TogoMCP

schema_info: title: Rhea - Annotated Reactions Database description: | Rhea is a comprehensive expert-curated database of biochemical reactions. It contains 17,078 reactions (including 34,156 directional and 17,078 bidirectional representations), 11,763 small molecule compounds, and 254 polymer structures. All reactions are atom-balanced, chemically annotated, and linked to standard compound vocabularies (ChEBI). Rhea provides extensive cross-references to metabolic pathway databases (KEGG, MetaCyc, Reactome), enzyme classifications (EC numbers), and gene/protein function annotations (Gene Ontology). Transport reactions (5,984 total) include cellular location information. Reactions are classified by approval status and include literature citations. Rhea serves as the reference reaction resource for UniProtKB enzyme annotation. endpoint: https://sparql.rhea-db.org/sparql base_uri: http://rdf.rhea-db.org/ graphs: - http://rdfportal.org/dataset/rhea version: mie_version: '1.0' mie_created: '2025-01-21' data_version: Release 2024 update_frequency: Quarterly license: data_license: CC BY 4.0 license_url: https://www.rhea-db.org/help/license access: rate_limiting: No explicit rate limit max_query_timeout: 60 seconds shape_expressions: | PREFIX rhea: <http://rdf.rhea-db.org/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX chebi: <http://purl.obolibrary.org/obo/> PREFIX uniprot: <http://purl.uniprot.org/enzyme/> # Reaction (master/unspecified direction) <ReactionShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:Reaction ] ; rdfs:label xsd:string ; rhea:accession xsd:string ; rhea:id xsd:integer ; rhea:equation xsd:string ; rhea:htmlEquation xsd:string ; rhea:status IRI ; # rhea:Approved, rhea:Preliminary, rhea:Obsolete rhea:isChemicallyBalanced xsd:boolean ; rhea:isTransport xsd:boolean ; rhea:side IRI + ; # Links to ReactionSide rhea:directionalReaction IRI + ; # Links to DirectionalReaction rhea:bidirectionalReaction IRI ? ; rhea:ec IRI * ; # Links to UniProt enzyme rdfs:seeAlso IRI * ; # Cross-references to GO, KEGG, etc. rdfs:comment xsd:string ? # Literature citations } # DirectionalReaction (left-to-right or right-to-left) <DirectionalReactionShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:DirectionalReaction ] * ; rdfs:subClassOf IRI + # Links to parent Reaction } # BidirectionalReaction (reversible) <BidirectionalReactionShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:BidirectionalReaction ] * ; rdfs:subClassOf IRI + } # ReactionSide (left or right side of reaction) <ReactionSideShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:ReactionSide ] ; rhea:contains IRI + ; # Links to Participant rhea:contains1 IRI * ; # Stoichiometry = 1 rhea:contains2 IRI * ; # Stoichiometry = 2 rhea:contains3 IRI * ; # Stoichiometry = 3 rhea:containsN IRI * ; # Stoichiometry > 3 rhea:curatedOrder xsd:integer ; # Display order rhea:transformableTo IRI ? # Links to opposite side } # ReactionParticipant (compound in a reaction) <ParticipantShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:ReactionParticipant ] ; rdfs:subClassOf IRI + ; rhea:compound IRI ; # Links to Compound rhea:location IRI ? # rhea:In or rhea:Out for transport } # SmallMolecule compound <SmallMoleculeShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:SmallMolecule ] ; rdfs:subClassOf IRI * ; # Links to ChEBI rhea:id xsd:integer ; rhea:accession xsd:string ; # CHEBI ID rhea:name xsd:string ; rhea:htmlName xsd:string ; rhea:formula xsd:string ; rhea:charge xsd:integer ; rhea:chebi IRI # ChEBI URI } # Polymer compound <PolymerShape> { a [ rdfs:Class ] ; rdfs:subClassOf [ rhea:Polymer ] ; rhea:id xsd:integer ; rhea:accession xsd:string ; # POLYMER:XXXXX rhea:name xsd:string ; rhea:htmlName xsd:string ; rhea:formula xsd:string ; # Contains (n) or (n-1) rhea:charge xsd:string ; # May contain (n) notation rhea:polymerizationIndex xsd:string ; # e.g., "n", "n-1" rhea:underlyingChebi IRI ? # ChEBI of repeating unit } sample_rdf_entries: - title: Master Reaction (Unspecified Direction) description: A master reaction entry representing pentanamide hydrolysis. Links to directional and bidirectional forms, EC number, and external databases. rdf: | <http://rdf.rhea-db.org/10000> a rdfs:Class ; rdfs:subClassOf rhea:Reaction ; rdfs:label "H2O + pentanamide = NH4(+) + pentanoate" ; rdfs:comment "Published in: Friedich, C.G. and Mitrenga, G. ..." ; rdfs:seeAlso <http://purl.obolibrary.org/obo/GO_0050168> ; rhea:accession "RHEA:10000" ; rhea:id 10000 ; rhea:equation "H2O + pentanamide = NH4(+) + pentanoate" ; rhea:htmlEquation "H<small>₂</small>O + pentanamide = ..." ; rhea:status rhea:Approved ; rhea:isChemicallyBalanced 1 ; rhea:isTransport 0 ; rhea:ec <http://purl.uniprot.org/enzyme/3.5.1.50> ; rhea:side <http://rdf.rhea-db.org/10000_L> ; rhea:side <http://rdf.rhea-db.org/10000_R> ; rhea:directionalReaction <http://rdf.rhea-db.org/10001> ; rhea:directionalReaction <http://rdf.rhea-db.org/10002> ; rhea:bidirectionalReaction <http://rdf.rhea-db.org/10003> . - title: Reaction Side with Participants description: Left side of a reaction, containing two participants (compounds) with defined stoichiometry and transformability to the opposite side. rdf: | <http://rdf.rhea-db.org/10000_L> a rdfs:Class ; rdfs:subClassOf rhea:ReactionSide ; rhea:contains <http://rdf.rhea-db.org/Participant_10000_compound_1283> ; rhea:contains <http://rdf.rhea-db.org/Participant_10000_compound_4808> ; rhea:contains1 <http://rdf.rhea-db.org/Participant_10000_compound_1283> ; rhea:contains1 <http://rdf.rhea-db.org/Participant_10000_compound_4808> ; rhea:curatedOrder 1 ; rhea:transformableTo <http://rdf.rhea-db.org/10000_R> . - title: Small Molecule Compound description: A small molecule compound (water) with chemical formula, charge, and ChEBI cross-reference. rdf: | <http://rdf.rhea-db.org/Compound_1283> a rdfs:Class ; rdfs:subClassOf rhea:SmallMolecule ; rdfs:subClassOf <http://purl.obolibrary.org/obo/CHEBI_15377> ; rhea:id 1283 ; rhea:accession "CHEBI:15377" ; rhea:name "H2O" ; rhea:htmlName "H<small>₂</small>O" ; rhea:formula "H2O" ; rhea:charge 0 ; rhea:chebi <http://purl.obolibrary.org/obo/CHEBI_15377> . - title: Polymer Compound description: A polymer structure representing a polysaccharide chain with polymerization index notation and underlying ChEBI reference. rdf: | <http://rdf.rhea-db.org/Compound_10035> a rdfs:Class ; rdfs:subClassOf rhea:Polymer ; rhea:id 10035 ; rhea:accession "POLYMER:10035" ; rhea:name "[(1->4)-beta-D-glucosyl](n-1)" ; rhea:htmlName "[(1&#8594;4)-&#946;-<small>D</small>-glucosyl]<small>_(<i>n</i>-1)</small>" ; rhea:formula "H2O(C6H10O5)<i>_n-1</i>" ; rhea:charge "(0)(0)<i>_n-1</i>" ; rhea:polymerizationIndex "n-1" ; rhea:underlyingChebi <http://purl.obolibrary.org/obo/CHEBI_18246> . - title: Transport Reaction Participant with Location description: Participant in a transport reaction with cellular location annotation indicating substrate is inside the cell. rdf: | <http://rdf.rhea-db.org/Participant_20621_compound_1073_in> a rdfs:Class ; rdfs:subClassOf rhea:ReactionParticipant ; rdfs:subClassOf <http://rdf.rhea-db.org/Compound_1073> ; rhea:compound <http://rdf.rhea-db.org/Compound_1073> ; rhea:location rhea:In . sparql_query_examples: - title: Search Reactions by Keyword description: Find approved reactions containing specific keywords (e.g., "ATP") using full-text search with relevance ranking. question: What are some approved reactions involving ATP? complexity: basic sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation ?label WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rdfs:label ?label ; rhea:status rhea:Approved . ?equation bif:contains "'atp'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 20 - title: Get Reaction Details by Accession description: Retrieve complete information for a specific Rhea reaction using its accession ID. question: What are the details of reaction RHEA:10000? complexity: basic sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?property ?value WHERE { ?reaction rhea:accession "RHEA:10000" ; ?property ?value . } - title: Find Transport Reactions description: Identify reactions that involve transport across cellular membranes with their substrates and locations. question: Which reactions are classified as transport reactions? complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation ?participant ?compound ?location WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rhea:isTransport 1 ; rhea:side ?side . ?side rhea:contains ?participant . ?participant rhea:compound ?compound ; rhea:location ?location . } LIMIT 50 - title: Get Reactions with EC Number and GO Terms description: Find reactions annotated with both enzyme commission numbers and Gene Ontology molecular function terms. question: Which reactions have EC classification and GO annotations? complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> PREFIX go: <http://purl.obolibrary.org/obo/> SELECT DISTINCT ?reaction ?equation ?ec ?goTerm WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rhea:ec ?ec ; rdfs:seeAlso ?goTerm . FILTER(STRSTARTS(STR(?goTerm), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 50 - title: Complex Keyword Search with Boolean Operators description: Find reactions containing multiple keywords using AND/OR operators with relevance ranking. question: What reactions involve both glucose and phosphate? complexity: intermediate sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rhea:status rhea:Approved . ?equation bif:contains "'glucose' AND 'phosphate'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 20 - title: Get Directional Variants of a Reaction description: For a master reaction, retrieve all directional and bidirectional representations with their relationships. question: What are all the directional forms of reaction RHEA:10000? complexity: advanced sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?masterReaction ?directional ?bidirectional ?type WHERE { ?masterReaction rhea:accession "RHEA:10000" . OPTIONAL { ?masterReaction rhea:directionalReaction ?directional . ?directional rdfs:subClassOf ?dirType . FILTER(?dirType = rhea:DirectionalReaction) BIND("directional" AS ?type) } OPTIONAL { ?masterReaction rhea:bidirectionalReaction ?bidirectional . BIND("bidirectional" AS ?type) } } - title: Complex Query - Reactions with Polymers and Citations description: Find reactions involving polymer substrates that have literature citations and cross-references to pathway databases. question: Which reactions involve polymers and have extensive literature support? complexity: advanced sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT DISTINCT ?reaction ?equation ?polymer ?citation ?kegg WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rhea:side ?side . ?side rhea:contains ?participant . ?participant rhea:compound ?compound . ?compound rdfs:subClassOf rhea:Polymer ; rhea:name ?polymer . OPTIONAL { ?reaction rdfs:comment ?citation . } OPTIONAL { ?reaction rdfs:seeAlso ?kegg . FILTER(CONTAINS(STR(?kegg), "kegg.reaction")) } } LIMIT 30 cross_references: - pattern: rdfs:seeAlso description: | Reactions link to external databases via rdfs:seeAlso. Cross-references use identifiers.org URIs or database-specific namespaces. Transport reactions include cellular compartment annotations (rhea:In, rhea:Out). Compounds link to ChEBI via rhea:chebi property and rdfs:subClassOf relationships. databases: Gene_Ontology: - GO (Molecular Function): High coverage via http://purl.obolibrary.org/obo/GO_XXXXXXX Metabolic_Pathways: - KEGG Reaction: Extensive via http://identifiers.org/kegg.reaction/RXXXXX - BioCyc/MetaCyc: Comprehensive via http://identifiers.org/biocyc/METACYC:XXX - Reactome: Selected pathways via http://identifiers.org/reactome/R-HSA-XXXXXX Enzyme_Mechanisms: - MACiE: Mechanism annotations via http://identifiers.org/macie/MXXXX Chemical_Structures: - ChEBI: All compounds via http://purl.obolibrary.org/obo/CHEBI_XXXXX Enzyme_Classification: - EC Numbers: Via http://purl.uniprot.org/enzyme/X.X.X.X sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation ?externalDB WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rdfs:seeAlso ?externalDB . } LIMIT 100 architectural_notes: schema_design: - Reactions have three representations - master (unspecified direction), directional (L→R, R→L), and bidirectional (reversible) - Each reaction ID forms a quartet - e.g., 10000 (master), 10001 (L→R), 10002 (R→L), 10003 (bidirectional) - Reaction sides (_L, _R suffixes) contain participants with stoichiometry encoded in property names (contains1, contains2, etc.) - Participants link to compounds via rhea:compound, with optional rhea:location for transport reactions - Compounds are either SmallMolecule (with ChEBI links) or Polymer (with polymerization indices) - All reactions are subclasses of rdfs:Class using OWL/RDFS vocabulary performance: - Use bif:contains for text search in equations and labels with relevance scoring - much faster than FILTER(CONTAINS()) - Boolean operators work in bif:contains - use 'glucose' AND 'phosphate' or 'atp' OR 'gtp' for complex searches - Filter by rhea:status early to focus on rhea:Approved reactions (66,740 vs 68,312 total) - When querying participants, start from reactions then traverse to compounds for better performance - Limit results when exploring relationships between reactions, sides, and participants - ORDER BY DESC(?sc) after bif:contains to get most relevant results first data_integration: - ChEBI integration via rdfs:subClassOf and rhea:chebi properties enables compound-level queries - EC numbers link to UniProt enzyme namespace for protein function connections - GO molecular function terms provide gene/protein annotation pathways - KEGG, MetaCyc, and Reactome links enable metabolic pathway mapping data_quality: - All approved reactions are chemically balanced (rhea:isChemicallyBalanced = 1) - Some reactions have Preliminary status (452) indicating ongoing curation - Obsolete reactions (1,120) are retained for historical reference - Literature citations in rdfs:comment use structured format but require text parsing - Polymers use specialized notation (n, n-1) in formulas and charges data_statistics: total_reactions: 17078 directional_reactions: 34156 bidirectional_reactions: 17078 small_molecules: 11763 polymers: 254 transport_reactions: 5984 reaction_status: approved: 66740 preliminary: 452 obsolete: 1120 coverage: reactions_with_ec: ~45% (based on enzyme classification overlap) reactions_with_go: ~55% (molecular function annotations) reactions_with_kegg: ~35% (metabolic pathway coverage) compounds_with_chebi: 100% (all small molecules have ChEBI IDs) cardinality: avg_participants_per_reaction: ~4-6 (substrates + products) avg_cross_refs_per_reaction: 1-5 (GO, KEGG, MetaCyc, etc.) performance_characteristics: - Simple reaction lookups by ID or accession: < 1 second - Keyword searches with bif:contains: < 1 second for 20 results - Complex joins (reactions-participants-compounds): 2-5 seconds with LIMIT 50 - Full traversal queries may timeout without proper LIMIT clauses data_quality_notes: - All approved reactions are atom-balanced and charge-balanced - Transport reactions consistently annotated with cellular locations - Polymer notation is standardized but may require parsing for applications anti_patterns: - title: Using FILTER(CONTAINS()) Instead of bif:contains problem: Standard FILTER(CONTAINS()) is much slower than Virtuoso's native full-text search and doesn't provide relevance ranking. wrong_sparql: | PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation WHERE { ?reaction rhea:equation ?equation . FILTER(CONTAINS(LCASE(?equation), "atp")) } correct_sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?equation WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rhea:status rhea:Approved . ?equation bif:contains "'atp'" option (score ?sc) . } ORDER BY DESC(?sc) LIMIT 20 explanation: Use bif:contains with single quotes around keywords for fast full-text search. Add ORDER BY DESC(?sc) to get most relevant results first. - title: Not Using LIMIT on Open-Ended Queries problem: Queries exploring relationships without LIMIT clauses can timeout on large result sets. wrong_sparql: | SELECT ?reaction ?participant ?compound WHERE { ?reaction rhea:side ?side . ?side rhea:contains ?participant . ?participant rhea:compound ?compound . } correct_sparql: | PREFIX rhea: <http://rdf.rhea-db.org/> SELECT ?reaction ?participant ?compound WHERE { ?reaction rhea:side ?side . ?side rhea:contains ?participant . ?participant rhea:compound ?compound . } LIMIT 100 explanation: Always include LIMIT when exploring relationships to prevent timeouts and get manageable result sets. - title: Confusing Reaction Types problem: Querying for master reactions but expecting directional properties, or vice versa. wrong_sparql: | # Trying to get directional info from master reaction directly SELECT ?reaction ?direction WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:direction ?direction . } correct_sparql: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> # Get master reaction and its directional variants SELECT ?masterReaction ?directionalReaction WHERE { ?masterReaction rdfs:subClassOf rhea:Reaction ; rhea:directionalReaction ?directionalReaction . } LIMIT 50 explanation: Master reactions link to directional forms via rhea:directionalReaction. Use the appropriate reaction type for your query needs. common_errors: - error: Query timeout when counting all reactions causes: - Not using LIMIT on large aggregation queries - Attempting to traverse entire reaction-participant-compound graph solutions: - Add LIMIT clause even to COUNT queries - Break complex queries into smaller focused queries - Use filters early (status, specific reaction IDs) to narrow results example_fix: | # Instead of: SELECT (COUNT(?reaction) as ?count) WHERE { ?reaction a ?type } # Use: SELECT (COUNT(?reaction) as ?count) WHERE { ?reaction rdfs:subClassOf rhea:Reaction . } LIMIT 1 - error: Empty results when searching for compound by name causes: - Compound names are on compound entities, not participant entities - Not following the reaction→side→participant→compound path correctly - Using FILTER(CONTAINS()) instead of bif:contains for text search solutions: - Always query compound properties from the compound entity (rhea:Compound_XXXX) - Use rhea:compound property to link participants to compounds - Use bif:contains for efficient text searching in compound names example_fix: | PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rhea: <http://rdf.rhea-db.org/> # Correct path with bif:contains SELECT ?reaction ?equation ?compoundName WHERE { ?compound rhea:name ?compoundName . ?compoundName bif:contains "'glucose'" option (score ?sc) . ?participant rhea:compound ?compound . ?side rhea:contains ?participant . ?reaction rhea:side ?side ; rhea:equation ?equation . } ORDER BY DESC(?sc) LIMIT 20 - error: Missing cross-references in results causes: - Using OPTIONAL without proper structure leads to cartesian products - Not filtering cross-references by database type solutions: - Use FILTER to specify cross-reference patterns (e.g., KEGG, GO, BioCyc) - Apply DISTINCT when querying multiple optional cross-references - Query one cross-reference type at a time for clearer results example_fix: | SELECT DISTINCT ?reaction ?equation ?goTerm WHERE { ?reaction rdfs:subClassOf rhea:Reaction ; rhea:equation ?equation ; rdfs:seeAlso ?goTerm . FILTER(STRSTARTS(STR(?goTerm), "http://purl.obolibrary.org/obo/GO_")) } LIMIT 50