TogoMCP

schema_info: title: Gene Ontology (GO) description: | The Gene Ontology provides a controlled vocabulary of terms for describing gene and gene product attributes across all organisms. GO terms are organized into three ontology domains: biological_process (30,804 terms describing biological objectives), molecular_function (12,793 terms describing molecular activities), and cellular_component (4,568 terms describing cellular locations). Each term includes definitions, synonyms, hierarchical relationships, and cross-references to external databases. The ontology enables standardized annotation of gene products and supports computational analysis of biological data. endpoint: https://rdfportal.org/primary/sparql base_uri: http://purl.obolibrary.org/obo/ graphs: - http://rdfportal.org/ontology/go - http://purl.jp/bio/11/goa version: mie_version: '1.0' mie_created: '2025-01-27' data_version: Latest GO Release update_frequency: Monthly license: data_license: Creative Commons Attribution 4.0 International (CC BY 4.0) license_url: https://creativecommons.org/licenses/by/4.0/ access: rate_limiting: 100 queries/min max_query_timeout: 60 seconds shape_expressions: | PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX oboinowl: <http://www.geneontology.org/formats/oboInOwl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> <GOTermShape> { a [ owl:Class ] ; oboinowl:id xsd:string ; rdfs:label xsd:string ; obo:IAO_0000115 xsd:string ; oboinowl:hasOBONamespace [ "biological_process" "molecular_function" "cellular_component" "external" ] ; rdfs:subClassOf IRI * ; oboinowl:hasExactSynonym xsd:string * ; oboinowl:hasRelatedSynonym xsd:string * ; oboinowl:hasNarrowSynonym xsd:string * ; oboinowl:hasBroadSynonym xsd:string * ; oboinowl:hasDbXref xsd:string * ; oboinowl:inSubset IRI * ; owl:deprecated xsd:boolean ? ; oboinowl:hasAlternativeId xsd:string * ; rdfs:comment xsd:string ? } sample_rdf_entries: - title: Biological Process Term - Chromatin Remodeling description: A biological process term describing dynamic chromatin reorganization. Includes hierarchical relationships. rdf: | @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix oboinowl: <http://www.geneontology.org/formats/oboInOwl#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . obo:GO_0006338 a owl:Class ; oboinowl:id "GO:0006338" ; rdfs:label "chromatin remodeling" ; obo:IAO_0000115 "A dynamic process of chromatin reorganization resulting in changes to chromatin structure." ; oboinowl:hasOBONamespace "biological_process" ; rdfs:subClassOf obo:GO_0006325 . - title: Cellular Component Term - Nucleus description: A cellular component term with multiple subsets and cross-references. Shows extensive synonym coverage and integration with GO slim subsets. rdf: | @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix oboinowl: <http://www.geneontology.org/formats/oboInOwl#> . obo:GO_0005634 a owl:Class ; oboinowl:id "GO:0005634" ; rdfs:label "nucleus" ; obo:IAO_0000115 "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated." ; oboinowl:hasOBONamespace "cellular_component" ; rdfs:subClassOf obo:GO_0043231 ; oboinowl:hasExactSynonym "cell nucleus" ; oboinowl:hasNarrowSynonym "horsetail nucleus" ; oboinowl:hasDbXref "NIF_Subcellular:sao1702920020" ; oboinowl:hasDbXref "Wikipedia:Cell_nucleus" ; oboinowl:inSubset obo:go#goslim_generic . - title: Molecular Function Term - Protein Kinase Activity description: A molecular function term describing catalytic activity with reaction details in the definition. rdf: | @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix oboinowl: <http://www.geneontology.org/formats/oboInOwl#> . obo:GO_0004672 a owl:Class ; oboinowl:id "GO:0004672" ; rdfs:label "protein kinase activity" ; obo:IAO_0000115 "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." ; oboinowl:hasOBONamespace "molecular_function" . - title: Term with External Cross-References description: GO term linked to external databases including Wikipedia for integrated knowledge access. rdf: | @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix oboinowl: <http://www.geneontology.org/formats/oboInOwl#> . obo:GO_0006935 a owl:Class ; oboinowl:id "GO:0006935" ; rdfs:label "chemotaxis" ; oboinowl:hasDbXref "Wikipedia:Chemotaxis" . - title: Obsolete Term with Deprecation Flag description: Example of deprecated GO term showing how obsolete terms are marked in the ontology. rdf: | @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . obo:GO_0005623 a owl:Class ; rdfs:label "obsolete cell" ; owl:deprecated true ; obo:IAO_0000115 "OBSOLETE. The basic structural and functional unit of all organisms." . sparql_query_examples: - title: Search GO terms by keyword description: Find GO terms matching specific keywords using full-text search question: Find all GO terms related to "apoptosis" complexity: basic sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT DISTINCT ?go ?label FROM <http://rdfportal.org/ontology/go> WHERE { ?go rdfs:label ?label . ?label bif:contains "'apoptosis'" . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 20 - title: Filter GO terms by namespace description: Retrieve terms from a specific GO domain question: What are some molecular function terms? complexity: basic sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX oboinowl: <http://www.geneontology.org/formats/oboInOwl#> SELECT DISTINCT ?go ?label ?namespace FROM <http://rdfportal.org/ontology/go> WHERE { ?go rdfs:label ?label . ?go oboinowl:hasOBONamespace ?namespace . FILTER(STR(?namespace) = "molecular_function") FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 10 - title: Search with keyword filtering and namespace description: Combine keyword search with namespace filtering for targeted results question: Find kinase-related molecular functions complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX oboinowl: <http://www.geneontology.org/formats/oboInOwl#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT DISTINCT ?go ?label ?definition ?namespace FROM <http://rdfportal.org/ontology/go> WHERE { ?go rdfs:label ?label . ?go obo:IAO_0000115 ?definition . ?go oboinowl:hasOBONamespace ?namespace . ?label bif:contains "'kinase'" . FILTER(STR(?namespace) = "molecular_function") FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 10 - title: Search definitions with complex keywords description: Use boolean operators in full-text search across definitions question: Find terms related to both mitochondria and transport complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT DISTINCT ?go ?label ?definition FROM <http://rdfportal.org/ontology/go> WHERE { ?go rdfs:label ?label . ?go obo:IAO_0000115 ?definition . ?definition bif:contains "('mitochondri*' AND 'transport')" . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 10 - title: Retrieve GO term with all properties description: Get complete information about a specific GO term including all annotations question: What are all the properties of GO:0005634 (nucleus)? complexity: intermediate sparql: | PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT ?property ?value FROM <http://rdfportal.org/ontology/go> WHERE { obo:GO_0005634 ?property ?value . } LIMIT 50 - title: Find hierarchical relationships description: Query parent-child relationships between GO terms question: What are the parent terms of chromatin remodeling? complexity: advanced sparql: | PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?child ?childLabel ?parent ?parentLabel FROM <http://rdfportal.org/ontology/go> WHERE { ?child rdfs:subClassOf ?parent . ?child rdfs:label ?childLabel . ?parent rdfs:label ?parentLabel . FILTER(?child = obo:GO_0006338) FILTER(STRSTARTS(STR(?parent), "http://purl.obolibrary.org/obo/GO_")) } - title: Count terms by namespace description: Aggregate statistics showing distribution of GO terms across namespaces question: How many terms are in each namespace? complexity: advanced sparql: | PREFIX oboinowl: <http://www.geneontology.org/formats/oboInOwl#> SELECT ?namespace (COUNT(DISTINCT ?go) as ?count) FROM <http://rdfportal.org/ontology/go> WHERE { ?go oboinowl:hasOBONamespace ?namespace . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } GROUP BY ?namespace ORDER BY DESC(?count) cross_references: - pattern: oboinowl:hasDbXref description: | GO terms include cross-references to external databases via hasDbXref property. These links connect GO terms to complementary resources including Wikipedia for general knowledge, pathway databases (Reactome, KEGG), disease/phenotype ontologies (MESH, SNOMEDCT, NCIt), and structural databases (NIF_Subcellular). Cross-references enable integrated analysis across biological knowledge bases. databases: general_knowledge: - Wikipedia: extensive coverage pathway_databases: - Reactome: biochemical pathways - KEGG_REACTION: metabolic reactions - RHEA: enzyme reactions - EC: enzyme classification disease_phenotype: - MESH: medical subject headings - SNOMEDCT: clinical terminology - NCIt: cancer terminology structural: - NIF_Subcellular: subcellular structures sparql: | PREFIX oboinowl: <http://www.geneontology.org/formats/oboInOwl#> SELECT DISTINCT ?go ?xref FROM <http://rdfportal.org/ontology/go> WHERE { ?go oboinowl:hasDbXref ?xref . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) FILTER(REGEX(?xref, "^Wikipedia:")) } LIMIT 20 architectural_notes: schema_design: - GO terms organized into three independent namespaces (biological_process, molecular_function, cellular_component) plus external - Hierarchical structure using rdfs:subClassOf for parent-child relationships forming directed acyclic graphs (DAGs) - Each term has unique GO ID (oboinowl:id) in format "GO:NNNNNNN" - Extensive synonym system with four types (exact, related, narrow, broad) for comprehensive term matching - Subset system (inSubset) provides organism-specific and application-specific GO slim views performance: - CRITICAL - Always use FROM clause to specify graph - Use bif:contains for keyword filtering instead of REGEX for better performance on Virtuoso backend - Use STR() for namespace comparisons to avoid datatype mismatch issues - Filter by namespace early in queries to reduce result set size - Limit STRSTARTS filters to GO_ prefix to avoid processing all ontology terms - Aggregation queries may timeout due to large dataset size; use LIMIT appropriately data_integration: - External database cross-references (hasDbXref) connect to 20+ resources - Many GO terms return duplicate rows in results; use DISTINCT to deduplicate data_quality: - Obsolete terms marked with owl:deprecated true flag - Alternative IDs (hasAlternativeId) track merged term history - Definitions (IAO_0000115) required for all non-obsolete terms - Created_by and creation_date properties track term provenance data_statistics: total_go_terms: 48165 terms_by_namespace: biological_process: 30804 molecular_function: 12793 cellular_component: 4568 external: 11 coverage: terms_with_definitions: ~100% terms_with_synonyms: ~80% terms_with_cross_references: ~52% deprecated_terms: ~25% cardinality: avg_synonyms_per_term: 1.6 avg_xrefs_per_term: 0.5 avg_subsets_per_term: 0.1 performance_characteristics: - Simple label searches: <1 second - Keyword searches with bif:contains: 1-3 seconds - Hierarchical queries: 1-5 seconds - Aggregation queries: may timeout, use LIMIT data_quality_notes: - Duplicate rows common in results due to multiple graph storage - Always use DISTINCT in SELECT queries - FILTER by GO_ prefix to exclude other ontology terms anti_patterns: - title: Missing FROM clause problem: Queries timeout or return no results without FROM clause wrong_sparql: | SELECT ?go ?label WHERE { ?go rdfs:label ?label . } correct_sparql: | SELECT ?go ?label FROM <http://rdfportal.org/ontology/go> WHERE { ?go rdfs:label ?label . } explanation: CRITICAL - FROM clause is required for GO queries at this endpoint. Without it, queries fail or timeout. - title: Namespace filter without STR() problem: Datatype mismatch causes namespace filters to fail wrong_sparql: | SELECT ?go ?label ?namespace WHERE { ?go oboinowl:hasOBONamespace ?namespace . FILTER(?namespace = "molecular_function") } correct_sparql: | SELECT ?go ?label ?namespace WHERE { ?go oboinowl:hasOBONamespace ?namespace . FILTER(STR(?namespace) = "molecular_function") } explanation: Use STR() to convert namespace values to plain strings for comparison to avoid datatype mismatch issues. - title: Using REGEX instead of bif:contains for keyword search problem: REGEX is slow on large text fields and doesn't leverage Virtuoso's full-text indexing wrong_sparql: | SELECT ?go ?label WHERE { ?go rdfs:label ?label . FILTER(REGEX(?label, "kinase", "i")) } correct_sparql: | SELECT ?go ?label WHERE { ?go rdfs:label ?label . ?label bif:contains "'kinase'" . } explanation: bif:contains uses Virtuoso's full-text index and is 10-100x faster than REGEX for keyword matching - title: Forgetting to filter by GO_ prefix problem: Returns terms from other ontologies (PRO, CHEBI, etc.) mixed with GO terms wrong_sparql: | SELECT ?term ?label WHERE { ?term rdfs:label ?label . ?label bif:contains "'apoptosis'" . } correct_sparql: | SELECT ?go ?label WHERE { ?go rdfs:label ?label . ?label bif:contains "'apoptosis'" . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } explanation: The GO graph contains terms from multiple OBO ontologies; always filter by GO_ prefix to get only GO terms - title: Not using DISTINCT with duplicate results problem: GO terms stored in multiple graphs cause duplicate rows in results wrong_sparql: | SELECT ?go ?label ?namespace WHERE { ?go rdfs:label ?label . ?go oboinowl:hasOBONamespace ?namespace . } correct_sparql: | SELECT DISTINCT ?go ?label ?namespace WHERE { ?go rdfs:label ?label . ?go oboinowl:hasOBONamespace ?namespace . } explanation: Always use DISTINCT to remove duplicate rows caused by multiple graph storage common_errors: - error: Query timeout or no results causes: - Missing FROM clause (CRITICAL) - Aggregating over all 48,000+ GO terms without filters - Complex COUNT or GROUP BY without LIMIT solutions: - Always add FROM <http://rdfportal.org/ontology/go> - Add namespace filter to reduce dataset size - Use LIMIT to cap result size - Filter by specific GO term ranges or keywords first example_fix: | # CRITICAL: Always include FROM clause SELECT ?namespace (COUNT(?go) as ?count) FROM <http://rdfportal.org/ontology/go> WHERE { ?go oboinowl:hasOBONamespace ?namespace . FILTER(STRSTARTS(STR(?go), "http://purl.obolibrary.org/obo/GO_")) } GROUP BY ?namespace - error: Empty results with namespace filter causes: - Datatype mismatch in namespace comparison - Querying wrong graph or missing FROM clause - Combining filters that exclude all results solutions: - CRITICAL - Use STR() for namespace comparisons - 'Verify namespace values: ''biological_process'', ''molecular_function'', ''cellular_component'' (not ''BP'', ''MF'', ''CC'')' - Check that GO term has the property being filtered - Test namespace filter separately before combining with other filters example_fix: | # Wrong: FILTER(?namespace = "molecular_function") # Correct: FILTER(STR(?namespace) = "molecular_function") - error: Boolean operators not working in bif:contains causes: - Incorrect syntax for AND/OR/NOT operators - Missing quotes or parentheses solutions: - Use single quotes around entire search expression - Use parentheses for operator precedence - 'Wildcard: use * for suffix matching' example_fix: | # Wrong: ?label bif:contains "kinase AND protein" # Correct: ?label bif:contains "'kinase' AND 'protein'" # With wildcards and NOT: ?label bif:contains "('phosph*' AND NOT 'kinase')"