TogoMCP

schema_info: title: DDBJ (DNA Data Bank of Japan) description: | DDBJ RDF provides nucleotide sequence data from the International Nucleotide Sequence Database Collaboration (INSDC). Contains entries with genomic annotations (genes, CDS, tRNA, rRNA) linked to organism metadata, taxonomic classification, functional annotations, and protein translations. Cross-referenced to BioProject, BioSample, NCBI Protein, and taxonomic databases. Uses FALDO for genomic coordinates, Sequence Ontology for feature types, and BFO/RO for biological relationships. endpoint: https://rdfportal.org/ddbj/sparql base_uri: http://identifiers.org/insdc/ graphs: - http://rdfportal.org/dataset/ddbj - http://rdfportal.org/ontology/nucleotide - http://rdfportal.org/ontology/so - http://rdfportal.org/ontology/faldo version: mie_version: '1.1' mie_created: '2024-12-08' data_version: DDBJ Release (continuous updates) update_frequency: Daily license: data_license: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license_url: https://creativecommons.org/publicdomain/zero/1.0/ access: rate_limiting: No strict rate limit, please use responsibly max_query_timeout: 60 seconds backend: Virtuoso (supports bif:contains) shape_expressions: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX bfo: <http://purl.obolibrary.org/obo/BFO_> PREFIX ro: <http://purl.obolibrary.org/obo/RO_> PREFIX sio: <http://semanticscience.org/resource/SIO_> PREFIX so: <http://purl.obolibrary.org/obo/SO_> <EntryShape> { a [ nuc:Entry ] ; rdfs:label xsd:string ; dcterms:identifier xsd:string ; nuc:definition xsd:string ; nuc:organism xsd:string ; nuc:taxonomy xsd:string ; nuc:division IRI ; nuc:sequence IRI ; nuc:sequence_version xsd:string ; nuc:sequence_date xsd:date ; nuc:dblink IRI* ; nuc:reference IRI* ; nuc:comment xsd:string ? ; nuc:source xsd:string ? } <GeneShape> { a [ nuc:Gene ] ; rdfs:subClassOf IRI+ ; rdfs:label xsd:string ; dcterms:identifier xsd:string ; skos:prefLabel xsd:string ; nuc:locus_tag xsd:string ; nuc:gene xsd:string ? ; nuc:location xsd:string ; faldo:location @<RegionShape> ; bfo:0000050 IRI ; bfo:0000051 IRI* ; ro:0002162 IRI } <CodingSequenceShape> { a [ nuc:Coding_Sequence ] ; rdfs:subClassOf IRI+ ; nuc:locus_tag xsd:string ; nuc:product xsd:string ; nuc:translation xsd:string ; nuc:codon_start xsd:integer ; nuc:transl_table xsd:integer ; faldo:location @<RegionShape> ; rdfs:seeAlso IRI ; sio:010081 IRI ; bfo:0000050 IRI ; ro:0002162 IRI } <TransferRNAShape> { a [ nuc:Transfer_RNA ] ; rdfs:subClassOf IRI+ ; faldo:location @<RegionShape> ; nuc:product xsd:string ? ; bfo:0000050 IRI ; ro:0002162 IRI } <RibosomalRNAShape> { a [ nuc:Ribosomal_RNA ] ; rdfs:subClassOf IRI+ ; faldo:location @<RegionShape> ; nuc:product xsd:string ? ; bfo:0000050 IRI ; ro:0002162 IRI } <SourceShape> { a [ nuc:Source ] ; rdfs:subClassOf IRI ; nuc:organism xsd:string ; nuc:mol_type xsd:string ; faldo:location @<RegionShape> ; rdfs:seeAlso IRI ; bfo:0000050 IRI ; ro:0002162 IRI } <RegionShape> { a [ faldo:Region ] ; faldo:begin @<PositionShape> ; faldo:end @<PositionShape> } <PositionShape> { a [ faldo:ExactPosition ] ; faldo:position xsd:integer ; faldo:reference IRI } sample_rdf_entries: - title: Entry with BioProject/BioSample Links description: Genome entry with organism metadata and external database links. rdf: | <http://identifiers.org/insdc/CP036276.1> a nuc:Entry ; rdfs:label "Symmachiella dynata strain Mal52 chromosome, complete genome." ; dcterms:identifier "CP036276.1" ; nuc:organism "Symmachiella dynata" ; nuc:dblink <http://identifiers.org/biosample/SAMN10954015> ; nuc:dblink <http://identifiers.org/bioproject/PRJNA485700> . - title: Gene with FALDO Location description: Gene feature with locus tag and genomic coordinates. rdf: | <http://identifiers.org/insdc/CP036276.1#feature:1001623-1002915:1:gene.47722> a nuc:Gene ; rdfs:subClassOf so:0000704 ; nuc:locus_tag "Mal52_08030" ; nuc:gene "clpX" ; faldo:location <http://identifiers.org/insdc/CP036276.1#region:1001623-1002915:1> ; bfo:0000050 <http://identifiers.org/insdc/CP036276.1#sequence> ; ro:0002162 <http://identifiers.org/taxonomy/2527995> . - title: CDS with Protein Link description: Coding sequence with product annotation and NCBI Protein reference. rdf: | <http://identifiers.org/insdc/CP036276.1#feature:1001623-1002915:1:CDS.47054> a nuc:Coding_Sequence ; nuc:locus_tag "Mal52_08030" ; nuc:product "ATP-dependent Clp protease ATP-binding subunit ClpX" ; nuc:translation "MPSGNDVTSGSRGATGKK..." ; rdfs:seeAlso <http://identifiers.org/ncbiprotein/QDU42347.1> ; sio:010081 <http://identifiers.org/insdc/CP036276.1#feature:1001623-1002915:1:gene.47722> . - title: Source with Taxonomy description: Source feature with organism and taxonomic identifier. rdf: | <http://identifiers.org/insdc/AB023775.1#feature:103-136:1:source.1> a nuc:Source ; nuc:organism "Lactobacillus phage phiFSW" ; nuc:mol_type "genomic DNA" ; rdfs:seeAlso <http://identifiers.org/taxonomy/91019> ; ro:0002162 <http://identifiers.org/taxonomy/1582> . - title: FALDO Region description: Genomic region with exact begin and end positions. rdf: | <http://identifiers.org/insdc/CP036276.1#region:1001623-1002915:1> a faldo:Region ; faldo:begin <http://identifiers.org/insdc/CP036276.1#position:1001623:1> ; faldo:end <http://identifiers.org/insdc/CP036276.1#position:1002915:1> . sparql_query_examples: - title: Search by Organism with bif:contains description: Find entries using full-text search with relevance scoring. question: What entries exist for Escherichia coli? complexity: basic sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> SELECT ?entry ?organism ?relevance FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?entry a nuc:Entry ; nuc:organism ?organism . ?organism bif:contains "'escherichia' AND 'coli'" option (score ?relevance) . } ORDER BY DESC(?relevance) LIMIT 10 - title: Get Gene by Locus Tag description: Retrieve gene annotations for a specific locus tag. question: What are annotations for locus Mal52_08030? complexity: basic sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> SELECT ?gene ?gene_symbol ?product FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?gene a nuc:Gene ; nuc:locus_tag "Mal52_08030" . OPTIONAL { ?gene nuc:gene ?gene_symbol } OPTIONAL { ?cds nuc:locus_tag "Mal52_08030" ; nuc:product ?product . } } - title: Genes with Coordinates description: Query genes with FALDO coordinates from specific entry. question: What are gene coordinates in CP036276.1? complexity: intermediate sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> SELECT ?locus_tag ?start ?end FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?gene a nuc:Gene ; nuc:locus_tag ?locus_tag ; faldo:location ?region . ?region faldo:begin/faldo:position ?start ; faldo:end/faldo:position ?end . FILTER(CONTAINS(STR(?gene), "CP036276.1")) } LIMIT 10 - title: Sample Feature Types description: List different feature types in an entry. question: What features are in CP036276.1? complexity: intermediate sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> SELECT ?feature_type ?locus_tag FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?feature a ?feature_type . FILTER(?feature_type IN (nuc:Gene, nuc:Coding_Sequence, nuc:Transfer_RNA, nuc:Ribosomal_RNA)) OPTIONAL { ?feature nuc:locus_tag ?locus_tag } FILTER(CONTAINS(STR(?feature), "CP036276.1")) } LIMIT 20 - title: Search Products by Entry with FILTER description: Find protease or peptidase genes within a specific entry. question: Find protease or peptidase genes in CP036276.1. complexity: intermediate sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> SELECT ?locus_tag ?product FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?cds a nuc:Coding_Sequence ; nuc:locus_tag ?locus_tag ; nuc:product ?product . FILTER(CONTAINS(STR(?cds), "CP036276.1")) FILTER(CONTAINS(LCASE(?product), "protease") || CONTAINS(LCASE(?product), "peptidase")) } LIMIT 50 - title: Gene-CDS-Protein Integration description: Complex query joining genes, CDS, and protein IDs. question: Get complete annotations for CP036276.1. complexity: advanced sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> PREFIX sio: <http://semanticscience.org/resource/SIO_> SELECT ?locus_tag ?product ?protein_id FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?gene a nuc:Gene ; nuc:locus_tag ?locus_tag . ?cds sio:010081 ?gene ; nuc:product ?product ; rdfs:seeAlso ?protein_id . FILTER(CONTAINS(STR(?protein_id), "ncbiprotein")) FILTER(CONTAINS(STR(?gene), "CP036276.1")) } LIMIT 100 - title: RNA Features by Type description: Find tRNA and rRNA using UNION. question: What RNA features exist? complexity: advanced sparql: | PREFIX nuc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> SELECT ?rna_type ?product FROM <http://rdfportal.org/dataset/ddbj> WHERE { { ?rna a nuc:Transfer_RNA ; nuc:product ?product . BIND("tRNA" AS ?rna_type) } UNION { ?rna a nuc:Ribosomal_RNA ; nuc:product ?product . BIND("rRNA" AS ?rna_type) } } LIMIT 20 cross_references: - pattern: nuc:dblink description: Entry links to BioProject and BioSample for experimental metadata. databases: project_metadata: - 'BioProject: Project organization' - 'BioSample: Specimen metadata' sparql: | SELECT ?entry ?bioproject ?biosample FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?entry a nuc:Entry ; nuc:dblink ?bioproject ; nuc:dblink ?biosample . FILTER(CONTAINS(STR(?bioproject), "bioproject")) FILTER(CONTAINS(STR(?biosample), "biosample")) } LIMIT 10 - pattern: rdfs:seeAlso description: Feature links to NCBI Protein, FASTA, and Taxonomy. databases: protein: - 'NCBI Protein: RefSeq sequences' taxonomy: - 'NCBI Taxonomy: Classification' sparql: | SELECT ?feature ?external FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?feature rdfs:seeAlso ?external . FILTER(CONTAINS(STR(?external), "ncbiprotein") || CONTAINS(STR(?external), "taxonomy")) } LIMIT 50 - pattern: ro:0002162 description: Taxonomic relationships via RO_0002162 (in taxon). databases: taxonomy: - 'NCBI Taxonomy: Full hierarchy' sparql: | SELECT ?feature ?taxon FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?feature ro:0002162 ?taxon . FILTER(CONTAINS(STR(?taxon), "taxonomy")) } LIMIT 50 - pattern: rdfs:subClassOf description: Sequence Ontology classification for features. databases: ontology: - 'Sequence Ontology: Feature types' sparql: | SELECT ?feature ?so_class FROM <http://rdfportal.org/dataset/ddbj> WHERE { ?feature rdfs:subClassOf ?so_class . FILTER(CONTAINS(STR(?so_class), "obo/SO_")) } LIMIT 50 architectural_notes: schema_design: - Entry-centric with hierarchical features via BFO_0000050/BFO_0000051 - FALDO coordinates for genomic positions - SO terms for semantic feature typing - Gene-CDS links via SIO_010081 performance: - CRITICAL - Always filter by entry ID before any complex queries - Use FILTER CONTAINS for product searches within entries - bif:contains best for organism name search at entry level - Filter by entry ID before FALDO queries - Avoid aggregation without entry filtering - Gene-CDS joins via sio:010081 are optimized data_integration: - identifiers.org URIs for cross-database linking - BioProject/BioSample for experimental context data_quality: - Locus tags more reliable than gene symbols - ~60% genes have symbols, >99% have locus tags - Mostly prokaryotic data data_statistics: coverage: entries_with_organism: '>99%' cds_with_product: '>95%' cds_with_translation: '>95%' genes_with_locus_tag: '>99%' features_with_faldo: '>99%' cardinality: genes_per_entry: 10-5000 (genome-dependent) trna_per_entry: 40-100 (bacteria) rrna_per_entry: 3-9 (bacteria) performance_characteristics: - Entry-specific queries by accession are fast - bif:contains for organism search at entry level is fast - Product searches require entry filtering - FALDO requires entry filtering first anti_patterns: - title: Aggregation Without Filtering problem: COUNT/GROUP BY without entry filter causes timeout. wrong_sparql: | SELECT (COUNT(*) as ?count) WHERE { ?entry a nuc:Entry } correct_sparql: | SELECT ?entry WHERE { ?entry a nuc:Entry } LIMIT 100 explanation: Replace aggregation with sampling. - title: FALDO Without Entry Filter problem: Coordinate queries without entry ID timeout. wrong_sparql: | SELECT ?gene ?start WHERE { ?gene a nuc:Gene ; faldo:location/faldo:begin/faldo:position ?start . FILTER(?start >= 1000000) } correct_sparql: | SELECT ?gene ?start WHERE { ?gene a nuc:Gene ; faldo:location/faldo:begin/faldo:position ?start . FILTER(CONTAINS(STR(?gene), "CP036276.1")) } explanation: Filter by entry URI before FALDO queries. - title: Product Search Without Entry Filter problem: Searching products across all entries causes timeout. wrong_sparql: | SELECT ?product WHERE { ?cds nuc:product ?product . ?product bif:contains "'protease'" } correct_sparql: | SELECT ?product WHERE { ?cds nuc:product ?product . FILTER(CONTAINS(STR(?cds), "CP036276.1")) FILTER(CONTAINS(LCASE(?product), "protease")) } explanation: Always filter by entry first when searching features. Use FILTER CONTAINS for product searches within an entry. common_errors: - error: Query timeout causes: - Aggregation without entry filter - FALDO without entry filter - Product search without entry filter - Using bif:contains on product field without entry filter solutions: - 'Add entry filter: FILTER(CONTAINS(STR(?var), ''ENTRY_ID''))' - Use FILTER CONTAINS for product searches within entries - Use bif:contains only for organism search at entry level - Sample with LIMIT instead of COUNT - error: Empty results causes: - Missing FROM clause - Required optional property - Wrong bif:contains syntax solutions: - Add FROM <http://rdfportal.org/dataset/ddbj> - Use OPTIONAL for nuc:gene - 'Use single quotes: bif:contains "''keyword''"' - error: Duplicates causes: - Missing DISTINCT - Multiple OPTIONAL multiplying results solutions: - Add SELECT DISTINCT - Test with LIMIT 5 first