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OrigeneBLOCK

mcp/gentel-lab/origene
MCP server by gentel-lab · Audited 2026-10-08
⚑ Report / re-scanSource ↗
Verdict
BLOCK
Grade
D
Trust score
69 /100
Exposed tools
200 376r · 23w · 0d
Transport
sse · stdio · streamable-http
License
—
Stars
39
01

Overview

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

OrigeneMCP is a core component of the OriGene ecosystem, a self-evolving multi-agent system designed to act as a virtual disease biologist. OriGene provides a unified platform for biomedical AI research and was officially launched at the 2025 WAIC.

Paper | OriGene Code | OrigeneMCP Code |

1. OrigeneMCP Overview

Recent updates: - 2026-02-24 🚀 Update new tools: DepMap, etc. - 2025-07-28 🚀 OriGene officially launched at WAIC 2025! - 2025-07-22 🔥 Integrated OrigeneMCP into the Bohrium AI for Science platform. - 2025-07-19 🔥 Integrated OrigeneMCP into CAMEL. - 2025-07-18 🚀 OrigeneMCP officially open-sourced!

OrigeneMCP is the MCP toolkit for the OriGene project that integrates over 600 tools and multiple databases (including ChEMBL, PubChem, FDA, OpenTargets, NCBI, UniProt, PDB, Ensembl, UCSC, KEGG, STRING, TCGA, Monarch, ClinicalTrials, and more) into an advanced integrated MCP server platform, combining disease biology and drug discovery tools to enable comprehensive multi-dimensional information retrieval across small molecules, proteins, genes, diseases, and other biological entities, serving as a unified interface for accessing and analyzing complex biomedical data to accelerate therapeutic research and development.

2. Deploy OrigeneMCP

Clone the repository:

git clone https://github.com/GENTEL-lab/OrigeneMCP.git

The dependencies of this repository are managed by uv. Before deployment, please make sure that uv is already installed. Use the following commands to install uv:

pip install uv
Read from source at commit 8eb8615c8696OBSERVED · 2026-10-08
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02
Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control. Replace the environment placeholders with a token scoped to the least it needs.
claude-code
claude mcp add mcp-tools --env FDA_API_KEY=${FDA_API_KEY} -- uvx mcp-tools
claude-desktop
{
  "mcpServers": {
    "mcp-tools": {
      "command": "uvx",
      "args": [
        "mcp-tools"
      ],
      "env": {
        "FDA_API_KEY": "${FDA_API_KEY}"
      }
    }
  }
}
03
Exposed tools (200)
376 read · 23 write · 0 destructive.
ToolRiskDescription
check_genome_accessionsreadCheck the validity of genome accessions
check_virus_accessionsreadCheck virus accessions validity
clinvar_find_single_mutationreadFind single amino acid mutation between mutant and reference sequences.
clinvar_get_best_refseqid_by_sequencereadFind best matching RefSeq ID for a protein sequence using BLASTP.
clinvar_query_sequence_variantsreadQuery ClinVar for multiple variants on a protein sequence.
clinvar_query_variant_significancereadQuery ClinVar for variant classification/significance.
depmap_comprehensive_analysisread
depmap_get_dependencyread
depmap_get_expressionread
depmap_get_mutationread
ensembl_get_genes_by_bandread
get_activityread
get_activity_by_idread
get_activity_by_idsread
get_activity_supplementary_data_by_activityread
get_activity_supplementary_data_by_activity_by_idread
get_activity_supplementary_data_by_activity_by_idsread
get_alignment_regionread
get_all_interaction_partners_of_the_protein_setwrite
get_archive_idread
get_assayread
get_assay_by_idread
get_assay_by_idsread
get_assay_classread
get_assay_class_by_idread
get_assay_class_by_idsread
get_assay_summary_by_cidread
get_assay_summary_by_sidread
get_assembly_region_inforead
get_atc_classread
get_atc_class_by_idread
get_atc_class_by_idsread
get_best_similarity_hits_between_speciesread
get_binding_siteread
get_binding_site_by_idread
get_binding_site_by_idsread
get_biosample_reportread
get_biotherapeuticread
get_biotherapeutic_by_idread
get_biotherapeutic_by_idsread
get_cafe_genetree_idread
get_cafe_genetree_member_idread
get_cafe_genetree_member_symbolread
get_cell_lineread
get_cell_line_by_idread
get_cell_line_by_idsread
get_chembl_id_lookupread
get_chembl_id_lookup_by_idread
get_chembl_id_lookup_by_idsread
get_chembl_releaseread
get_chembl_release_by_idread
get_chembl_release_by_idsread
get_chromosome_sequenceread
get_chromosome_summaryreadGet chromosome summary by taxon and annotation name
get_cids_by_formularead
get_cids_by_smilesread
get_compound_by_cidread
get_compound_by_nameread
get_compound_chembl_id_by_nameread
get_compound_dictread
get_compound_property_by_nameread
get_compound_recordread
get_compound_record_by_idread
get_compound_record_by_idsread
get_compound_structural_alertread
get_compound_structural_alert_by_idread
get_compound_structural_alert_by_idsread
get_compound_synonyms_by_nameread
get_compounds_3dread
get_compounds_by_formularead
get_compounds_by_smilesread
get_compounds_dictread
get_conformers_by_cidread
get_cytobandread
get_description_by_aidread
get_description_by_cidread
get_description_by_sidread
get_documentread
get_document_by_idread
get_document_by_idsread
get_document_similarityread
get_document_similarity_by_idread
get_document_similarity_by_idsread
get_drugread
get_drug_by_idread
get_drug_by_idsread
get_drug_indicationread
get_drug_indication_by_idread
get_drug_indication_by_idsread
get_drug_warningread
get_drug_warning_idread
get_drug_warning_idsread
get_enumsread
get_field_size_statsread
get_field_value_statsread
get_functional_annotationread
get_functional_enrichmentread
get_ga4gh_beaconread
get_ga4gh_beacon_queryread
get_ga4gh_callsetsread
get_ga4gh_datasetsread
get_ga4gh_featuresread
get_ga4gh_featuresetsread
get_ga4gh_referencesread
get_ga4gh_referencesetsread
get_ga4gh_variantannotationsetsread
get_ga4gh_variantsread
get_ga4gh_variantsetsread
get_gene_by_accessionread
get_gene_by_accession_dataset_reportread
get_gene_by_accession_product_reportread
get_gene_by_idsread
get_gene_by_symbol_dataset_reportreadGet dataset reports by taxons
get_gene_by_symbol_product_reportreadGet product reports by taxon
get_gene_by_taxonreadGet gene information by taxon
get_gene_by_taxon_dataset_reportreadGet gene dataset reports by taxonomic identifier
get_gene_by_taxon_product_reportreadGet gene product reports by taxonomic identifier
get_gene_centric_by_accessionread
get_gene_centric_by_proteomeread
get_gene_counts_by_taxonreadGet gene counts by taxon
get_gene_dataset_report_by_idreadGet gene information by dataset report
get_gene_dataset_report_by_locus_tagreadGet gene dataset reports by locus tag
get_gene_download_summary_by_idreadGet gene download summary by GeneID
get_gene_links_by_idreadGet gene links by gene ID
get_gene_metadata_by_gene_nameread
get_gene_orthologsreadGet gene orthologs by gene ID
get_gene_product_report_by_idreadGet gene product report by gene ID
get_gene_product_report_by_locus_tagreadGet gene product reports by locus tags
get_gene_specific_expression_in_cancer_typeread
get_gene_summary_by_geneidread
get_general_info_by_compound_nameread
get_general_info_by_protein_or_gene_nameread
get_genes_in_regionread
get_genetree_idread
get_genetree_member_idread
get_genetree_member_symbolread
get_genome_annotation_reportread
get_genome_annotation_summaryread
get_genome_by_accessionreadGet genome information by accession
get_genome_dataset_report_by_accessionreadGet dataset reports by accessions
get_genome_dataset_report_by_assembly_namereadGet dataset reports by assembly name
get_genome_dataset_report_by_bioprojectreadGet dataset reports by bioproject
get_genome_dataset_report_by_biosamplereadGet dataset reports by biosample id
get_genome_dataset_report_by_taxonreadGet dataset reports by taxons
get_genome_dataset_report_by_wgsreadGet dataset reports by wgs accession
get_genome_downloadreadGet a genome dataset by accession
get_genome_download_summaryreadPreview genome dataset download
get_genome_linksreadGet assembly links by accessions
get_genome_revision_historyreadGet revision history for assembly by accession
get_genome_sequence_reportsreadGet sequence reports by accessions
get_go_slimread
get_go_slim_idread
get_go_slim_idsread
get_homology_idread
get_homology_symbolread
get_imageread
get_info_analysisread
get_info_assemblyread
get_info_biotypesread
get_info_biotypes_groupsread
get_info_biotypes_nameread
get_info_compara_methodsread
get_info_compara_species_setsread
get_info_comparasread
get_info_dataread
get_info_divisionsread
get_info_eg_versionread
get_info_external_dbsread
get_info_genomesread
get_info_genomes_accessionread
get_info_genomes_assemblyread
get_info_genomes_divisionread
get_info_genomes_taxonomyread
get_info_pingread
get_info_restread
get_info_softwareread
get_info_speciesread
get_info_variationread
get_info_variation_consequence_typesread
get_info_variation_populationsread
get_isomeric_smilesread
get_iupac_nameread
get_ldread
get_ld_pairwiseread
get_ld_regionread
get_lookup_idread
get_lookup_symbolread
get_mapread
get_map_cdnaread
get_map_cdsread
get_map_translationread
get_mechanismread
get_mechanism_idread
get_mechanism_idsread
get_metabolismread
get_metabolism_idread
get_metabolism_idsread
get_metadataread
get_molecular_formularead
get_molecular_weightread
04
Trust audit
BLOCKgrade D · trust 69/100 Do not install this without reading the findings. The audit found something that could harm you or your machine.
LayerWhat it checksResult
L0Provenance & inventoryPASS
L1Static analysis of the codeFAIL
L2Instruction surface (what it tells the agent)PASS
L3Class-specific surfacePASS
L4Behavioural (sandbox)SKIPPED
What the source does
Filesystem
none-observed
Network
declared (10 observation(s))
Shell
declared (1 observation(s))
Dependencies
pinned
Secrets in source
none-found
Findings (11)
HIGHNetwork egress · net.tls_off · CWE-200, CWE-319
tools/tcga/tcga_analyse.py:315
response = self.session.get(url, stream=True, timeout=(15, 120), verify=False)
Why it matters. certificate verification is disabled
Fix. leave verification on
MEDIUMNetwork egress · net.beacon_words · CWE-200, CWE-319
tools/ensembl/ensembl_api.py:632
return self._make_request("GET", "ga4gh/beacon")
MEDIUMNetwork egress · net.beacon_words · CWE-200, CWE-319
tools/ensembl/ensembl_api.py:636
return self._make_request("GET", "ga4gh/beacon/query", params=params)
MEDIUMNetwork egress · net.beacon_words · CWE-200, CWE-319
tools/ensembl/ensembl_api.py:640
return self._make_request("POST", "ga4gh/beacon/query", data=data)
MEDIUMNetwork egress · net.raw_ip · CWE-200, CWE-319
dist/logs/mcp_traffic.csv:2
2025-07-14T17:00:54.558217,ncbi_mcp,POST,http://127.0.0.1:8788/ncbi_mcp/mcp/,127.0.0.1,"{'name': 'get_gene_metadata_by_gene_name', 'arguments': {'name': 'TP53'}}",{'status_code': 200}
LOWInventory / provenance · inv.no_license · CWE-1104
Why it matters. no LICENSE file and no repo licence
Fix. add a licence
LOWNetwork egress · net.raw_ip · CWE-200, CWE-319
README.md:85
"url": f"http://127.0.0.1:8788/{package}/mcp/"
LOWNetwork egress · net.raw_ip · CWE-200, CWE-319
README.md:158
"url": f"http://127.0.0.1:8788/{package}/mcp/"
LOWNetwork egress · net.raw_ip · CWE-200, CWE-319
tests/test.py:17
"url": f"http://127.0.0.1:8788/{package}/mcp/"
INFOInventory / provenance · inv.oversize · CWE-1104
tools/tcga/data/TCGA_CIBERSORT.tsv
tools/tcga/data/TCGA_CIBERSORT.tsv
Why it matters. 3818975 bytes not read
INFOInventory / provenance · inv.oversize · CWE-1104
tools/tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py
tools/tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py
Why it matters. 6510589 bytes not read
Gates applied: no_behavioural_pass, no_license.
Audited 2026-10-08 · audit v0.4.1 · source sha 8eb8615c8696full audit observations/trust-audit/mcp-server/gentel-lab__origene.json · Report an issue / request a re-scan
05
Audit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
DateSourceVerdictGradeScoreChange
2026-10-088eb8615c8696BLOCKD69first audit
06
Questions
What tools does Origene expose?
200 in total: 376 read-only, 23 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is Origene safe to connect to an agent?
No — not without reading the findings first. The audit graded it D (69/100) and found 1 critical or high issue in the source. Each one is listed on this page with the file and line it is on.
What credentials does Origene need?
It reads FDA_API_KEY from the environment. Give it a token scoped to the least it needs — an agent that can be talked into calling a tool can be talked into calling it with your credentials.
How does Origene run?
It speaks sse, stdio and streamable-http, so it runs as a local process your client starts. It is published on PyPI as mcp-tools.
How current is this page?
The grade is for one exact copy of the source (8eb8615c8696), read on 2026-10-08. The repository is watched and re-audited when it changes.
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