TogoMCP

schema_info: title: Ensembl RDF description: | Ensembl is a comprehensive genomics database providing genome annotations for 100+ species. Contains genes, transcripts, proteins, and exons with genomic locations. Main entities include EnsemblGene (genes with biotypes), EnsemblTranscript (transcript variants with quality flags), EnsemblProtein (translated products), and EnsemblExon (exon regions). Cross-referenced to UniProt, HGNC, NCBI Gene, Reactome, and OMIM. endpoint: https://rdfportal.org/ebi/sparql base_uri: http://rdf.ebi.ac.uk/resource/ensembl/ graphs: - http://rdfportal.org/dataset/ensembl - http://rdfportal.org/dataset/ensembl_grch38 - http://rdfportal.org/dataset/ensembl_grch37 version: mie_version: '1.1' mie_created: '2024-12-08' data_version: Release 114 update_frequency: Quarterly license: data_license: Creative Commons Attribution 4.0 International license_url: https://www.ensembl.org/info/about/legal/index.html access: rate_limiting: Reasonable use policy max_query_timeout: 60 seconds backend: Virtuoso (supports bif:contains) shape_expressions: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX sio: <http://semanticscience.org/resource/> <EnsemblGeneShape> { a [ terms:EnsemblGene ] ; rdfs:label xsd:string ; dcterms:identifier xsd:string ; dcterms:description xsd:string ; terms:has_biotype IRI ; obo:RO_0002162 IRI ; so:part_of IRI + ; faldo:location BNode ; rdfs:seeAlso IRI * } <EnsemblTranscriptShape> { a [ terms:EnsemblTranscript ] ; dcterms:identifier xsd:string ; terms:has_biotype IRI ; so:transcribed_from @<EnsemblGeneShape> ; so:translates_to @<EnsemblProteinShape> ? ; terms:has_transcript_flag IRI * ; faldo:location BNode ; sio:SIO_000974 @<EnsemblOrderedExonShape> + } <EnsemblProteinShape> { a [ terms:EnsemblProtein ] ; dcterms:identifier xsd:string ; so:translation_of @<EnsemblTranscriptShape> ; rdfs:seeAlso IRI * } <EnsemblExonShape> { a [ terms:EnsemblExon ] ; dcterms:identifier xsd:string ; faldo:location BNode } <EnsemblOrderedExonShape> { a [ terms:EnsemblOrderedExon ] ; sio:SIO_000628 @<EnsemblExonShape> ; sio:SIO_000300 xsd:integer } sample_rdf_entries: - title: Human BRCA1 Gene description: Protein-coding gene on chromosome 17 with genomic coordinates and cross-references. rdf: | ensg:ENSG00000012048 a terms:EnsemblGene ; rdfs:label "BRCA1" ; dcterms:identifier "ENSG00000012048" ; dcterms:description "BRCA1 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1100]" ; terms:has_biotype <http://ensembl.org/glossary/ENSGLOSSARY_0000026> ; obo:RO_0002162 <http://identifiers.org/taxonomy/9606> ; so:part_of <http://rdf.ebi.ac.uk/resource/ensembl/114/homo_sapiens/GRCh38/17> ; faldo:location [ faldo:begin [ faldo:position 43044295 ; rdf:type faldo:ReverseStrandPosition ] ; faldo:end [ faldo:position 43170245 ; rdf:type faldo:ReverseStrandPosition ] ] ; rdfs:seeAlso <http://purl.uniprot.org/uniprot/P38398> ; rdfs:seeAlso <http://identifiers.org/hgnc/HGNC:1100> . - title: Transcript with Quality Flags description: BRCA1 transcript with MANE Select and canonical flags showing quality annotations. rdf: | enst:ENST00000468300 a terms:EnsemblTranscript ; dcterms:identifier "ENST00000468300" ; terms:has_biotype <http://ensembl.org/glossary/ENSGLOSSARY_0000026> ; so:transcribed_from <http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000012048> ; so:translates_to <http://rdf.ebi.ac.uk/resource/ensembl.protein/ENSP00000418960> ; terms:has_transcript_flag <http://ensembl.org/glossary/ENSGLOSSARY_0000023> ; terms:has_transcript_flag <http://ensembl.org/glossary/ENSGLOSSARY_0000365> . - title: Protein with UniProt Link description: Translated protein product with UniProt cross-reference. rdf: | ensp:ENSP00000418960 a terms:EnsemblProtein ; dcterms:identifier "ENSP00000418960" ; so:translation_of <http://rdf.ebi.ac.uk/resource/ensembl.transcript/ENST00000468300> ; rdfs:seeAlso <http://purl.uniprot.org/uniprot/P38398> . - title: Ordered Exon description: Exon with sequential ordering showing transcript structure. rdf: | <http://rdf.ebi.ac.uk/resource/ensembl.transcript/ENST00000468300#Exon_1> a terms:EnsemblOrderedExon ; sio:SIO_000628 ense:ENSE00003884397 ; sio:SIO_000300 1 . ense:ENSE00003884397 a terms:EnsemblExon ; dcterms:identifier "ENSE00003884397" ; faldo:location [ faldo:begin [ faldo:position 43170245 ] ; faldo:end [ faldo:position 43170403 ] ] . - title: microRNA Gene description: Gene classified as microRNA with biotype annotation. rdf: | ensg:ENSG00000266085 a terms:EnsemblGene ; rdfs:label "MIR6723" ; dcterms:identifier "ENSG00000266085" ; terms:has_biotype <http://ensembl.org/glossary/ENSGLOSSARY_0000038> ; obo:RO_0002162 <http://identifiers.org/taxonomy/9606> . sparql_query_examples: - title: Search Genes by Symbol with bif:contains description: Find genes using full-text search with wildcard and relevance scoring. question: Find human genes starting with BRCA. complexity: basic sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX taxonomy: <http://identifiers.org/taxonomy/> SELECT ?gene ?id ?label ?description FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?id ; rdfs:label ?label ; dcterms:description ?description ; obo:RO_0002162 taxonomy:9606 . ?label bif:contains "'BRCA*'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 10 - title: List Genes on Chromosome description: Retrieve protein-coding genes from specific chromosome. question: What are protein-coding genes on chromosome X? complexity: basic sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX taxonomy: <http://identifiers.org/taxonomy/> SELECT ?gene ?id ?label FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?id ; rdfs:label ?label ; so:part_of ?chr ; terms:has_biotype <http://ensembl.org/glossary/ENSGLOSSARY_0000026> ; obo:RO_0002162 taxonomy:9606 . FILTER(CONTAINS(STR(?chr), "GRCh38/X")) } LIMIT 100 - title: Search by Functional Keywords description: Find genes using keyword search in descriptions with boolean operators. question: Find genes involved in kinase receptor activity. complexity: intermediate sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX taxonomy: <http://identifiers.org/taxonomy/> SELECT ?gene ?id ?label ?description FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?id ; rdfs:label ?label ; dcterms:description ?description ; obo:RO_0002162 taxonomy:9606 . ?description bif:contains "('kinase' AND 'receptor')" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 20 - title: Get Gene Genomic Coordinates description: Retrieve gene location with start, end, strand, and chromosome using FALDO. question: What are genomic coordinates of BRCA1? complexity: intermediate sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX taxonomy: <http://identifiers.org/taxonomy/> SELECT DISTINCT ?gene ?id ?label ?start ?end ?strand ?chr FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?id ; rdfs:label ?label ; faldo:location ?loc ; so:part_of ?chr ; obo:RO_0002162 taxonomy:9606 . ?loc faldo:begin/faldo:position ?start ; faldo:end/faldo:position ?end ; faldo:begin/rdf:type ?strand_type . BIND(IF(?strand_type = faldo:ForwardStrandPosition, "+", "-") AS ?strand) FILTER(?id = "ENSG00000012048") } - title: Gene-Transcript-Protein Mapping description: Navigate gene to protein hierarchy with UniProt cross-references. question: What proteins are encoded by BRCA1 with UniProt IDs? complexity: intermediate sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX taxonomy: <http://identifiers.org/taxonomy/> SELECT ?gene_id ?gene_label ?transcript_id ?protein_id ?uniprot FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?gene_id ; rdfs:label ?gene_label ; obo:RO_0002162 taxonomy:9606 . ?transcript so:transcribed_from ?gene ; dcterms:identifier ?transcript_id ; so:translates_to ?protein . ?protein dcterms:identifier ?protein_id ; rdfs:seeAlso ?uniprot . FILTER(STRSTARTS(STR(?uniprot), "http://purl.uniprot.org/uniprot/")) FILTER(?gene_label = "BRCA1") } LIMIT 20 - title: Retrieve Ordered Exons description: Get exons in sequential order with coordinates for transcript. question: What are exons of ENST00000700182 in order? complexity: advanced sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX sio: <http://semanticscience.org/resource/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> SELECT ?transcript_id ?exon_id ?order ?start ?end FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?transcript a terms:EnsemblTranscript ; dcterms:identifier ?transcript_id ; sio:SIO_000974 ?ordered_exon . ?ordered_exon sio:SIO_000628 ?exon ; sio:SIO_000300 ?order . ?exon dcterms:identifier ?exon_id ; faldo:location/faldo:begin/faldo:position ?start ; faldo:location/faldo:end/faldo:position ?end . FILTER(?transcript_id = "ENST00000700182") } ORDER BY ?order LIMIT 100 - title: Species Gene Distribution description: Count genes by species to see database coverage. question: How many genes per species? complexity: advanced sparql: | PREFIX terms: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT ?taxonomy (COUNT(?gene) as ?gene_count) FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; obo:RO_0002162 ?taxonomy . } GROUP BY ?taxonomy ORDER BY DESC(?gene_count) LIMIT 50 cross_references: - pattern: rdfs:seeAlso description: External database cross-references linking to proteins, gene nomenclature, pathways, and clinical databases. databases: proteins: - UniProt - UniParc genes: - HGNC (human) - MGI (mouse) - NCBI Gene - GeneCards pathways: - Reactome clinical: - OMIM sparql: | SELECT ?gene_id ?xref FROM <http://rdfportal.org/dataset/ensembl> WHERE { ?gene a terms:EnsemblGene ; dcterms:identifier ?gene_id ; rdfs:seeAlso ?xref . FILTER(?gene_id = "ENSG00000012048") } architectural_notes: schema_design: - Hierarchical Gene → Transcript → Protein following central dogma - FALDO ontology for genomic coordinates with strand information - SO (Sequence Ontology) defines feature relationships - SIO ontology enables ordered exon structures - Biotypes classify genes/transcripts into functional categories performance: - Use bif:contains for text search with relevance scoring and wildcards - Filter by species (obo:RO_0002162) early in queries - 'Chromosome filtering: CONTAINS(STR(?chr), ''GRCh38/X'')' - Limit FALDO queries to specific genes - Always use DISTINCT with FALDO location queries data_integration: - Multiple genome assemblies (GRCh38, GRCh37) in separate graphs - Species via NCBI Taxonomy IDs - External IDs use identifiers.org and purl.uniprot.org data_quality: - Not all transcripts encode proteins (non-coding RNAs) - Transcript flags indicate confidence (MANE, APPRIS, TSL) - FALDO positions may have duplicate entries data_statistics: total_genes: 3000000 total_transcripts: 4000000 total_proteins: 2000000 species_coverage: 100+ vertebrate species major_species: human: 87,688 genes mouse: 744,820 genes rat: 143,695 genes coverage: genes_with_description: ~95% transcripts_with_proteins: ~40% genes_with_uniprot_xrefs: ~60% cardinality: transcripts_per_gene: 1-100+ exons_per_transcript: 1-300+ performance_characteristics: - 'Gene symbol searches: <1s' - 'Chromosome queries: 1-3s' - 'Gene-transcript-protein: 2-5s' - 'Exon retrieval: <1s' anti_patterns: - title: FILTER/REGEX vs bif:contains problem: FILTER with regex is slow and doesn't support ranking. wrong_sparql: | SELECT ?gene ?label WHERE { ?gene rdfs:label ?label . FILTER(REGEX(?label, "^BRCA", "i")) } correct_sparql: | SELECT ?gene ?label WHERE { ?gene rdfs:label ?label . ?label bif:contains "'BRCA*'" option (score ?sc) . } ORDER BY DESC(?sc) explanation: Use bif:contains with wildcard (*) and scoring for faster, ranked results. - title: Missing Species Filter problem: Querying without species returns mixed results from all organisms. wrong_sparql: | SELECT ?gene ?label WHERE { ?gene a terms:EnsemblGene ; rdfs:label ?label . FILTER(?label = "TP53") } correct_sparql: | SELECT ?gene ?label WHERE { ?gene a terms:EnsemblGene ; rdfs:label ?label ; obo:RO_0002162 taxonomy:9606 . FILTER(?label = "TP53") } explanation: Always filter by species taxonomy ID (9606 for human). - title: Incorrect Strand Detection problem: Trying to get strand from non-existent property. wrong_sparql: | SELECT ?gene ?strand WHERE { ?gene faldo:location/faldo:strand ?strand . } correct_sparql: | SELECT ?gene ?strand WHERE { ?gene faldo:location/faldo:begin/rdf:type ?strand_type . BIND(IF(?strand_type = faldo:ForwardStrandPosition, "+", "-") AS ?strand) } explanation: Strand is encoded in position type (ForwardStrandPosition/ReverseStrandPosition). common_errors: - error: Query timeout on broad searches causes: - Querying all genes without species filter - Scanning all FALDO locations without constraints solutions: - Include species filter (obo:RO_0002162 taxonomy:XXXX) - Use LIMIT to restrict results - Use bif:contains for text searches - Start with specific gene or chromosome constraints - error: Empty results for proteins causes: - Not all transcripts encode proteins (lncRNA, miRNA) - Using required pattern instead of OPTIONAL solutions: - Use OPTIONAL for so:translates_to - Filter by protein-coding biotype (ENSGLOSSARY_0000026) - Check transcript biotype before expecting proteins - error: Duplicate results with FALDO causes: - FALDO stores begin/end positions separately - Not using DISTINCT solutions: - Always use DISTINCT with location queries - Use LIMIT to control result size - error: Missing prefix causes 400 error causes: - Using so:part_of without defining PREFIX so: - Other properties from ontologies without prefixes solutions: - Always define all prefixes at the start of queries - Common prefixes needed - so:, obo:, faldo:, sio:, terms: