TogoMCP

schema_info: title: Medical Subject Headings (MeSH) RDF description: | National Library of Medicine's controlled vocabulary thesaurus for biomedical literature indexing. Hierarchical structure with descriptors, qualifiers, supplementary chemical/disease records across 16 main categories. endpoint: https://rdfportal.org/primary/sparql base_uri: http://id.nlm.nih.gov/mesh/ graphs: - http://id.nlm.nih.gov/mesh version: mie_version: '1.0' mie_created: '2025-12-08' data_version: '2024' update_frequency: Annual license: data_license: Public Domain (U.S. Government) license_url: https://www.nlm.nih.gov/databases/download/terms_and_conditions.html access: rate_limiting: No strict limits max_query_timeout: 60 seconds shape_expressions: | PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> <TopicalDescriptorShape> { a [ meshv:TopicalDescriptor ] ; rdfs:label xsd:string ; meshv:identifier xsd:string ; meshv:treeNumber @<TreeNumberShape> * ; meshv:broaderDescriptor @<TopicalDescriptorShape> * ; meshv:annotation xsd:string ? ; meshv:preferredConcept @<ConceptShape> ; meshv:allowableQualifier @<QualifierShape> * } <ConceptShape> { a [ meshv:Concept ] ; rdfs:label xsd:string ; meshv:preferredTerm @<TermShape> } <TermShape> { a [ meshv:Term ] ; rdfs:label xsd:string ; meshv:prefLabel xsd:string } <TreeNumberShape> { a [ meshv:TreeNumber ] ; rdfs:label xsd:string } <QualifierShape> { a [ meshv:Qualifier ] OR [ meshv:TopicalDescriptor ] ; rdfs:label xsd:string } sample_rdf_entries: - title: Topical Descriptor with Tree Numbers description: Main subject heading with hierarchical classification. rdf: | mesh:D003920 a meshv:TopicalDescriptor ; rdfs:label "Diabetes Mellitus" ; meshv:identifier "D003920" ; meshv:treeNumber mesh:C18.452.394.750 ; meshv:annotation "general or unspecified; prefer specifics..." . - title: Descriptor with Broader Relationship description: Subject heading showing parent-child hierarchy. rdf: | mesh:D003924 a meshv:TopicalDescriptor ; rdfs:label "Diabetes Mellitus, Type 2" ; meshv:identifier "D003924" ; meshv:broaderDescriptor mesh:D003920 . - title: Supplementary Chemical Record description: Chemical substance entry in MeSH. rdf: | mesh:C517652 a meshv:SCR_Chemical ; rdfs:label "Insulin Glargine" ; meshv:identifier "C517652" ; meshv:registryNumber "2ZM8CX04RZ" . - title: Descriptor with Concept and Term description: Complete descriptor with preferred concept and term. rdf: | mesh:D002318 a meshv:TopicalDescriptor ; rdfs:label "Cardiovascular Diseases" ; meshv:preferredConcept [ a meshv:Concept ; meshv:preferredTerm [ a meshv:Term ; rdfs:label "Cardiovascular Diseases" ] ] . - title: Descriptor with Allowable Qualifiers description: Subject heading with permitted subheadings. rdf: | mesh:D003920 a meshv:TopicalDescriptor ; rdfs:label "Diabetes Mellitus" ; meshv:allowableQualifier mesh:Q000188 . mesh:Q000188 a meshv:Qualifier ; rdfs:label "drug therapy" . sparql_query_examples: - title: Search Descriptors by Keyword with bif:contains description: Full-text search with relevance scoring question: Which descriptors relate to diabetes? complexity: basic sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> SELECT ?descriptor ?label FROM <http://id.nlm.nih.gov/mesh> WHERE { ?descriptor a meshv:TopicalDescriptor ; rdfs:label ?label . ?label bif:contains "'diabetes'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 20 - title: Get Biological Annotations for Descriptor description: Retrieve annotations, tree numbers, and hierarchy question: What are the annotations for diabetes mellitus descriptor? complexity: basic sparql: | PREFIX mesh: <http://id.nlm.nih.gov/mesh/> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?label ?annotation ?treeNumber ?broaderLabel FROM <http://id.nlm.nih.gov/mesh> WHERE { mesh:D003920 rdfs:label ?label . OPTIONAL { mesh:D003920 meshv:annotation ?annotation } OPTIONAL { mesh:D003920 meshv:treeNumber ?tree . ?tree rdfs:label ?treeNumber } OPTIONAL { mesh:D003920 meshv:broaderDescriptor ?broader . ?broader rdfs:label ?broaderLabel } } - title: Get Hierarchical Classification Path description: Retrieve all parent descriptors in tree structure question: What are all parent categories of a descriptor? complexity: intermediate sparql: | PREFIX mesh: <http://id.nlm.nih.gov/mesh/> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?parent ?parentLabel FROM <http://id.nlm.nih.gov/mesh> WHERE { mesh:D003920 meshv:broaderDescriptor+ ?parent . ?parent rdfs:label ?parentLabel . } - title: Count Descriptors by Tree Category description: Aggregate counts by major MeSH tree categories question: How many descriptors in each major category? complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> SELECT ?category (COUNT(DISTINCT ?descriptor) as ?count) FROM <http://id.nlm.nih.gov/mesh> WHERE { ?descriptor a meshv:TopicalDescriptor ; meshv:treeNumber ?tree . ?tree rdfs:label ?treeLabel . BIND(SUBSTR(?treeLabel, 1, 1) as ?category) } GROUP BY ?category ORDER BY DESC(?count) - title: Find Chemicals by Name description: Search supplementary chemical records question: Which chemical records contain "insulin"? complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> SELECT ?chemical ?label ?registryNumber FROM <http://id.nlm.nih.gov/mesh> WHERE { ?chemical a meshv:SCR_Chemical ; rdfs:label ?label . OPTIONAL { ?chemical meshv:registryNumber ?registryNumber } ?label bif:contains "'insulin'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 20 - title: Get Allowable Qualifiers for Descriptor description: Retrieve permitted subheadings for subject heading question: Which qualifiers can be used with diabetes descriptor? complexity: advanced sparql: | PREFIX mesh: <http://id.nlm.nih.gov/mesh/> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?qualifier ?qualifierLabel FROM <http://id.nlm.nih.gov/mesh> WHERE { mesh:D003920 meshv:allowableQualifier ?qualifier . ?qualifier rdfs:label ?qualifierLabel . } - title: Multi-Faceted Descriptor Analysis description: Comprehensive query with annotations, tree numbers, and hierarchy question: Get complete information for cancer-related descriptors complexity: advanced sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> SELECT DISTINCT ?descriptor ?label ?annotation ?treeNum ?broaderLabel FROM <http://id.nlm.nih.gov/mesh> WHERE { ?descriptor a meshv:TopicalDescriptor ; rdfs:label ?label . OPTIONAL { ?descriptor meshv:annotation ?annotation } OPTIONAL { ?descriptor meshv:treeNumber/rdfs:label ?treeNum } OPTIONAL { ?descriptor meshv:broaderDescriptor/rdfs:label ?broaderLabel } ?label bif:contains "'cancer'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 10 cross_references: - pattern: meshv:thesaurusID description: | Cross-references to external databases via thesaurusID property. Coverage: 916K total references across all entities. databases: pharmaceutical: FDA SRS (22.6K), FDA UNII (22.6K), INN (8.8K) genetic: OMIM (12.5K), GHR (3.8K) specialized: ChEBI (2.5K), FMA (1.1K), SNOMED CT (800+) sparql: | PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#> SELECT ?entity ?xref FROM <http://id.nlm.nih.gov/mesh> WHERE { ?entity meshv:thesaurusID ?xref . FILTER(CONTAINS(STR(?xref), "OMIM")) } LIMIT 50 architectural_notes: schema_design: - CRITICAL - Use meshv:broaderDescriptor (NOT meshv:broader) for hierarchical relationships - CRITICAL - Use meshv:annotation (NOT meshv:scopeNote) for scope notes and indexing guidance - CRITICAL - Terms use meshv:prefLabel (NOT rdfs:label) for their labels - Tree numbers provide alphanumeric hierarchical codes for classification - Descriptor-Concept-Term three-level structure - Allowable qualifiers constrain descriptor-qualifier combinations performance: - Use bif:contains for label searches (full-text index + relevance scoring) - Tree number filtering with STRSTARTS or REGEX is efficient - broaderDescriptor+ transitive queries work well from specific descriptors - Always use LIMIT for exploratory queries (2.5M+ entities) data_integration: - FDA SRS/UNII for pharmaceutical substances - OMIM for genetic disorders - ChEBI for chemical entities - SNOMED CT for clinical terminology data_quality: - Topical descriptors are primary subject headings (30,248) - Annotations available for ~40% of descriptors - Tree numbers available for ~95% of descriptors - broaderDescriptor relationships for ~99.6% of descriptors data_statistics: total_entities: 2456909 topical_descriptors: 30248 terms: 869536 concepts: 466976 chemicals: 250445 coverage: descriptors_with_labels: 100% descriptors_with_annotations: ~40% descriptors_with_tree_numbers: ~95% descriptors_with_broader_relationships: ~99.6% entities_with_thesaurus_ids: ~37% cardinality: avg_tree_numbers_per_descriptor: 2.7 avg_terms_per_concept: 1.9 avg_qualifiers_per_descriptor: 22 performance_characteristics: - bif:contains efficient for label searches with relevance ranking - Tree number filtering fast with STRSTARTS or REGEX patterns - Transitive broaderDescriptor+ queries work from specific starting descriptors - Recommend LIMIT 50 for exploratory queries anti_patterns: - title: Using meshv:broader Instead of meshv:broaderDescriptor problem: Property name is incorrect - meshv:broader does not exist wrong_sparql: | SELECT ?parent WHERE { mesh:D003920 meshv:broader+ ?parent . } correct_sparql: | SELECT ?parent FROM <http://id.nlm.nih.gov/mesh> WHERE { mesh:D003920 meshv:broaderDescriptor+ ?parent . ?parent a meshv:TopicalDescriptor . } explanation: The correct property is meshv:broaderDescriptor, not meshv:broader - title: Using meshv:scopeNote Instead of meshv:annotation problem: Property name is incorrect - meshv:scopeNote does not exist wrong_sparql: | SELECT ?descriptor ?scopeNote WHERE { ?descriptor meshv:scopeNote ?scopeNote . } correct_sparql: | SELECT ?descriptor ?annotation FROM <http://id.nlm.nih.gov/mesh> WHERE { ?descriptor meshv:annotation ?annotation . } explanation: The correct property is meshv:annotation, not meshv:scopeNote or skos:scopeNote - title: Using FILTER Instead of bif:contains problem: No full-text index or relevance ranking wrong_sparql: | SELECT ?label WHERE { ?descriptor rdfs:label ?label . FILTER(CONTAINS(LCASE(?label), "diabetes")) } correct_sparql: | SELECT ?label WHERE { ?descriptor rdfs:label ?label . ?label bif:contains "'diabetes'" option (score ?sc) } ORDER BY DESC(?sc) explanation: bif:contains uses full-text index and provides relevance scoring - title: No LIMIT on Large Datasets problem: 2.5M+ entities can cause timeout without pagination wrong_sparql: | SELECT ?term ?label WHERE { ?term a meshv:Term ; meshv:prefLabel ?label } correct_sparql: | SELECT ?term ?label FROM <http://id.nlm.nih.gov/mesh> WHERE { ?term a meshv:Term ; meshv:prefLabel ?label } LIMIT 100 explanation: Always add LIMIT for exploratory queries on large datasets. Note that Terms use meshv:prefLabel, not rdfs:label. common_errors: - error: Empty results when querying broader relationships causes: - Using wrong property name meshv:broader instead of meshv:broaderDescriptor - Not starting from a specific descriptor for transitive queries solutions: - CRITICAL - Use meshv:broaderDescriptor, not meshv:broader - Start transitive queries (broaderDescriptor+) from specific descriptors - Use tree numbers as an alternative for category-based navigation example_fix: | # Wrong - incorrect property name SELECT ?parent WHERE { mesh:D003920 meshv:broader ?parent . } # Correct - use broaderDescriptor SELECT ?parent ?parentLabel FROM <http://id.nlm.nih.gov/mesh> WHERE { mesh:D003920 meshv:broaderDescriptor+ ?parent . ?parent rdfs:label ?parentLabel . } - error: Empty results when querying scope notes causes: - Using wrong property name meshv:scopeNote instead of meshv:annotation - Using skos:scopeNote which doesn't exist in MeSH RDF solutions: - CRITICAL - Use meshv:annotation, not meshv:scopeNote - Remember only ~40% of descriptors have annotations - Always use OPTIONAL for annotation property example_fix: | # Wrong - incorrect property name SELECT ?descriptor ?scopeNote WHERE { ?descriptor meshv:scopeNote ?scopeNote . } # Correct - use annotation SELECT ?descriptor ?annotation FROM <http://id.nlm.nih.gov/mesh> WHERE { ?descriptor a meshv:TopicalDescriptor . OPTIONAL { ?descriptor meshv:annotation ?annotation } } LIMIT 50 - error: Query timeout on term searches causes: - Searching 869K terms without filters - Missing LIMIT clause solutions: - Filter by descriptor type first - Use bif:contains for keyword searches - Add LIMIT 50-100 for exploratory queries