TogoMCP

schema_info: title: ChEMBL RDF description: | ChEMBL is a manually curated database of bioactive molecules with drug-like properties containing 2.4M+ compounds, 1.6M assays, 20M bioactivity measurements, and cross-references to external databases (UniProt, PDB, PubChem, DrugBank). Major entities include small molecules, proteins, targets, assays, activities, documents, drug mechanisms, and drug indications. Enables queries for compound-target-activity relationships, mechanism of action, and drug repositioning. endpoint: https://rdfportal.org/backend/ebi/sparql base_uri: http://rdf.ebi.ac.uk/resource/chembl/ graphs: - http://rdf.ebi.ac.uk/dataset/chembl version: mie_version: '1.1' mie_created: '2024-12-08' data_version: ChEMBL 34 update_frequency: Quarterly license: data_license: CC BY-SA 3.0 license_url: https://creativecommons.org/licenses/by-sa/3.0/ access: rate_limiting: No strict limit, reasonable use expected max_query_timeout: 60 seconds backend: Virtuoso (supports bif:contains) shape_expressions: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX bibo: <http://purl.org/ontology/bibo/> <MoleculeShape> { a [ cco:SmallMolecule ] ; rdfs:label xsd:string ; skos:prefLabel xsd:string ; cco:chemblId xsd:string ; cco:highestDevelopmentPhase xsd:integer ? ; cco:atcClassification xsd:string * ; cco:substanceType xsd:string ; cco:hasActivity @<ActivityShape> * ; cco:hasDrugIndication @<DrugIndicationShape> * ; cco:hasMechanism @<DrugMechanismShape> * ; cco:moleculeXref IRI * ; skos:exactMatch IRI * } <ActivityShape> { a [ cco:Activity ] ; cco:chemblId xsd:string ; cco:standardType xsd:string ; cco:standardValue xsd:string ? ; cco:standardUnits xsd:string ? ; cco:pChembl xsd:string ? ; cco:hasMolecule @<MoleculeShape> ; cco:hasAssay @<AssayShape> } <AssayShape> { a [ cco:Assay ] ; cco:chemblId xsd:string ; cco:assayType xsd:string ; cco:organismName xsd:string * ; cco:hasTarget @<TargetShape> } <TargetShape> { a [ cco:SingleProtein cco:ProteinComplex cco:ProteinFamily ] ; rdfs:label xsd:string ; cco:chemblId xsd:string ; cco:targetType xsd:string ; cco:organismName xsd:string * ; cco:hasTargetComponent @<TargetComponentShape> * } <TargetComponentShape> { a [ cco:TargetComponent ] ; cco:chemblId xsd:string ; skos:exactMatch IRI * } <DrugMechanismShape> { a [ cco:Mechanism ] ; cco:mechanismActionType xsd:string ? ; cco:hasMolecule @<MoleculeShape> ; cco:hasTarget @<TargetShape> ? } <DrugIndicationShape> { a [ cco:DrugIndication ] ; cco:hasMolecule @<MoleculeShape> ; cco:hasMesh IRI ; cco:hasMeshHeading xsd:string ; cco:highestDevelopmentPhase xsd:integer } sample_rdf_entries: - title: Small Molecule with Drug Development description: Marketed drug with ATC classification, cross-references, and drug indications. rdf: | chembl_molecule:CHEMBL1004 a cco:SmallMolecule ; rdfs:label "DOXYLAMINE" ; cco:chemblId "CHEMBL1004" ; cco:atcClassification "R06AA09" ; cco:highestDevelopmentPhase 4 ; cco:substanceType "Small molecule" ; cco:moleculeXref <http://www.drugbank.ca/drugs/DB00366> ; cco:moleculeXref <http://pubchem.ncbi.nlm.nih.gov/compound/3162> ; skos:exactMatch <http://purl.obolibrary.org/obo/CHEBI_51380> . - title: Bioactivity Measurement description: Ki binding measurement linking molecule, assay, and document. rdf: | chembl_activity:CHEMBL_ACT_1000385 a cco:Activity ; cco:chemblId "CHEMBL_ACT_1000385" ; cco:standardType "Ki" ; cco:standardValue "16.7" ; cco:standardUnits "nM" ; cco:hasMolecule chembl_molecule:CHEMBL331696 ; cco:hasAssay chembl_assay:CHEMBL696974 . - title: Target with UniProt Link description: Single protein target with organism and UniProt cross-reference. rdf: | chembl_target:CHEMBL1808 a cco:SingleProtein ; rdfs:label "Angiotensin-converting enzyme" ; cco:chemblId "CHEMBL1808" ; cco:targetType "SINGLE PROTEIN" ; cco:organismName "Homo sapiens" ; cco:hasTargetComponent chembl_target_cmpt:CHEMBL_TC_1332 . chembl_target_cmpt:CHEMBL_TC_1332 skos:exactMatch <http://purl.uniprot.org/uniprot/P12527> . - title: Drug Mechanism description: Inhibitor mechanism linking molecule and target. rdf: | chembl_drug_mechanism:CHEMBL_MEC_100 a cco:Mechanism ; cco:mechanismActionType "INHIBITOR" ; cco:hasMolecule chembl_molecule:CHEMBL1200475 ; cco:hasTarget chembl_target:CHEMBL1806 . - title: Drug Indication description: Clinical indication with MeSH disease term and development phase. rdf: | chembl_drug_indication:CHEMBL_IND_107436 a cco:DrugIndication ; cco:hasMolecule chembl_molecule:CHEMBL491473 ; cco:hasMeshHeading "Melanoma" ; cco:hasMesh <http://identifiers.org/mesh/D008545> ; cco:highestDevelopmentPhase 1 . sparql_query_examples: - title: Search Molecules with bif:contains description: Find molecules by name using full-text search with relevance ranking. question: Find molecules containing aspirin. complexity: basic sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?molecule ?label ?sc FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?molecule a cco:SmallMolecule ; rdfs:label ?label . ?label bif:contains "'aspirin'" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 100 - title: Get Human Protein Targets description: Find all human protein targets. question: What are human protein targets? complexity: basic sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?target ?label ?targetType FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?target a cco:SingleProtein ; rdfs:label ?label ; cco:targetType ?targetType ; cco:organismName "Homo sapiens" . } LIMIT 100 - title: Find Bioactivities for Molecule description: Retrieve activity measurements with assay and target information. question: What are bioactivities for CHEMBL1004? complexity: intermediate sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?activity ?type ?value ?units ?target FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?activity a cco:Activity ; cco:hasMolecule <http://rdf.ebi.ac.uk/resource/chembl/molecule/CHEMBL1004> ; cco:standardType ?type ; cco:hasAssay/cco:hasTarget ?target . OPTIONAL { ?activity cco:standardValue ?value } OPTIONAL { ?activity cco:standardUnits ?units } } LIMIT 100 - title: Keyword Search with Boolean Operators description: Find serine/threonine kinases excluding tyrosine kinases. question: Find kinases that are not tyrosine kinases. complexity: intermediate sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?target ?label ?sc FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?target a cco:SingleProtein ; rdfs:label ?label ; cco:organismName "Homo sapiens" . ?label bif:contains "('kinase' AND NOT 'tyrosine')" option (score ?sc) } ORDER BY DESC(?sc) LIMIT 100 - title: Drug Indications in Clinical Trials description: Get disease indications for molecules in advanced clinical development. question: What are drug indications in phase 3+? complexity: intermediate sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?molecule ?moleculeLabel ?disease ?phase FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?indication a cco:DrugIndication ; cco:hasMolecule ?molecule ; cco:hasMeshHeading ?disease ; cco:highestDevelopmentPhase ?phase . ?molecule rdfs:label ?moleculeLabel . FILTER(?phase >= 3) } ORDER BY DESC(?phase) LIMIT 100 - title: Potent Kinase Inhibitors description: Find potent inhibitors (IC50 < 100 nM) tested against kinase targets. question: What are potent kinase inhibitors? complexity: advanced sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT ?molecule ?label ?target ?targetLabel ?value FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?activity a cco:Activity ; cco:standardType "IC50" ; cco:standardValue ?value ; cco:standardUnits "nM" ; cco:hasMolecule ?molecule ; cco:hasAssay/cco:hasTarget ?target . ?target rdfs:label ?targetLabel . ?molecule rdfs:label ?label . ?targetLabel bif:contains "'kinase'" option (score ?sc) FILTER(xsd:decimal(?value) < 100) } ORDER BY DESC(?sc) LIMIT 100 - title: Cross-Database Integration description: Link ChEMBL molecules to DrugBank and UniProt targets. question: How to link ChEMBL to DrugBank and UniProt? complexity: advanced sparql: | PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> SELECT ?molecule ?moleculeLabel ?drugbankId ?uniprot ?targetLabel FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?molecule a cco:SmallMolecule ; rdfs:label ?moleculeLabel ; cco:moleculeXref ?drugbankId ; cco:hasActivity/cco:hasAssay/cco:hasTarget ?target . ?target cco:hasTargetComponent/skos:exactMatch ?uniprot ; rdfs:label ?targetLabel . FILTER(STRSTARTS(STR(?drugbankId), "http://www.drugbank.ca/drugs/")) FILTER(STRSTARTS(STR(?uniprot), "http://purl.uniprot.org/uniprot/")) } LIMIT 100 cross_references: - pattern: cco:moleculeXref description: Molecules link to external databases via cco:moleculeXref using database-specific URI patterns. databases: chemical: - PubChem (2.2M+) - ZINC (1.2M+) - ChEBI (35k) drug: - DrugBank (8.4k) - FDA SRS (32k) - HMDB (12k) research: - LINCS (16k) - SureChEMBL (540k) - Wikipedia sparql: | SELECT ?molecule ?xref FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?molecule a cco:SmallMolecule ; cco:moleculeXref ?xref . FILTER(STRSTARTS(STR(?xref), "http://www.drugbank.ca/")) } LIMIT 100 - pattern: skos:exactMatch description: Target components link to UniProt proteins for sequence and functional data. databases: protein: - UniProt (11k) - Ensembl - PDB (64k) sparql: | SELECT ?targetComponent ?uniprot FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?targetComponent a cco:TargetComponent ; skos:exactMatch ?uniprot . FILTER(STRSTARTS(STR(?uniprot), "http://purl.uniprot.org/")) } LIMIT 100 - pattern: cco:hasMesh / cco:hasEFO description: Drug indications link to MeSH and EFO disease ontologies. databases: disease: - MeSH (51k indications) - EFO (subset) sparql: | SELECT ?indication ?mesh ?meshHeading ?efo FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?indication a cco:DrugIndication ; cco:hasMesh ?mesh ; cco:hasMeshHeading ?meshHeading . OPTIONAL { ?indication cco:hasEFO ?efo } } LIMIT 100 - pattern: bibo:pmid description: Documents link to PubMed for literature tracking. databases: literature: - PubMed (88k docs) - DOI sparql: | SELECT ?document ?pmid ?doi FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?document a cco:Document ; bibo:pmid ?pmid . OPTIONAL { ?document bibo:doi ?doi } } LIMIT 100 - pattern: cco:taxonomy description: NCBI Taxonomy links for organism information on targets, assays, and cell lines. databases: taxonomy: - NCBI Taxonomy sparql: | SELECT ?target ?organism ?taxonomy FROM <http://rdf.ebi.ac.uk/dataset/chembl> WHERE { ?target a cco:SingleProtein ; cco:organismName ?organism ; cco:taxonomy ?taxonomy . } LIMIT 100 architectural_notes: schema_design: - Molecule-Activity-Assay-Target core model for bioactivity measurements - TargetComponent bridges Targets to UniProt identifiers - Drug mechanisms separate molecular interactions from bioactivities - Hierarchical protein classification using SKOS performance: - Always specify FROM graph clause - Use bif:contains for keyword searches (faster than FILTER/REGEX) - Boolean operators in bif:contains work efficiently (AND, OR, NOT) - Filter on development phase, assay type, or activity type well-indexed - Start with specific target types (cco:SingleProtein) data_integration: - UniProt mappings via TargetComponent for protein data - PubChem/DrugBank/ChEBI for chemical structure enrichment - MeSH/EFO for disease ontology queries - NCBI Taxonomy for organism-specific filtering data_quality: - Not all molecules have chemical descriptors - Activity values may lack units - always check cco:standardUnits - Some targets lack UniProt mappings (non-human organisms) - Development phase most complete for marketed drugs data_statistics: total_molecules: 2400000 total_activities: 20000000 total_assays: 1600000 total_targets: 13000 coverage: molecules_with_activities: ~80% targets_with_uniprot: ~85% activities_with_standard_values: ~70% molecules_with_pubchem: ~90% cardinality: avg_activities_per_molecule: 8.5 avg_assays_per_target: 120 avg_xrefs_per_molecule: 4.2 performance_characteristics: - 'Simple lookups: <1s for 100 results' - 'Activity queries with filters: 2-5s' - 'bif:contains keyword search: very fast' anti_patterns: - title: FILTER/REGEX vs bif:contains problem: FILTER/REGEX is slow and not optimized for large text searches. wrong_sparql: | SELECT ?molecule ?label WHERE { ?molecule a cco:SmallMolecule ; rdfs:label ?label . FILTER(REGEX(?label, "kinase", "i")) } correct_sparql: | SELECT ?molecule ?label ?sc WHERE { ?molecule a cco:SmallMolecule ; rdfs:label ?label . ?label bif:contains "'kinase'" option (score ?sc) } ORDER BY DESC(?sc) explanation: Use bif:contains for Virtuoso-optimized full-text search with relevance ranking and Boolean operators. - title: Forgetting Activity Units problem: Comparing activity values without checking units leads to incorrect conclusions. wrong_sparql: | SELECT ?molecule ?value WHERE { ?activity cco:hasMolecule ?molecule ; cco:standardValue ?value . FILTER(xsd:decimal(?value) < 100) } correct_sparql: | SELECT ?molecule ?value ?units WHERE { ?activity cco:hasMolecule ?molecule ; cco:standardValue ?value ; cco:standardUnits ?units . FILTER(xsd:decimal(?value) < 100 && ?units = "nM") } explanation: Always filter by cco:standardUnits when comparing activity values (nM, uM, %, etc.). - title: Inefficient Target Component Queries problem: Querying target components without specifying target type is slow. wrong_sparql: | SELECT ?component ?uniprot WHERE { ?component a cco:TargetComponent ; skos:exactMatch ?uniprot . FILTER(STRSTARTS(STR(?uniprot), "http://purl.uniprot.org")) } correct_sparql: | SELECT ?target ?component ?uniprot WHERE { ?target a cco:SingleProtein ; cco:hasTargetComponent ?component . ?component skos:exactMatch ?uniprot . FILTER(STRSTARTS(STR(?uniprot), "http://purl.uniprot.org/uniprot/")) } explanation: Start from specific target types and use precise FILTER patterns. common_errors: - error: Query timeout causes: - Missing FROM clause or GRAPH specification - Using FILTER/REGEX instead of bif:contains - Missing LIMIT clause solutions: - Always include FROM <http://rdf.ebi.ac.uk/dataset/chembl> - Use bif:contains for text searches - Add type constraints before text filtering - Use LIMIT appropriately (100-10000) - error: Empty results for cross-references causes: - Incorrect URI pattern for external database - Querying wrong entity type solutions: - Check sample data for exact URI patterns - Use STRSTARTS for URI matching - Verify entity type supports cross-reference property - Use OPTIONAL for cross-references that may not exist - error: Incorrect activity comparisons causes: - Comparing without checking standardType - Missing units check (mixing nM and uM) - Not handling NULL values solutions: - Always filter by cco:standardType (IC50, EC50, Ki) - Include cco:standardUnits in WHERE and filter - Use OPTIONAL with FILTER for numeric values - Consider cco:pChembl for normalized comparison