tooluniverse 0.1.4__py3-none-any.whl → 1.0.0__py3-none-any.whl
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- tooluniverse/__init__.py +340 -4
- tooluniverse/admetai_tool.py +84 -0
- tooluniverse/agentic_tool.py +563 -0
- tooluniverse/alphafold_tool.py +96 -0
- tooluniverse/base_tool.py +129 -6
- tooluniverse/boltz_tool.py +207 -0
- tooluniverse/chem_tool.py +192 -0
- tooluniverse/compose_scripts/__init__.py +1 -0
- tooluniverse/compose_scripts/biomarker_discovery.py +293 -0
- tooluniverse/compose_scripts/comprehensive_drug_discovery.py +186 -0
- tooluniverse/compose_scripts/drug_safety_analyzer.py +89 -0
- tooluniverse/compose_scripts/literature_tool.py +34 -0
- tooluniverse/compose_scripts/output_summarizer.py +279 -0
- tooluniverse/compose_scripts/tool_description_optimizer.py +681 -0
- tooluniverse/compose_scripts/tool_discover.py +705 -0
- tooluniverse/compose_scripts/tool_graph_composer.py +448 -0
- tooluniverse/compose_tool.py +371 -0
- tooluniverse/ctg_tool.py +1002 -0
- tooluniverse/custom_tool.py +81 -0
- tooluniverse/dailymed_tool.py +108 -0
- tooluniverse/data/admetai_tools.json +155 -0
- tooluniverse/data/agentic_tools.json +1156 -0
- tooluniverse/data/alphafold_tools.json +87 -0
- tooluniverse/data/boltz_tools.json +9 -0
- tooluniverse/data/chembl_tools.json +16 -0
- tooluniverse/data/clait_tools.json +108 -0
- tooluniverse/data/clinicaltrials_gov_tools.json +326 -0
- tooluniverse/data/compose_tools.json +202 -0
- tooluniverse/data/dailymed_tools.json +70 -0
- tooluniverse/data/dataset_tools.json +646 -0
- tooluniverse/data/disease_target_score_tools.json +712 -0
- tooluniverse/data/efo_tools.json +17 -0
- tooluniverse/data/embedding_tools.json +319 -0
- tooluniverse/data/enrichr_tools.json +31 -0
- tooluniverse/data/europe_pmc_tools.json +22 -0
- tooluniverse/data/expert_feedback_tools.json +10 -0
- tooluniverse/data/fda_drug_adverse_event_tools.json +491 -0
- tooluniverse/data/fda_drug_labeling_tools.json +544 -168
- tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py +76929 -148860
- tooluniverse/data/finder_tools.json +209 -0
- tooluniverse/data/gene_ontology_tools.json +113 -0
- tooluniverse/data/gwas_tools.json +1082 -0
- tooluniverse/data/hpa_tools.json +333 -0
- tooluniverse/data/humanbase_tools.json +47 -0
- tooluniverse/data/idmap_tools.json +74 -0
- tooluniverse/data/mcp_client_tools_example.json +113 -0
- tooluniverse/data/mcpautoloadertool_defaults.json +28 -0
- tooluniverse/data/medlineplus_tools.json +141 -0
- tooluniverse/data/monarch_tools.json +1 -1
- tooluniverse/data/openalex_tools.json +36 -0
- tooluniverse/data/opentarget_tools.json +82 -58
- tooluniverse/data/output_summarization_tools.json +101 -0
- tooluniverse/data/packages/bioinformatics_core_tools.json +1756 -0
- tooluniverse/data/packages/categorized_tools.txt +206 -0
- tooluniverse/data/packages/cheminformatics_tools.json +347 -0
- tooluniverse/data/packages/earth_sciences_tools.json +74 -0
- tooluniverse/data/packages/genomics_tools.json +776 -0
- tooluniverse/data/packages/image_processing_tools.json +38 -0
- tooluniverse/data/packages/machine_learning_tools.json +789 -0
- tooluniverse/data/packages/neuroscience_tools.json +62 -0
- tooluniverse/data/packages/original_tools.txt +0 -0
- tooluniverse/data/packages/physics_astronomy_tools.json +62 -0
- tooluniverse/data/packages/scientific_computing_tools.json +560 -0
- tooluniverse/data/packages/single_cell_tools.json +453 -0
- tooluniverse/data/packages/software_tools.json +4954 -0
- tooluniverse/data/packages/structural_biology_tools.json +396 -0
- tooluniverse/data/packages/visualization_tools.json +399 -0
- tooluniverse/data/pubchem_tools.json +215 -0
- tooluniverse/data/pubtator_tools.json +68 -0
- tooluniverse/data/rcsb_pdb_tools.json +1332 -0
- tooluniverse/data/reactome_tools.json +19 -0
- tooluniverse/data/semantic_scholar_tools.json +26 -0
- tooluniverse/data/special_tools.json +2 -25
- tooluniverse/data/tool_composition_tools.json +88 -0
- tooluniverse/data/toolfinderkeyword_defaults.json +34 -0
- tooluniverse/data/txagent_client_tools.json +9 -0
- tooluniverse/data/uniprot_tools.json +211 -0
- tooluniverse/data/url_fetch_tools.json +94 -0
- tooluniverse/data/uspto_downloader_tools.json +9 -0
- tooluniverse/data/uspto_tools.json +811 -0
- tooluniverse/data/xml_tools.json +3275 -0
- tooluniverse/dataset_tool.py +296 -0
- tooluniverse/default_config.py +165 -0
- tooluniverse/efo_tool.py +42 -0
- tooluniverse/embedding_database.py +630 -0
- tooluniverse/embedding_sync.py +396 -0
- tooluniverse/enrichr_tool.py +266 -0
- tooluniverse/europe_pmc_tool.py +52 -0
- tooluniverse/execute_function.py +1775 -95
- tooluniverse/extended_hooks.py +444 -0
- tooluniverse/gene_ontology_tool.py +194 -0
- tooluniverse/graphql_tool.py +158 -36
- tooluniverse/gwas_tool.py +358 -0
- tooluniverse/hpa_tool.py +1645 -0
- tooluniverse/humanbase_tool.py +389 -0
- tooluniverse/logging_config.py +254 -0
- tooluniverse/mcp_client_tool.py +764 -0
- tooluniverse/mcp_integration.py +413 -0
- tooluniverse/mcp_tool_registry.py +925 -0
- tooluniverse/medlineplus_tool.py +337 -0
- tooluniverse/openalex_tool.py +228 -0
- tooluniverse/openfda_adv_tool.py +283 -0
- tooluniverse/openfda_tool.py +393 -160
- tooluniverse/output_hook.py +1122 -0
- tooluniverse/package_tool.py +195 -0
- tooluniverse/pubchem_tool.py +158 -0
- tooluniverse/pubtator_tool.py +168 -0
- tooluniverse/rcsb_pdb_tool.py +38 -0
- tooluniverse/reactome_tool.py +108 -0
- tooluniverse/remote/boltz/boltz_mcp_server.py +50 -0
- tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py +442 -0
- tooluniverse/remote/expert_feedback/human_expert_mcp_tools.py +2013 -0
- tooluniverse/remote/expert_feedback/simple_test.py +23 -0
- tooluniverse/remote/expert_feedback/start_web_interface.py +188 -0
- tooluniverse/remote/expert_feedback/web_only_interface.py +0 -0
- tooluniverse/remote/expert_feedback_mcp/human_expert_mcp_server.py +1611 -0
- tooluniverse/remote/expert_feedback_mcp/simple_test.py +34 -0
- tooluniverse/remote/expert_feedback_mcp/start_web_interface.py +91 -0
- tooluniverse/remote/immune_compass/compass_tool.py +327 -0
- tooluniverse/remote/pinnacle/pinnacle_tool.py +328 -0
- tooluniverse/remote/transcriptformer/transcriptformer_tool.py +586 -0
- tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +61 -0
- tooluniverse/remote/uspto_downloader/uspto_downloader_tool.py +120 -0
- tooluniverse/remote_tool.py +99 -0
- tooluniverse/restful_tool.py +53 -30
- tooluniverse/scripts/generate_tool_graph.py +408 -0
- tooluniverse/scripts/visualize_tool_graph.py +829 -0
- tooluniverse/semantic_scholar_tool.py +62 -0
- tooluniverse/smcp.py +2452 -0
- tooluniverse/smcp_server.py +975 -0
- tooluniverse/test/mcp_server_test.py +0 -0
- tooluniverse/test/test_admetai_tool.py +370 -0
- tooluniverse/test/test_agentic_tool.py +129 -0
- tooluniverse/test/test_alphafold_tool.py +71 -0
- tooluniverse/test/test_chem_tool.py +37 -0
- tooluniverse/test/test_compose_lieraturereview.py +63 -0
- tooluniverse/test/test_compose_tool.py +448 -0
- tooluniverse/test/test_dailymed.py +69 -0
- tooluniverse/test/test_dataset_tool.py +200 -0
- tooluniverse/test/test_disease_target_score.py +56 -0
- tooluniverse/test/test_drugbank_filter_examples.py +179 -0
- tooluniverse/test/test_efo.py +31 -0
- tooluniverse/test/test_enrichr_tool.py +21 -0
- tooluniverse/test/test_europe_pmc_tool.py +20 -0
- tooluniverse/test/test_fda_adv.py +95 -0
- tooluniverse/test/test_fda_drug_labeling.py +91 -0
- tooluniverse/test/test_gene_ontology_tools.py +66 -0
- tooluniverse/test/test_gwas_tool.py +139 -0
- tooluniverse/test/test_hpa.py +625 -0
- tooluniverse/test/test_humanbase_tool.py +20 -0
- tooluniverse/test/test_idmap_tools.py +61 -0
- tooluniverse/test/test_mcp_server.py +211 -0
- tooluniverse/test/test_mcp_tool.py +247 -0
- tooluniverse/test/test_medlineplus.py +220 -0
- tooluniverse/test/test_openalex_tool.py +32 -0
- tooluniverse/test/test_opentargets.py +28 -0
- tooluniverse/test/test_pubchem_tool.py +116 -0
- tooluniverse/test/test_pubtator_tool.py +37 -0
- tooluniverse/test/test_rcsb_pdb_tool.py +86 -0
- tooluniverse/test/test_reactome.py +54 -0
- tooluniverse/test/test_semantic_scholar_tool.py +24 -0
- tooluniverse/test/test_software_tools.py +147 -0
- tooluniverse/test/test_tool_description_optimizer.py +49 -0
- tooluniverse/test/test_tool_finder.py +26 -0
- tooluniverse/test/test_tool_finder_llm.py +252 -0
- tooluniverse/test/test_tools_find.py +195 -0
- tooluniverse/test/test_uniprot_tools.py +74 -0
- tooluniverse/test/test_uspto_tool.py +72 -0
- tooluniverse/test/test_xml_tool.py +113 -0
- tooluniverse/tool_finder_embedding.py +267 -0
- tooluniverse/tool_finder_keyword.py +693 -0
- tooluniverse/tool_finder_llm.py +699 -0
- tooluniverse/tool_graph_web_ui.py +955 -0
- tooluniverse/tool_registry.py +416 -0
- tooluniverse/uniprot_tool.py +155 -0
- tooluniverse/url_tool.py +253 -0
- tooluniverse/uspto_tool.py +240 -0
- tooluniverse/utils.py +369 -41
- tooluniverse/xml_tool.py +369 -0
- tooluniverse-1.0.0.dist-info/METADATA +377 -0
- tooluniverse-1.0.0.dist-info/RECORD +186 -0
- {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/WHEEL +1 -1
- tooluniverse-1.0.0.dist-info/entry_points.txt +9 -0
- tooluniverse-0.1.4.dist-info/METADATA +0 -141
- tooluniverse-0.1.4.dist-info/RECORD +0 -18
- {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/licenses/LICENSE +0 -0
- {tooluniverse-0.1.4.dist-info → tooluniverse-1.0.0.dist-info}/top_level.txt +0 -0
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[
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{
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"type": "XMLTool",
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"name": "mesh_get_subjects_by_pharmacological_action",
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"description": "Find MeSH (Medical Subject Heading) subjects with matching pharmacological actions.",
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"settings": {
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"hf_dataset_path": {
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"repo_id": "agenticx/MeSH2025",
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"path_in_repo": "MeSH_desc2025.xml",
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"token": null,
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"save_to_local_dir": "src/tooluniverse/test"
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},
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"record_xpath": "DescriptorRecord",
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"search_fields": ["pharmacological_actions"],
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"field_mappings": {
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"subject_name": "DescriptorName/String",
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"subject_id": "DescriptorUI",
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"pharmacological_actions": ".//PharmacologicalAction/DescriptorReferredTo/DescriptorName/String",
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"key_concepts": ".//Concept/ConceptName/String",
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"concept_synonyms": ".//Term/String",
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"subject_scope": ".//ScopeNote",
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"subject_hierarchy_tree_numbers": ".//TreeNumber",
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"entry_creation_date": "DateCreated/Year",
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"entry_last_revised_date": "DateRevised/Year",
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"related_subjects": ".//SeeRelatedDescriptor/DescriptorReferredTo/DescriptorName/String"
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"query": {
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"type": "string",
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"description": "Pharmacological action to search for in MeSH subjects",
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"minLength": 1
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"description": "Select True to perform a case-sensitive search for the pharmacological action query",
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"default": false
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"description": "Select True to require an exact match for the pharmacological action query",
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"default": false
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"limit": {
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"description": "Maximum number of results to return",
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"default": 50,
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"minimum": 1,
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"maximum": 1000
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"required": ["query"]
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"description": "Error message (if any)"
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"query": {
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"description": "Number of results returned in this response"
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"pharmacological_actions": {
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"description": "MeSH tree numbers indicating hierarchical classification. Parents have a prefix of the tree number, up to the last '.' character. If multiple tree numbers present, they are separated by ' | '"
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"matched_fields": {
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"description": "List of fields that matched the search query"
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"description": "Whether the search was case-sensitive"
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"exact_match": {
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"limit": {
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"type": "XMLTool",
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"name": "mesh_get_subjects_by_subject_scope_or_definition",
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"description": "Find MeSH (Medical Subject Heading) subjects with matching scopes (definitions).",
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"settings": {
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"hf_dataset_path": {
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"repo_id": "agenticx/MeSH2025",
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"path_in_repo": "MeSH_desc2025.xml",
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"token": null,
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"save_to_local_dir": "src/tooluniverse/test"
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},
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"record_xpath": "DescriptorRecord",
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"search_fields": ["subject_scope"],
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"field_mappings": {
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"subject_name": "DescriptorName/String",
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"subject_id": "DescriptorUI",
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"pharmacological_actions": ".//PharmacologicalAction/DescriptorReferredTo/DescriptorName/String",
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"key_concepts": ".//Concept/ConceptName/String",
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"concept_synonyms": ".//Term/String",
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"subject_scope": ".//ScopeNote",
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"subject_hierarchy_tree_numbers": ".//TreeNumber",
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"entry_creation_date": "DateCreated/Year",
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"entry_last_revised_date": "DateRevised/Year",
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"related_subjects": ".//SeeRelatedDescriptor/DescriptorReferredTo/DescriptorName/String"
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}
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},
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"query": {
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"type": "string",
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"description": "Query string to search for in the scope notes of MeSH subjects",
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"minLength": 1
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},
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"case_sensitive": {
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"type": "boolean",
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"description": "Select True to perform a case-sensitive search for the query",
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"default": false
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},
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"exact_match": {
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"type": "boolean",
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"description": "Select True to require an exact match for the query",
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"default": false
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},
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"limit": {
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"type": "integer",
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"description": "Maximum number of results to return",
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"default": 50,
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"minimum": 1,
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"maximum": 1000
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}
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},
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"required": ["query"]
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},
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"return_schema": {
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"properties": {
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"error": {
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"type": "string",
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"description": "Error message (if any)"
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},
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"query": {
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"type": "string",
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"description": "The original search query"
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},
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"total_matches": {
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"type": "integer",
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"description": "Total number of matching records found"
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},
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"total_returned_results": {
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"description": "Number of results returned in this response"
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},
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"results": {
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"type": "array",
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"items": {
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"properties": {
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"_tag": {
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"type": "string",
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"description": "XML tag name of the record element"
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},
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"_text": {
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"type": "string",
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"description": "Text content of the record element"
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},
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"_attributes": {
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"type": "object",
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"description": "Attributes of the record element"
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},
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"subject_name": {
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"type": "string",
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"description": "Name of the MeSH subject"
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},
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"subject_id": {
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"type": "string",
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"description": "MeSH subject ID (Descriptor UI)"
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},
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"pharmacological_actions": {
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"type": "string",
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"description": "Pharmacological actions associated with the subject, separated by ' | '"
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},
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"key_concepts": {
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"type": "string",
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"description": "Key concepts related to the subject, separated by ' | '"
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},
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"concept_synonyms": {
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"type": "string",
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"description": "Synonyms for the subject concepts, separated by ' | '"
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},
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"subject_scope": {
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"type": "string",
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"description": "Scope note or definition of the subject. If multiple, they are separated by ' | '"
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},
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"subject_hierarchy_tree_numbers": {
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"type": "string",
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"description": "MeSH tree numbers indicating hierarchical classification. Parents have a prefix of the tree number, up to the last '.' character. If multiple tree numbers present, they are separated by ' | '"
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},
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"entry_creation_date": {
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"type": "string",
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"description": "Year the entry was created"
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},
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"entry_last_revised_date": {
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|
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"type": "string",
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"description": "Year the entry was last revised"
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},
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|
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"related_subjects": {
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|
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"type": "string",
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|
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"description": "Related MeSH subjects, separated by ' | '"
|
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|
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},
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|
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"matched_fields": {
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|
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"type": "array",
|
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|
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"items": {
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|
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"type": "string"
|
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|
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},
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|
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"description": "List of fields that matched the search query"
|
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|
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}
|
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|
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}
|
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|
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}
|
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},
|
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|
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"search_parameters": {
|
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|
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"type": "object",
|
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|
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"properties": {
|
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|
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"case_sensitive": {
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|
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"type": "boolean",
|
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|
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"description": "Whether the search was case-sensitive"
|
|
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|
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},
|
|
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|
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"exact_match": {
|
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|
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"type": "boolean",
|
|
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|
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"description": "Whether exact matching was used"
|
|
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|
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},
|
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313
|
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"limit": {
|
|
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|
+
"type": "integer",
|
|
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|
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"description": "Maximum number of results requested"
|
|
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|
+
}
|
|
317
|
+
}
|
|
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|
+
}
|
|
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|
+
}
|
|
320
|
+
}
|
|
321
|
+
},
|
|
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|
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{
|
|
323
|
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"type": "XMLTool",
|
|
324
|
+
"name": "mesh_get_subjects_by_subject_name",
|
|
325
|
+
"description": "Find MeSH (Medical Subject Heading) subjects with matching names.",
|
|
326
|
+
"settings": {
|
|
327
|
+
"hf_dataset_path": {
|
|
328
|
+
"repo_id": "agenticx/MeSH2025",
|
|
329
|
+
"path_in_repo": "MeSH_desc2025.xml",
|
|
330
|
+
"token": null,
|
|
331
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
332
|
+
},
|
|
333
|
+
"record_xpath": "DescriptorRecord",
|
|
334
|
+
"search_fields": ["subject_name","key_concepts","concept_synonyms"],
|
|
335
|
+
"field_mappings": {
|
|
336
|
+
"subject_name": "DescriptorName/String",
|
|
337
|
+
"subject_id": "DescriptorUI",
|
|
338
|
+
"pharmacological_actions": ".//PharmacologicalAction/DescriptorReferredTo/DescriptorName/String",
|
|
339
|
+
"key_concepts": ".//Concept/ConceptName/String",
|
|
340
|
+
"concept_synonyms": ".//Term/String",
|
|
341
|
+
"subject_scope": ".//ScopeNote",
|
|
342
|
+
"subject_hierarchy_tree_numbers": ".//TreeNumber",
|
|
343
|
+
"entry_creation_date": "DateCreated/Year",
|
|
344
|
+
"entry_last_revised_date": "DateRevised/Year",
|
|
345
|
+
"related_subjects": ".//SeeRelatedDescriptor/DescriptorReferredTo/DescriptorName/String"
|
|
346
|
+
}
|
|
347
|
+
},
|
|
348
|
+
"parameter": {
|
|
349
|
+
"type": "object",
|
|
350
|
+
"properties": {
|
|
351
|
+
"query": {
|
|
352
|
+
"type": "string",
|
|
353
|
+
"description": "Query string to search for in the name of each MeSH subject and the names of the subject's key concepts and concept synonyms.",
|
|
354
|
+
"minLength": 1
|
|
355
|
+
},
|
|
356
|
+
"case_sensitive": {
|
|
357
|
+
"type": "boolean",
|
|
358
|
+
"description": "Select True to perform a case-sensitive search for the query",
|
|
359
|
+
"default": false
|
|
360
|
+
},
|
|
361
|
+
"exact_match": {
|
|
362
|
+
"type": "boolean",
|
|
363
|
+
"description": "Select True to require an exact match for the query",
|
|
364
|
+
"default": false
|
|
365
|
+
},
|
|
366
|
+
"limit": {
|
|
367
|
+
"type": "integer",
|
|
368
|
+
"description": "Maximum number of results to return",
|
|
369
|
+
"default": 50,
|
|
370
|
+
"minimum": 1,
|
|
371
|
+
"maximum": 1000
|
|
372
|
+
}
|
|
373
|
+
},
|
|
374
|
+
"required": ["query"]
|
|
375
|
+
},
|
|
376
|
+
"return_schema": {
|
|
377
|
+
"type": "object",
|
|
378
|
+
"properties": {
|
|
379
|
+
"error": {
|
|
380
|
+
"type": "string",
|
|
381
|
+
"description": "Error message (if any)"
|
|
382
|
+
},
|
|
383
|
+
"query": {
|
|
384
|
+
"type": "string",
|
|
385
|
+
"description": "The original search query"
|
|
386
|
+
},
|
|
387
|
+
"total_matches": {
|
|
388
|
+
"type": "integer",
|
|
389
|
+
"description": "Total number of matching records found"
|
|
390
|
+
},
|
|
391
|
+
"total_returned_results": {
|
|
392
|
+
"type": "integer",
|
|
393
|
+
"description": "Number of results returned in this response"
|
|
394
|
+
},
|
|
395
|
+
"results": {
|
|
396
|
+
"type": "array",
|
|
397
|
+
"items": {
|
|
398
|
+
"type": "object",
|
|
399
|
+
"properties": {
|
|
400
|
+
"_tag": {
|
|
401
|
+
"type": "string",
|
|
402
|
+
"description": "XML tag name of the record element"
|
|
403
|
+
},
|
|
404
|
+
"_text": {
|
|
405
|
+
"type": "string",
|
|
406
|
+
"description": "Text content of the record element"
|
|
407
|
+
},
|
|
408
|
+
"_attributes": {
|
|
409
|
+
"type": "object",
|
|
410
|
+
"description": "Attributes of the record element"
|
|
411
|
+
},
|
|
412
|
+
"subject_name": {
|
|
413
|
+
"type": "string",
|
|
414
|
+
"description": "Name of the MeSH subject"
|
|
415
|
+
},
|
|
416
|
+
"subject_id": {
|
|
417
|
+
"type": "string",
|
|
418
|
+
"description": "MeSH subject ID (Descriptor UI)"
|
|
419
|
+
},
|
|
420
|
+
"pharmacological_actions": {
|
|
421
|
+
"type": "string",
|
|
422
|
+
"description": "Pharmacological actions associated with the subject, separated by ' | '"
|
|
423
|
+
},
|
|
424
|
+
"key_concepts": {
|
|
425
|
+
"type": "string",
|
|
426
|
+
"description": "Key concepts related to the subject, separated by ' | '"
|
|
427
|
+
},
|
|
428
|
+
"concept_synonyms": {
|
|
429
|
+
"type": "string",
|
|
430
|
+
"description": "Synonyms for the subject concepts, separated by ' | '"
|
|
431
|
+
},
|
|
432
|
+
"subject_scope": {
|
|
433
|
+
"type": "string",
|
|
434
|
+
"description": "Scope note or definition of the subject. If multiple, they are separated by ' | '"
|
|
435
|
+
},
|
|
436
|
+
"subject_hierarchy_tree_numbers": {
|
|
437
|
+
"type": "string",
|
|
438
|
+
"description": "MeSH tree numbers indicating hierarchical classification. Parents have a prefix of the tree number, up to the last '.' character. If multiple tree numbers present, they are separated by ' | '"
|
|
439
|
+
},
|
|
440
|
+
"entry_creation_date": {
|
|
441
|
+
"type": "string",
|
|
442
|
+
"description": "Year the entry was created"
|
|
443
|
+
},
|
|
444
|
+
"entry_last_revised_date": {
|
|
445
|
+
"type": "string",
|
|
446
|
+
"description": "Year the entry was last revised"
|
|
447
|
+
},
|
|
448
|
+
"related_subjects": {
|
|
449
|
+
"type": "string",
|
|
450
|
+
"description": "Related MeSH subjects, separated by ' | '"
|
|
451
|
+
},
|
|
452
|
+
"matched_fields": {
|
|
453
|
+
"type": "array",
|
|
454
|
+
"items": {
|
|
455
|
+
"type": "string"
|
|
456
|
+
},
|
|
457
|
+
"description": "List of fields that matched the search query"
|
|
458
|
+
}
|
|
459
|
+
}
|
|
460
|
+
}
|
|
461
|
+
},
|
|
462
|
+
"search_parameters": {
|
|
463
|
+
"type": "object",
|
|
464
|
+
"properties": {
|
|
465
|
+
"case_sensitive": {
|
|
466
|
+
"type": "boolean",
|
|
467
|
+
"description": "Whether the search was case-sensitive"
|
|
468
|
+
},
|
|
469
|
+
"exact_match": {
|
|
470
|
+
"type": "boolean",
|
|
471
|
+
"description": "Whether exact matching was used"
|
|
472
|
+
},
|
|
473
|
+
"limit": {
|
|
474
|
+
"type": "integer",
|
|
475
|
+
"description": "Maximum number of results requested"
|
|
476
|
+
}
|
|
477
|
+
}
|
|
478
|
+
}
|
|
479
|
+
}
|
|
480
|
+
}
|
|
481
|
+
},
|
|
482
|
+
{
|
|
483
|
+
"type": "XMLTool",
|
|
484
|
+
"name": "mesh_get_subjects_by_subject_id",
|
|
485
|
+
"description": "Find MeSH (Medical Subject Heading) subjects with a matching subject ID (also called Descriptor UI).",
|
|
486
|
+
"settings": {
|
|
487
|
+
"hf_dataset_path": {
|
|
488
|
+
"repo_id": "agenticx/MeSH2025",
|
|
489
|
+
"path_in_repo": "MeSH_desc2025.xml",
|
|
490
|
+
"token": null,
|
|
491
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
492
|
+
},
|
|
493
|
+
"record_xpath": "DescriptorRecord",
|
|
494
|
+
"search_fields": ["subject_id"],
|
|
495
|
+
"field_mappings": {
|
|
496
|
+
"subject_name": "DescriptorName/String",
|
|
497
|
+
"subject_id": "DescriptorUI",
|
|
498
|
+
"pharmacological_actions": ".//PharmacologicalAction/DescriptorReferredTo/DescriptorName/String",
|
|
499
|
+
"key_concepts": ".//Concept/ConceptName/String",
|
|
500
|
+
"concept_synonyms": ".//Term/String",
|
|
501
|
+
"subject_scope": ".//ScopeNote",
|
|
502
|
+
"subject_hierarchy_tree_numbers": ".//TreeNumber",
|
|
503
|
+
"entry_creation_date": "DateCreated/Year",
|
|
504
|
+
"entry_last_revised_date": "DateRevised/Year",
|
|
505
|
+
"related_subjects": ".//SeeRelatedDescriptor/DescriptorReferredTo/DescriptorName/String"
|
|
506
|
+
}
|
|
507
|
+
},
|
|
508
|
+
"parameter": {
|
|
509
|
+
"type": "object",
|
|
510
|
+
"properties": {
|
|
511
|
+
"query": {
|
|
512
|
+
"type": "string",
|
|
513
|
+
"description": "Query ID to search for among the MeSH subject IDs",
|
|
514
|
+
"minLength": 1
|
|
515
|
+
},
|
|
516
|
+
"case_sensitive": {
|
|
517
|
+
"type": "boolean",
|
|
518
|
+
"description": "Select True to perform a case-sensitive search for the query",
|
|
519
|
+
"default": false
|
|
520
|
+
},
|
|
521
|
+
"exact_match": {
|
|
522
|
+
"type": "boolean",
|
|
523
|
+
"description": "Select True to require an exact match for the query",
|
|
524
|
+
"default": false
|
|
525
|
+
},
|
|
526
|
+
"limit": {
|
|
527
|
+
"type": "integer",
|
|
528
|
+
"description": "Maximum number of results to return",
|
|
529
|
+
"default": 50,
|
|
530
|
+
"minimum": 1,
|
|
531
|
+
"maximum": 1000
|
|
532
|
+
}
|
|
533
|
+
},
|
|
534
|
+
"required": ["query"]
|
|
535
|
+
},
|
|
536
|
+
"return_schema": {
|
|
537
|
+
"type": "object",
|
|
538
|
+
"properties": {
|
|
539
|
+
"error": {
|
|
540
|
+
"type": "string",
|
|
541
|
+
"description": "Error message (if any)"
|
|
542
|
+
},
|
|
543
|
+
"query": {
|
|
544
|
+
"type": "string",
|
|
545
|
+
"description": "The original search query"
|
|
546
|
+
},
|
|
547
|
+
"total_matches": {
|
|
548
|
+
"type": "integer",
|
|
549
|
+
"description": "Total number of matching records found"
|
|
550
|
+
},
|
|
551
|
+
"total_returned_results": {
|
|
552
|
+
"type": "integer",
|
|
553
|
+
"description": "Number of results returned in this response"
|
|
554
|
+
},
|
|
555
|
+
"results": {
|
|
556
|
+
"type": "array",
|
|
557
|
+
"items": {
|
|
558
|
+
"type": "object",
|
|
559
|
+
"properties": {
|
|
560
|
+
"_tag": {
|
|
561
|
+
"type": "string",
|
|
562
|
+
"description": "XML tag name of the record element"
|
|
563
|
+
},
|
|
564
|
+
"_text": {
|
|
565
|
+
"type": "string",
|
|
566
|
+
"description": "Text content of the record element"
|
|
567
|
+
},
|
|
568
|
+
"_attributes": {
|
|
569
|
+
"type": "object",
|
|
570
|
+
"description": "Attributes of the record element"
|
|
571
|
+
},
|
|
572
|
+
"subject_name": {
|
|
573
|
+
"type": "string",
|
|
574
|
+
"description": "Name of the MeSH subject"
|
|
575
|
+
},
|
|
576
|
+
"subject_id": {
|
|
577
|
+
"type": "string",
|
|
578
|
+
"description": "MeSH subject ID (Descriptor UI)"
|
|
579
|
+
},
|
|
580
|
+
"pharmacological_actions": {
|
|
581
|
+
"type": "string",
|
|
582
|
+
"description": "Pharmacological actions associated with the subject, separated by ' | '"
|
|
583
|
+
},
|
|
584
|
+
"key_concepts": {
|
|
585
|
+
"type": "string",
|
|
586
|
+
"description": "Key concepts related to the subject, separated by ' | '"
|
|
587
|
+
},
|
|
588
|
+
"concept_synonyms": {
|
|
589
|
+
"type": "string",
|
|
590
|
+
"description": "Synonyms for the subject concepts, separated by ' | '"
|
|
591
|
+
},
|
|
592
|
+
"subject_scope": {
|
|
593
|
+
"type": "string",
|
|
594
|
+
"description": "Scope note or definition of the subject. If multiple, they are separated by ' | '"
|
|
595
|
+
},
|
|
596
|
+
"subject_hierarchy_tree_numbers": {
|
|
597
|
+
"type": "string",
|
|
598
|
+
"description": "MeSH tree numbers indicating hierarchical classification. Parents have a prefix of the tree number, up to the last '.' character. If multiple tree numbers present, they are separated by ' | '"
|
|
599
|
+
},
|
|
600
|
+
"entry_creation_date": {
|
|
601
|
+
"type": "string",
|
|
602
|
+
"description": "Year the entry was created"
|
|
603
|
+
},
|
|
604
|
+
"entry_last_revised_date": {
|
|
605
|
+
"type": "string",
|
|
606
|
+
"description": "Year the entry was last revised"
|
|
607
|
+
},
|
|
608
|
+
"related_subjects": {
|
|
609
|
+
"type": "string",
|
|
610
|
+
"description": "Related MeSH subjects, separated by ' | '"
|
|
611
|
+
},
|
|
612
|
+
"matched_fields": {
|
|
613
|
+
"type": "array",
|
|
614
|
+
"items": {
|
|
615
|
+
"type": "string"
|
|
616
|
+
},
|
|
617
|
+
"description": "List of fields that matched the search query"
|
|
618
|
+
}
|
|
619
|
+
}
|
|
620
|
+
}
|
|
621
|
+
},
|
|
622
|
+
"search_parameters": {
|
|
623
|
+
"type": "object",
|
|
624
|
+
"properties": {
|
|
625
|
+
"case_sensitive": {
|
|
626
|
+
"type": "boolean",
|
|
627
|
+
"description": "Whether the search was case-sensitive"
|
|
628
|
+
},
|
|
629
|
+
"exact_match": {
|
|
630
|
+
"type": "boolean",
|
|
631
|
+
"description": "Whether exact matching was used"
|
|
632
|
+
},
|
|
633
|
+
"limit": {
|
|
634
|
+
"type": "integer",
|
|
635
|
+
"description": "Maximum number of results requested"
|
|
636
|
+
}
|
|
637
|
+
}
|
|
638
|
+
}
|
|
639
|
+
}
|
|
640
|
+
}
|
|
641
|
+
},
|
|
642
|
+
{
|
|
643
|
+
"type": "XMLTool",
|
|
644
|
+
"name": "drugbank_get_drug_basic_info_by_drug_name_or_drugbank_id",
|
|
645
|
+
"description": "Get basic drug information including name, description, CAS number, and approval status by drug name or DrugBank ID.",
|
|
646
|
+
"settings": {
|
|
647
|
+
"hf_dataset_path": {
|
|
648
|
+
"repo_id": "agenticx/DrugBank",
|
|
649
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
650
|
+
"token": null,
|
|
651
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
652
|
+
},
|
|
653
|
+
"namespaces": {
|
|
654
|
+
"db": "http://www.drugbank.ca"
|
|
655
|
+
},
|
|
656
|
+
"record_xpath": "db:drug",
|
|
657
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
658
|
+
"field_mappings": {
|
|
659
|
+
"drug_name": "db:name",
|
|
660
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
661
|
+
"secondary_ids": "db:drugbank-id[not(@primary='true')]",
|
|
662
|
+
"description": "db:description",
|
|
663
|
+
"cas_number": "db:cas-number",
|
|
664
|
+
"unii": "db:unii",
|
|
665
|
+
"state": "db:state",
|
|
666
|
+
"drug_type": "@type",
|
|
667
|
+
"approval_groups": "db:groups/db:group",
|
|
668
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
669
|
+
"entry_creation_date": "@created",
|
|
670
|
+
"entry_last_updated": "@updated"
|
|
671
|
+
}
|
|
672
|
+
},
|
|
673
|
+
"parameter": {
|
|
674
|
+
"type": "object",
|
|
675
|
+
"properties": {
|
|
676
|
+
"query": {
|
|
677
|
+
"type": "string",
|
|
678
|
+
"description": "Drug name or DrugBank ID to search for",
|
|
679
|
+
"minLength": 1
|
|
680
|
+
},
|
|
681
|
+
"case_sensitive": {
|
|
682
|
+
"type": "boolean",
|
|
683
|
+
"description": "Select True to perform a case-sensitive search",
|
|
684
|
+
"default": false
|
|
685
|
+
},
|
|
686
|
+
"exact_match": {
|
|
687
|
+
"type": "boolean",
|
|
688
|
+
"description": "Select True to require an exact match with the queried name or ID",
|
|
689
|
+
"default": false
|
|
690
|
+
},
|
|
691
|
+
"limit": {
|
|
692
|
+
"type": "integer",
|
|
693
|
+
"description": "Maximum number of results to return",
|
|
694
|
+
"default": 10,
|
|
695
|
+
"minimum": 1,
|
|
696
|
+
"maximum": 100
|
|
697
|
+
}
|
|
698
|
+
},
|
|
699
|
+
"required": ["query"]
|
|
700
|
+
},
|
|
701
|
+
"return_schema": {
|
|
702
|
+
"type": "object",
|
|
703
|
+
"properties": {
|
|
704
|
+
"error": {
|
|
705
|
+
"type": "string",
|
|
706
|
+
"description": "Error message (if any)"
|
|
707
|
+
},
|
|
708
|
+
"query": {
|
|
709
|
+
"type": "string",
|
|
710
|
+
"description": "The original search query"
|
|
711
|
+
},
|
|
712
|
+
"total_matches": {
|
|
713
|
+
"type": "integer",
|
|
714
|
+
"description": "Total number of matching records found"
|
|
715
|
+
},
|
|
716
|
+
"total_returned_results": {
|
|
717
|
+
"type": "integer",
|
|
718
|
+
"description": "Number of results returned in this response"
|
|
719
|
+
},
|
|
720
|
+
"results": {
|
|
721
|
+
"type": "array",
|
|
722
|
+
"items": {
|
|
723
|
+
"type": "object",
|
|
724
|
+
"properties": {
|
|
725
|
+
"_tag": {
|
|
726
|
+
"type": "string",
|
|
727
|
+
"description": "XML tag name of the record element"
|
|
728
|
+
},
|
|
729
|
+
"_text": {
|
|
730
|
+
"type": "string",
|
|
731
|
+
"description": "Text content of the record element"
|
|
732
|
+
},
|
|
733
|
+
"_attributes": {
|
|
734
|
+
"type": "object",
|
|
735
|
+
"description": "Attributes of the record element"
|
|
736
|
+
},
|
|
737
|
+
"drug_name": {
|
|
738
|
+
"type": "string",
|
|
739
|
+
"description": "Name of the drug"
|
|
740
|
+
},
|
|
741
|
+
"drugbank_id": {
|
|
742
|
+
"type": "string",
|
|
743
|
+
"description": "Primary DrugBank ID"
|
|
744
|
+
},
|
|
745
|
+
"secondary_ids": {
|
|
746
|
+
"type": "string",
|
|
747
|
+
"description": "Secondary DrugBank IDs, separated by ' | '"
|
|
748
|
+
},
|
|
749
|
+
"description": {
|
|
750
|
+
"type": "string",
|
|
751
|
+
"description": "Drug description"
|
|
752
|
+
},
|
|
753
|
+
"cas_number": {
|
|
754
|
+
"type": "string",
|
|
755
|
+
"description": "Chemical Abstracts Service registry number"
|
|
756
|
+
},
|
|
757
|
+
"unii": {
|
|
758
|
+
"type": "string",
|
|
759
|
+
"description": "Unique Ingredient Identifier"
|
|
760
|
+
},
|
|
761
|
+
"state": {
|
|
762
|
+
"type": "string",
|
|
763
|
+
"description": "Physical state of the drug"
|
|
764
|
+
},
|
|
765
|
+
"drug_type": {
|
|
766
|
+
"type": "string",
|
|
767
|
+
"description": "Type of drug (e.g., small molecule, biotech)"
|
|
768
|
+
},
|
|
769
|
+
"approval_groups": {
|
|
770
|
+
"type": "string",
|
|
771
|
+
"description": "Drug approval status groups, separated by ' | '"
|
|
772
|
+
},
|
|
773
|
+
"synonyms": {
|
|
774
|
+
"type": "string",
|
|
775
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
776
|
+
},
|
|
777
|
+
"entry_creation_date": {
|
|
778
|
+
"type": "string",
|
|
779
|
+
"description": "Date when the entry was created"
|
|
780
|
+
},
|
|
781
|
+
"entry_last_updated": {
|
|
782
|
+
"type": "string",
|
|
783
|
+
"description": "Date when the entry was last updated"
|
|
784
|
+
},
|
|
785
|
+
"matched_fields": {
|
|
786
|
+
"type": "array",
|
|
787
|
+
"items": {
|
|
788
|
+
"type": "string"
|
|
789
|
+
},
|
|
790
|
+
"description": "List of fields that matched the search query"
|
|
791
|
+
}
|
|
792
|
+
}
|
|
793
|
+
}
|
|
794
|
+
},
|
|
795
|
+
"search_parameters": {
|
|
796
|
+
"type": "object",
|
|
797
|
+
"properties": {
|
|
798
|
+
"case_sensitive": {
|
|
799
|
+
"type": "boolean",
|
|
800
|
+
"description": "Whether the search was case-sensitive"
|
|
801
|
+
},
|
|
802
|
+
"exact_match": {
|
|
803
|
+
"type": "boolean",
|
|
804
|
+
"description": "Whether exact matching was used"
|
|
805
|
+
},
|
|
806
|
+
"limit": {
|
|
807
|
+
"type": "integer",
|
|
808
|
+
"description": "Maximum number of results requested"
|
|
809
|
+
}
|
|
810
|
+
}
|
|
811
|
+
}
|
|
812
|
+
}
|
|
813
|
+
}
|
|
814
|
+
},
|
|
815
|
+
{
|
|
816
|
+
"type": "XMLTool",
|
|
817
|
+
"name": "drugbank_get_indications_by_drug_name_or_drugbank_id",
|
|
818
|
+
"description": "Get drug indications and therapeutic uses by drug name or DrugBank ID.",
|
|
819
|
+
"settings": {
|
|
820
|
+
"hf_dataset_path": {
|
|
821
|
+
"repo_id": "agenticx/DrugBank",
|
|
822
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
823
|
+
"token": null,
|
|
824
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
825
|
+
},
|
|
826
|
+
"namespaces": {
|
|
827
|
+
"db": "http://www.drugbank.ca"
|
|
828
|
+
},
|
|
829
|
+
"record_xpath": "db:drug",
|
|
830
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
831
|
+
"field_mappings": {
|
|
832
|
+
"drug_name": "db:name",
|
|
833
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
834
|
+
"indication": "db:indication",
|
|
835
|
+
"categories": "db:categories/db:category/db:category",
|
|
836
|
+
"atc_codes": {
|
|
837
|
+
"parent_path": "db:atc-codes/db:atc-code",
|
|
838
|
+
"subfields": {
|
|
839
|
+
"code": "@code",
|
|
840
|
+
"children_names": "db:level",
|
|
841
|
+
"children_codes": "db:level/@code"
|
|
842
|
+
}
|
|
843
|
+
},
|
|
844
|
+
"synonyms": "db:synonyms/db:synonym"
|
|
845
|
+
}
|
|
846
|
+
},
|
|
847
|
+
"parameter": {
|
|
848
|
+
"type": "object",
|
|
849
|
+
"properties": {
|
|
850
|
+
"query": {
|
|
851
|
+
"type": "string",
|
|
852
|
+
"description": "Drug name or ID to search for",
|
|
853
|
+
"minLength": 1
|
|
854
|
+
},
|
|
855
|
+
"case_sensitive": {
|
|
856
|
+
"type": "boolean",
|
|
857
|
+
"description": "Select True to perform a case-sensitive search",
|
|
858
|
+
"default": false
|
|
859
|
+
},
|
|
860
|
+
"exact_match": {
|
|
861
|
+
"type": "boolean",
|
|
862
|
+
"description": "Select True to require an exact match",
|
|
863
|
+
"default": false
|
|
864
|
+
},
|
|
865
|
+
"limit": {
|
|
866
|
+
"type": "integer",
|
|
867
|
+
"description": "Maximum number of results to return",
|
|
868
|
+
"default": 10,
|
|
869
|
+
"minimum": 1,
|
|
870
|
+
"maximum": 100
|
|
871
|
+
}
|
|
872
|
+
},
|
|
873
|
+
"required": ["query"]
|
|
874
|
+
},
|
|
875
|
+
"return_schema": {
|
|
876
|
+
"type": "object",
|
|
877
|
+
"properties": {
|
|
878
|
+
"error": {
|
|
879
|
+
"type": "string",
|
|
880
|
+
"description": "Error message (if any)"
|
|
881
|
+
},
|
|
882
|
+
"query": {
|
|
883
|
+
"type": "string",
|
|
884
|
+
"description": "The original search query"
|
|
885
|
+
},
|
|
886
|
+
"total_matches": {
|
|
887
|
+
"type": "integer",
|
|
888
|
+
"description": "Total number of matching records found"
|
|
889
|
+
},
|
|
890
|
+
"total_returned_results": {
|
|
891
|
+
"type": "integer",
|
|
892
|
+
"description": "Number of results returned in this response"
|
|
893
|
+
},
|
|
894
|
+
"results": {
|
|
895
|
+
"type": "array",
|
|
896
|
+
"items": {
|
|
897
|
+
"type": "object",
|
|
898
|
+
"properties": {
|
|
899
|
+
"_tag": {
|
|
900
|
+
"type": "string",
|
|
901
|
+
"description": "XML tag name of the record element"
|
|
902
|
+
},
|
|
903
|
+
"_text": {
|
|
904
|
+
"type": "string",
|
|
905
|
+
"description": "Text content of the record element"
|
|
906
|
+
},
|
|
907
|
+
"_attributes": {
|
|
908
|
+
"type": "object",
|
|
909
|
+
"description": "Attributes of the record element"
|
|
910
|
+
},
|
|
911
|
+
"drug_name": {
|
|
912
|
+
"type": "string",
|
|
913
|
+
"description": "Name of the drug"
|
|
914
|
+
},
|
|
915
|
+
"drugbank_id": {
|
|
916
|
+
"type": "string",
|
|
917
|
+
"description": "Primary DrugBank ID"
|
|
918
|
+
},
|
|
919
|
+
"indication": {
|
|
920
|
+
"type": "string",
|
|
921
|
+
"description": "Drug indication and therapeutic uses"
|
|
922
|
+
},
|
|
923
|
+
"categories": {
|
|
924
|
+
"type": "string",
|
|
925
|
+
"description": "Categories the drug belongs to, separated by ' | '"
|
|
926
|
+
},
|
|
927
|
+
"atc_codes": {
|
|
928
|
+
"type": "array",
|
|
929
|
+
"items": {
|
|
930
|
+
"type": "object",
|
|
931
|
+
"properties": {
|
|
932
|
+
"code": {
|
|
933
|
+
"type": "string",
|
|
934
|
+
"description": "ATC code"
|
|
935
|
+
},
|
|
936
|
+
"children_names": {
|
|
937
|
+
"type": "string",
|
|
938
|
+
"description": "Child level names in the ATC hierarchy, separated by ' | '"
|
|
939
|
+
},
|
|
940
|
+
"children_codes": {
|
|
941
|
+
"type": "string",
|
|
942
|
+
"description": "Child level codes in the ATC hierarchy, separated by ' | '"
|
|
943
|
+
}
|
|
944
|
+
}
|
|
945
|
+
},
|
|
946
|
+
"description": "ATC (Anatomical Therapeutic Chemical) codes and hierarchy"
|
|
947
|
+
},
|
|
948
|
+
"synonyms": {
|
|
949
|
+
"type": "string",
|
|
950
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
951
|
+
},
|
|
952
|
+
"matched_fields": {
|
|
953
|
+
"type": "array",
|
|
954
|
+
"items": {
|
|
955
|
+
"type": "string"
|
|
956
|
+
},
|
|
957
|
+
"description": "List of fields that matched the search query"
|
|
958
|
+
}
|
|
959
|
+
}
|
|
960
|
+
}
|
|
961
|
+
},
|
|
962
|
+
"search_parameters": {
|
|
963
|
+
"type": "object",
|
|
964
|
+
"properties": {
|
|
965
|
+
"case_sensitive": {
|
|
966
|
+
"type": "boolean",
|
|
967
|
+
"description": "Whether the search was case-sensitive"
|
|
968
|
+
},
|
|
969
|
+
"exact_match": {
|
|
970
|
+
"type": "boolean",
|
|
971
|
+
"description": "Whether exact matching was used"
|
|
972
|
+
},
|
|
973
|
+
"limit": {
|
|
974
|
+
"type": "integer",
|
|
975
|
+
"description": "Maximum number of results requested"
|
|
976
|
+
}
|
|
977
|
+
}
|
|
978
|
+
}
|
|
979
|
+
}
|
|
980
|
+
}
|
|
981
|
+
},
|
|
982
|
+
{
|
|
983
|
+
"type": "XMLTool",
|
|
984
|
+
"name": "drugbank_get_drug_name_and_description_by_indication",
|
|
985
|
+
"description": "Get drug name, Drugbank ID, and description by its indication.",
|
|
986
|
+
"settings": {
|
|
987
|
+
"hf_dataset_path": {
|
|
988
|
+
"repo_id": "agenticx/DrugBank",
|
|
989
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
990
|
+
"token": null,
|
|
991
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
992
|
+
},
|
|
993
|
+
"namespaces": {
|
|
994
|
+
"db": "http://www.drugbank.ca"
|
|
995
|
+
},
|
|
996
|
+
"record_xpath": "db:drug",
|
|
997
|
+
"search_fields": ["indication"],
|
|
998
|
+
"field_mappings": {
|
|
999
|
+
"drug_name": "db:name",
|
|
1000
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1001
|
+
"indication": "db:indication",
|
|
1002
|
+
"description": "db:description"
|
|
1003
|
+
}
|
|
1004
|
+
},
|
|
1005
|
+
"parameter": {
|
|
1006
|
+
"type": "object",
|
|
1007
|
+
"properties": {
|
|
1008
|
+
"query": {
|
|
1009
|
+
"type": "string",
|
|
1010
|
+
"description": "Drug indication to search for",
|
|
1011
|
+
"minLength": 1
|
|
1012
|
+
},
|
|
1013
|
+
"case_sensitive": {
|
|
1014
|
+
"type": "boolean",
|
|
1015
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1016
|
+
"default": false
|
|
1017
|
+
},
|
|
1018
|
+
"exact_match": {
|
|
1019
|
+
"type": "boolean",
|
|
1020
|
+
"description": "Select True to require an exact match",
|
|
1021
|
+
"default": false
|
|
1022
|
+
},
|
|
1023
|
+
"limit": {
|
|
1024
|
+
"type": "integer",
|
|
1025
|
+
"description": "Maximum number of results to return",
|
|
1026
|
+
"default": 10,
|
|
1027
|
+
"minimum": 1,
|
|
1028
|
+
"maximum": 100
|
|
1029
|
+
}
|
|
1030
|
+
},
|
|
1031
|
+
"required": ["query"]
|
|
1032
|
+
},
|
|
1033
|
+
"return_schema": {
|
|
1034
|
+
"type": "object",
|
|
1035
|
+
"properties": {
|
|
1036
|
+
"error": {
|
|
1037
|
+
"type": "string",
|
|
1038
|
+
"description": "Error message (if any)"
|
|
1039
|
+
},
|
|
1040
|
+
"query": {
|
|
1041
|
+
"type": "string",
|
|
1042
|
+
"description": "The original search query"
|
|
1043
|
+
},
|
|
1044
|
+
"total_matches": {
|
|
1045
|
+
"type": "integer",
|
|
1046
|
+
"description": "Total number of matching records found"
|
|
1047
|
+
},
|
|
1048
|
+
"total_returned_results": {
|
|
1049
|
+
"type": "integer",
|
|
1050
|
+
"description": "Number of results returned in this response"
|
|
1051
|
+
},
|
|
1052
|
+
"results": {
|
|
1053
|
+
"type": "array",
|
|
1054
|
+
"items": {
|
|
1055
|
+
"type": "object",
|
|
1056
|
+
"properties": {
|
|
1057
|
+
"_tag": {
|
|
1058
|
+
"type": "string",
|
|
1059
|
+
"description": "XML tag name of the record element"
|
|
1060
|
+
},
|
|
1061
|
+
"_text": {
|
|
1062
|
+
"type": "string",
|
|
1063
|
+
"description": "Text content of the record element"
|
|
1064
|
+
},
|
|
1065
|
+
"_attributes": {
|
|
1066
|
+
"type": "object",
|
|
1067
|
+
"description": "Attributes of the record element"
|
|
1068
|
+
},
|
|
1069
|
+
"drug_name": {
|
|
1070
|
+
"type": "string",
|
|
1071
|
+
"description": "Name of the drug"
|
|
1072
|
+
},
|
|
1073
|
+
"drugbank_id": {
|
|
1074
|
+
"type": "string",
|
|
1075
|
+
"description": "Primary DrugBank ID"
|
|
1076
|
+
},
|
|
1077
|
+
"indication": {
|
|
1078
|
+
"type": "string",
|
|
1079
|
+
"description": "Drug indication and therapeutic uses"
|
|
1080
|
+
},
|
|
1081
|
+
"description": {
|
|
1082
|
+
"type": "string",
|
|
1083
|
+
"description": "Drug description"
|
|
1084
|
+
},
|
|
1085
|
+
"matched_fields": {
|
|
1086
|
+
"type": "array",
|
|
1087
|
+
"items": {
|
|
1088
|
+
"type": "string"
|
|
1089
|
+
},
|
|
1090
|
+
"description": "List of fields that matched the search query"
|
|
1091
|
+
}
|
|
1092
|
+
}
|
|
1093
|
+
}
|
|
1094
|
+
},
|
|
1095
|
+
"search_parameters": {
|
|
1096
|
+
"type": "object",
|
|
1097
|
+
"properties": {
|
|
1098
|
+
"case_sensitive": {
|
|
1099
|
+
"type": "boolean",
|
|
1100
|
+
"description": "Whether the search was case-sensitive"
|
|
1101
|
+
},
|
|
1102
|
+
"exact_match": {
|
|
1103
|
+
"type": "boolean",
|
|
1104
|
+
"description": "Whether exact matching was used"
|
|
1105
|
+
},
|
|
1106
|
+
"limit": {
|
|
1107
|
+
"type": "integer",
|
|
1108
|
+
"description": "Maximum number of results requested"
|
|
1109
|
+
}
|
|
1110
|
+
}
|
|
1111
|
+
}
|
|
1112
|
+
}
|
|
1113
|
+
}
|
|
1114
|
+
},
|
|
1115
|
+
{
|
|
1116
|
+
"type": "XMLTool",
|
|
1117
|
+
"name": "drugbank_get_pharmacology_by_drug_name_or_drugbank_id",
|
|
1118
|
+
"description": "Get drug pharmacodynamics, mechanism of action, and pharmacokinetics by drug name or Drugbank ID.",
|
|
1119
|
+
"settings": {
|
|
1120
|
+
"hf_dataset_path": {
|
|
1121
|
+
"repo_id": "agenticx/DrugBank",
|
|
1122
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
1123
|
+
"token": null,
|
|
1124
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
1125
|
+
},
|
|
1126
|
+
"namespaces": {
|
|
1127
|
+
"db": "http://www.drugbank.ca"
|
|
1128
|
+
},
|
|
1129
|
+
"record_xpath": "db:drug",
|
|
1130
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
1131
|
+
"field_mappings": {
|
|
1132
|
+
"drug_name": "db:name",
|
|
1133
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1134
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
1135
|
+
"pharmacodynamics": "db:pharmacodynamics",
|
|
1136
|
+
"mechanism_of_action": "db:mechanism-of-action",
|
|
1137
|
+
"absorption": "db:absorption",
|
|
1138
|
+
"metabolism": "db:metabolism",
|
|
1139
|
+
"half_life": "db:half-life",
|
|
1140
|
+
"protein_binding": "db:protein-binding",
|
|
1141
|
+
"route_of_elimination": "db:route-of-elimination",
|
|
1142
|
+
"volume_of_distribution": "db:volume-of-distribution",
|
|
1143
|
+
"clearance": "db:clearance"
|
|
1144
|
+
}
|
|
1145
|
+
},
|
|
1146
|
+
"parameter": {
|
|
1147
|
+
"type": "object",
|
|
1148
|
+
"properties": {
|
|
1149
|
+
"query": {
|
|
1150
|
+
"type": "string",
|
|
1151
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
1152
|
+
"minLength": 1
|
|
1153
|
+
},
|
|
1154
|
+
"case_sensitive": {
|
|
1155
|
+
"type": "boolean",
|
|
1156
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1157
|
+
"default": false
|
|
1158
|
+
},
|
|
1159
|
+
"exact_match": {
|
|
1160
|
+
"type": "boolean",
|
|
1161
|
+
"description": "Select True to require an exact match",
|
|
1162
|
+
"default": false
|
|
1163
|
+
},
|
|
1164
|
+
"limit": {
|
|
1165
|
+
"type": "integer",
|
|
1166
|
+
"description": "Maximum number of results to return",
|
|
1167
|
+
"default": 10,
|
|
1168
|
+
"minimum": 1,
|
|
1169
|
+
"maximum": 100
|
|
1170
|
+
}
|
|
1171
|
+
},
|
|
1172
|
+
"required": ["query"]
|
|
1173
|
+
},
|
|
1174
|
+
"return_schema": {
|
|
1175
|
+
"type": "object",
|
|
1176
|
+
"properties": {
|
|
1177
|
+
"error": {
|
|
1178
|
+
"type": "string",
|
|
1179
|
+
"description": "Error message (if any)"
|
|
1180
|
+
},
|
|
1181
|
+
"query": {
|
|
1182
|
+
"type": "string",
|
|
1183
|
+
"description": "The original search query"
|
|
1184
|
+
},
|
|
1185
|
+
"total_matches": {
|
|
1186
|
+
"type": "integer",
|
|
1187
|
+
"description": "Total number of matching records found"
|
|
1188
|
+
},
|
|
1189
|
+
"total_returned_results": {
|
|
1190
|
+
"type": "integer",
|
|
1191
|
+
"description": "Number of results returned in this response"
|
|
1192
|
+
},
|
|
1193
|
+
"results": {
|
|
1194
|
+
"type": "array",
|
|
1195
|
+
"items": {
|
|
1196
|
+
"type": "object",
|
|
1197
|
+
"properties": {
|
|
1198
|
+
"_tag": {
|
|
1199
|
+
"type": "string",
|
|
1200
|
+
"description": "XML tag name of the record element"
|
|
1201
|
+
},
|
|
1202
|
+
"_text": {
|
|
1203
|
+
"type": "string",
|
|
1204
|
+
"description": "Text content of the record element"
|
|
1205
|
+
},
|
|
1206
|
+
"_attributes": {
|
|
1207
|
+
"type": "object",
|
|
1208
|
+
"description": "Attributes of the record element"
|
|
1209
|
+
},
|
|
1210
|
+
"drug_name": {
|
|
1211
|
+
"type": "string",
|
|
1212
|
+
"description": "Name of the drug"
|
|
1213
|
+
},
|
|
1214
|
+
"drugbank_id": {
|
|
1215
|
+
"type": "string",
|
|
1216
|
+
"description": "Primary DrugBank ID"
|
|
1217
|
+
},
|
|
1218
|
+
"synonyms": {
|
|
1219
|
+
"type": "string",
|
|
1220
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
1221
|
+
},
|
|
1222
|
+
"pharmacodynamics": {
|
|
1223
|
+
"type": "string",
|
|
1224
|
+
"description": "Pharmacodynamics information describing the drug's effects on the body"
|
|
1225
|
+
},
|
|
1226
|
+
"mechanism_of_action": {
|
|
1227
|
+
"type": "string",
|
|
1228
|
+
"description": "Mechanism of action describing how the drug works at the molecular level"
|
|
1229
|
+
},
|
|
1230
|
+
"absorption": {
|
|
1231
|
+
"type": "string",
|
|
1232
|
+
"description": "Information about drug absorption and bioavailability"
|
|
1233
|
+
},
|
|
1234
|
+
"metabolism": {
|
|
1235
|
+
"type": "string",
|
|
1236
|
+
"description": "Information about drug metabolism and metabolic pathways"
|
|
1237
|
+
},
|
|
1238
|
+
"half_life": {
|
|
1239
|
+
"type": "string",
|
|
1240
|
+
"description": "Plasma elimination half-life of the drug"
|
|
1241
|
+
},
|
|
1242
|
+
"protein_binding": {
|
|
1243
|
+
"type": "string",
|
|
1244
|
+
"description": "Information about protein binding properties"
|
|
1245
|
+
},
|
|
1246
|
+
"route_of_elimination": {
|
|
1247
|
+
"type": "string",
|
|
1248
|
+
"description": "Information about how the drug is eliminated from the body"
|
|
1249
|
+
},
|
|
1250
|
+
"volume_of_distribution": {
|
|
1251
|
+
"type": "string",
|
|
1252
|
+
"description": "Volume of distribution of the drug"
|
|
1253
|
+
},
|
|
1254
|
+
"clearance": {
|
|
1255
|
+
"type": "string",
|
|
1256
|
+
"description": "Information about drug clearance"
|
|
1257
|
+
},
|
|
1258
|
+
"matched_fields": {
|
|
1259
|
+
"type": "array",
|
|
1260
|
+
"items": {
|
|
1261
|
+
"type": "string"
|
|
1262
|
+
},
|
|
1263
|
+
"description": "List of fields that matched the search query"
|
|
1264
|
+
}
|
|
1265
|
+
}
|
|
1266
|
+
}
|
|
1267
|
+
},
|
|
1268
|
+
"search_parameters": {
|
|
1269
|
+
"type": "object",
|
|
1270
|
+
"properties": {
|
|
1271
|
+
"case_sensitive": {
|
|
1272
|
+
"type": "boolean",
|
|
1273
|
+
"description": "Whether the search was case-sensitive"
|
|
1274
|
+
},
|
|
1275
|
+
"exact_match": {
|
|
1276
|
+
"type": "boolean",
|
|
1277
|
+
"description": "Whether exact matching was used"
|
|
1278
|
+
},
|
|
1279
|
+
"limit": {
|
|
1280
|
+
"type": "integer",
|
|
1281
|
+
"description": "Maximum number of results requested"
|
|
1282
|
+
}
|
|
1283
|
+
}
|
|
1284
|
+
}
|
|
1285
|
+
}
|
|
1286
|
+
}
|
|
1287
|
+
},
|
|
1288
|
+
{
|
|
1289
|
+
"type": "XMLTool",
|
|
1290
|
+
"name": "drugbank_get_drug_name_description_pharmacology_by_mechanism_of_action",
|
|
1291
|
+
"description": "Get drug name, ID, description, pharmacodynamics, mechanism of action, and pharmacokinetics by drug mechanism of action.",
|
|
1292
|
+
"settings": {
|
|
1293
|
+
"hf_dataset_path": {
|
|
1294
|
+
"repo_id": "agenticx/DrugBank",
|
|
1295
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
1296
|
+
"token": null,
|
|
1297
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
1298
|
+
},
|
|
1299
|
+
"namespaces": {
|
|
1300
|
+
"db": "http://www.drugbank.ca"
|
|
1301
|
+
},
|
|
1302
|
+
"record_xpath": "db:drug",
|
|
1303
|
+
"search_fields": ["mechanism_of_action"],
|
|
1304
|
+
"field_mappings": {
|
|
1305
|
+
"drug_name": "db:name",
|
|
1306
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1307
|
+
"description": "db:description",
|
|
1308
|
+
"pharmacodynamics": "db:pharmacodynamics",
|
|
1309
|
+
"mechanism_of_action": "db:mechanism-of-action",
|
|
1310
|
+
"absorption": "db:absorption",
|
|
1311
|
+
"metabolism": "db:metabolism",
|
|
1312
|
+
"half_life": "db:half-life",
|
|
1313
|
+
"protein_binding": "db:protein-binding",
|
|
1314
|
+
"route_of_elimination": "db:route-of-elimination",
|
|
1315
|
+
"volume_of_distribution": "db:volume-of-distribution",
|
|
1316
|
+
"clearance": "db:clearance"
|
|
1317
|
+
}
|
|
1318
|
+
},
|
|
1319
|
+
"parameter": {
|
|
1320
|
+
"type": "object",
|
|
1321
|
+
"properties": {
|
|
1322
|
+
"query": {
|
|
1323
|
+
"type": "string",
|
|
1324
|
+
"description": "Query string to search for in mechanism of action descriptions",
|
|
1325
|
+
"minLength": 1
|
|
1326
|
+
},
|
|
1327
|
+
"case_sensitive": {
|
|
1328
|
+
"type": "boolean",
|
|
1329
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1330
|
+
"default": false
|
|
1331
|
+
},
|
|
1332
|
+
"exact_match": {
|
|
1333
|
+
"type": "boolean",
|
|
1334
|
+
"description": "Select True to require an exact match",
|
|
1335
|
+
"default": false
|
|
1336
|
+
},
|
|
1337
|
+
"limit": {
|
|
1338
|
+
"type": "integer",
|
|
1339
|
+
"description": "Maximum number of results to return",
|
|
1340
|
+
"default": 10,
|
|
1341
|
+
"minimum": 1,
|
|
1342
|
+
"maximum": 100
|
|
1343
|
+
}
|
|
1344
|
+
},
|
|
1345
|
+
"required": ["query"]
|
|
1346
|
+
},
|
|
1347
|
+
"return_schema": {
|
|
1348
|
+
"type": "object",
|
|
1349
|
+
"properties": {
|
|
1350
|
+
"error": {
|
|
1351
|
+
"type": "string",
|
|
1352
|
+
"description": "Error message (if any)"
|
|
1353
|
+
},
|
|
1354
|
+
"query": {
|
|
1355
|
+
"type": "string",
|
|
1356
|
+
"description": "The original search query"
|
|
1357
|
+
},
|
|
1358
|
+
"total_matches": {
|
|
1359
|
+
"type": "integer",
|
|
1360
|
+
"description": "Total number of matching records found"
|
|
1361
|
+
},
|
|
1362
|
+
"total_returned_results": {
|
|
1363
|
+
"type": "integer",
|
|
1364
|
+
"description": "Number of results returned in this response"
|
|
1365
|
+
},
|
|
1366
|
+
"results": {
|
|
1367
|
+
"type": "array",
|
|
1368
|
+
"items": {
|
|
1369
|
+
"type": "object",
|
|
1370
|
+
"properties": {
|
|
1371
|
+
"_tag": {
|
|
1372
|
+
"type": "string",
|
|
1373
|
+
"description": "XML tag name of the record element"
|
|
1374
|
+
},
|
|
1375
|
+
"_text": {
|
|
1376
|
+
"type": "string",
|
|
1377
|
+
"description": "Text content of the record element"
|
|
1378
|
+
},
|
|
1379
|
+
"_attributes": {
|
|
1380
|
+
"type": "object",
|
|
1381
|
+
"description": "Attributes of the record element"
|
|
1382
|
+
},
|
|
1383
|
+
"drug_name": {
|
|
1384
|
+
"type": "string",
|
|
1385
|
+
"description": "Name of the drug"
|
|
1386
|
+
},
|
|
1387
|
+
"drugbank_id": {
|
|
1388
|
+
"type": "string",
|
|
1389
|
+
"description": "Primary DrugBank ID"
|
|
1390
|
+
},
|
|
1391
|
+
"description": {
|
|
1392
|
+
"type": "string",
|
|
1393
|
+
"description": "Drug description"
|
|
1394
|
+
},
|
|
1395
|
+
"pharmacodynamics": {
|
|
1396
|
+
"type": "string",
|
|
1397
|
+
"description": "Pharmacodynamics information describing the drug's effects on the body"
|
|
1398
|
+
},
|
|
1399
|
+
"mechanism_of_action": {
|
|
1400
|
+
"type": "string",
|
|
1401
|
+
"description": "Mechanism of action describing how the drug works at the molecular level"
|
|
1402
|
+
},
|
|
1403
|
+
"absorption": {
|
|
1404
|
+
"type": "string",
|
|
1405
|
+
"description": "Information about drug absorption and bioavailability"
|
|
1406
|
+
},
|
|
1407
|
+
"metabolism": {
|
|
1408
|
+
"type": "string",
|
|
1409
|
+
"description": "Information about drug metabolism and metabolic pathways"
|
|
1410
|
+
},
|
|
1411
|
+
"half_life": {
|
|
1412
|
+
"type": "string",
|
|
1413
|
+
"description": "Plasma elimination half-life of the drug"
|
|
1414
|
+
},
|
|
1415
|
+
"protein_binding": {
|
|
1416
|
+
"type": "string",
|
|
1417
|
+
"description": "Information about protein binding properties"
|
|
1418
|
+
},
|
|
1419
|
+
"route_of_elimination": {
|
|
1420
|
+
"type": "string",
|
|
1421
|
+
"description": "Information about how the drug is eliminated from the body"
|
|
1422
|
+
},
|
|
1423
|
+
"volume_of_distribution": {
|
|
1424
|
+
"type": "string",
|
|
1425
|
+
"description": "Volume of distribution of the drug"
|
|
1426
|
+
},
|
|
1427
|
+
"clearance": {
|
|
1428
|
+
"type": "string",
|
|
1429
|
+
"description": "Information about drug clearance"
|
|
1430
|
+
},
|
|
1431
|
+
"matched_fields": {
|
|
1432
|
+
"type": "array",
|
|
1433
|
+
"items": {
|
|
1434
|
+
"type": "string"
|
|
1435
|
+
},
|
|
1436
|
+
"description": "List of fields that matched the search query"
|
|
1437
|
+
}
|
|
1438
|
+
}
|
|
1439
|
+
}
|
|
1440
|
+
},
|
|
1441
|
+
"search_parameters": {
|
|
1442
|
+
"type": "object",
|
|
1443
|
+
"properties": {
|
|
1444
|
+
"case_sensitive": {
|
|
1445
|
+
"type": "boolean",
|
|
1446
|
+
"description": "Whether the search was case-sensitive"
|
|
1447
|
+
},
|
|
1448
|
+
"exact_match": {
|
|
1449
|
+
"type": "boolean",
|
|
1450
|
+
"description": "Whether exact matching was used"
|
|
1451
|
+
},
|
|
1452
|
+
"limit": {
|
|
1453
|
+
"type": "integer",
|
|
1454
|
+
"description": "Maximum number of results requested"
|
|
1455
|
+
}
|
|
1456
|
+
}
|
|
1457
|
+
}
|
|
1458
|
+
}
|
|
1459
|
+
}
|
|
1460
|
+
},
|
|
1461
|
+
{
|
|
1462
|
+
"type": "XMLTool",
|
|
1463
|
+
"name": "drugbank_get_drug_interactions_by_drug_name_or_drugbank_id",
|
|
1464
|
+
"description": "Get drug interactions and contraindications by drug name or DrugBank ID.",
|
|
1465
|
+
"settings": {
|
|
1466
|
+
"hf_dataset_path": {
|
|
1467
|
+
"repo_id": "agenticx/DrugBank",
|
|
1468
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
1469
|
+
"token": null,
|
|
1470
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
1471
|
+
},
|
|
1472
|
+
"namespaces": {
|
|
1473
|
+
"db": "http://www.drugbank.ca"
|
|
1474
|
+
},
|
|
1475
|
+
"record_xpath": "db:drug",
|
|
1476
|
+
"search_fields": ["drug_name", "drugbank_id"],
|
|
1477
|
+
"field_mappings": {
|
|
1478
|
+
"drug_name": "db:name",
|
|
1479
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1480
|
+
"interacting_drugs": {
|
|
1481
|
+
"parent_path": "db:drug-interactions/db:drug-interaction",
|
|
1482
|
+
"subfields": {
|
|
1483
|
+
"id": "db:drugbank-id",
|
|
1484
|
+
"name": "db:name",
|
|
1485
|
+
"description": "db:description"
|
|
1486
|
+
}
|
|
1487
|
+
},
|
|
1488
|
+
"food_interactions": "db:food-interactions/db:food-interaction"
|
|
1489
|
+
}
|
|
1490
|
+
},
|
|
1491
|
+
"parameter": {
|
|
1492
|
+
"type": "object",
|
|
1493
|
+
"properties": {
|
|
1494
|
+
"query": {
|
|
1495
|
+
"type": "string",
|
|
1496
|
+
"description": "Drug name to search for interactions",
|
|
1497
|
+
"minLength": 1
|
|
1498
|
+
},
|
|
1499
|
+
"case_sensitive": {
|
|
1500
|
+
"type": "boolean",
|
|
1501
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1502
|
+
"default": false
|
|
1503
|
+
},
|
|
1504
|
+
"exact_match": {
|
|
1505
|
+
"type": "boolean",
|
|
1506
|
+
"description": "Select True to require an exact match",
|
|
1507
|
+
"default": false
|
|
1508
|
+
},
|
|
1509
|
+
"limit": {
|
|
1510
|
+
"type": "integer",
|
|
1511
|
+
"description": "Maximum number of results to return",
|
|
1512
|
+
"default": 10,
|
|
1513
|
+
"minimum": 1,
|
|
1514
|
+
"maximum": 100
|
|
1515
|
+
}
|
|
1516
|
+
},
|
|
1517
|
+
"required": ["query"]
|
|
1518
|
+
},
|
|
1519
|
+
"return_schema": {
|
|
1520
|
+
"type": "object",
|
|
1521
|
+
"properties": {
|
|
1522
|
+
"error": {
|
|
1523
|
+
"type": "string",
|
|
1524
|
+
"description": "Error message (if any)"
|
|
1525
|
+
},
|
|
1526
|
+
"query": {
|
|
1527
|
+
"type": "string",
|
|
1528
|
+
"description": "The original search query"
|
|
1529
|
+
},
|
|
1530
|
+
"total_matches": {
|
|
1531
|
+
"type": "integer",
|
|
1532
|
+
"description": "Total number of matching records found"
|
|
1533
|
+
},
|
|
1534
|
+
"total_returned_results": {
|
|
1535
|
+
"type": "integer",
|
|
1536
|
+
"description": "Number of results returned in this response"
|
|
1537
|
+
},
|
|
1538
|
+
"results": {
|
|
1539
|
+
"type": "array",
|
|
1540
|
+
"items": {
|
|
1541
|
+
"type": "object",
|
|
1542
|
+
"properties": {
|
|
1543
|
+
"_tag": {
|
|
1544
|
+
"type": "string",
|
|
1545
|
+
"description": "XML tag name of the record element"
|
|
1546
|
+
},
|
|
1547
|
+
"_text": {
|
|
1548
|
+
"type": "string",
|
|
1549
|
+
"description": "Text content of the record element"
|
|
1550
|
+
},
|
|
1551
|
+
"_attributes": {
|
|
1552
|
+
"type": "object",
|
|
1553
|
+
"description": "Attributes of the record element"
|
|
1554
|
+
},
|
|
1555
|
+
"drug_name": {
|
|
1556
|
+
"type": "string",
|
|
1557
|
+
"description": "Name of the drug"
|
|
1558
|
+
},
|
|
1559
|
+
"drugbank_id": {
|
|
1560
|
+
"type": "string",
|
|
1561
|
+
"description": "Primary DrugBank ID"
|
|
1562
|
+
},
|
|
1563
|
+
"interacting_drugs": {
|
|
1564
|
+
"type": "array",
|
|
1565
|
+
"items": {
|
|
1566
|
+
"type": "object",
|
|
1567
|
+
"properties": {
|
|
1568
|
+
"id": {
|
|
1569
|
+
"type": "string",
|
|
1570
|
+
"description": "DrugBank ID of the interacting drug"
|
|
1571
|
+
},
|
|
1572
|
+
"name": {
|
|
1573
|
+
"type": "string",
|
|
1574
|
+
"description": "Name of the interacting drug"
|
|
1575
|
+
},
|
|
1576
|
+
"description": {
|
|
1577
|
+
"type": "string",
|
|
1578
|
+
"description": "Description of the drug interaction"
|
|
1579
|
+
}
|
|
1580
|
+
}
|
|
1581
|
+
},
|
|
1582
|
+
"description": "List of drugs that interact with the queried drug"
|
|
1583
|
+
},
|
|
1584
|
+
"food_interactions": {
|
|
1585
|
+
"type": "string",
|
|
1586
|
+
"description": "Food interactions and dietary considerations, separated by ' | '"
|
|
1587
|
+
},
|
|
1588
|
+
"matched_fields": {
|
|
1589
|
+
"type": "array",
|
|
1590
|
+
"items": {
|
|
1591
|
+
"type": "string"
|
|
1592
|
+
},
|
|
1593
|
+
"description": "List of fields that matched the search query"
|
|
1594
|
+
}
|
|
1595
|
+
}
|
|
1596
|
+
}
|
|
1597
|
+
},
|
|
1598
|
+
"search_parameters": {
|
|
1599
|
+
"type": "object",
|
|
1600
|
+
"properties": {
|
|
1601
|
+
"case_sensitive": {
|
|
1602
|
+
"type": "boolean",
|
|
1603
|
+
"description": "Whether the search was case-sensitive"
|
|
1604
|
+
},
|
|
1605
|
+
"exact_match": {
|
|
1606
|
+
"type": "boolean",
|
|
1607
|
+
"description": "Whether exact matching was used"
|
|
1608
|
+
},
|
|
1609
|
+
"limit": {
|
|
1610
|
+
"type": "integer",
|
|
1611
|
+
"description": "Maximum number of results requested"
|
|
1612
|
+
}
|
|
1613
|
+
}
|
|
1614
|
+
}
|
|
1615
|
+
}
|
|
1616
|
+
}
|
|
1617
|
+
},
|
|
1618
|
+
{
|
|
1619
|
+
"type": "XMLTool",
|
|
1620
|
+
"name": "drugbank_get_targets_by_drug_name_or_drugbank_id",
|
|
1621
|
+
"description": "Get drug targets, enzymes, carriers, and transporters by drug name or DrugBank ID.",
|
|
1622
|
+
"settings": {
|
|
1623
|
+
"hf_dataset_path": {
|
|
1624
|
+
"repo_id": "agenticx/DrugBank",
|
|
1625
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
1626
|
+
"token": null,
|
|
1627
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
1628
|
+
},
|
|
1629
|
+
"namespaces": {
|
|
1630
|
+
"db": "http://www.drugbank.ca"
|
|
1631
|
+
},
|
|
1632
|
+
"record_xpath": "db:drug",
|
|
1633
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
1634
|
+
"field_mappings": {
|
|
1635
|
+
"drug_name": "db:name",
|
|
1636
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1637
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
1638
|
+
"targets": {
|
|
1639
|
+
"parent_path": "db:targets/db:target",
|
|
1640
|
+
"subfields": {
|
|
1641
|
+
"id": "db:id",
|
|
1642
|
+
"name": "db:name",
|
|
1643
|
+
"organism": "db:organism",
|
|
1644
|
+
"actions": "db:actions/db:action"
|
|
1645
|
+
}
|
|
1646
|
+
},
|
|
1647
|
+
"enzymes": {
|
|
1648
|
+
"parent_path": "db:enzymes/db:enzyme",
|
|
1649
|
+
"subfields": {
|
|
1650
|
+
"id": "db:id",
|
|
1651
|
+
"name": "db:name",
|
|
1652
|
+
"organism": "db:organism",
|
|
1653
|
+
"actions": "db:actions/db:action"
|
|
1654
|
+
}
|
|
1655
|
+
},
|
|
1656
|
+
"carriers": {
|
|
1657
|
+
"parent_path": "db:carriers/db:carrier",
|
|
1658
|
+
"subfields": {
|
|
1659
|
+
"id": "db:id",
|
|
1660
|
+
"name": "db:name",
|
|
1661
|
+
"organism": "db:organism",
|
|
1662
|
+
"actions": "db:actions/db:action"
|
|
1663
|
+
}
|
|
1664
|
+
},
|
|
1665
|
+
"transporters": {
|
|
1666
|
+
"parent_path": "db:transporters/db:transporter",
|
|
1667
|
+
"subfields": {
|
|
1668
|
+
"id": "db:id",
|
|
1669
|
+
"name": "db:name",
|
|
1670
|
+
"organism": "db:organism",
|
|
1671
|
+
"actions": "db:actions/db:action"
|
|
1672
|
+
}
|
|
1673
|
+
}
|
|
1674
|
+
}
|
|
1675
|
+
},
|
|
1676
|
+
"parameter": {
|
|
1677
|
+
"type": "object",
|
|
1678
|
+
"properties": {
|
|
1679
|
+
"query": {
|
|
1680
|
+
"type": "string",
|
|
1681
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
1682
|
+
"minLength": 1
|
|
1683
|
+
},
|
|
1684
|
+
"case_sensitive": {
|
|
1685
|
+
"type": "boolean",
|
|
1686
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1687
|
+
"default": false
|
|
1688
|
+
},
|
|
1689
|
+
"exact_match": {
|
|
1690
|
+
"type": "boolean",
|
|
1691
|
+
"description": "Select True to require an exact match",
|
|
1692
|
+
"default": false
|
|
1693
|
+
},
|
|
1694
|
+
"limit": {
|
|
1695
|
+
"type": "integer",
|
|
1696
|
+
"description": "Maximum number of results to return",
|
|
1697
|
+
"default": 10,
|
|
1698
|
+
"minimum": 1,
|
|
1699
|
+
"maximum": 100
|
|
1700
|
+
}
|
|
1701
|
+
},
|
|
1702
|
+
"required": ["query"]
|
|
1703
|
+
},
|
|
1704
|
+
"return_schema": {
|
|
1705
|
+
"type": "object",
|
|
1706
|
+
"properties": {
|
|
1707
|
+
"error": {
|
|
1708
|
+
"type": "string",
|
|
1709
|
+
"description": "Error message (if any)"
|
|
1710
|
+
},
|
|
1711
|
+
"query": {
|
|
1712
|
+
"type": "string",
|
|
1713
|
+
"description": "The original search query"
|
|
1714
|
+
},
|
|
1715
|
+
"total_matches": {
|
|
1716
|
+
"type": "integer",
|
|
1717
|
+
"description": "Total number of matching records found"
|
|
1718
|
+
},
|
|
1719
|
+
"total_returned_results": {
|
|
1720
|
+
"type": "integer",
|
|
1721
|
+
"description": "Number of results returned in this response"
|
|
1722
|
+
},
|
|
1723
|
+
"results": {
|
|
1724
|
+
"type": "array",
|
|
1725
|
+
"items": {
|
|
1726
|
+
"type": "object",
|
|
1727
|
+
"properties": {
|
|
1728
|
+
"_tag": {
|
|
1729
|
+
"type": "string",
|
|
1730
|
+
"description": "XML tag name of the record element"
|
|
1731
|
+
},
|
|
1732
|
+
"_text": {
|
|
1733
|
+
"type": "string",
|
|
1734
|
+
"description": "Text content of the record element"
|
|
1735
|
+
},
|
|
1736
|
+
"_attributes": {
|
|
1737
|
+
"type": "object",
|
|
1738
|
+
"description": "Attributes of the record element"
|
|
1739
|
+
},
|
|
1740
|
+
"drug_name": {
|
|
1741
|
+
"type": "string",
|
|
1742
|
+
"description": "Name of the drug"
|
|
1743
|
+
},
|
|
1744
|
+
"drugbank_id": {
|
|
1745
|
+
"type": "string",
|
|
1746
|
+
"description": "Primary DrugBank ID"
|
|
1747
|
+
},
|
|
1748
|
+
"synonyms": {
|
|
1749
|
+
"type": "string",
|
|
1750
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
1751
|
+
},
|
|
1752
|
+
"targets": {
|
|
1753
|
+
"type": "array",
|
|
1754
|
+
"items": {
|
|
1755
|
+
"type": "object",
|
|
1756
|
+
"properties": {
|
|
1757
|
+
"id": {
|
|
1758
|
+
"type": "string",
|
|
1759
|
+
"description": "Target ID"
|
|
1760
|
+
},
|
|
1761
|
+
"name": {
|
|
1762
|
+
"type": "string",
|
|
1763
|
+
"description": "Target name"
|
|
1764
|
+
},
|
|
1765
|
+
"organism": {
|
|
1766
|
+
"type": "string",
|
|
1767
|
+
"description": "Target organism"
|
|
1768
|
+
},
|
|
1769
|
+
"actions": {
|
|
1770
|
+
"type": "string",
|
|
1771
|
+
"description": "Target actions, separated by ' | '"
|
|
1772
|
+
}
|
|
1773
|
+
}
|
|
1774
|
+
},
|
|
1775
|
+
"description": "Drug targets"
|
|
1776
|
+
},
|
|
1777
|
+
"enzymes": {
|
|
1778
|
+
"type": "array",
|
|
1779
|
+
"items": {
|
|
1780
|
+
"type": "object",
|
|
1781
|
+
"properties": {
|
|
1782
|
+
"id": {
|
|
1783
|
+
"type": "string",
|
|
1784
|
+
"description": "Enzyme ID"
|
|
1785
|
+
},
|
|
1786
|
+
"name": {
|
|
1787
|
+
"type": "string",
|
|
1788
|
+
"description": "Enzyme name"
|
|
1789
|
+
},
|
|
1790
|
+
"organism": {
|
|
1791
|
+
"type": "string",
|
|
1792
|
+
"description": "Enzyme organism"
|
|
1793
|
+
},
|
|
1794
|
+
"actions": {
|
|
1795
|
+
"type": "string",
|
|
1796
|
+
"description": "Enzyme actions, separated by ' | '"
|
|
1797
|
+
}
|
|
1798
|
+
}
|
|
1799
|
+
},
|
|
1800
|
+
"description": "Drug enzymes"
|
|
1801
|
+
},
|
|
1802
|
+
"carriers": {
|
|
1803
|
+
"type": "array",
|
|
1804
|
+
"items": {
|
|
1805
|
+
"type": "object",
|
|
1806
|
+
"properties": {
|
|
1807
|
+
"id": {
|
|
1808
|
+
"type": "string",
|
|
1809
|
+
"description": "Carrier ID"
|
|
1810
|
+
},
|
|
1811
|
+
"name": {
|
|
1812
|
+
"type": "string",
|
|
1813
|
+
"description": "Carrier name"
|
|
1814
|
+
},
|
|
1815
|
+
"organism": {
|
|
1816
|
+
"type": "string",
|
|
1817
|
+
"description": "Carrier organism"
|
|
1818
|
+
},
|
|
1819
|
+
"actions": {
|
|
1820
|
+
"type": "string",
|
|
1821
|
+
"description": "Carrier actions, separated by ' | '"
|
|
1822
|
+
}
|
|
1823
|
+
}
|
|
1824
|
+
},
|
|
1825
|
+
"description": "Drug carriers"
|
|
1826
|
+
},
|
|
1827
|
+
"transporters": {
|
|
1828
|
+
"type": "array",
|
|
1829
|
+
"items": {
|
|
1830
|
+
"type": "object",
|
|
1831
|
+
"properties": {
|
|
1832
|
+
"id": {
|
|
1833
|
+
"type": "string",
|
|
1834
|
+
"description": "Transporter ID"
|
|
1835
|
+
},
|
|
1836
|
+
"name": {
|
|
1837
|
+
"type": "string",
|
|
1838
|
+
"description": "Transporter name"
|
|
1839
|
+
},
|
|
1840
|
+
"organism": {
|
|
1841
|
+
"type": "string",
|
|
1842
|
+
"description": "Transporter organism"
|
|
1843
|
+
},
|
|
1844
|
+
"actions": {
|
|
1845
|
+
"type": "string",
|
|
1846
|
+
"description": "Transporter actions, separated by ' | '"
|
|
1847
|
+
}
|
|
1848
|
+
}
|
|
1849
|
+
},
|
|
1850
|
+
"description": "Drug transporters"
|
|
1851
|
+
},
|
|
1852
|
+
"matched_fields": {
|
|
1853
|
+
"type": "array",
|
|
1854
|
+
"items": {
|
|
1855
|
+
"type": "string"
|
|
1856
|
+
},
|
|
1857
|
+
"description": "List of fields that matched the search query"
|
|
1858
|
+
}
|
|
1859
|
+
}
|
|
1860
|
+
}
|
|
1861
|
+
},
|
|
1862
|
+
"search_parameters": {
|
|
1863
|
+
"type": "object",
|
|
1864
|
+
"properties": {
|
|
1865
|
+
"case_sensitive": {
|
|
1866
|
+
"type": "boolean",
|
|
1867
|
+
"description": "Whether the search was case-sensitive"
|
|
1868
|
+
},
|
|
1869
|
+
"exact_match": {
|
|
1870
|
+
"type": "boolean",
|
|
1871
|
+
"description": "Whether exact matching was used"
|
|
1872
|
+
},
|
|
1873
|
+
"limit": {
|
|
1874
|
+
"type": "integer",
|
|
1875
|
+
"description": "Maximum number of results requested"
|
|
1876
|
+
}
|
|
1877
|
+
}
|
|
1878
|
+
}
|
|
1879
|
+
}
|
|
1880
|
+
}
|
|
1881
|
+
},
|
|
1882
|
+
{
|
|
1883
|
+
"type": "XMLTool",
|
|
1884
|
+
"name": "drugbank_get_drug_name_and_description_by_target_name",
|
|
1885
|
+
"description": "Get associated drug names and descriptions for a particular target, enzyme, carrier, or transporter protein.",
|
|
1886
|
+
"settings": {
|
|
1887
|
+
"hf_dataset_path": {
|
|
1888
|
+
"repo_id": "agenticx/DrugBank",
|
|
1889
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
1890
|
+
"token": null,
|
|
1891
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
1892
|
+
},
|
|
1893
|
+
"namespaces": {
|
|
1894
|
+
"db": "http://www.drugbank.ca"
|
|
1895
|
+
},
|
|
1896
|
+
"record_xpath": "db:drug",
|
|
1897
|
+
"search_fields": ["target_names", "enzyme_names", "carrier_names", "transporter_names"],
|
|
1898
|
+
"field_mappings": {
|
|
1899
|
+
"drug_name": "db:name",
|
|
1900
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
1901
|
+
"description": "db:description",
|
|
1902
|
+
"target_names": "db:targets/db:target/db:name",
|
|
1903
|
+
"enzyme_names": "db:enzymes/db:enzyme/db:name",
|
|
1904
|
+
"carrier_names": "db:carriers/db:carrier/db:name",
|
|
1905
|
+
"transporter_names": "db:transporters/db:transporter/db:name"
|
|
1906
|
+
}
|
|
1907
|
+
},
|
|
1908
|
+
"parameter": {
|
|
1909
|
+
"type": "object",
|
|
1910
|
+
"properties": {
|
|
1911
|
+
"query": {
|
|
1912
|
+
"type": "string",
|
|
1913
|
+
"description": "Target, enzyme, carrier, or transporter name to search for",
|
|
1914
|
+
"minLength": 1
|
|
1915
|
+
},
|
|
1916
|
+
"case_sensitive": {
|
|
1917
|
+
"type": "boolean",
|
|
1918
|
+
"description": "Select True to perform a case-sensitive search",
|
|
1919
|
+
"default": false
|
|
1920
|
+
},
|
|
1921
|
+
"exact_match": {
|
|
1922
|
+
"type": "boolean",
|
|
1923
|
+
"description": "Select True to require an exact match",
|
|
1924
|
+
"default": false
|
|
1925
|
+
},
|
|
1926
|
+
"limit": {
|
|
1927
|
+
"type": "integer",
|
|
1928
|
+
"description": "Maximum number of results to return",
|
|
1929
|
+
"default": 10,
|
|
1930
|
+
"minimum": 1,
|
|
1931
|
+
"maximum": 100
|
|
1932
|
+
}
|
|
1933
|
+
},
|
|
1934
|
+
"required": ["query"]
|
|
1935
|
+
},
|
|
1936
|
+
"return_schema": {
|
|
1937
|
+
"type": "object",
|
|
1938
|
+
"properties": {
|
|
1939
|
+
"error": {
|
|
1940
|
+
"type": "string",
|
|
1941
|
+
"description": "Error message (if any)"
|
|
1942
|
+
},
|
|
1943
|
+
"query": {
|
|
1944
|
+
"type": "string",
|
|
1945
|
+
"description": "The original search query"
|
|
1946
|
+
},
|
|
1947
|
+
"total_matches": {
|
|
1948
|
+
"type": "integer",
|
|
1949
|
+
"description": "Total number of matching records found"
|
|
1950
|
+
},
|
|
1951
|
+
"total_returned_results": {
|
|
1952
|
+
"type": "integer",
|
|
1953
|
+
"description": "Number of results returned in this response"
|
|
1954
|
+
},
|
|
1955
|
+
"results": {
|
|
1956
|
+
"type": "array",
|
|
1957
|
+
"items": {
|
|
1958
|
+
"type": "object",
|
|
1959
|
+
"properties": {
|
|
1960
|
+
"_tag": {
|
|
1961
|
+
"type": "string",
|
|
1962
|
+
"description": "XML tag name of the record element"
|
|
1963
|
+
},
|
|
1964
|
+
"_text": {
|
|
1965
|
+
"type": "string",
|
|
1966
|
+
"description": "Text content of the record element"
|
|
1967
|
+
},
|
|
1968
|
+
"_attributes": {
|
|
1969
|
+
"type": "object",
|
|
1970
|
+
"description": "Attributes of the record element"
|
|
1971
|
+
},
|
|
1972
|
+
"drug_name": {
|
|
1973
|
+
"type": "string",
|
|
1974
|
+
"description": "Name of the drug"
|
|
1975
|
+
},
|
|
1976
|
+
"drugbank_id": {
|
|
1977
|
+
"type": "string",
|
|
1978
|
+
"description": "Primary DrugBank ID"
|
|
1979
|
+
},
|
|
1980
|
+
"description": {
|
|
1981
|
+
"type": "string",
|
|
1982
|
+
"description": "Drug description"
|
|
1983
|
+
},
|
|
1984
|
+
"target_names": {
|
|
1985
|
+
"type": "string",
|
|
1986
|
+
"description": "Names of targets associated with the drug, separated by ' | '"
|
|
1987
|
+
},
|
|
1988
|
+
"enzyme_names": {
|
|
1989
|
+
"type": "string",
|
|
1990
|
+
"description": "Names of enzymes associated with the drug, separated by ' | '"
|
|
1991
|
+
},
|
|
1992
|
+
"carrier_names": {
|
|
1993
|
+
"type": "string",
|
|
1994
|
+
"description": "Names of carriers associated with the drug, separated by ' | '"
|
|
1995
|
+
},
|
|
1996
|
+
"transporter_names": {
|
|
1997
|
+
"type": "string",
|
|
1998
|
+
"description": "Names of transporters associated with the drug, separated by ' | '"
|
|
1999
|
+
},
|
|
2000
|
+
"matched_fields": {
|
|
2001
|
+
"type": "array",
|
|
2002
|
+
"items": {
|
|
2003
|
+
"type": "string"
|
|
2004
|
+
},
|
|
2005
|
+
"description": "List of fields that matched the search query"
|
|
2006
|
+
}
|
|
2007
|
+
}
|
|
2008
|
+
}
|
|
2009
|
+
},
|
|
2010
|
+
"search_parameters": {
|
|
2011
|
+
"type": "object",
|
|
2012
|
+
"properties": {
|
|
2013
|
+
"case_sensitive": {
|
|
2014
|
+
"type": "boolean",
|
|
2015
|
+
"description": "Whether the search was case-sensitive"
|
|
2016
|
+
},
|
|
2017
|
+
"exact_match": {
|
|
2018
|
+
"type": "boolean",
|
|
2019
|
+
"description": "Whether exact matching was used"
|
|
2020
|
+
},
|
|
2021
|
+
"limit": {
|
|
2022
|
+
"type": "integer",
|
|
2023
|
+
"description": "Maximum number of results requested"
|
|
2024
|
+
}
|
|
2025
|
+
}
|
|
2026
|
+
}
|
|
2027
|
+
}
|
|
2028
|
+
}
|
|
2029
|
+
},
|
|
2030
|
+
{
|
|
2031
|
+
"type": "XMLTool",
|
|
2032
|
+
"name": "drugbank_get_drug_products_by_name_or_drugbank_id",
|
|
2033
|
+
"description": "Get commercial drug products, dosage forms, and pricing informatiomon by drug name or DrugBank ID.",
|
|
2034
|
+
"settings": {
|
|
2035
|
+
"hf_dataset_path": {
|
|
2036
|
+
"repo_id": "agenticx/DrugBank",
|
|
2037
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2038
|
+
"token": null,
|
|
2039
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2040
|
+
},
|
|
2041
|
+
"namespaces": {
|
|
2042
|
+
"db": "http://www.drugbank.ca"
|
|
2043
|
+
},
|
|
2044
|
+
"record_xpath": "db:drug",
|
|
2045
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
2046
|
+
"field_mappings": {
|
|
2047
|
+
"drug_name": "db:name",
|
|
2048
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2049
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
2050
|
+
"products": {
|
|
2051
|
+
"parent_path": "db:products/db:product",
|
|
2052
|
+
"subfields": {
|
|
2053
|
+
"name": "db:name",
|
|
2054
|
+
"labeller": "db:labeller",
|
|
2055
|
+
"dosage_form": "db:dosage-form",
|
|
2056
|
+
"strength": "db:strength",
|
|
2057
|
+
"route": "db:route",
|
|
2058
|
+
"ndc_product_code": "db:ndc-product-code",
|
|
2059
|
+
"marketing_start": "db:started-marketing-on",
|
|
2060
|
+
"marketing_end": "db:ended-marketing-on",
|
|
2061
|
+
"country": "db:country",
|
|
2062
|
+
"approval_status": "db:approved",
|
|
2063
|
+
"generic_status": "db:generic"
|
|
2064
|
+
}
|
|
2065
|
+
},
|
|
2066
|
+
"prices": {
|
|
2067
|
+
"parent_path": "db:prices/db:price",
|
|
2068
|
+
"subfields": {
|
|
2069
|
+
"cost": "db:cost",
|
|
2070
|
+
"currency": "db:cost/@currency",
|
|
2071
|
+
"unit": "db:unit"
|
|
2072
|
+
}
|
|
2073
|
+
}
|
|
2074
|
+
}
|
|
2075
|
+
},
|
|
2076
|
+
"parameter": {
|
|
2077
|
+
"type": "object",
|
|
2078
|
+
"properties": {
|
|
2079
|
+
"query": {
|
|
2080
|
+
"type": "string",
|
|
2081
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
2082
|
+
"minLength": 1
|
|
2083
|
+
},
|
|
2084
|
+
"case_sensitive": {
|
|
2085
|
+
"type": "boolean",
|
|
2086
|
+
"description": "Select True to perform a case-sensitive search",
|
|
2087
|
+
"default": false
|
|
2088
|
+
},
|
|
2089
|
+
"exact_match": {
|
|
2090
|
+
"type": "boolean",
|
|
2091
|
+
"description": "Select True to require an exact match",
|
|
2092
|
+
"default": false
|
|
2093
|
+
},
|
|
2094
|
+
"limit": {
|
|
2095
|
+
"type": "integer",
|
|
2096
|
+
"description": "Maximum number of results to return",
|
|
2097
|
+
"default": 10,
|
|
2098
|
+
"minimum": 1,
|
|
2099
|
+
"maximum": 100
|
|
2100
|
+
}
|
|
2101
|
+
},
|
|
2102
|
+
"required": ["query"]
|
|
2103
|
+
},
|
|
2104
|
+
"return_schema":{
|
|
2105
|
+
"type": "object",
|
|
2106
|
+
"properties": {
|
|
2107
|
+
"error": {
|
|
2108
|
+
"type": "string",
|
|
2109
|
+
"description": "Error message (if any)"
|
|
2110
|
+
},
|
|
2111
|
+
"query": {
|
|
2112
|
+
"type": "string",
|
|
2113
|
+
"description": "The original search query"
|
|
2114
|
+
},
|
|
2115
|
+
"total_matches": {
|
|
2116
|
+
"type": "integer",
|
|
2117
|
+
"description": "Total number of matching records found"
|
|
2118
|
+
},
|
|
2119
|
+
"total_returned_results": {
|
|
2120
|
+
"type": "integer",
|
|
2121
|
+
"description": "Number of results returned in this response"
|
|
2122
|
+
},
|
|
2123
|
+
"results": {
|
|
2124
|
+
"type": "array",
|
|
2125
|
+
"items": {
|
|
2126
|
+
"type": "object",
|
|
2127
|
+
"properties": {
|
|
2128
|
+
"_tag": {
|
|
2129
|
+
"type": "string",
|
|
2130
|
+
"description": "XML tag name of the record element"
|
|
2131
|
+
},
|
|
2132
|
+
"_text": {
|
|
2133
|
+
"type": "string",
|
|
2134
|
+
"description": "Text content of the record element"
|
|
2135
|
+
},
|
|
2136
|
+
"_attributes": {
|
|
2137
|
+
"type": "object",
|
|
2138
|
+
"description": "Attributes of the record element"
|
|
2139
|
+
},
|
|
2140
|
+
"drug_name": {
|
|
2141
|
+
"type": "string",
|
|
2142
|
+
"description": "Name of the drug"
|
|
2143
|
+
},
|
|
2144
|
+
"drugbank_id": {
|
|
2145
|
+
"type": "string",
|
|
2146
|
+
"description": "Primary DrugBank ID"
|
|
2147
|
+
},
|
|
2148
|
+
"synonyms": {
|
|
2149
|
+
"type": "string",
|
|
2150
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
2151
|
+
},
|
|
2152
|
+
"products": {
|
|
2153
|
+
"type": "array",
|
|
2154
|
+
"items": {
|
|
2155
|
+
"type": "object",
|
|
2156
|
+
"properties": {
|
|
2157
|
+
"name": {
|
|
2158
|
+
"type": "string",
|
|
2159
|
+
"description": "Product name"
|
|
2160
|
+
},
|
|
2161
|
+
"labeller": {
|
|
2162
|
+
"type": "string",
|
|
2163
|
+
"description": "Product labeller/manufacturer"
|
|
2164
|
+
},
|
|
2165
|
+
"dosage_form": {
|
|
2166
|
+
"type": "string",
|
|
2167
|
+
"description": "Dosage form (e.g., Tablet, Kit, Capsule)"
|
|
2168
|
+
},
|
|
2169
|
+
"strength": {
|
|
2170
|
+
"type": "string",
|
|
2171
|
+
"description": "Drug strength/concentration"
|
|
2172
|
+
},
|
|
2173
|
+
"route": {
|
|
2174
|
+
"type": "string",
|
|
2175
|
+
"description": "Route of administration (e.g., Oral, Topical)"
|
|
2176
|
+
},
|
|
2177
|
+
"ndc_product_code": {
|
|
2178
|
+
"type": "string",
|
|
2179
|
+
"description": "National Drug Code (NDC) product identifier"
|
|
2180
|
+
},
|
|
2181
|
+
"marketing_start": {
|
|
2182
|
+
"type": "string",
|
|
2183
|
+
"description": "Marketing start date"
|
|
2184
|
+
},
|
|
2185
|
+
"marketing_end": {
|
|
2186
|
+
"type": "string",
|
|
2187
|
+
"description": "Marketing end date"
|
|
2188
|
+
},
|
|
2189
|
+
"country": {
|
|
2190
|
+
"type": "string",
|
|
2191
|
+
"description": "Country where the product is marketed"
|
|
2192
|
+
},
|
|
2193
|
+
"approval_status": {
|
|
2194
|
+
"type": "string",
|
|
2195
|
+
"description": "Product approval status (true/false)"
|
|
2196
|
+
},
|
|
2197
|
+
"generic_status": {
|
|
2198
|
+
"type": "string",
|
|
2199
|
+
"description": "Generic product status (true/false)"
|
|
2200
|
+
}
|
|
2201
|
+
}
|
|
2202
|
+
},
|
|
2203
|
+
"description": "Commercial drug products and formulations"
|
|
2204
|
+
},
|
|
2205
|
+
"prices": {
|
|
2206
|
+
"type": "array",
|
|
2207
|
+
"items": {
|
|
2208
|
+
"type": "object",
|
|
2209
|
+
"properties": {
|
|
2210
|
+
"cost": {
|
|
2211
|
+
"type": "string",
|
|
2212
|
+
"description": "Cost/price amount"
|
|
2213
|
+
},
|
|
2214
|
+
"currency": {
|
|
2215
|
+
"type": "string",
|
|
2216
|
+
"description": "Currency type"
|
|
2217
|
+
},
|
|
2218
|
+
"unit": {
|
|
2219
|
+
"type": "string",
|
|
2220
|
+
"description": "Unit of measurement for pricing (e.g., patch, g, ml)"
|
|
2221
|
+
}
|
|
2222
|
+
}
|
|
2223
|
+
},
|
|
2224
|
+
"description": "Pricing information for the drug"
|
|
2225
|
+
},
|
|
2226
|
+
"matched_fields": {
|
|
2227
|
+
"type": "array",
|
|
2228
|
+
"items": {
|
|
2229
|
+
"type": "string"
|
|
2230
|
+
},
|
|
2231
|
+
"description": "List of fields that matched the search query"
|
|
2232
|
+
}
|
|
2233
|
+
}
|
|
2234
|
+
}
|
|
2235
|
+
},
|
|
2236
|
+
"search_parameters": {
|
|
2237
|
+
"type": "object",
|
|
2238
|
+
"properties": {
|
|
2239
|
+
"case_sensitive": {
|
|
2240
|
+
"type": "boolean",
|
|
2241
|
+
"description": "Whether the search was case-sensitive"
|
|
2242
|
+
},
|
|
2243
|
+
"exact_match": {
|
|
2244
|
+
"type": "boolean",
|
|
2245
|
+
"description": "Whether exact matching was used"
|
|
2246
|
+
},
|
|
2247
|
+
"limit": {
|
|
2248
|
+
"type": "integer",
|
|
2249
|
+
"description": "Maximum number of results requested"
|
|
2250
|
+
}
|
|
2251
|
+
}
|
|
2252
|
+
}
|
|
2253
|
+
}
|
|
2254
|
+
}
|
|
2255
|
+
},
|
|
2256
|
+
{
|
|
2257
|
+
"type": "XMLTool",
|
|
2258
|
+
"name": "drugbank_get_safety_by_drug_name_or_drugbank_id",
|
|
2259
|
+
"description": "Get drug toxicity, contraindications, and safety information by drug name or DrugBank ID.",
|
|
2260
|
+
"settings": {
|
|
2261
|
+
"hf_dataset_path": {
|
|
2262
|
+
"repo_id": "agenticx/DrugBank",
|
|
2263
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2264
|
+
"token": null,
|
|
2265
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2266
|
+
},
|
|
2267
|
+
"namespaces": {
|
|
2268
|
+
"db": "http://www.drugbank.ca"
|
|
2269
|
+
},
|
|
2270
|
+
"record_xpath": "db:drug",
|
|
2271
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
2272
|
+
"field_mappings": {
|
|
2273
|
+
"drug_name": "db:name",
|
|
2274
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2275
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
2276
|
+
"toxicity": "db:toxicity",
|
|
2277
|
+
"affected_organisms": "db:affected-organisms/db:affected-organism",
|
|
2278
|
+
"food_interactions": "db:food-interactions/db:food-interaction"
|
|
2279
|
+
}
|
|
2280
|
+
},
|
|
2281
|
+
"parameter": {
|
|
2282
|
+
"type": "object",
|
|
2283
|
+
"properties": {
|
|
2284
|
+
"query": {
|
|
2285
|
+
"type": "string",
|
|
2286
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
2287
|
+
"minLength": 1
|
|
2288
|
+
},
|
|
2289
|
+
"case_sensitive": {
|
|
2290
|
+
"type": "boolean",
|
|
2291
|
+
"description": "Select True to perform a case-sensitive search",
|
|
2292
|
+
"default": false
|
|
2293
|
+
},
|
|
2294
|
+
"exact_match": {
|
|
2295
|
+
"type": "boolean",
|
|
2296
|
+
"description": "Select True to require an exact match",
|
|
2297
|
+
"default": false
|
|
2298
|
+
},
|
|
2299
|
+
"limit": {
|
|
2300
|
+
"type": "integer",
|
|
2301
|
+
"description": "Maximum number of results to return",
|
|
2302
|
+
"default": 10,
|
|
2303
|
+
"minimum": 1,
|
|
2304
|
+
"maximum": 100
|
|
2305
|
+
}
|
|
2306
|
+
},
|
|
2307
|
+
"required": ["query"]
|
|
2308
|
+
},
|
|
2309
|
+
"return_schema":{
|
|
2310
|
+
"type": "object",
|
|
2311
|
+
"properties": {
|
|
2312
|
+
"error": {
|
|
2313
|
+
"type": "string",
|
|
2314
|
+
"description": "Error message (if any)"
|
|
2315
|
+
},
|
|
2316
|
+
"query": {
|
|
2317
|
+
"type": "string",
|
|
2318
|
+
"description": "The original search query"
|
|
2319
|
+
},
|
|
2320
|
+
"total_matches": {
|
|
2321
|
+
"type": "integer",
|
|
2322
|
+
"description": "Total number of matching records found"
|
|
2323
|
+
},
|
|
2324
|
+
"total_returned_results": {
|
|
2325
|
+
"type": "integer",
|
|
2326
|
+
"description": "Number of results returned in this response"
|
|
2327
|
+
},
|
|
2328
|
+
"results": {
|
|
2329
|
+
"type": "array",
|
|
2330
|
+
"items": {
|
|
2331
|
+
"type": "object",
|
|
2332
|
+
"properties": {
|
|
2333
|
+
"_tag": {
|
|
2334
|
+
"type": "string",
|
|
2335
|
+
"description": "XML tag name of the record element"
|
|
2336
|
+
},
|
|
2337
|
+
"_text": {
|
|
2338
|
+
"type": "string",
|
|
2339
|
+
"description": "Text content of the record element"
|
|
2340
|
+
},
|
|
2341
|
+
"_attributes": {
|
|
2342
|
+
"type": "object",
|
|
2343
|
+
"description": "Attributes of the record element"
|
|
2344
|
+
},
|
|
2345
|
+
"drug_name": {
|
|
2346
|
+
"type": "string",
|
|
2347
|
+
"description": "Name of the drug"
|
|
2348
|
+
},
|
|
2349
|
+
"drugbank_id": {
|
|
2350
|
+
"type": "string",
|
|
2351
|
+
"description": "Primary DrugBank ID"
|
|
2352
|
+
},
|
|
2353
|
+
"synonyms": {
|
|
2354
|
+
"type": "string",
|
|
2355
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
2356
|
+
},
|
|
2357
|
+
"toxicity": {
|
|
2358
|
+
"type": "string",
|
|
2359
|
+
"description": "Toxicity information and safety warnings"
|
|
2360
|
+
},
|
|
2361
|
+
"affected_organisms": {
|
|
2362
|
+
"type": "string",
|
|
2363
|
+
"description": "Organisms affected by the drug, separated by ' | '"
|
|
2364
|
+
},
|
|
2365
|
+
"food_interactions": {
|
|
2366
|
+
"type": "string",
|
|
2367
|
+
"description": "Food interactions and dietary considerations, separated by ' | '"
|
|
2368
|
+
},
|
|
2369
|
+
"matched_fields": {
|
|
2370
|
+
"type": "array",
|
|
2371
|
+
"items": {
|
|
2372
|
+
"type": "string"
|
|
2373
|
+
},
|
|
2374
|
+
"description": "List of fields that matched the search query"
|
|
2375
|
+
}
|
|
2376
|
+
}
|
|
2377
|
+
}
|
|
2378
|
+
},
|
|
2379
|
+
"search_parameters": {
|
|
2380
|
+
"type": "object",
|
|
2381
|
+
"properties": {
|
|
2382
|
+
"case_sensitive": {
|
|
2383
|
+
"type": "boolean",
|
|
2384
|
+
"description": "Whether the search was case-sensitive"
|
|
2385
|
+
},
|
|
2386
|
+
"exact_match": {
|
|
2387
|
+
"type": "boolean",
|
|
2388
|
+
"description": "Whether exact matching was used"
|
|
2389
|
+
},
|
|
2390
|
+
"limit": {
|
|
2391
|
+
"type": "integer",
|
|
2392
|
+
"description": "Maximum number of results requested"
|
|
2393
|
+
}
|
|
2394
|
+
}
|
|
2395
|
+
}
|
|
2396
|
+
}
|
|
2397
|
+
}
|
|
2398
|
+
},
|
|
2399
|
+
{
|
|
2400
|
+
"type": "XMLTool",
|
|
2401
|
+
"name": "drugbank_get_drug_chemistry_by_drug_name_or_drugbank_id",
|
|
2402
|
+
"description": "Get drug chemical properties including molecular formula, weight, and structure by drug name or DrugBank ID.",
|
|
2403
|
+
"settings": {
|
|
2404
|
+
"hf_dataset_path": {
|
|
2405
|
+
"repo_id": "agenticx/DrugBank",
|
|
2406
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2407
|
+
"token": null,
|
|
2408
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2409
|
+
},
|
|
2410
|
+
"namespaces": {
|
|
2411
|
+
"db": "http://www.drugbank.ca"
|
|
2412
|
+
},
|
|
2413
|
+
"record_xpath": "db:drug",
|
|
2414
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
2415
|
+
"field_mappings": {
|
|
2416
|
+
"drug_name": "db:name",
|
|
2417
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2418
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
2419
|
+
"cas_number": "db:cas-number",
|
|
2420
|
+
"unii": "db:unii",
|
|
2421
|
+
"molecular_formula": "db:experimental-properties/db:property[db:kind='Molecular Formula']/db:value",
|
|
2422
|
+
"molecular_weight": "db:experimental-properties/db:property[db:kind='Molecular Weight']/db:value",
|
|
2423
|
+
"melting_point": "db:experimental-properties/db:property[db:kind='Melting Point']/db:value",
|
|
2424
|
+
"water_solubility": "db:experimental-properties/db:property[db:kind='Water Solubility']/db:value",
|
|
2425
|
+
"isoelectric_point": "db:experimental-properties/db:property[db:kind='Isoelectric Point']/db:value",
|
|
2426
|
+
"classification": "db:classification",
|
|
2427
|
+
"kingdom": "db:classification/db:kingdom",
|
|
2428
|
+
"superclass": "db:classification/db:superclass",
|
|
2429
|
+
"class": "db:classification/db:class",
|
|
2430
|
+
"subclass": "db:classification/db:subclass",
|
|
2431
|
+
"sequences": "db:sequences/db:sequence"
|
|
2432
|
+
}
|
|
2433
|
+
},
|
|
2434
|
+
"parameter": {
|
|
2435
|
+
"type": "object",
|
|
2436
|
+
"properties": {
|
|
2437
|
+
"query": {
|
|
2438
|
+
"type": "string",
|
|
2439
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
2440
|
+
"minLength": 1
|
|
2441
|
+
},
|
|
2442
|
+
"case_sensitive": {
|
|
2443
|
+
"type": "boolean",
|
|
2444
|
+
"description": "Select True to perform a case-sensitive search",
|
|
2445
|
+
"default": false
|
|
2446
|
+
},
|
|
2447
|
+
"exact_match": {
|
|
2448
|
+
"type": "boolean",
|
|
2449
|
+
"description": "Select True to require an exact match",
|
|
2450
|
+
"default": false
|
|
2451
|
+
},
|
|
2452
|
+
"limit": {
|
|
2453
|
+
"type": "integer",
|
|
2454
|
+
"description": "Maximum number of results to return",
|
|
2455
|
+
"default": 10,
|
|
2456
|
+
"minimum": 1,
|
|
2457
|
+
"maximum": 100
|
|
2458
|
+
}
|
|
2459
|
+
},
|
|
2460
|
+
"required": ["query"]
|
|
2461
|
+
},
|
|
2462
|
+
"return_schema": {
|
|
2463
|
+
"type": "object",
|
|
2464
|
+
"properties": {
|
|
2465
|
+
"error": {
|
|
2466
|
+
"type": "string",
|
|
2467
|
+
"description": "Error message (if any)"
|
|
2468
|
+
},
|
|
2469
|
+
"query": {
|
|
2470
|
+
"type": "string",
|
|
2471
|
+
"description": "The original search query"
|
|
2472
|
+
},
|
|
2473
|
+
"total_matches": {
|
|
2474
|
+
"type": "integer",
|
|
2475
|
+
"description": "Total number of matching records found"
|
|
2476
|
+
},
|
|
2477
|
+
"total_returned_results": {
|
|
2478
|
+
"type": "integer",
|
|
2479
|
+
"description": "Number of results returned in this response"
|
|
2480
|
+
},
|
|
2481
|
+
"results": {
|
|
2482
|
+
"type": "array",
|
|
2483
|
+
"items": {
|
|
2484
|
+
"type": "object",
|
|
2485
|
+
"properties": {
|
|
2486
|
+
"_tag": {
|
|
2487
|
+
"type": "string",
|
|
2488
|
+
"description": "XML tag name of the record element"
|
|
2489
|
+
},
|
|
2490
|
+
"_text": {
|
|
2491
|
+
"type": "string",
|
|
2492
|
+
"description": "Text content of the record element"
|
|
2493
|
+
},
|
|
2494
|
+
"_attributes": {
|
|
2495
|
+
"type": "object",
|
|
2496
|
+
"description": "Attributes of the record element"
|
|
2497
|
+
},
|
|
2498
|
+
"drug_name": {
|
|
2499
|
+
"type": "string",
|
|
2500
|
+
"description": "Name of the drug"
|
|
2501
|
+
},
|
|
2502
|
+
"drugbank_id": {
|
|
2503
|
+
"type": "string",
|
|
2504
|
+
"description": "Primary DrugBank ID"
|
|
2505
|
+
},
|
|
2506
|
+
"synonyms": {
|
|
2507
|
+
"type": "string",
|
|
2508
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
2509
|
+
},
|
|
2510
|
+
"cas_number": {
|
|
2511
|
+
"type": "string",
|
|
2512
|
+
"description": "Chemical Abstracts Service registry number"
|
|
2513
|
+
},
|
|
2514
|
+
"unii": {
|
|
2515
|
+
"type": "string",
|
|
2516
|
+
"description": "Unique Ingredient Identifier"
|
|
2517
|
+
},
|
|
2518
|
+
"molecular_formula": {
|
|
2519
|
+
"type": "string",
|
|
2520
|
+
"description": "Molecular formula of the drug"
|
|
2521
|
+
},
|
|
2522
|
+
"molecular_weight": {
|
|
2523
|
+
"type": "string",
|
|
2524
|
+
"description": "Molecular weight of the drug"
|
|
2525
|
+
},
|
|
2526
|
+
"melting_point": {
|
|
2527
|
+
"type": "string",
|
|
2528
|
+
"description": "Melting point of the drug"
|
|
2529
|
+
},
|
|
2530
|
+
"water_solubility": {
|
|
2531
|
+
"type": "string",
|
|
2532
|
+
"description": "Water solubility properties of the drug"
|
|
2533
|
+
},
|
|
2534
|
+
"isoelectric_point": {
|
|
2535
|
+
"type": "string",
|
|
2536
|
+
"description": "Isoelectric point of the drug"
|
|
2537
|
+
},
|
|
2538
|
+
"classification": {
|
|
2539
|
+
"type": "string",
|
|
2540
|
+
"description": "Chemical classification information"
|
|
2541
|
+
},
|
|
2542
|
+
"kingdom": {
|
|
2543
|
+
"type": "string",
|
|
2544
|
+
"description": "Chemical classification kingdom"
|
|
2545
|
+
},
|
|
2546
|
+
"superclass": {
|
|
2547
|
+
"type": "string",
|
|
2548
|
+
"description": "Chemical classification superclass"
|
|
2549
|
+
},
|
|
2550
|
+
"class": {
|
|
2551
|
+
"type": "string",
|
|
2552
|
+
"description": "Chemical classification class"
|
|
2553
|
+
},
|
|
2554
|
+
"subclass": {
|
|
2555
|
+
"type": "string",
|
|
2556
|
+
"description": "Chemical classification subclass"
|
|
2557
|
+
},
|
|
2558
|
+
"sequences": {
|
|
2559
|
+
"type": "string",
|
|
2560
|
+
"description": "Sequence information for the drug, separated by ' | '"
|
|
2561
|
+
},
|
|
2562
|
+
"matched_fields": {
|
|
2563
|
+
"type": "array",
|
|
2564
|
+
"items": {
|
|
2565
|
+
"type": "string"
|
|
2566
|
+
},
|
|
2567
|
+
"description": "List of fields that matched the search query"
|
|
2568
|
+
}
|
|
2569
|
+
}
|
|
2570
|
+
}
|
|
2571
|
+
},
|
|
2572
|
+
"search_parameters": {
|
|
2573
|
+
"type": "object",
|
|
2574
|
+
"properties": {
|
|
2575
|
+
"case_sensitive": {
|
|
2576
|
+
"type": "boolean",
|
|
2577
|
+
"description": "Whether the search was case-sensitive"
|
|
2578
|
+
},
|
|
2579
|
+
"exact_match": {
|
|
2580
|
+
"type": "boolean",
|
|
2581
|
+
"description": "Whether exact matching was used"
|
|
2582
|
+
},
|
|
2583
|
+
"limit": {
|
|
2584
|
+
"type": "integer",
|
|
2585
|
+
"description": "Maximum number of results requested"
|
|
2586
|
+
}
|
|
2587
|
+
}
|
|
2588
|
+
}
|
|
2589
|
+
}
|
|
2590
|
+
}
|
|
2591
|
+
},
|
|
2592
|
+
{
|
|
2593
|
+
"type": "XMLTool",
|
|
2594
|
+
"name": "drugbank_get_drug_references_by_drug_name_or_drugbank_id",
|
|
2595
|
+
"description": "Get drug literature references, patents, and external links by drug name or DrugBank ID.",
|
|
2596
|
+
"settings": {
|
|
2597
|
+
"hf_dataset_path": {
|
|
2598
|
+
"repo_id": "agenticx/DrugBank",
|
|
2599
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2600
|
+
"token": null,
|
|
2601
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2602
|
+
},
|
|
2603
|
+
"namespaces": {
|
|
2604
|
+
"db": "http://www.drugbank.ca"
|
|
2605
|
+
},
|
|
2606
|
+
"record_xpath": "db:drug",
|
|
2607
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
2608
|
+
"field_mappings": {
|
|
2609
|
+
"drug_name": "db:name",
|
|
2610
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2611
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
2612
|
+
"articles": {
|
|
2613
|
+
"parent_path": "db:general-references/db:articles/db:article",
|
|
2614
|
+
"subfields": {
|
|
2615
|
+
"pubmed_id": "db:pubmed-id",
|
|
2616
|
+
"citations": "db:citation"
|
|
2617
|
+
}
|
|
2618
|
+
},
|
|
2619
|
+
"patents": {
|
|
2620
|
+
"parent_path": "db:general-references/db:patents/db:patent",
|
|
2621
|
+
"subfields": {
|
|
2622
|
+
"number": "db:number",
|
|
2623
|
+
"country": "db:country",
|
|
2624
|
+
"approved": "db:approved",
|
|
2625
|
+
"expires": "db:expires"
|
|
2626
|
+
}
|
|
2627
|
+
},
|
|
2628
|
+
"external_identifiers": "db:external-identifiers/db:external-identifier",
|
|
2629
|
+
"external_links": "db:external-links/db:external-link"
|
|
2630
|
+
}
|
|
2631
|
+
},
|
|
2632
|
+
"parameter": {
|
|
2633
|
+
"type": "object",
|
|
2634
|
+
"properties": {
|
|
2635
|
+
"query": {
|
|
2636
|
+
"type": "string",
|
|
2637
|
+
"description": "Drug name or Drugbank ID to search for references",
|
|
2638
|
+
"minLength": 1
|
|
2639
|
+
},
|
|
2640
|
+
"case_sensitive": {
|
|
2641
|
+
"type": "boolean",
|
|
2642
|
+
"description": "Select True to perform a case-sensitive search",
|
|
2643
|
+
"default": false
|
|
2644
|
+
},
|
|
2645
|
+
"exact_match": {
|
|
2646
|
+
"type": "boolean",
|
|
2647
|
+
"description": "Select True to require an exact match",
|
|
2648
|
+
"default": false
|
|
2649
|
+
},
|
|
2650
|
+
"limit": {
|
|
2651
|
+
"type": "integer",
|
|
2652
|
+
"description": "Maximum number of results to return",
|
|
2653
|
+
"default": 10,
|
|
2654
|
+
"minimum": 1,
|
|
2655
|
+
"maximum": 100
|
|
2656
|
+
}
|
|
2657
|
+
},
|
|
2658
|
+
"required": ["query"]
|
|
2659
|
+
},
|
|
2660
|
+
"return_schema": {
|
|
2661
|
+
"type": "object",
|
|
2662
|
+
"properties": {
|
|
2663
|
+
"error": {
|
|
2664
|
+
"type": "string",
|
|
2665
|
+
"description": "Error message (if any)"
|
|
2666
|
+
},
|
|
2667
|
+
"query": {
|
|
2668
|
+
"type": "string",
|
|
2669
|
+
"description": "The original search query"
|
|
2670
|
+
},
|
|
2671
|
+
"total_matches": {
|
|
2672
|
+
"type": "integer",
|
|
2673
|
+
"description": "Total number of matching records found"
|
|
2674
|
+
},
|
|
2675
|
+
"total_returned_results": {
|
|
2676
|
+
"type": "integer",
|
|
2677
|
+
"description": "Number of results returned in this response"
|
|
2678
|
+
},
|
|
2679
|
+
"results": {
|
|
2680
|
+
"type": "array",
|
|
2681
|
+
"items": {
|
|
2682
|
+
"type": "object",
|
|
2683
|
+
"properties": {
|
|
2684
|
+
"_tag": {
|
|
2685
|
+
"type": "string",
|
|
2686
|
+
"description": "XML tag name of the record element"
|
|
2687
|
+
},
|
|
2688
|
+
"_text": {
|
|
2689
|
+
"type": "string",
|
|
2690
|
+
"description": "Text content of the record element"
|
|
2691
|
+
},
|
|
2692
|
+
"_attributes": {
|
|
2693
|
+
"type": "object",
|
|
2694
|
+
"description": "Attributes of the record element"
|
|
2695
|
+
},
|
|
2696
|
+
"drug_name": {
|
|
2697
|
+
"type": "string",
|
|
2698
|
+
"description": "Name of the drug"
|
|
2699
|
+
},
|
|
2700
|
+
"drugbank_id": {
|
|
2701
|
+
"type": "string",
|
|
2702
|
+
"description": "Primary DrugBank ID"
|
|
2703
|
+
},
|
|
2704
|
+
"synonyms": {
|
|
2705
|
+
"type": "string",
|
|
2706
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
2707
|
+
},
|
|
2708
|
+
"articles": {
|
|
2709
|
+
"type": "array",
|
|
2710
|
+
"items": {
|
|
2711
|
+
"type": "object",
|
|
2712
|
+
"properties": {
|
|
2713
|
+
"pubmed_id": {
|
|
2714
|
+
"type": "string",
|
|
2715
|
+
"description": "PubMed ID of the article"
|
|
2716
|
+
},
|
|
2717
|
+
"citations": {
|
|
2718
|
+
"type": "string",
|
|
2719
|
+
"description": "Article citation information"
|
|
2720
|
+
}
|
|
2721
|
+
}
|
|
2722
|
+
},
|
|
2723
|
+
"description": "Literature references and articles related to the drug"
|
|
2724
|
+
},
|
|
2725
|
+
"patents": {
|
|
2726
|
+
"type": "array",
|
|
2727
|
+
"items": {
|
|
2728
|
+
"type": "object",
|
|
2729
|
+
"properties": {
|
|
2730
|
+
"number": {
|
|
2731
|
+
"type": "string",
|
|
2732
|
+
"description": "Patent number"
|
|
2733
|
+
},
|
|
2734
|
+
"country": {
|
|
2735
|
+
"type": "string",
|
|
2736
|
+
"description": "Country where patent is filed"
|
|
2737
|
+
},
|
|
2738
|
+
"approved": {
|
|
2739
|
+
"type": "string",
|
|
2740
|
+
"description": "Patent approval date"
|
|
2741
|
+
},
|
|
2742
|
+
"expires": {
|
|
2743
|
+
"type": "string",
|
|
2744
|
+
"description": "Patent expiration date"
|
|
2745
|
+
}
|
|
2746
|
+
}
|
|
2747
|
+
},
|
|
2748
|
+
"description": "Patents associated with the drug"
|
|
2749
|
+
},
|
|
2750
|
+
"external_identifiers": {
|
|
2751
|
+
"type": "string",
|
|
2752
|
+
"description": "External database identifiers, separated by ' | '"
|
|
2753
|
+
},
|
|
2754
|
+
"external_links": {
|
|
2755
|
+
"type": "string",
|
|
2756
|
+
"description": "External links and resources, separated by ' | '"
|
|
2757
|
+
},
|
|
2758
|
+
"matched_fields": {
|
|
2759
|
+
"type": "array",
|
|
2760
|
+
"items": {
|
|
2761
|
+
"type": "string"
|
|
2762
|
+
},
|
|
2763
|
+
"description": "List of fields that matched the search query"
|
|
2764
|
+
}
|
|
2765
|
+
}
|
|
2766
|
+
}
|
|
2767
|
+
},
|
|
2768
|
+
"search_parameters": {
|
|
2769
|
+
"type": "object",
|
|
2770
|
+
"properties": {
|
|
2771
|
+
"case_sensitive": {
|
|
2772
|
+
"type": "boolean",
|
|
2773
|
+
"description": "Whether the search was case-sensitive"
|
|
2774
|
+
},
|
|
2775
|
+
"exact_match": {
|
|
2776
|
+
"type": "boolean",
|
|
2777
|
+
"description": "Whether exact matching was used"
|
|
2778
|
+
},
|
|
2779
|
+
"limit": {
|
|
2780
|
+
"type": "integer",
|
|
2781
|
+
"description": "Maximum number of results requested"
|
|
2782
|
+
}
|
|
2783
|
+
}
|
|
2784
|
+
}
|
|
2785
|
+
}
|
|
2786
|
+
}
|
|
2787
|
+
},
|
|
2788
|
+
{
|
|
2789
|
+
"type": "XMLTool",
|
|
2790
|
+
"name": "drugbank_get_drug_pathways_and_reactions_by_drug_name_or_drugbank_id",
|
|
2791
|
+
"description": "Get drug pathways and metabolic reactions by drug name or DrugBank ID.",
|
|
2792
|
+
"settings": {
|
|
2793
|
+
"hf_dataset_path": {
|
|
2794
|
+
"repo_id": "agenticx/DrugBank",
|
|
2795
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2796
|
+
"token": null,
|
|
2797
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2798
|
+
},
|
|
2799
|
+
"namespaces": {
|
|
2800
|
+
"db": "http://www.drugbank.ca"
|
|
2801
|
+
},
|
|
2802
|
+
"record_xpath": "db:drug",
|
|
2803
|
+
"search_fields": ["drug_name", "drugbank_id", "synonyms"],
|
|
2804
|
+
"field_mappings": {
|
|
2805
|
+
"drug_name": "db:name",
|
|
2806
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2807
|
+
"synonyms": "db:synonyms/db:synonym",
|
|
2808
|
+
"pathways": {
|
|
2809
|
+
"parent_path": "db:pathways/db:pathway",
|
|
2810
|
+
"subfields": {
|
|
2811
|
+
"id": "db:smpdb-id",
|
|
2812
|
+
"name": "db:name",
|
|
2813
|
+
"category": "db:category"
|
|
2814
|
+
}
|
|
2815
|
+
},
|
|
2816
|
+
"reactions": {
|
|
2817
|
+
"parent_path": "db:reactions/db:reaction",
|
|
2818
|
+
"subfields": {
|
|
2819
|
+
"reaction_sequence": "db:sequence",
|
|
2820
|
+
"reaction_left_element": "db:left-element/db:name",
|
|
2821
|
+
"reaction_right_element": "db:right-element/db:name"
|
|
2822
|
+
}
|
|
2823
|
+
}
|
|
2824
|
+
}
|
|
2825
|
+
},
|
|
2826
|
+
"parameter": {
|
|
2827
|
+
"type": "object",
|
|
2828
|
+
"properties": {
|
|
2829
|
+
"query": {
|
|
2830
|
+
"type": "string",
|
|
2831
|
+
"description": "Drug name or Drugbank ID to search for",
|
|
2832
|
+
"minLength": 1
|
|
2833
|
+
},
|
|
2834
|
+
"case_sensitive": {
|
|
2835
|
+
"type": "boolean",
|
|
2836
|
+
"description": "Select True to perform a case-sensitive search",
|
|
2837
|
+
"default": false
|
|
2838
|
+
},
|
|
2839
|
+
"exact_match": {
|
|
2840
|
+
"type": "boolean",
|
|
2841
|
+
"description": "Select True to require an exact match",
|
|
2842
|
+
"default": false
|
|
2843
|
+
},
|
|
2844
|
+
"limit": {
|
|
2845
|
+
"type": "integer",
|
|
2846
|
+
"description": "Maximum number of results to return",
|
|
2847
|
+
"default": 10,
|
|
2848
|
+
"minimum": 1,
|
|
2849
|
+
"maximum": 100
|
|
2850
|
+
}
|
|
2851
|
+
},
|
|
2852
|
+
"required": ["query"]
|
|
2853
|
+
},
|
|
2854
|
+
"return_schema": {
|
|
2855
|
+
"type": "object",
|
|
2856
|
+
"properties": {
|
|
2857
|
+
"error": {
|
|
2858
|
+
"type": "string",
|
|
2859
|
+
"description": "Error message (if any)"
|
|
2860
|
+
},
|
|
2861
|
+
"query": {
|
|
2862
|
+
"type": "string",
|
|
2863
|
+
"description": "The original search query"
|
|
2864
|
+
},
|
|
2865
|
+
"total_matches": {
|
|
2866
|
+
"type": "integer",
|
|
2867
|
+
"description": "Total number of matching records found"
|
|
2868
|
+
},
|
|
2869
|
+
"total_returned_results": {
|
|
2870
|
+
"type": "integer",
|
|
2871
|
+
"description": "Number of results returned in this response"
|
|
2872
|
+
},
|
|
2873
|
+
"results": {
|
|
2874
|
+
"type": "array",
|
|
2875
|
+
"items": {
|
|
2876
|
+
"type": "object",
|
|
2877
|
+
"properties": {
|
|
2878
|
+
"_tag": {
|
|
2879
|
+
"type": "string",
|
|
2880
|
+
"description": "XML tag name of the record element"
|
|
2881
|
+
},
|
|
2882
|
+
"_text": {
|
|
2883
|
+
"type": "string",
|
|
2884
|
+
"description": "Text content of the record element"
|
|
2885
|
+
},
|
|
2886
|
+
"_attributes": {
|
|
2887
|
+
"type": "object",
|
|
2888
|
+
"description": "Attributes of the record element"
|
|
2889
|
+
},
|
|
2890
|
+
"drug_name": {
|
|
2891
|
+
"type": "string",
|
|
2892
|
+
"description": "Name of the drug"
|
|
2893
|
+
},
|
|
2894
|
+
"drugbank_id": {
|
|
2895
|
+
"type": "string",
|
|
2896
|
+
"description": "Primary DrugBank ID"
|
|
2897
|
+
},
|
|
2898
|
+
"synonyms": {
|
|
2899
|
+
"type": "string",
|
|
2900
|
+
"description": "Drug synonyms, separated by ' | '"
|
|
2901
|
+
},
|
|
2902
|
+
"pathways": {
|
|
2903
|
+
"type": "array",
|
|
2904
|
+
"items": {
|
|
2905
|
+
"type": "object",
|
|
2906
|
+
"properties": {
|
|
2907
|
+
"id": {
|
|
2908
|
+
"type": "string",
|
|
2909
|
+
"description": "SMPDB ID of the pathway"
|
|
2910
|
+
},
|
|
2911
|
+
"name": {
|
|
2912
|
+
"type": "string",
|
|
2913
|
+
"description": "Name of the pathway"
|
|
2914
|
+
},
|
|
2915
|
+
"category": {
|
|
2916
|
+
"type": "string",
|
|
2917
|
+
"description": "Category of the pathway (e.g., metabolic, disease)"
|
|
2918
|
+
}
|
|
2919
|
+
}
|
|
2920
|
+
},
|
|
2921
|
+
"description": "Drug pathways and metabolic pathways"
|
|
2922
|
+
},
|
|
2923
|
+
"reactions": {
|
|
2924
|
+
"type": "array",
|
|
2925
|
+
"items": {
|
|
2926
|
+
"type": "object",
|
|
2927
|
+
"properties": {
|
|
2928
|
+
"reaction_sequence": {
|
|
2929
|
+
"type": "string",
|
|
2930
|
+
"description": "Sequence identifier of the reaction"
|
|
2931
|
+
},
|
|
2932
|
+
"reaction_left_element": {
|
|
2933
|
+
"type": "string",
|
|
2934
|
+
"description": "Left side element(s) of the reaction"
|
|
2935
|
+
},
|
|
2936
|
+
"reaction_right_element": {
|
|
2937
|
+
"type": "string",
|
|
2938
|
+
"description": "Right side element(s) of the reaction"
|
|
2939
|
+
}
|
|
2940
|
+
}
|
|
2941
|
+
},
|
|
2942
|
+
"description": "Drug metabolic reactions"
|
|
2943
|
+
},
|
|
2944
|
+
"matched_fields": {
|
|
2945
|
+
"type": "array",
|
|
2946
|
+
"items": {
|
|
2947
|
+
"type": "string"
|
|
2948
|
+
},
|
|
2949
|
+
"description": "List of fields that matched the search query"
|
|
2950
|
+
}
|
|
2951
|
+
}
|
|
2952
|
+
}
|
|
2953
|
+
},
|
|
2954
|
+
"search_parameters": {
|
|
2955
|
+
"type": "object",
|
|
2956
|
+
"properties": {
|
|
2957
|
+
"case_sensitive": {
|
|
2958
|
+
"type": "boolean",
|
|
2959
|
+
"description": "Whether the search was case-sensitive"
|
|
2960
|
+
},
|
|
2961
|
+
"exact_match": {
|
|
2962
|
+
"type": "boolean",
|
|
2963
|
+
"description": "Whether exact matching was used"
|
|
2964
|
+
},
|
|
2965
|
+
"limit": {
|
|
2966
|
+
"type": "integer",
|
|
2967
|
+
"description": "Maximum number of results requested"
|
|
2968
|
+
}
|
|
2969
|
+
}
|
|
2970
|
+
}
|
|
2971
|
+
}
|
|
2972
|
+
}
|
|
2973
|
+
},
|
|
2974
|
+
{
|
|
2975
|
+
"type": "XMLTool",
|
|
2976
|
+
"name": "drugbank_get_drug_name_and_description_by_pathway_name",
|
|
2977
|
+
"description": "Get drug names and descriptions by pathway name.",
|
|
2978
|
+
"settings": {
|
|
2979
|
+
"hf_dataset_path": {
|
|
2980
|
+
"repo_id": "agenticx/DrugBank",
|
|
2981
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
2982
|
+
"token": null,
|
|
2983
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
2984
|
+
},
|
|
2985
|
+
"namespaces": {
|
|
2986
|
+
"db": "http://www.drugbank.ca"
|
|
2987
|
+
},
|
|
2988
|
+
"record_xpath": "db:drug",
|
|
2989
|
+
"search_fields": ["pathways_name"],
|
|
2990
|
+
"field_mappings": {
|
|
2991
|
+
"drug_name": "db:name",
|
|
2992
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
2993
|
+
"pathways": {
|
|
2994
|
+
"parent_path": "db:pathways/db:pathway",
|
|
2995
|
+
"subfields": {
|
|
2996
|
+
"id": "db:smpdb-id",
|
|
2997
|
+
"name": "db:name",
|
|
2998
|
+
"category": "db:category"
|
|
2999
|
+
}
|
|
3000
|
+
},
|
|
3001
|
+
"reactions": {
|
|
3002
|
+
"parent_path": "db:reactions/db:reaction",
|
|
3003
|
+
"subfields": {
|
|
3004
|
+
"reaction_sequence": "db:sequence",
|
|
3005
|
+
"reaction_left_element": "db:left-element/db:name",
|
|
3006
|
+
"reaction_right_element": "db:right-element/db:name"
|
|
3007
|
+
}
|
|
3008
|
+
}
|
|
3009
|
+
}
|
|
3010
|
+
},
|
|
3011
|
+
"parameter": {
|
|
3012
|
+
"type": "object",
|
|
3013
|
+
"properties": {
|
|
3014
|
+
"query": {
|
|
3015
|
+
"type": "string",
|
|
3016
|
+
"description": "Pathway name to search for",
|
|
3017
|
+
"minLength": 1
|
|
3018
|
+
},
|
|
3019
|
+
"case_sensitive": {
|
|
3020
|
+
"type": "boolean",
|
|
3021
|
+
"description": "Select True to perform a case-sensitive search",
|
|
3022
|
+
"default": false
|
|
3023
|
+
},
|
|
3024
|
+
"exact_match": {
|
|
3025
|
+
"type": "boolean",
|
|
3026
|
+
"description": "Select True to require an exact match",
|
|
3027
|
+
"default": false
|
|
3028
|
+
},
|
|
3029
|
+
"limit": {
|
|
3030
|
+
"type": "integer",
|
|
3031
|
+
"description": "Maximum number of results to return",
|
|
3032
|
+
"default": 10,
|
|
3033
|
+
"minimum": 1,
|
|
3034
|
+
"maximum": 100
|
|
3035
|
+
}
|
|
3036
|
+
},
|
|
3037
|
+
"required": ["query"]
|
|
3038
|
+
},
|
|
3039
|
+
"return_schema": {
|
|
3040
|
+
"type": "object",
|
|
3041
|
+
"properties": {
|
|
3042
|
+
"error": {
|
|
3043
|
+
"type": "string",
|
|
3044
|
+
"description": "Error message (if any)"
|
|
3045
|
+
},
|
|
3046
|
+
"query": {
|
|
3047
|
+
"type": "string",
|
|
3048
|
+
"description": "The original search query"
|
|
3049
|
+
},
|
|
3050
|
+
"total_matches": {
|
|
3051
|
+
"type": "integer",
|
|
3052
|
+
"description": "Total number of matching records found"
|
|
3053
|
+
},
|
|
3054
|
+
"total_returned_results": {
|
|
3055
|
+
"type": "integer",
|
|
3056
|
+
"description": "Number of results returned in this response"
|
|
3057
|
+
},
|
|
3058
|
+
"results": {
|
|
3059
|
+
"type": "array",
|
|
3060
|
+
"items": {
|
|
3061
|
+
"type": "object",
|
|
3062
|
+
"properties": {
|
|
3063
|
+
"_tag": {
|
|
3064
|
+
"type": "string",
|
|
3065
|
+
"description": "XML tag name of the record element"
|
|
3066
|
+
},
|
|
3067
|
+
"_text": {
|
|
3068
|
+
"type": "string",
|
|
3069
|
+
"description": "Text content of the record element"
|
|
3070
|
+
},
|
|
3071
|
+
"_attributes": {
|
|
3072
|
+
"type": "object",
|
|
3073
|
+
"description": "Attributes of the record element"
|
|
3074
|
+
},
|
|
3075
|
+
"drug_name": {
|
|
3076
|
+
"type": "string",
|
|
3077
|
+
"description": "Name of the drug"
|
|
3078
|
+
},
|
|
3079
|
+
"drugbank_id": {
|
|
3080
|
+
"type": "string",
|
|
3081
|
+
"description": "Primary DrugBank ID"
|
|
3082
|
+
},
|
|
3083
|
+
"pathways": {
|
|
3084
|
+
"type": "array",
|
|
3085
|
+
"items": {
|
|
3086
|
+
"type": "object",
|
|
3087
|
+
"properties": {
|
|
3088
|
+
"id": {
|
|
3089
|
+
"type": "string",
|
|
3090
|
+
"description": "SMPDB ID of the pathway"
|
|
3091
|
+
},
|
|
3092
|
+
"name": {
|
|
3093
|
+
"type": "string",
|
|
3094
|
+
"description": "Name of the pathway"
|
|
3095
|
+
},
|
|
3096
|
+
"category": {
|
|
3097
|
+
"type": "string",
|
|
3098
|
+
"description": "Category of the pathway (e.g., metabolic, disease)"
|
|
3099
|
+
}
|
|
3100
|
+
}
|
|
3101
|
+
},
|
|
3102
|
+
"description": "Drug pathways and metabolic pathways"
|
|
3103
|
+
},
|
|
3104
|
+
"reactions": {
|
|
3105
|
+
"type": "array",
|
|
3106
|
+
"items": {
|
|
3107
|
+
"type": "object",
|
|
3108
|
+
"properties": {
|
|
3109
|
+
"reaction_sequence": {
|
|
3110
|
+
"type": "string",
|
|
3111
|
+
"description": "Sequence identifier of the reaction"
|
|
3112
|
+
},
|
|
3113
|
+
"reaction_left_element": {
|
|
3114
|
+
"type": "string",
|
|
3115
|
+
"description": "Left side element(s) of the reaction"
|
|
3116
|
+
},
|
|
3117
|
+
"reaction_right_element": {
|
|
3118
|
+
"type": "string",
|
|
3119
|
+
"description": "Right side element(s) of the reaction"
|
|
3120
|
+
}
|
|
3121
|
+
}
|
|
3122
|
+
},
|
|
3123
|
+
"description": "Drug metabolic reactions"
|
|
3124
|
+
},
|
|
3125
|
+
"matched_fields": {
|
|
3126
|
+
"type": "array",
|
|
3127
|
+
"items": {
|
|
3128
|
+
"type": "string"
|
|
3129
|
+
},
|
|
3130
|
+
"description": "List of fields that matched the search query"
|
|
3131
|
+
}
|
|
3132
|
+
}
|
|
3133
|
+
}
|
|
3134
|
+
},
|
|
3135
|
+
"search_parameters": {
|
|
3136
|
+
"type": "object",
|
|
3137
|
+
"properties": {
|
|
3138
|
+
"case_sensitive": {
|
|
3139
|
+
"type": "boolean",
|
|
3140
|
+
"description": "Whether the search was case-sensitive"
|
|
3141
|
+
},
|
|
3142
|
+
"exact_match": {
|
|
3143
|
+
"type": "boolean",
|
|
3144
|
+
"description": "Whether exact matching was used"
|
|
3145
|
+
},
|
|
3146
|
+
"limit": {
|
|
3147
|
+
"type": "integer",
|
|
3148
|
+
"description": "Maximum number of results requested"
|
|
3149
|
+
}
|
|
3150
|
+
}
|
|
3151
|
+
}
|
|
3152
|
+
}
|
|
3153
|
+
}
|
|
3154
|
+
},
|
|
3155
|
+
{
|
|
3156
|
+
"type": "XMLTool",
|
|
3157
|
+
"name": "drugbank_filter_drugs_by_name",
|
|
3158
|
+
"description": "Filter DrugBank records based on conditions applied to drug names. For example, find drugs whose names end with 'cillin' (penicillin antibiotics), contain 'mab', or are exactly 'Insulin'.",
|
|
3159
|
+
"settings": {
|
|
3160
|
+
"hf_dataset_path": {
|
|
3161
|
+
"repo_id": "agenticx/DrugBank",
|
|
3162
|
+
"path_in_repo": "drugbank_full_database.xml",
|
|
3163
|
+
"token": null,
|
|
3164
|
+
"save_to_local_dir": "src/tooluniverse/test"
|
|
3165
|
+
},
|
|
3166
|
+
"namespaces": {
|
|
3167
|
+
"db": "http://www.drugbank.ca"
|
|
3168
|
+
},
|
|
3169
|
+
"record_xpath": "db:drug",
|
|
3170
|
+
"filter_field": "drug_name",
|
|
3171
|
+
"field_mappings": {
|
|
3172
|
+
"drug_name": "db:name",
|
|
3173
|
+
"drugbank_id": "db:drugbank-id[@primary='true']",
|
|
3174
|
+
"description": "db:description"
|
|
3175
|
+
}
|
|
3176
|
+
},
|
|
3177
|
+
"parameter": {
|
|
3178
|
+
"type": "object",
|
|
3179
|
+
"properties": {
|
|
3180
|
+
"condition": {
|
|
3181
|
+
"type": "string",
|
|
3182
|
+
"description": "The condition to apply for filtering.",
|
|
3183
|
+
"enum": ["contains", "starts_with", "ends_with", "exact", "not_empty", "has_attribute"]
|
|
3184
|
+
},
|
|
3185
|
+
"value": {
|
|
3186
|
+
"type": "string",
|
|
3187
|
+
"description": "The value to use with the condition (e.g., 'Aspirin' for 'starts_with'). Required for 'contains', 'starts_with', 'ends_with', and 'exact' conditions.",
|
|
3188
|
+
"minLength": 1
|
|
3189
|
+
},
|
|
3190
|
+
"limit": {
|
|
3191
|
+
"type": "integer",
|
|
3192
|
+
"description": "Maximum number of results to return.",
|
|
3193
|
+
"default": 10,
|
|
3194
|
+
"minimum": 1,
|
|
3195
|
+
"maximum": 100
|
|
3196
|
+
}
|
|
3197
|
+
},
|
|
3198
|
+
"required": ["condition"]
|
|
3199
|
+
},
|
|
3200
|
+
"return_schema":{
|
|
3201
|
+
"type": "object",
|
|
3202
|
+
"properties": {
|
|
3203
|
+
"error": {
|
|
3204
|
+
"type": "string",
|
|
3205
|
+
"description": "Error message (if any)"
|
|
3206
|
+
},
|
|
3207
|
+
"total_matches": {
|
|
3208
|
+
"type": "integer",
|
|
3209
|
+
"description": "Total number of matching records found"
|
|
3210
|
+
},
|
|
3211
|
+
"total_returned_results": {
|
|
3212
|
+
"type": "integer",
|
|
3213
|
+
"description": "Number of results returned in this response"
|
|
3214
|
+
},
|
|
3215
|
+
"results": {
|
|
3216
|
+
"type": "array",
|
|
3217
|
+
"items": {
|
|
3218
|
+
"type": "object",
|
|
3219
|
+
"properties": {
|
|
3220
|
+
"_tag": {
|
|
3221
|
+
"type": "string",
|
|
3222
|
+
"description": "XML tag name of the record element"
|
|
3223
|
+
},
|
|
3224
|
+
"_text": {
|
|
3225
|
+
"type": "string",
|
|
3226
|
+
"description": "Text content of the record element"
|
|
3227
|
+
},
|
|
3228
|
+
"_attributes": {
|
|
3229
|
+
"type": "object",
|
|
3230
|
+
"description": "Attributes of the record element"
|
|
3231
|
+
},
|
|
3232
|
+
"drug_name": {
|
|
3233
|
+
"type": "string",
|
|
3234
|
+
"description": "Name of the drug"
|
|
3235
|
+
},
|
|
3236
|
+
"drugbank_id": {
|
|
3237
|
+
"type": "string",
|
|
3238
|
+
"description": "Primary DrugBank ID"
|
|
3239
|
+
},
|
|
3240
|
+
"description": {
|
|
3241
|
+
"type": "string",
|
|
3242
|
+
"description": "Drug description"
|
|
3243
|
+
}
|
|
3244
|
+
}
|
|
3245
|
+
}
|
|
3246
|
+
},
|
|
3247
|
+
"applied_filter": {
|
|
3248
|
+
"type": "string",
|
|
3249
|
+
"description": "Human-readable description of the filter that was applied"
|
|
3250
|
+
},
|
|
3251
|
+
"filter_parameters": {
|
|
3252
|
+
"type": "object",
|
|
3253
|
+
"properties": {
|
|
3254
|
+
"field": {
|
|
3255
|
+
"type": "string",
|
|
3256
|
+
"description": "The field that was filtered on"
|
|
3257
|
+
},
|
|
3258
|
+
"condition": {
|
|
3259
|
+
"type": "string",
|
|
3260
|
+
"description": "The filter condition that was applied"
|
|
3261
|
+
},
|
|
3262
|
+
"value": {
|
|
3263
|
+
"type": "string",
|
|
3264
|
+
"description": "The value used for filtering (null for 'not_empty' and 'has_attribute' conditions)"
|
|
3265
|
+
},
|
|
3266
|
+
"limit": {
|
|
3267
|
+
"type": "integer",
|
|
3268
|
+
"description": "Maximum number of results requested"
|
|
3269
|
+
}
|
|
3270
|
+
}
|
|
3271
|
+
}
|
|
3272
|
+
}
|
|
3273
|
+
}
|
|
3274
|
+
}
|
|
3275
|
+
]
|