TogoMCP

schema_info: title: BacDive - The Bacterial Diversity Metadatabase description: | BacDive provides standardized bacterial and archaeal strain information covering taxonomy, morphology, physiology, cultivation conditions, and molecular data. Contains 97,000+ strain records with phenotypic and genotypic characterizations. Major entities include Strains (core records), Phenotypes (morphology, Gram staining, enzyme activities, oxygen tolerance), CultureConditions (media, temperature, pH), Sequences (16S rRNA, genomes), and GeographicOrigin. Cross-referenced to culture collections and sequence databases. endpoint: https://rdfportal.org/primary/sparql base_uri: https://purl.dsmz.de/ graphs: - http://rdfportal.org/dataset/bacdive version: mie_version: '1.2' mie_created: '2024-12-08' data_version: BacDive 2024 update_frequency: Quarterly license: data_license: CC BY 4.0 license_url: https://bacdive.dsmz.de/about access: rate_limiting: 100 queries/min max_query_timeout: 60 seconds backend: Virtuoso (supports bif:contains) shape_expressions: | PREFIX schema: <https://purl.dsmz.de/schema/> <StrainShape> { a [ schema:Strain ] ; rdfs:label xsd:string ; rdfs:hasScientificName xsd:string ; schema:hasBacDiveID xsd:integer ; schema:hasTaxID xsd:integer ; schema:hasGenus xsd:string ; schema:hasSpecies xsd:string ; schema:hasFamily xsd:string ? ; schema:hasDomain xsd:string ? ; schema:hasDesignation xsd:string ? ; schema:isTypeStrain xsd:boolean ? ; dct:description xsd:string ? } <EnzymeShape> { a [ schema:Enzyme ] ; rdfs:label xsd:string ; schema:describesStrain @<StrainShape> ; schema:hasActivity xsd:string ; schema:hasECNumber xsd:string ? } <GramStainShape> { a [ schema:GramStain ] ; schema:describesStrain @<StrainShape> ; schema:hasGramStain xsd:string } <CellMotilityShape> { a [ schema:CellMotility ] ; schema:describesStrain @<StrainShape> ; schema:isMotile xsd:boolean } <OxygenToleranceShape> { a [ schema:OxygenTolerance ] ; schema:describesStrain @<StrainShape> ; schema:hasOxygenTolerance xsd:string } <CultureMediumShape> { a [ schema:CultureMedium ] ; rdfs:label xsd:string ; schema:describesStrain @<StrainShape> ; schema:hasMediaLink IRI ? } <CultureTemperatureShape> { a [ schema:CultureTemperature ] ; schema:describesStrain @<StrainShape> ; schema:hasTemperatureRangeStart xsd:float ? ; schema:hasTemperatureRangeEnd xsd:float ? } <CulturePHShape> { a [ schema:CulturePH ] ; schema:describesStrain @<StrainShape> ; schema:hasPHRangeStart xsd:float ? ; schema:hasPHRangeEnd xsd:float ? } <Sequence16SShape> { a [ schema:16SSequence ] ; rdfs:label xsd:string ; schema:describesStrain @<StrainShape> ; schema:hasSequenceAccession xsd:string ; schema:fromSequenceDB xsd:string ; schema:hasTaxID xsd:integer } <GenomeSequenceShape> { a [ schema:GenomeSequence ] ; schema:describesStrain @<StrainShape> ; schema:hasSequenceAccession xsd:string ; schema:fromSequenceDB xsd:string } <CultureCollectionNumberShape> { a [ schema:CultureCollectionNumber ] ; rdfs:label xsd:string ; schema:describesStrain @<StrainShape> ; schema:hasLink IRI ? } <LocationShape> { a [ schema:LocationOfOrigin ] ; rdfs:label xsd:string ; schema:describesStrain @<StrainShape> ; schema:hasCountry xsd:string ? ; schema:hasLatitude xsd:float ? ; schema:hasLongitude xsd:float ? } sample_rdf_entries: - title: Strain with Taxonomic Hierarchy description: Core strain entry with complete taxonomic classification and identifiers. rdf: | strain:1 a schema:Strain ; rdfs:label "Acetobacter aceti 1" ; rdfs:hasScientificName "Acetobacter aceti (Pasteur 1864) Beijerinck 1898" ; schema:hasBacDiveID 1 ; schema:hasTaxID 435 ; schema:hasGenus "Acetobacter" ; schema:hasSpecies "Acetobacter aceti" ; schema:hasDomain "Bacteria" . - title: Enzyme Activity description: Enzyme phenotype with activity status linked to strain. rdf: | enzyme:10 a schema:Enzyme ; rdfs:label "gelatinase" ; schema:describesStrain strain:1290 ; schema:hasActivity "+" . - title: 16S Sequence with Accession description: Ribosomal RNA sequence with external database accession. rdf: | sequence_16S:JN000316 a schema:16SSequence ; rdfs:label "Compostimonas suwonensis 16S rRNA gene" ; schema:describesStrain strain:7514 ; schema:fromSequenceDB "ena" ; schema:hasSequenceAccession "JN000316" ; schema:hasSequenceLength 1422 . - title: Culture Collection Link description: External culture collection identifier with institutional URL. rdf: | culture_collection_number:2749 a schema:CultureCollectionNumber ; rdfs:label "DSM 30652" ; schema:describesStrain strain:XXX ; schema:hasLink <https://www.dsmz.de/collection/catalogue/details/culture/DSM-30652> . - title: Geographic Location description: Isolation location with country and coordinates. rdf: | location:12345 a schema:LocationOfOrigin ; rdfs:label "Japan" ; schema:describesStrain strain:7514 ; schema:hasCountry "Japan" ; schema:hasLatitude 37.5665 ; schema:hasLongitude 126.9780 . sparql_query_examples: - title: Search Strains with bif:contains description: Find strains using full-text search with boolean operators and relevance scoring. question: Find Escherichia coli strains. complexity: basic sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?label ?sc FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; rdfs:label ?label . ?label bif:contains "'escherichia' AND 'coli'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 100 - title: Search Descriptions with Boolean Logic description: Complex keyword search in descriptions with AND/NOT operators. question: Find aerobic Gram-negative bacteria excluding plant pathogens. complexity: basic sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> PREFIX dct: <http://purl.org/dc/terms/> SELECT ?strain ?description ?sc FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; dct:description ?description . ?description bif:contains "'aerobic' AND 'gram-negative' AND NOT 'plant'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 50 - title: Strains with 16S Sequences description: Find strains with 16S rRNA data and accessions. question: Which strains have 16S sequences? complexity: intermediate sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?strainLabel ?accession ?length FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; rdfs:label ?strainLabel . ?seq a schema:16SSequence ; schema:describesStrain ?strain ; schema:hasSequenceAccession ?accession ; schema:hasSequenceLength ?length . } LIMIT 100 - title: Enzyme Activities by Strain description: Retrieve positive enzyme activities for strains. question: What enzymes show positive activity? complexity: intermediate sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strainLabel ?enzymeLabel ?activity FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; rdfs:label ?strainLabel . ?enzyme a schema:Enzyme ; schema:describesStrain ?strain ; rdfs:label ?enzymeLabel ; schema:hasActivity ?activity . FILTER(?activity = "+") } LIMIT 100 - title: Keyword Search with Phenotypes description: Combine bif:contains with structured phenotype queries. question: Find thermophilic bacteria with Gram stain and temperature data. complexity: intermediate sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> PREFIX dct: <http://purl.org/dc/terms/> SELECT ?strain ?description ?gramStain ?tempStart ?tempEnd ?sc FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; dct:description ?description . ?description bif:contains "'thermophilic'" option (score ?sc) . OPTIONAL { ?gs a schema:GramStain ; schema:describesStrain ?strain ; schema:hasGramStain ?gramStain . } OPTIONAL { ?temp a schema:CultureTemperature ; schema:describesStrain ?strain ; schema:hasTemperatureRangeStart ?tempStart ; schema:hasTemperatureRangeEnd ?tempEnd . } } ORDER BY DESC(?sc) LIMIT 50 - title: Growth Conditions Profile description: Query culture medium, temperature, and pH together. question: What are growth conditions for Bacillus? complexity: advanced sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?label ?medium ?tempStart ?tempEnd ?phStart ?phEnd FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; rdfs:label ?label ; schema:hasGenus ?genus . FILTER(CONTAINS(LCASE(?genus), "bacillus")) OPTIONAL { ?m a schema:CultureMedium ; schema:describesStrain ?strain ; rdfs:label ?medium . } OPTIONAL { ?temp a schema:CultureTemperature ; schema:describesStrain ?strain ; schema:hasTemperatureRangeStart ?tempStart ; schema:hasTemperatureRangeEnd ?tempEnd . } OPTIONAL { ?ph a schema:CulturePH ; schema:describesStrain ?strain ; schema:hasPHRangeStart ?phStart ; schema:hasPHRangeEnd ?phEnd . } } LIMIT 50 - title: Multi-Phenotype with Complex Keywords description: Combine complex boolean keyword search with multiple phenotypes. question: Find human pathogens with complete phenotypic profiles. complexity: advanced sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> PREFIX dct: <http://purl.org/dc/terms/> SELECT ?label ?description ?gramStain ?isMotile ?sc FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; rdfs:label ?label ; dct:description ?description . ?description bif:contains "('pathogen' OR 'pathogenic') AND NOT 'plant'" option (score ?sc) . OPTIONAL { ?gs a schema:GramStain ; schema:describesStrain ?strain ; schema:hasGramStain ?gramStain . } OPTIONAL { ?cm a schema:CellMotility ; schema:describesStrain ?strain ; schema:isMotile ?isMotile . } } ORDER BY DESC(?sc) LIMIT 50 cross_references: - pattern: schema:hasLink description: Culture collection links through CultureCollectionNumber entities to institutional databases. databases: collections: - DSMZ (>90%) - JCM (~40%) - KCTC (~30%) - CCUG (~25%) sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?collectionLabel ?link FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain . ?ccn a schema:CultureCollectionNumber ; schema:describesStrain ?strain ; rdfs:label ?collectionLabel ; schema:hasLink ?link . } LIMIT 50 - pattern: schema:hasTaxID description: NCBI Taxonomy IDs on all strains and sequences for standardized classification. databases: taxonomy: - NCBI Taxonomy (100%) sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?taxID ?genus ?species FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain ; schema:hasTaxID ?taxID ; schema:hasGenus ?genus ; schema:hasSpecies ?species . } LIMIT 50 - pattern: schema:hasSequenceAccession description: Sequence accessions from ENA/NCBI with database source indicator. databases: sequence: - ENA (~60% 16S) - NCBI GenBank (~40% genomes) sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?accession ?seqDB ?seqType FROM <http://rdfportal.org/dataset/bacdive> WHERE { { ?seq a schema:16SSequence ; schema:describesStrain ?strain ; schema:hasSequenceAccession ?accession ; schema:fromSequenceDB ?seqDB . BIND("16S" as ?seqType) } UNION { ?seq a schema:GenomeSequence ; schema:describesStrain ?strain ; schema:hasSequenceAccession ?accession ; schema:fromSequenceDB ?seqDB . BIND("Genome" as ?seqType) } } LIMIT 50 - pattern: schema:hasMediaLink description: Links to MediaDive for detailed culture medium recipes. databases: media: - MediaDive (~20%) - CIP Media (~10%) sparql: | PREFIX schema: <https://purl.dsmz.de/schema/> SELECT ?strain ?mediumLabel ?mediaLink FROM <http://rdfportal.org/dataset/bacdive> WHERE { ?strain a schema:Strain . ?medium a schema:CultureMedium ; schema:describesStrain ?strain ; rdfs:label ?mediumLabel ; schema:hasMediaLink ?mediaLink . } LIMIT 50 architectural_notes: schema_design: - Hub-and-spoke with Strain as central entity - Phenotypes connect via schema:describesStrain - Multiple inheritance for entity types - Full taxonomic lineage in Strain entities performance: - Use bif:contains for keywords with boolean operators (AND, OR, NOT, parentheses) - bif:contains as triple pattern with option (score ?var) for relevance - Genus/species filters are efficient - Use OPTIONAL for phenotypes (incomplete coverage) - Always use LIMIT to prevent timeouts data_integration: - NCBI Taxonomy IDs for cross-database joins - Culture collection numbers for strain repositories - Sequence accessions (ENA/NCBI) for sequence databases data_quality: - Not all strains have complete phenotypes - use OPTIONAL - 16S coverage (~35%) higher than genomes - Type strains have more complete data data_statistics: total_strains: 97334 total_enzymes: 573112 total_16s_sequences: 87045 coverage: strains_with_gram_stain: ~40% strains_with_16s_sequence: ~35% strains_with_culture_collections: ~60% strains_with_enzyme_data: ~55% cardinality: avg_enzymes_per_strain: 5.9 avg_culture_collections_per_strain: 1.5 performance_characteristics: - Simple strain queries complete in <2s - bif:contains searches are very fast with complex boolean logic - Multi-join phenotype queries may take 5-10s anti_patterns: - title: bif:contains in FILTER problem: bif:contains must be triple pattern, not in FILTER. wrong_sparql: | SELECT ?strain ?description WHERE { ?strain dct:description ?description . FILTER(bif:contains(?description, "'thermophilic'")) } correct_sparql: | SELECT ?strain ?description ?sc WHERE { ?strain dct:description ?description . ?description bif:contains "'thermophilic'" option (score ?sc) . } ORDER BY DESC(?sc) explanation: Use as triple pattern (?var bif:contains 'keywords') with single-quoted keywords. - title: Using Reserved Variable ?score problem: Variable name ?score conflicts with score keyword. wrong_sparql: | SELECT ?strain ?score WHERE { ?strain rdfs:label ?label . ?label bif:contains "'escherichia'" option (score ?score) . } correct_sparql: | SELECT ?strain ?sc WHERE { ?strain rdfs:label ?label . ?label bif:contains "'escherichia'" option (score ?sc) . } explanation: Never use ?score as variable name - use ?sc or any other name. - title: Required Phenotypes problem: Requiring phenotypes excludes strains with missing data. wrong_sparql: | SELECT ?strain ?gramStain ?motile WHERE { ?strain a schema:Strain . ?gs schema:describesStrain ?strain ; schema:hasGramStain ?gramStain . ?cm schema:describesStrain ?strain ; schema:isMotile ?motile . } correct_sparql: | SELECT ?strain ?gramStain ?motile WHERE { ?strain a schema:Strain . OPTIONAL { ?gs schema:describesStrain ?strain ; schema:hasGramStain ?gramStain . } OPTIONAL { ?cm schema:describesStrain ?strain ; schema:isMotile ?motile . } } explanation: Use OPTIONAL for phenotypes since coverage is incomplete (~40%). common_errors: - error: 400 Bad Request with bif:contains causes: - Using bif:contains in FILTER instead of as triple pattern - Using ?score as variable name - Missing single quotes around keywords solutions: - 'Use as triple: ?var bif:contains "''keyword''" option (score ?sc)' - Never use ?score - use ?sc or other name - 'Always wrap keywords in single quotes: ''keyword''' - 'Boolean syntax: "''keyword1'' AND ''keyword2''", "''keyword1'' OR ''keyword2''"' - error: Empty results with phenotypes causes: - Assuming all strains have phenotypes - Missing OPTIONAL clauses solutions: - Always use OPTIONAL for phenotype properties - Check coverage statistics (~40% Gram stain, ~35% 16S) - Use FILTER(BOUND(?var)) to require specific data - error: Query timeout causes: - Joining many phenotypes without LIMIT - Querying all strains without filters solutions: - Add LIMIT to prevent processing entire database - Use bif:contains to filter by keywords first - Filter by genus/family to reduce scope - Query phenotypes separately rather than all at once