// SCAN REPORT

OrigeneMCP

439 tools. 8 can modify or destroy data without limits.

6 write tools that can modify data. Rate limits recommended.

Last updated:

8 can modify or destroy data
431 read-only
439 tools total

Community server · catalogue entry verified 11/06/2026

How to control OrigeneMCP ↓

TOOL MAP

What OrigeneMCP exposes to your agents

Read (431) Write / Execute (6) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS
High Risk

The most dangerous OrigeneMCP tools

Execute · Medium post_vep_hgvs VEP (Variant Effect Predictor) is a bioinformatics tool that runs computational analysis on genomic variants. Execute · Medium post_vep_id VEP (Variant Effect Predictor) is a well-known bioinformatics tool that runs variant annotation analysis. Write · Medium post_archive_id The 'post_' prefix indicates a write operation that creates or modifies data. Write · Medium post_sequence_id The 'post' prefix strongly suggests this tool creates or submits sequence data.

8 of OrigeneMCP's 439 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control OrigeneMCP

PolicyLayer is an MCP gateway — it sits between your AI agents and OrigeneMCP, and nothing reaches the server without passing your rules. These are the rules we recommend:

Rate limit write operations
{
  "post_archive_id": {
    "limits": [
      {
        "counter": "post_archive_id_per_hour",
        "window": "hour",
        "max": 30,
        "scope": "grant"
      }
    ]
  }
}

Prevents bulk unintended modifications from agents caught in loops.

Cap read operations
{
  "check_genome_accessions": {
    "limits": [
      {
        "counter": "check_genome_accessions_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

  1. Create a free account and register OrigeneMCP — nothing to install.
  2. Add these rules — paste them, or build them visually. Tune the limits to your setup.
  3. Point your MCP client (Claude, Cursor, anything) at your gateway URL.
ENFORCE POLICY ON ORIGENEMCP →

Free to start. No card required.

FULL CATALOGUE

All 439 OrigeneMCP tools

EXECUTE 2 tools
Execute post_vep_hgvs post_vep_hgvs Execute post_vep_id post_vep_id
WRITE 4 tools
Write post_archive_id post_archive_id Write post_sequence_id post_sequence_id Write post_variant_recoder post_variant_recoder Write post_variation post_variation
READ 431 tools
Read check_genome_accessions Check the validity of genome accessions Read check_virus_accessions Check virus accessions validity Read clinvar_find_single_mutation clinvar_find_single_mutation Read clinvar_get_best_refseqid_by_sequence clinvar_get_best_refseqid_by_sequence Read clinvar_query_sequence_variants clinvar_query_sequence_variants Read clinvar_query_variant_significance clinvar_query_variant_significance Read depmap_comprehensive_analysis depmap_comprehensive_analysis Read depmap_get_dependency depmap_get_dependency Read depmap_get_expression depmap_get_expression Read depmap_get_mutation depmap_get_mutation Read ensembl_get_genes_by_band Extract genes in a cytogenetic band region (e.g., 'chr10q21'). Read get_activity get_activity Read get_activity_by_id get_activity_by_id Read get_activity_by_ids get_activity_by_ids Read get_activity_supplementary_data_by_activity get_activity_supplementary_data_by_activity Read get_activity_supplementary_data_by_activity_by_id Retrieve single activitysupplementarydatabyactivity object details by ID. Read get_activity_supplementary_data_by_activity_by_ids Retrieve multiple activitysupplementarydatabyactivity objects by IDs. Read get_alignment_region get_alignment_region Read get_all_interaction_partners_of_the_protein_set get_all_interaction_partners_of_the_protein_set Read get_archive_id get_archive_id Read get_assay get_assay Read get_assay_by_id get_assay_by_id Read get_assay_by_ids get_assay_by_ids Read get_assay_class get_assay_class Read get_assay_class_by_id get_assay_class_by_id Read get_assay_class_by_ids get_assay_class_by_ids Read get_assay_summary_by_cid get_assay_summary_by_cid Read get_assay_summary_by_sid get_assay_summary_by_sid Read get_assembly_region_info get_assembly_region_info Read get_associated_diseases_by_drug_name Retrieve the list of diseases associated with a specific drug based on clinical trial data or post-marketed dr Read get_associated_diseases_phenotypes_by_target_name Find diseases or phenotypes associated with a specific target. Read get_associated_drugs_by_disease_name Retrieve known drugs associated with a specific disease by disease name. Read get_associated_drugs_by_target_name Get known drugs associated with a specific target, including clinical trial phase and mechanism of action of t Read get_associated_phenotypes_by_disease_name Find HPO phenotypes asosciated with the specified disease. Read get_associated_targets_by_disease_name Find targets associated with a specific disease or phenotype based on its name. Read get_associated_targets_by_drug_name Retrieve the list of targets linked to a specific drug based on its mechanism of action. Read get_atc_class get_atc_class Read get_atc_class_by_id get_atc_class_by_id Read get_atc_class_by_ids get_atc_class_by_ids Read get_best_similarity_hits_between_species get_best_similarity_hits_between_species Read get_binding_site get_binding_site Read get_binding_site_by_id get_binding_site_by_id Read get_binding_site_by_ids get_binding_site_by_ids Read get_biological_mouse_models_by_target_name Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a specific targe Read get_biosample_report Get biosample report. Read get_biotherapeutic get_biotherapeutic Read get_biotherapeutic_by_id get_biotherapeutic_by_id Read get_biotherapeutic_by_ids get_biotherapeutic_by_ids Read get_cafe_genetree_id get_cafe_genetree_id Read get_cafe_genetree_member_id get_cafe_genetree_member_id Read get_cafe_genetree_member_symbol get_cafe_genetree_member_symbol Read get_cell_line get_cell_line Read get_cell_line_by_id get_cell_line_by_id Read get_cell_line_by_ids get_cell_line_by_ids Read get_chembl_id_lookup Retrieve chembl_id_lookup object list. Read get_chembl_id_lookup_by_id get_chembl_id_lookup_by_id Read get_chembl_id_lookup_by_ids get_chembl_id_lookup_by_ids Read get_chembl_release Retrieve chembl_release object list. Read get_chembl_release_by_id get_chembl_release_by_id Read get_chembl_release_by_ids get_chembl_release_by_ids Read get_chemical_probes_by_target_name Retrieve chemical probes associated with a specific target. Read get_chromosome_sequence Get sequence for an entire chromosome. Read get_chromosome_summary Get chromosome summary by taxon and annotation name Read get_cids_by_formula Get a list of CIDs by molecular formula. Read get_cids_by_smiles Obtain the CID corresponding to the drug smiles Read get_compound_by_cid Get compound information by PubChem CID. Read get_compound_by_name get_compound_by_name Read get_compound_chembl_id_by_name Get compound ChEMBL ID by name. Read get_compound_dict Get a dictionary of a compound's properties. Read get_compound_property_by_name get_compound_property_by_name Read get_compound_record Retrieve compound record object list. Read get_compound_record_by_id get_compound_record_by_id Read get_compound_record_by_ids get_compound_record_by_ids Read get_compound_structural_alert Retrieve compound structural alert object list. Read get_compound_structural_alert_by_id get_compound_structural_alert_by_id Read get_compound_structural_alert_by_ids get_compound_structural_alert_by_ids Read get_compound_synonyms_by_name get_compound_synonyms_by_name Read get_compounds_3d Get a list of compound objects with 3D structures. Read get_compounds_by_formula get_compounds_by_formula Read get_compounds_by_smiles get_compounds_by_smiles Read get_compounds_dict Get a dictionary representation of a compound by CID. Read get_conformers_by_cid get_conformers_by_cid Read get_cytoband get_cytoband Read get_description_by_aid get_description_by_aid Read get_description_by_cid get_description_by_cid Read get_description_by_sid get_description_by_sid Read get_disease_ancestors_parents_by_name Retrieve the ancestors and parents of a specific disease. Read get_disease_descendants_children_by_name Retrieve the descendants and children of a specific disease. Read get_disease_description_by_name Retrieve the description of a specific disease. Read get_disease_efo_id Get disease EFO ID by disease name. Read get_disease_locations_by_name Retrieve the locations of a specific disease. Read get_disease_synonyms_by_name Retrieve synonyms for a specific disease. Read get_disease_therapeutic_areas_by_name Retrieve the therapeutic areas associated with a specific disease. Read get_document Retrieve document object list. Read get_document_by_id get_document_by_id Read get_document_by_ids get_document_by_ids Read get_document_similarity Retrieve document similarity object list. Read get_document_similarity_by_id get_document_similarity_by_id Read get_document_similarity_by_ids get_document_similarity_by_ids Read get_drug Retrieve drug object list. Read get_drug_by_id get_drug_by_id Read get_drug_by_ids get_drug_by_ids Read get_drug_chembl_id_by_name Find drug ChEMBL ID by drug name. Read get_drug_indication Retrieve drug indication object list. Read get_drug_indication_by_id get_drug_indication_by_id Read get_drug_indication_by_ids Retrieve multiple drus objects by IDs. Read get_drug_indications_by_name Fetch indications (treatable phenotypes/diseases) for a given drug. Read get_drug_mechanisms_of_action_by_name Retrieve the mechanisms of action associated with a specific drug. Read get_drug_warning Retrieve drug_warning object list Read get_drug_warning_id get_drug_warning_id Read get_drug_warning_ids get_drug_warning_ids Read get_drug_warnings_by_name Retrieve warnings for a specific drug. Read get_enums Get enumeration types and values. Read get_field_size_stats Get size statistics for list/array fields. Read get_field_value_stats Get value statistics for fields. Read get_functional_annotation get_functional_annotation Read get_functional_enrichment get_functional_enrichment Read get_ga4gh_beacon Get Beacon information. Read get_ga4gh_beacon_query Query Beacon. Read get_ga4gh_callsets Get the GA4GH record for a specific CallSet given its identifier Read get_ga4gh_datasets Get the GA4GH record for a specific dataset given its identifier Read get_ga4gh_features Get GA4GH features by ID. Read get_ga4gh_featuresets Return the GA4GH record for a specific featureSet given its identifier Read get_ga4gh_references Return data for a specific reference in GA4GH format by id Read get_ga4gh_referencesets get_ga4gh_referencesets Read get_ga4gh_variantannotationsets Return meta data for a specific annotation set in GA4GH format by ID Read get_ga4gh_variants Get GA4GH variant by ID. Read get_ga4gh_variantsets Return the GA4GH record for a specific VariantSet given its identifier Read get_gene_by_accession Get gene information by accession. Read get_gene_by_accession_dataset_report Get dataset reports by accession IDs Read get_gene_by_accession_product_report Get gene product reports by accession IDs Read get_gene_by_ids Get gene information by gene IDs. Read get_gene_by_symbol_dataset_report Get dataset reports by taxons Read get_gene_by_symbol_product_report Get product reports by taxon Read get_gene_by_taxon Get gene information by taxon Read get_gene_by_taxon_dataset_report Get gene dataset reports by taxonomic identifier Read get_gene_by_taxon_product_report Get gene product reports by taxonomic identifier Read get_gene_centric_by_accession get_gene_centric_by_accession Read get_gene_centric_by_proteome get_gene_centric_by_proteome Read get_gene_counts_by_taxon Get gene counts by taxon Read get_gene_dataset_report_by_id Get gene information by dataset report Read get_gene_dataset_report_by_locus_tag Get gene dataset reports by locus tag Read get_gene_download_summary_by_id Get gene download summary by GeneID Read get_gene_links_by_id Get gene links by gene ID Read get_gene_metadata_by_gene_name get_gene_metadata_by_gene_name Read get_gene_orthologs Get gene orthologs by gene ID Read get_gene_product_report_by_id Get gene product report by gene ID Read get_gene_product_report_by_locus_tag Get gene product reports by locus tags Read get_gene_specific_expression_in_cancer_type get_gene_specific_expression_in_cancer_type Read get_gene_summary_by_geneid Get summary information for a gene by Gene ID. Read get_general_info_by_compound_name Get detailed description of a compound by name, including overall information, drug and medication information Read get_general_info_by_disease_name get_general_info_by_disease_name Read get_general_info_by_protein_or_gene_name Get general information of a protein or gene by name from UniProt database. Read get_genes_in_region Query Ensembl REST API to get genes within a specific genomic region. Read get_genetree_id get_genetree_id Read get_genetree_member_id get_genetree_member_id Read get_genetree_member_symbol Get gene tree by symbol. Read get_genome_annotation_report Get genome annotation reports by genome accession. Read get_genome_annotation_summary Get genome annotation report summary information. Read get_genome_by_accession Get genome information by accession Read get_genome_dataset_report_by_accession Get dataset reports by accessions Read get_genome_dataset_report_by_assembly_name Get dataset reports by assembly name Read get_genome_dataset_report_by_bioproject Get dataset reports by bioproject Read get_genome_dataset_report_by_biosample Get dataset reports by biosample id Read get_genome_dataset_report_by_taxon Get dataset reports by taxons Read get_genome_dataset_report_by_wgs Get dataset reports by wgs accession Read get_genome_download Get a genome dataset by accession Read get_genome_download_summary Preview genome dataset download Read get_genome_links Get assembly links by accessions Read get_genome_revision_history Get revision history for assembly by accession Read get_genome_sequence_reports Get sequence reports by accessions Read get_go_slim get_go_slim Read get_go_slim_id get_go_slim_id Read get_go_slim_ids get_go_slim_ids Read get_homology_id get_homology_id Read get_homology_symbol get_homology_symbol Read get_image get_image Read get_info_analysis get_info_analysis Read get_info_assembly get_info_assembly Read get_info_biotypes get_info_biotypes Read get_info_biotypes_groups get_info_biotypes_groups Read get_info_biotypes_name get_info_biotypes_name Read get_info_compara_methods Get comparative analysis methods used in Ensembl Compara. Read get_info_compara_species_sets List all collections of species analysed with the specified compara method. Read get_info_comparas get_info_comparas Read get_info_data Get data release information. Read get_info_divisions Get Ensembl divisions. Read get_info_eg_version Get Ensembl Genomes version. Read get_info_external_dbs get_info_external_dbs Read get_info_genomes Find information about a given genome. Read get_info_genomes_accession get_info_genomes_accession Read get_info_genomes_assembly get_info_genomes_assembly Read get_info_genomes_division get_info_genomes_division Read get_info_genomes_taxonomy get_info_genomes_taxonomy Read get_info_ping Checks if the service is alive. Read get_info_rest Shows the current version of the Ensembl REST API. Read get_info_software Shows the current version of the Ensembl API used by the REST server. Read get_info_species get_info_species Read get_info_variation get_info_variation Read get_info_variation_consequence_types Lists all variant consequence types used by Ensembl. Read get_info_variation_populations get_info_variation_populations Read get_isomeric_smiles Get the isomeric SMILES of a compound. Read get_iupac_name Get the IUPAC name of a compound. Read get_ld get_ld Read get_ld_pairwise get_ld_pairwise Read get_ld_region get_ld_region Read get_lookup_id get_lookup_id Read get_lookup_symbol get_lookup_symbol Read get_map Map coordinates between assemblies. Read get_map_cdna get_map_cdna Read get_map_cds get_map_cds Read get_map_translation get_map_translation Read get_mechanism get_mechanism Read get_mechanism_id get_mechanism_id Read get_mechanism_ids get_mechanism_ids Read get_metabolism get_metabolism Read get_metabolism_id Retrieve single metabolism object details by ID. Read get_metabolism_ids get_metabolism_ids Read get_metadata Get metadata about available study fields. Read get_molecular_formula Get the molecular formula of a compound. Read get_molecular_weight Get the molecular weight of a compound. Read get_molecule get_molecule Read get_molecule_form get_molecule_form Read get_molecule_form_id get_molecule_form_id Read get_molecule_form_ids get_molecule_form_ids Read get_molecule_id get_molecule_id Read get_molecule_ids get_molecule_ids Read get_ontology_ancestors get_ontology_ancestors Read get_ontology_ancestors_chart Reconstruct the entire ancestry of a term from is_a and part_of relationships. Read get_ontology_descendants get_ontology_descendants Read get_ontology_id get_ontology_id Read get_ontology_name Get ontology by name. Read get_organelle_by_taxon_dataset_report Get organelle dataset report by taxon. Read get_organelle_dataset_report Get organelle dataset report. Read get_organelle_download Download organelle data Read get_organism get_organism Read get_organism_id get_organism_id Read get_organism_ids get_organism_ids Read get_overlap_id get_overlap_id Read get_overlap_region get_overlap_region Read get_overlap_translation get_overlap_translation Read get_phenotype_accession get_phenotype_accession Read get_phenotype_gene get_phenotype_gene Read get_phenotype_region get_phenotype_region Read get_ppi_enrichment get_ppi_enrichment Read get_prokaryote_gene_dataset_by_refseq_protein_accession Get a prokaryote gene dataset by RefSeq protein accession Read get_protein_classification get_protein_classification Read get_protein_classification_id get_protein_classification_id Read get_protein_classification_ids get_protein_classification_ids Read get_protein_summary_by_accession get_protein_summary_by_accession Read get_proteome_by_id Retrieve a proteome by UniProt Proteome ID. Read get_pubchem_compound_by_cid get_pubchem_compound_by_cid Read get_publications_by_disease_name Retrieve publications related to a disease name, including PubMed IDs and publication dates. Read get_publications_by_drug_name Retrieve publications related to a drug, including PubMed IDs and publication dates. Read get_publications_by_target_name Retrieve publications related to a target, including PubMed IDs and publication dates. Read get_search_areas Get available search documents and areas. Read get_sequence get_sequence Read get_sequence_assemblies Get assembly accessions for a sequence accession Read get_sequence_id get_sequence_id Read get_sequence_region get_sequence_region Read get_sids_by_name Get a list of SIDs by name. Read get_similar_entities_by_disease_name Retrieve similar entities for a given disease using a model trained with PubMed. Read get_similar_entities_by_drug_name Retrieve similar entities for a given drug using a model trained with PubMed. Read get_similar_entities_by_target_name Retrieve similar entities for a given target using a model trained with PubMed. Read get_similarity_scores_of_the_protein_set get_similarity_scores_of_the_protein_set Read get_similarity_smiles get_similarity_smiles Read get_source Retrieve source object list. Read get_source_id Retrieve single source object details by ID. Read get_source_ids Retrieve multiple source object details by IDs. Read get_species_binding_matrix get_species_binding_matrix Read get_status Retrieve status object list. Read get_string_network_interaction get_string_network_interaction Read get_studies get_studies Read get_study get_study Read get_study_size_stats Get statistics about study record sizes. Read get_substance_by_name Get substance information by name. Read get_substance_by_sid Get substance information by PubChem SID. Read get_substance_by_sid_pcp Get a Substance object by SID using PubChemPy. Read get_substances_by_name_pcp Get a list of Substance objects by name using PubChemPy. Read get_substances_source_id get_substances_source_id Read get_substances_synonyms Get the synonyms (Different names or identifiers for the same chemical substance) of a substance by SID. Read get_substructure_cas Get CAS Registry Numbers for compounds containing a specified substructure. Read get_synonyms Get the synonyms of a compound. Read get_target Retrieve target object list. Read get_target_classes_by_name Retrieve the target classes associated with a specific target. Read get_target_component get_target_component Read get_target_component_id get_target_component_id Read get_target_component_ids get_target_component_ids Read get_target_constraint_info_by_name Retrieve genetic constraint information for a specific target, including expected and observed values, and sco Read get_target_disease_evidence_by_name get_target_disease_evidence_by_name Read get_target_enabling_packages_by_name Retrieve the Target Enabling Packages (TEP) associated with a specific target. Read get_target_ensembl_id Get target Ensembl ID by target name. Read get_target_gene_ontology_by_name Retrieve Gene Ontology annotations for a specific target. Read get_target_genomic_location_by_name Retrieve genomic location data for a specific target, including chromosome, start, end, and strand. Read get_target_homologues_by_name Fetch homologues for a specific target. Read get_target_id get_target_id Read get_target_ids get_target_ids Read get_target_interactions_by_name Retrieve interaction data for a specific target, including interaction partners and evidence. Read get_target_relation Retrieve target relation object list. Read get_target_relation_id get_target_relation_id Read get_target_relation_ids get_target_relation_ids Read get_target_safety_profile_by_name Retrieve known target safety liabilities for a specific target. Read get_target_subcellular_locations_by_name Retrieve information about subcellular locations for a specific target. Read get_target_synonyms_by_name Retrieve synonyms for specified target, including alternative names and symbols. Read get_target_tractability_by_name Retrieve tractability assessments, including modality and values. Read get_taxonomy Get taxonomy information. Read get_taxonomy_classification Return the taxonomic classification of a taxon node. Read get_taxonomy_dataset_report Get taxonomy dataset report. Read get_taxonomy_download Download taxonomy data Read get_taxonomy_filtered_subtree Get filtered taxonomy subtree Read get_taxonomy_id Search for a taxonomic term by its identifier or name Read get_taxonomy_links Get taxonomy links Read get_taxonomy_name Search for a taxonomic id by a non-scientific name. Read get_taxonomy_name_report Get taxonomy name report Read get_taxonomy_related_ids Get related taxonomy IDs Read get_taxonomy_summary_by_taxonomyid get_taxonomy_summary_by_taxonomyid Read get_taxonomy_taxon_suggest Get taxonomy suggestions Read get_tissue Retrieve tissue object list Read get_tissue_id get_tissue_id Read get_tissue_ids Retrieve single tissue object details by IDs. Read get_track_data get_track_data Read get_transcript_haplotypes get_transcript_haplotypes Read get_uniparc_cross_references_by_upi get_uniparc_cross_references_by_upi Read get_uniparc_entry_by_upi get_uniparc_entry_by_upi Read get_uniparc_light_entry_by_upi get_uniparc_light_entry_by_upi Read get_uniprotkb_entry_by_accession get_uniprotkb_entry_by_accession Read get_uniref_cluster_by_id get_uniref_cluster_by_id Read get_uniref_cluster_members_by_id get_uniref_cluster_members_by_id Read get_uniref_light_cluster_by_id get_uniref_light_cluster_by_id Read get_variant_recoder get_variant_recoder Read get_variation get_variation Read get_variation_pmcid get_variation_pmcid Read get_variation_pmid get_variation_pmid Read get_vep_hgvs get_vep_hgvs Read get_vep_id get_vep_id Read get_vep_region get_vep_region Read get_version Get current version of all services. Read get_virus_annotation_report Get virus annotation report by accessions. Read get_virus_by_taxon_annotation_report Get virus annotation report by taxon Read get_virus_by_taxon_genome Get virus genome by taxon Read get_virus_by_taxon_genome_table Get virus genome table by taxon Read get_virus_dataset_report Get virus dataset report by accessions Read get_virus_genome_download Download virus genome by accessions Read get_xlogp Get the XLogP value of a compound. Read get_xref_source Retrieve xref_source object list Read get_xref_source_id get_xref_source_id Read get_xref_source_ids get_xref_source_ids Read get_xrefs_id Get cross references by ID. Read get_xrefs_name get_xrefs_name Read get_xrefs_symbol get_xrefs_symbol Read gsea_get_genelist_from_genesetname gsea_get_genelist_from_genesetname Read gtrd_entry_to_target_genes gtrd_entry_to_target_genes Read gtrd_gene_to_entry gtrd_gene_to_entry Read jina_search Run the jina DeepSearch engine with a given query, retrieving and filtering results. Read kegg_conv kegg_conv Read kegg_find kegg_find Read kegg_get kegg_get Read kegg_info kegg_info Read kegg_link kegg_link Read kegg_list kegg_list Read list_chromosomes list_chromosomes Read list_genomes Get all supported genome assemblies from UCSC Genome Browser. Read list_hub_tracks list_hub_tracks Read list_public_hubs list_public_hubs Read list_tcga_cancer_types List all supported TCGA cancer types. Read list_tracks List all tracks for a specific genome assembly. Read mapping_identifiers mapping_identifiers Read mirdb_get_geneset_by_mirname mirdb_get_geneset_by_mirname Read mousemine_get_geneset_from_mpid mousemine_get_geneset_from_mpid Read paper_search Run the openalex search engine with a given query, retrieving and filtering results. Read pdb_get_aggregation_group_provenance pdb_get_aggregation_group_provenance Read pdb_get_branched_entity pdb_get_branched_entity Read pdb_get_branched_entity_instance pdb_get_branched_entity_instance Read pdb_get_chemical_component pdb_get_chemical_component Read pdb_get_drugbank_annotations pdb_get_drugbank_annotations Read pdb_get_entry_groups pdb_get_entry_groups Read pdb_get_nonpolymer_entity pdb_get_nonpolymer_entity Read pdb_get_nonpolymer_entity_groups pdb_get_nonpolymer_entity_groups Read pdb_get_nonpolymer_entity_instance pdb_get_nonpolymer_entity_instance Read pdb_get_pdb_cluster_data_aggregation pdb_get_pdb_cluster_data_aggregation Read pdb_get_pdb_cluster_data_aggregation_method pdb_get_pdb_cluster_data_aggregation_method Read pdb_get_polymer_entity pdb_get_polymer_entity Read pdb_get_polymer_entity_groups pdb_get_polymer_entity_groups Read pdb_get_polymer_entity_instance pdb_get_polymer_entity_instance Read pdb_get_polymer_interface pdb_get_polymer_interface Read pdb_get_pubmed_annotations pdb_get_pubmed_annotations Read pdb_get_residue_chains pdb_get_residue_chains Read pdb_get_structural_assembly pdb_get_structural_assembly Read pdb_get_structure pdb_get_structure Read pdb_get_uniprot_annotations pdb_get_uniprot_annotations Read phipster_get_hpid_list_by_vpid phipster_get_hpid_list_by_vpid Read phipster_hpid_list_to_hpname_list phipster_hpid_list_to_hpname_list Read phipster_vpname2vpid phipster_vpname2vpid Read search_activity search_activity Read search_assay search_assay Read search_chembl_id_lookup search_chembl_id_lookup Read search_document search_document Read search_gene_centric Search GeneCentric entries with pagination. Read search_molecule search_molecule Read search_protein_classification search_protein_classification Read search_proteomes Search Proteome entries with pagination. Read search_pubchem_advanced search_pubchem_advanced Read search_pubchem_by_name search_pubchem_by_name Read search_pubchem_by_smiles Search PubChem for compounds matching a SMILES string. Read search_target search_target Read search_uniparc_entries search_uniparc_entries Read search_uniprotkb_entries search_uniprotkb_entries Read search_uniref_clusters search_uniref_clusters Read stream_gene_centric Stream GeneCentric entries matching a query (max 10M entries). Read stream_proteomes Stream Proteome entries matching a query (max 10M entries). Read stream_uniparc_cross_references_by_upi stream_uniparc_cross_references_by_upi Read stream_uniparc_entries stream_uniparc_entries Read stream_uniprotkb_entries stream_uniprotkb_entries Read stream_uniref_clusters stream_uniref_clusters Read substructure_info substructure_info Read tavily_search Run the search engine with a given query, retrieving and filtering results. Read tcga_differential_expression_analysis tcga_differential_expression_analysis Read tcga_immune_correlation_analysis tcga_immune_correlation_analysis Read post_ga4gh_beacon_query Query Beacon with POST. Read post_ga4gh_callsets_search Search GA4GH callsets. Read post_ga4gh_datasets_search Get a list of datasets in GA4GH format Read post_ga4gh_featuresets_search Search GA4GH feature sets. Read post_ga4gh_references_search post_ga4gh_references_search Read post_ga4gh_referencesets_search post_ga4gh_referencesets_search Read post_ga4gh_variantannotations_search post_ga4gh_variantannotations_search Read post_ga4gh_variantannotationsets_search Return a list of annotation sets in GA4GH format Read post_ga4gh_variants_search post_ga4gh_variants_search Read post_ga4gh_variantsets_search Search GA4GH variant sets. Read post_lookup_symbol post_lookup_symbol Read post_sequence_region Get sequences by multiple regions. Read post_vep_region Get variant effect predictions by multiple regions.
OTHER 2 tools
Other post_ga4gh_features_search post_ga4gh_features_search Other post_lookup_id post_lookup_id
FAQ

Questions about OrigeneMCP

How do I prevent bulk modifications through OrigeneMCP? +

The OrigeneMCP server has 4 write tools including post_archive_id, post_sequence_id, post_variant_recoder. Set a rate limit in your policy -- for example, 10 calls per hour prevents an agent from making more than 10 modifications per hour. PolicyLayer enforces this at the gateway, before calls reach OrigeneMCP.

How many tools does the Origene MCP server expose? +

439 tools across 2 categories: Read, Write. 431 are read-only. 8 can modify, create, or delete data.

How do I enforce a policy on OrigeneMCP? +

Register the Origene MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every OrigeneMCP tool call.

Deterministic rules across all 439 OrigeneMCP tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON ORIGENEMCP →

Free to start. No card required.

439 OrigeneMCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.

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