TogoMCP

schema_info: title: GlyCosmos RDF Database description: | Comprehensive glycoscience portal integrating glycan structures (GlyTouCan), glycoproteins, glycosylation sites, glycogenes, glycoepitopes, and lectin-glycan interactions across 100+ named graphs for multi-species glycobiology research and biomarker discovery. endpoint: https://ts.glycosmos.org/sparql base_uri: http://rdf.glycoinfo.org/ graphs: - http://rdf.glytoucan.org/core - http://rdf.glycosmos.org/glycoprotein - http://rdf.glycosmos.org/glycogenes - http://rdf.glycoinfo.org/glycoepitope - http://rdf.glycosmos.org/sugarbind - http://rdf.glycosmos.org/pathway - http://rdf.glycosmos.org/disease version: mie_version: "1.1" mie_created: "2025-12-08" data_version: "Release 2024.12" update_frequency: "Quarterly" license: data_license: "CC BY 4.0" license_url: "https://creativecommons.org/licenses/by/4.0/" access: rate_limiting: "No strict limits, reasonable use" max_query_timeout: "120 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 xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#> PREFIX glycoconjugate: <http://purl.jp/bio/12/glyco/conjugate#> PREFIX glycoepitope: <http://www.glycoepitope.jp/epitopes/glycoepitope.owl#> PREFIX sugarbind: <http://rdf.glycoinfo.org/SugarBind/ontology#> PREFIX sio: <http://semanticscience.org/resource/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> <SaccharideShape> { a [ glycan:Saccharide ] ; glytoucan:has_primary_id xsd:string ; glycan:has_Resource_entry IRI * } <ResourceEntryShape> { a [ glycan:Resource_entry ] ; rdfs:label xsd:string ? ; dcterms:identifier xsd:string ? } <GlycoproteinShape> { a [ glycan:Glycoprotein ] ; rdfs:label xsd:string ; rdfs:seeAlso IRI * ; glycan:has_taxon IRI ? ; glycoconjugate:glycosylated_at @<GlycosylationSiteShape> * } <GlycosylationSiteShape> { a [ glycoconjugate:Glycosylation_Site ] ; sio:SIO_000772 IRI ; faldo:location @<FaldoLocationShape> ? ; dcterms:references IRI * ; glycoconjugate:has_saccharide IRI * } <FaldoLocationShape> { a [ faldo:ExactPosition ] OR [ faldo:FuzzyPosition ] ; faldo:position xsd:integer } <GlycogeneShape> { a [ glycan:Glycogene ] AND [ sio:SIO_010035 ] ; rdfs:label xsd:string ; rdfs:seeAlso IRI * ; glycan:has_taxon IRI ? ; dcterms:description xsd:string ? } <GlycanEpitopeShape> { a [ glycan:Glycan_epitope ] ; rdfs:label xsd:string ; skos:altLabel xsd:string * ; glycan:has_glycosequence IRI * ; glycoepitope:has_antibody IRI * ; glycoepitope:organism IRI * ; glycoepitope:tissue IRI * } <LectinShape> { a [ sugarbind:Lectin ] ; rdfs:label xsd:string ; rdfs:seeAlso IRI * ; sugarbind:uniprotId IRI * } sample_rdf_entries: - title: Glycan with GlyTouCan ID description: Core glycan entry with accession and external database link. rdf: | glycoinfo:glycan/G00051MO a glycan:Saccharide ; glytoucan:has_primary_id "G00051MO" ; glycan:has_Resource_entry glycoinfo:resource-entry/G00051MO . - title: Glycan with ChEBI Cross-Reference description: External database entry linking glycan to ChEBI chemical database. rdf: | <http://purl.obolibrary.org/obo/CHEBI_146500> a glycan:Resource_entry ; rdfs:label "ChEBI" ; dcterms:identifier "146500" . glycoinfo:glycan/G01416HI glycan:has_resource_entry <http://purl.obolibrary.org/obo/CHEBI_146500> . - title: Glycoprotein with Glycosylation Site description: Human protein with N-glycosylation site at specific sequence position. rdf: | glycosmos:glycoprotein/P02763 a glycan:Glycoprotein ; rdfs:label "Alpha-1-acid glycoprotein 1" ; glycan:has_taxon <http://identifiers.org/taxonomy/9606> ; glycoconjugate:glycosylated_at glycosmos:glycosylationsite/SITE00187901 . glycosmos:glycosylationsite/SITE00187901 a glycoconjugate:Glycosylation_Site ; sio:SIO_000772 glycoinfo:dbid/glygen/P02763 ; faldo:location [ a faldo:ExactPosition ; faldo:position 33 ] . - title: Glycogene Entry description: Gene involved in glycosylation with functional description. rdf: | glycosmos:glycogene/1436 a glycan:Glycogene, sio:SIO_010035 ; rdfs:label "CSF1R" ; glycan:has_taxon <http://identifiers.org/taxonomy/9606> ; dcterms:description "colony stimulating factor 1 receptor" . - title: Glycan Epitope description: Immunological epitope with alternative nomenclature. rdf: | <http://www.glycoepitope.jp/epitopes/EP0007> a glycan:Glycan_epitope ; rdfs:label "Lewis a" ; skos:altLabel "Le^a" ; glycan:has_glycosequence <http://www.glycoepitope.jp/epitopes/EP0007/glycoct> . sparql_query_examples: - title: Search Epitopes by Keyword with bif:contains description: Full-text search with relevance scoring question: Which epitopes contain "Lewis" in their name? complexity: basic sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?epitope ?label FROM <http://rdf.glycoinfo.org/glycoepitope> WHERE { ?epitope a glycan:Glycan_epitope ; rdfs:label ?label . ?label bif:contains "'Lewis'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 20 - title: Get Epitope Functional Annotations description: Retrieve biological context for specific epitopes question: What are the antibodies and tissues for epitope EP0007? complexity: basic sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glycoepitope: <http://www.glycoepitope.jp/epitopes/glycoepitope.owl#> SELECT ?antibody ?organism ?tissue FROM <http://rdf.glycoinfo.org/glycoepitope> WHERE { <http://www.glycoepitope.jp/epitopes/EP0007> a glycan:Glycan_epitope . OPTIONAL { <http://www.glycoepitope.jp/epitopes/EP0007> glycoepitope:has_antibody ?antibody } OPTIONAL { <http://www.glycoepitope.jp/epitopes/EP0007> glycoepitope:organism ?organism } OPTIONAL { <http://www.glycoepitope.jp/epitopes/EP0007> glycoepitope:tissue ?tissue } } - title: Count Glycoproteins by Species description: Aggregate statistics by taxonomy question: How many glycoproteins per species? complexity: intermediate sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> SELECT ?taxon (COUNT(DISTINCT ?protein) as ?count) FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?protein a glycan:Glycoprotein ; glycan:has_taxon ?taxon . } GROUP BY ?taxon ORDER BY DESC(?count) LIMIT 20 - title: Find Human Glycosylation Sites with Positions description: Retrieve sequence positions for human proteins question: Which human proteins have glycosylation sites at which positions? complexity: intermediate sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glycoconjugate: <http://purl.jp/bio/12/glyco/conjugate#> PREFIX faldo: <http://biohackathon.org/resource/faldo#> SELECT ?protein ?site ?position FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?protein a glycan:Glycoprotein ; glycan:has_taxon <http://identifiers.org/taxonomy/9606> ; glycoconjugate:glycosylated_at ?site . ?site faldo:location/faldo:position ?position . } LIMIT 50 - title: Search Glycogene Descriptions description: Filter genes by functional annotations question: Which glycogenes have "receptor" in their description? complexity: intermediate sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX dcterms: <http://purl.org/dc/terms/> SELECT ?gene ?symbol ?description FROM <http://rdf.glycosmos.org/glycogenes> WHERE { ?gene a glycan:Glycogene ; rdfs:label ?symbol ; dcterms:description ?description . FILTER(CONTAINS(LCASE(?description), "receptor")) } LIMIT 20 - title: Glycan-Protein-Gene Integration description: Multi-entity join across graphs question: For glycan G00051MO, find associated proteins and genes complexity: advanced sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#> PREFIX glycoconjugate: <http://purl.jp/bio/12/glyco/conjugate#> PREFIX sio: <http://semanticscience.org/resource/> SELECT DISTINCT ?protein ?gene FROM <http://rdf.glytoucan.org/core> FROM <http://rdf.glycosmos.org/glycoprotein> FROM <http://rdf.glycosmos.org/glycogenes> WHERE { ?glycan glytoucan:has_primary_id "G00051MO" . OPTIONAL { ?site glycoconjugate:has_saccharide ?glycan ; sio:SIO_000772 ?proteinRef . ?protein rdfs:seeAlso ?proteinRef . OPTIONAL { ?protein rdfs:seeAlso ?uniprotRef . FILTER(CONTAINS(STR(?uniprotRef), "uniprot")) ?gene rdfs:seeAlso ?uniprotRef . } } } LIMIT 100 - title: Human Glycobiology Network Statistics description: Aggregate analysis with multiple joins question: Compute statistics for human glycoproteins complexity: advanced sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glycoconjugate: <http://purl.jp/bio/12/glyco/conjugate#> SELECT (COUNT(DISTINCT ?protein) as ?totalProteins) (COUNT(DISTINCT ?site) as ?totalSites) (AVG(?siteCount) as ?avgSitesPerProtein) WHERE { { SELECT ?protein (COUNT(?site) as ?siteCount) FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?protein a glycan:Glycoprotein ; glycan:has_taxon <http://identifiers.org/taxonomy/9606> ; glycoconjugate:glycosylated_at ?site . } GROUP BY ?protein LIMIT 1000 } } cross_references: - pattern: glycan:has_Resource_entry description: | Glycans link to external databases via Resource_entry objects. Coverage: 101,600/117,864 glycans (~86%). databases: structure: Carbbank (44K), GlycomeDB (39K), GLYCOSCIENCES.de (22K), JCGGDB (22K), BCSDB (8K), CFG (8K) chemical: PubChem Substance (32K), PubChem Compound (32K), ChEBI (11K), KEGG (10K) protein_structure: PDB (6K) sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX glytoucan: <http://www.glytoucan.org/glyco/owl/glytoucan#> SELECT ?glycanId ?dbName ?dbId FROM <http://rdf.glytoucan.org/core> WHERE { ?glycan glytoucan:has_primary_id ?glycanId ; glycan:has_Resource_entry ?entry . ?entry rdfs:label ?dbName . OPTIONAL { ?entry dcterms:identifier ?dbId } } LIMIT 50 - pattern: rdfs:seeAlso (Glycoproteins) description: | Protein database links via rdfs:seeAlso. Total: 153,178 glycoproteins. databases: protein: UniProt (139K), PubChem (16K), ACGG GPDB2 (14K), GlyGen (12K), GlyConnect (2K) sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> SELECT ?protein ?externalDB FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?protein a glycan:Glycoprotein ; rdfs:seeAlso ?externalDB . # FILTER(CONTAINS(STR(?externalDB), "purl.uniprot.org/uniprot")) } LIMIT 50 - pattern: rdfs:seeAlso (Glycogenes) description: | Gene database links via rdfs:seeAlso. Total: 423,164 glycogenes. databases: gene: NCBI Gene (423K), KEGG Genes (381K) sparql: | PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> SELECT ?gene ?externalDB FROM <http://rdf.glycosmos.org/glycogenes> WHERE { ?gene a glycan:Glycogene ; rdfs:seeAlso ?externalDB . # FILTER(CONTAINS(STR(?externalDB), "ncbigene")) } LIMIT 50 - pattern: sio:SIO_000772 description: | Glycosylation sites reference parent proteins. Total: 414,798 sites. databases: protein: UniProt, GlyGen, GlyConnect, ACGG GPDB2, O-GlcNAc Database sparql: | PREFIX glycoconjugate: <http://purl.jp/bio/12/glyco/conjugate#> PREFIX sio: <http://semanticscience.org/resource/> SELECT ?site ?proteinRef ?position FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?site a glycoconjugate:Glycosylation_Site ; sio:SIO_000772 ?proteinRef . OPTIONAL { ?site faldo:location/faldo:position ?position } } LIMIT 50 architectural_notes: schema_design: - Multi-graph architecture (100+ graphs) for modular data management - FALDO for sequence positions, SIO for semantic relationships - Resource_entry pattern for external database cross-references performance: - Always specify FROM graph to reduce search space significantly - Use bif:contains for label searches (full-text index + relevance scoring) - Early taxonomy filtering for glycoprotein queries - Pagination essential for 414K+ glycosylation sites data_integration: - ChEBI, PubChem for chemical IDs; UniProt for proteins; NCBI Gene for genes - KEGG/Reactome for pathways; PDB for structures data_quality: - GlyTouCan IDs: G[0-9]{5}[A-Z]{2} pattern - Label coverage varies: glycans <1%, proteins 17%, genes 32% - Taxon coverage: proteins 18%, genes 0.4% data_statistics: total_entities: glycans: 117864 glycoproteins: 153178 glycosylation_sites: 414798 glycogenes: 423164 glycoepitopes: 173 lectins: 739 coverage: glycans_with_primary_id: "~99.8%" glycans_with_resource_entry: "~86%" glycoproteins_with_labels: "~17%" glycosylation_sites_with_positions: ">90%" glycogenes_with_descriptions: "~8%" cardinality: avg_glycosylation_sites_per_protein: 2.6 max_glycosylation_sites_per_protein: 276 performance_characteristics: - FROM clause improves speed 10-100x on multi-graph queries - bif:contains fast for 173 epitopes, use FILTER for 414K sites with early filters - Multi-graph joins require explicit FROM for each graph anti_patterns: - title: "Omitting FROM Clause" problem: "Searches all 100+ graphs causing timeouts" wrong_sparql: | SELECT ?epitope WHERE { ?epitope a glycan:Glycan_epitope } correct_sparql: | SELECT ?epitope FROM <http://rdf.glycoinfo.org/glycoepitope> WHERE { ?epitope a glycan:Glycan_epitope } explanation: "FROM clause limits search to relevant graph, critical for performance" - title: "Using FILTER Instead of bif:contains" problem: "No full-text index or relevance ranking" wrong_sparql: | SELECT ?label WHERE { ?epitope rdfs:label ?label . FILTER(CONTAINS(LCASE(?label), "lewis")) } correct_sparql: | SELECT ?label WHERE { ?epitope rdfs:label ?label . ?label bif:contains "'Lewis'" option (score ?sc) } ORDER BY DESC(?sc) explanation: "bif:contains uses full-text index and provides relevance scoring" - title: "No Pagination on Large Datasets" problem: "414K sites cause timeout" wrong_sparql: | SELECT ?site WHERE { ?site a glycoconjugate:Glycosylation_Site } correct_sparql: | SELECT ?site FROM <http://rdf.glycosmos.org/glycoprotein> WHERE { ?protein glycan:has_taxon <http://identifiers.org/taxonomy/9606> ; glycoconjugate:glycosylated_at ?site . } LIMIT 100 explanation: "Filter early by taxon, always add LIMIT for large datasets" common_errors: - error: "Query timeout" causes: - "Missing FROM clause" - "No early filters or LIMIT on large datasets" solutions: - "Add FROM clause with specific graph(s)" - "Add early filters (taxon, ID) and LIMIT" - error: "No label results" causes: - "Glycan labels rarely populated (<1%)" - "Protein/gene labels partial (17%/32%)" solutions: - "Use GlyTouCan IDs for glycans" - "Use rdfs:seeAlso external database links" - error: "bif:contains fails on descriptions" causes: - "Full-text index optimized for rdfs:label only" solutions: - "Use bif:contains only on rdfs:label/skos:altLabel" - "Use FILTER(CONTAINS()) for other properties"