// MCP TOOL REFERENCE

ORIGENEMCP TOOLS

439 tools from the OrigeneMCP MCP Server, categorised by risk level.

View the OrigeneMCP policy →
// ALL 439 ORIGENEMCP TOOLS
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... 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 o... 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 ta... 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 informat... 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 ... 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.
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
EXECUTE 2 tools
Execute post_vep_hgvs post_vep_hgvs Execute post_vep_id post_vep_id
OTHER 2 tools
Other post_ga4gh_features_search post_ga4gh_features_search Other post_lookup_id post_lookup_id

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// FAQ
How many tools does the OrigeneMCP MCP server have? +

The OrigeneMCP MCP server exposes 439 tools across 4 categories: Read, Write, Execute, Other.

How do I enforce policies on OrigeneMCP tools? +

Route the OrigeneMCP server through the PolicyLayer gateway. Define allow, deny, or approval rules per tool in the dashboard; they are enforced on every call before it reaches the server.

What risk categories do OrigeneMCP tools fall into? +

OrigeneMCP tools are categorised as Read (431), Write (4), Execute (2), Other (2). Each category has a recommended default policy.

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