bd10357a954423d520cfd33fd85945bb84edaed912c546e82a994aa2bc_get_recruiting_studies_by_locationFind recruiting clinical trials by geographic location. Returns paginated results with summary breakdowns. Returns: dict: Studies list with summary containing search location, total studies, study type/phase/condition breakdowns, recruiting locations or error message.Find recruiting clinical trials by geographic location. Returns paginated results with summary breakdowns. Returns: dict: Studies list with summary containing search location, total studies, study type/phase/condition breakdowns, recruiting locations or error message.
pin e78a2364a52608fa1eac1c3fd8b345f7a7cb6938472a55cc6e36162c06ec9521bc_get_string_idMap protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability. Returns: str or dict: STRING ID string (e.g., '9606.ENSP00000269305') or dict with error message.Map protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability. Returns: str or dict: STRING ID string (e.g., '9606.ENSP00000269305') or dict with error message.
pin df0cc3ded7be33226d9dea3ad584f6d68019ebdb78166c25467b07dbb135d80ebc_get_string_interactionsRetrieve protein-protein interactions for a given protein with scores above threshold. Always provide species parameter. Returns: list or dict: Protein interactions array with stringId_A, stringId_B, preferredName_A/B, score, evidence channels or error message.Retrieve protein-protein interactions for a given protein with scores above threshold. Always provide species parameter. Returns: list or dict: Protein interactions array with stringId_A, stringId_B, preferredName_A/B, score, evidence channels or error message.
pin 2f623771a69a0a6782420771086f0d413ed56e0588cf431747e3485066468974bc_get_string_network_imageGenerate protein-protein interaction network image from STRING database. Always provide species parameter. Returns: Image or dict: Network visualization as PNG image object or error message.Generate protein-protein interaction network image from STRING database. Always provide species parameter. Returns: Image or dict: Network visualization as PNG image object or error message.
pin d924805831c004f84719db6815349a48f616a448f13a85588a5b6afbcd90deecbc_get_string_similarity_scoresRetrieve protein homology similarity scores from STRING database based on Smith-Waterman bit scores. Only scores above 50 reported. Returns: list or dict: Similarity scores array with stringId_A, stringId_B, bitscore or error message.Retrieve protein homology similarity scores from STRING database based on Smith-Waterman bit scores. Only scores above 50 reported. Returns: list or dict: Similarity scores array with stringId_A, stringId_B, bitscore or error message.
pin 914c3fcbebde176a463e44d7f45ace3cb108b602718dca2658ce60e40cb20bdcbc_get_studies_by_conditionSearch trials by condition with summary statistics. Returns paginated results with breakdowns by status, study type, and phase. Returns: dict: Studies list with summary containing condition searched, total studies, status/study type/phase breakdowns or error message.Search trials by condition with summary statistics. Returns paginated results with breakdowns by status, study type, and phase. Returns: dict: Studies list with summary containing condition searched, total studies, status/study type/phase breakdowns or error message.
pin 6a59a07874e96480713acd2513505883e81fca3fdf43b526882d8a27a45c29eebc_get_studies_by_interventionSearch trials by intervention with condition and phase filters. Returns paginated results with breakdowns. Returns: dict: Studies list with summary containing intervention searched, total studies, status/phase breakdowns, top conditions/sponsors or error message.Search trials by intervention with condition and phase filters. Returns paginated results with breakdowns. Returns: dict: Studies list with summary containing intervention searched, total studies, status/phase breakdowns, top conditions/sponsors or error message.
pin 3ae00259791ce5ab84a952fd7d7994a3a469149d93f10483c7976748dfaf04f3bc_get_study_detailsGet complete trial details by NCT ID. Retrieves study design, eligibility, outcomes, locations, contacts, and metadata. Returns: dict: Study details with protocol sections including identification, status, sponsors, description, conditions, design, interventions, outcomes, eligibility, locations or error message.Get complete trial details by NCT ID. Retrieves study design, eligibility, outcomes, locations, contacts, and metadata. Returns: dict: Study details with protocol sections including identification, status, sponsors, description, conditions, design, interventions, outcomes, eligibility, locations or error message.
pin d75f3a3c4d6e9de029f331295caca4a829f2bd9eaaf362011673c89a5bec3744bc_get_term_detailsGet comprehensive details about a specific ontology term including definition, synonyms, hierarchical relationships. Returns: dict: Term details with id, label, definition, synonyms, hierarchical info, num_descendants or error message.Get comprehensive details about a specific ontology term including definition, synonyms, hierarchical relationships. Returns: dict: Term details with id, label, definition, synonyms, hierarchical info, num_descendants or error message.
pin c97951e9e49e9a5d1a54cae997093fef40ccda0209b49616796dabe53866da94bc_get_term_hierarchical_childrenGet hierarchical children of an ontology term from OLS. Includes subclasses and hierarchical properties. Returns: dict: Parent term, hierarchical_children array with id/label/definition, total_children, page_info or error message.Get hierarchical children of an ontology term from OLS. Includes subclasses and hierarchical properties. Returns: dict: Parent term, hierarchical_children array with id/label/definition, total_children, page_info or error message.
pin cb27e54f9041a427188d9a3554c897bb886f86a4db9953e1a44cbd6db8692fe4bc_get_uniprot_id_by_protein_symbolRetrieve the UniProt accession for a gene symbol and species. Prefers reviewed (Swiss-Prot) entries. Returns: dict: accession, gene, protein_name, reviewed, match_type ('gene', 'synonym' or 'protein_name') and other candidates, or error message (with candidates if ambiguous or only partially matching).Retrieve the UniProt accession for a gene symbol and species. Prefers reviewed (Swiss-Prot) entries. Returns: dict: accession, gene, protein_name, reviewed, match_type ('gene', 'synonym' or 'protein_name') and other candidates, or error message (with candidates if ambiguous or only partially matching).
pin 197fa086cdf46fe3a90bfb2c46767e420918e348fc9a055fca404001e793d142bc_get_uniprot_protein_infoRetrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol. Returns: dict: Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references or error message.Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol. Returns: dict: Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references or error message.
pin 1d4790eb8b0eba54117a036d75b8aa81414cb8612f4bc89365d564e6665fa9eabc_query_open_targets_graphqlExecute GraphQL queries against the Open Targets API. Use get_open_targets_query_examples() or get_open_targets_graphql_schema() first. Returns: dict: GraphQL response with data field containing targets, diseases, drugs, variants, studies or error message.Execute GraphQL queries against the Open Targets API. Use get_open_targets_query_examples() or get_open_targets_graphql_schema() first. Returns: dict: GraphQL response with data field containing targets, diseases, drugs, variants, studies or error message.
pin 317461c3060ef80b3500aee4a00b319da9d749c3c92681c53244a37fb5535f5dbc_search_drugs_by_therapeutic_classSearch for drugs by therapeutic or pharmacologic class. Use get_available_pharmacologic_classes() first for exact terms. Returns: dict: FDA drug results array with application info, products, sponsor names or error message.Search for drugs by therapeutic or pharmacologic class. Use get_available_pharmacologic_classes() first for exact terms. Returns: dict: FDA drug results array with application info, products, sponsor names or error message.
pin ed191ce740c904d9a67db35a562ca063d41edad2f608e76e19902dc0c2c6ea5dbc_search_drugs_fdaSearch FDA Drugs@FDA database for approved drug products. Supports multiple search criteria. Returns: dict: Results array with drug products including application numbers, sponsors, products array or error message.Search FDA Drugs@FDA database for approved drug products. Supports multiple search criteria. Returns: dict: Results array with drug products including application numbers, sponsors, products array or error message.
pin 95eeedc64760d5a4ddf02c7c391c1b9e7f157cbb53795e3c3961ff3d268c726ebc_search_grants_govSearch grants.gov by keyword, agency, or other criteria. Returns opportunity listings with deadlines and eligibility. Returns: dict: Grant opportunities list with titles, agencies, deadlines, funding amounts, eligibility criteria or error message.Search grants.gov by keyword, agency, or other criteria. Returns opportunity listings with deadlines and eligibility. Returns: dict: Grant opportunities list with titles, agencies, deadlines, funding amounts, eligibility criteria or error message.
pin 876ca41593a0be390801f1d68b79bba1bfe91aff1e838d8f85d5e2a48b8b3902bc_search_interpro_entriesSearch InterPro entries by name, type, database, GO term, or species. Returns matching entries with metadata. Returns: dict: Search results with results array (InterPro entries), count, total_available, search_criteria or error message.Search InterPro entries by name, type, database, GO term, or species. Returns matching entries with metadata. Returns: dict: Search results with results array (InterPro entries), count, total_available, search_criteria or error message.
pin 686826275f809b3b9264ee1b446f91ae32cb6f6b5bbb691eecbd39e9124f78e0bc_search_ontology_termsSearch for terms across multiple ontologies in OLS. Use get_available_ontologies() first to discover ontologies. Returns: dict: Terms array, terms_by_ontology grouped results, total_results, ontologies_found list or error message.Search for terms across multiple ontologies in OLS. Use get_available_ontologies() first to discover ontologies. Returns: dict: Terms array, terms_by_ontology grouped results, total_results, ontologies_found list or error message.
pin 2cc6bc3ee1ef190d18e5afddd431c5a371efe2cb78825179e32f0be474af8757bc_search_pride_projectsSearch PRIDE database for mass spectrometry proteomics projects using keywords and filters. Returns: dict: Results array with project accessions, titles, descriptions, organisms, instruments, experiment types, count, search_criteria or error message.Search PRIDE database for mass spectrometry proteomics projects using keywords and filters. Returns: dict: Results array with project accessions, titles, descriptions, organisms, instruments, experiment types, count, search_criteria or error message.
pin 630c2afbb4c512df362e3e4d0a701cfb56f9ffa10ce076512973d00134d6d3c4bc_search_pride_proteinsSearch for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets. Returns: dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets. Returns: dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.
pin 70a2990b50516df38ae441ceceacdb2b0dcd66ee27a581316bba2789ac910224bc_search_studiesAdvanced search for trials with flexible multi-field filtering. Specify at least one search parameter. Returns: dict: Paginated search results containing studies list with trial metadata or error message.Advanced search for trials with flexible multi-field filtering. Specify at least one search parameter. Returns: dict: Paginated search results containing studies list with trial metadata or error message.
pin bf724e9c0df90e66c71662be6007613ee2f02e8b9f1b627f06c6ef5fd7dd631a
runs · 1
the latest tests of this entry by the hub and its workers, newest first| date | worker | method | status | sandbox | reason |
|---|---|---|---|---|---|
| 2026-10-17 19:18 | local-mac-vm | dockermcp 2025-06-18 | ok49 tools | gvisor | — |