TogoMCP

schema_info: title: NCBI Taxonomy RDF description: | Comprehensive biological taxonomic classification covering 3M+ organisms from bacteria to mammals with hierarchical relationships, scientific/common names, and genetic code assignments. Essential for biological data integration. endpoint: https://rdfportal.org/primary/sparql base_uri: http://identifiers.org/taxonomy/ graphs: - http://rdfportal.org/ontology/taxonomy version: mie_version: "1.0" mie_created: "2025-12-08" data_version: "2024" update_frequency: Monthly license: data_license: Public Domain (U.S. Government) license_url: https://www.ncbi.nlm.nih.gov/home/about/policies/ 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 owl: <http://www.w3.org/2002/07/owl#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> <Taxon> { a [ tax:Taxon ] ; rdfs:label xsd:string ; dcterms:identifier xsd:string ; tax:rank @<Rank> ; rdfs:subClassOf @<Taxon> * ; owl:sameAs IRI * ; rdfs:seeAlso IRI * ; tax:scientificName xsd:string ? ; tax:authority xsd:string ? ; tax:commonName xsd:string * ; tax:synonym xsd:string * ; tax:geneticCode @<GeneticCode> ? ; tax:geneticCodeMt @<GeneticCode> ? } <Rank> { a [ tax:Rank ] ; rdfs:label xsd:string } <GeneticCode> { rdfs:label xsd:string } sample_rdf_entries: - title: Human Species with Complete Metadata description: Homo sapiens with hierarchy, names, and cross-references. rdf: | taxon:9606 a tax:Taxon ; rdfs:label "Homo sapiens" ; rdfs:subClassOf taxon:9605 ; dcterms:identifier "9606" ; tax:rank tax:Species ; tax:scientificName "Homo sapiens" ; tax:authority "Homo sapiens Linnaeus, 1758" ; tax:commonName "human" ; tax:geneticCode tax:GeneticCode1 ; owl:sameAs obo:NCBITaxon_9606 ; rdfs:seeAlso <http://purl.uniprot.org/taxonomy/9606> . - title: Bacterial Strain Entry description: Bacterial strain with complete taxonomic information. rdf: | taxon:1086030 a tax:Taxon ; rdfs:label "Shigella flexneri 5a str. M90T" ; rdfs:subClassOf taxon:424718 ; dcterms:identifier "1086030" ; tax:rank tax:Strain ; tax:scientificName "Shigella flexneri 5a str. M90T" ; tax:equivalentName "Shigella flexneri 5a strain M90T" ; tax:geneticCode tax:GeneticCode11 ; rdfs:seeAlso <http://purl.uniprot.org/taxonomy/1086030> . - title: Genus Level Classification description: Genus showing intermediate taxonomic rank. rdf: | taxon:561 a tax:Taxon ; rdfs:label "Escherichia" ; rdfs:subClassOf taxon:543 ; dcterms:identifier "561" ; tax:rank tax:Genus ; tax:scientificName "Escherichia" ; rdfs:seeAlso <http://purl.uniprot.org/taxonomy/561> . - title: Kingdom Level description: High-level classification (Animal kingdom). rdf: | taxon:33208 a tax:Taxon ; rdfs:label "Metazoa" ; rdfs:subClassOf taxon:2759 ; dcterms:identifier "33208" ; tax:rank tax:Kingdom ; tax:scientificName "Metazoa" ; tax:commonName "animals" . - title: Root of Taxonomy Tree description: Top-level root node of entire taxonomy. rdf: | taxon:1 a tax:Taxon ; rdfs:label "root" ; dcterms:identifier "1" ; tax:rank tax:NoRank . sparql_query_examples: - title: Search Taxa by Name with bif:contains description: Full-text search with relevance scoring question: Which taxa have "mouse" in their names? complexity: basic sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX dcterms: <http://purl.org/dc/terms/> SELECT ?taxon ?id ?label FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?taxon a tax:Taxon ; rdfs:label ?label ; dcterms:identifier ?id . ?label bif:contains "'mouse'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 20 - title: Get Biological Annotations for Taxa description: Retrieve complete biological annotations and classifications question: What are the biological annotations for taxonomy IDs 9606 and 10090? complexity: basic sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX taxon: <http://identifiers.org/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX dcterms: <http://purl.org/dc/terms/> SELECT ?taxon ?label ?id ?rank ?scientificName ?authority ?commonName ?geneticCode FROM <http://rdfportal.org/ontology/taxonomy> WHERE { VALUES ?taxon { taxon:9606 taxon:10090 } ?taxon a tax:Taxon ; rdfs:label ?label ; dcterms:identifier ?id ; tax:rank ?rank . OPTIONAL { ?taxon tax:scientificName ?scientificName } OPTIONAL { ?taxon tax:authority ?authority } OPTIONAL { ?taxon tax:commonName ?commonName } OPTIONAL { ?taxon tax:geneticCode ?geneticCode } } - title: Get Complete Lineage description: Retrieve full taxonomic lineage for an organism question: What is the complete lineage of humans? complexity: intermediate sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX taxon: <http://identifiers.org/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX dcterms: <http://purl.org/dc/terms/> SELECT ?ancestor ?rank ?label ?id FROM <http://rdfportal.org/ontology/taxonomy> WHERE { taxon:9606 rdfs:subClassOf* ?ancestor . ?ancestor a tax:Taxon ; tax:rank ?rank ; rdfs:label ?label ; dcterms:identifier ?id . } ORDER BY DESC(?id) - title: Find Species in Genus description: Get all species within a specific genus question: What species are in genus Escherichia? complexity: intermediate sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX dcterms: <http://purl.org/dc/terms/> SELECT ?species ?label ?id FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?species a tax:Taxon ; rdfs:label ?label ; dcterms:identifier ?id ; tax:rank tax:Species ; rdfs:subClassOf ?genus . ?genus rdfs:label "Escherichia" ; tax:rank tax:Genus . } LIMIT 20 - title: Find Taxa with UniProt Cross-References description: Retrieve organisms with UniProt Taxonomy links question: Which organisms have UniProt Taxonomy references? complexity: intermediate sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?taxon ?label ?uniprotLink FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?taxon a tax:Taxon ; rdfs:label ?label ; rdfs:seeAlso ?uniprotLink . FILTER(CONTAINS(STR(?uniprotLink), "purl.uniprot.org")) } LIMIT 20 - title: Count Species Per Genus with Aggregation description: Biodiversity analysis counting species in genera question: Which genera have most species? complexity: advanced sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?genus ?genus_label (COUNT(?species) AS ?count) FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?species a tax:Taxon ; tax:rank tax:Species ; rdfs:subClassOf ?genus . ?genus tax:rank tax:Genus ; rdfs:label ?genus_label . } GROUP BY ?genus ?genus_label ORDER BY DESC(?count) LIMIT 20 - title: Calculate Lineage Depth for Specific Species description: Count taxonomic hierarchy levels for given species question: What is the hierarchy depth from humans to root through major ranks? complexity: advanced sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX taxon: <http://identifiers.org/taxonomy/> SELECT (COUNT(?ancestor) as ?depth) FROM <http://rdfportal.org/ontology/taxonomy> WHERE { taxon:9606 rdfs:subClassOf+ ?ancestor . ?ancestor tax:rank ?rank . FILTER(?rank IN (tax:Genus, tax:Family, tax:Order, tax:Class, tax:Phylum, tax:Kingdom, tax:Superkingdom)) } cross_references: - pattern: owl:sameAs description: | Taxonomic identifier equivalences across ontology and database systems. Coverage: ~100% of all taxa (5 identifiers per taxon on average). databases: ontologies: OBO NCBITaxon (100%), OBO OWL (100%), Berkeley BOP (100%) databases: DDBJ (100%), NCBI Web (100%) sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?taxon ?label ?sameAs FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?taxon a tax:Taxon ; rdfs:label ?label ; owl:sameAs ?sameAs . } LIMIT 30 - pattern: rdfs:seeAlso description: | Links to UniProt Taxonomy database for protein-related information. Coverage: ~100% of taxa. databases: protein: UniProt Taxonomy (purl.uniprot.org/taxonomy/) sparql: | PREFIX tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?taxon ?label ?uniprotLink FROM <http://rdfportal.org/ontology/taxonomy> WHERE { ?taxon a tax:Taxon ; rdfs:label ?label ; rdfs:seeAlso ?uniprotLink . FILTER(CONTAINS(STR(?uniprotLink), "purl.uniprot.org")) } LIMIT 30 architectural_notes: schema_design: - Hierarchical classification via rdfs:subClassOf for parent-child relationships - owl:sameAs provides cross-database identifier equivalences (5 per taxon) - rdfs:seeAlso links to UniProt Taxonomy for protein database integration - Multiple naming systems (scientific, common, synonym, equivalent) for diverse contexts - Genetic code properties for both nuclear and mitochondrial genomes performance: - Use bif:contains for label searches (full-text index + relevance scoring) - 3M+ taxa require LIMIT clauses for all exploratory queries - Hierarchical queries with rdfs:subClassOf* expensive on deep lineages - Filtering by tax:rank improves performance significantly - Always start transitive queries from specific taxa, not all taxa data_integration: - OBO NCBITaxon for ontology interoperability - UniProt Taxonomy (rdfs:seeAlso) for protein database integration - TogoID relations available in separate graphs for cross-database links - Use owl:sameAs for identifier conversion across systems data_quality: - All taxa have complete identity cross-references (owl:sameAs ~100%) - Scientific names >99% complete - Common names ~30% complete (higher for vertebrates) - UniProt links ~100% coverage via rdfs:seeAlso data_statistics: total_taxa: 2698386 estimated_species: 1500000 taxonomic_ranks: 47 coverage: taxa_with_owl_sameAs: ~100% taxa_with_scientific_names: '>99%' taxa_with_common_names: ~30% taxa_with_genetic_codes: ~100% taxa_with_uniprot_links: ~100% cardinality: avg_owl_sameAs_per_taxon: 5.0 avg_common_names_per_taxon: 1-3 avg_synonyms_per_taxon: 0.1 performance_characteristics: - bif:contains efficient for label searches with relevance ranking - Identity queries (owl:sameAs, rdfs:seeAlso) well-optimized - Lineage traversal (rdfs:subClassOf*) can be slow for deep hierarchies - Recommend LIMIT 100 for exploratory queries - tax:rank filtering significantly improves performance anti_patterns: - title: Using FILTER Instead of bif:contains problem: No full-text index or relevance ranking wrong_sparql: | SELECT ?label WHERE { ?taxon rdfs:label ?label . FILTER(CONTAINS(LCASE(?label), "mouse")) } correct_sparql: | SELECT ?label WHERE { ?taxon rdfs:label ?label . ?label bif:contains "'mouse'" option (score ?sc) } ORDER BY DESC(?sc) explanation: bif:contains uses full-text index and provides relevance scoring - title: Unbounded Lineage Traversal problem: rdfs:subClassOf* without constraints causes timeout on 3M+ taxa wrong_sparql: | SELECT ?ancestor WHERE { ?taxon rdfs:subClassOf* ?ancestor } correct_sparql: | SELECT ?ancestor FROM <http://rdfportal.org/ontology/taxonomy> WHERE { taxon:9606 rdfs:subClassOf* ?ancestor . ?ancestor tax:rank ?rank . } LIMIT 50 explanation: Start from specific taxon and add LIMIT for transitive queries - title: Expensive Queries on All Species problem: Running transitive queries on all species causes timeout wrong_sparql: | SELECT ?species (COUNT(?ancestor) as ?depth) WHERE { ?species tax:rank tax:Species ; rdfs:subClassOf+ ?ancestor . } GROUP BY ?species correct_sparql: | SELECT (COUNT(?ancestor) as ?depth) FROM <http://rdfportal.org/ontology/taxonomy> WHERE { taxon:9606 rdfs:subClassOf+ ?ancestor . ?ancestor tax:rank ?rank . FILTER(?rank IN (tax:Genus, tax:Family, tax:Order)) } explanation: Query specific taxa instead of all species, add rank filters common_errors: - error: Query timeout on lineage queries causes: - Unbounded rdfs:subClassOf* traversal - Missing specific starting taxon - No LIMIT clause solutions: - Start from specific taxon ID (e.g., taxon:9606) - Add LIMIT 50-100 for exploratory queries - Use rdfs:subClassOf+ for ancestors-only - Add tax:rank filters to reduce traversal - error: Empty results for cross-database queries causes: - Looking for TogoID properties in wrong graph - TogoID relations are in separate graphs like http://rdfportal.org/dataset/togoid/relation/* solutions: - Use owl:sameAs and rdfs:seeAlso in the taxonomy graph - Query TogoID relation graphs separately for cross-database links - Use rdfs:seeAlso for UniProt Taxonomy links - error: Poor search results for organism names causes: - Using FILTER(CONTAINS()) instead of bif:contains - Case-sensitive searches solutions: - Use bif:contains for full-text search with relevance - Order by score with ORDER BY DESC(?sc) - Search both scientific and common names with OPTIONAL