Summary
The below examples can be queried against the latest version of UniCarbKB 2.0 using the GlycoCoO 1.3.2 ontology
For more information and example RDF files refer to the GlycoCoO GitHub site
UniCarbKB data releases (CSV and SPARQL) are available from our GitLab repo
Prefixes
GlycoCoO 1.3.2 Prefixes
Copy prefix gc: <http://www.oegov.org/core/owl/gc#>
prefix sio: <http://semanticscience.org/resource/>
prefix gl: <http://schema.geolink.org/>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix ms: <http://www.berkeleybop.org/ontologies/ms.owl>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix gco: <http://purl.jp/bio/12/glyco/conjugate#>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix unicarbkb: <http://purl.org/unicarbkb>
prefix faldo: <http://www.biohackathon.org/resource/faldo/>
prefix pato: <http://purl.obolibrary.org/obo/uo.owl>
prefix dcterms: <http://purl.org/dc/terms/>
prefix bibo: <http://purl.org/ontology/bibo/>
prefix uniprot: <http://purl.uniprot.org/core/>
prefix foaf: <http://xmlns.com/foaf/0.1/>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix glycan: <http://purl.jp/bio/12/glyco/glycan#> Endpoint
http://sparql.unicarbkb.org (http://130.56.249.35:40935/unicarbkb/query)
License
Please note this data is CC 4.0 licensed. All users are required to cite UniCarbKB (https://www.ncbi.nlm.nih.gov › pmc › articles › PMC3964942 ) and funding from ARDC-NeCTAR and the NIH Glycoscience Common Fund project GlyGen . Data provenance must be acknowledged and cross-referencing is recommended. The developers acknowledge GlycoSuiteDB, EUROCarbDB, GlycoBase (now GlycoStore) and all biocurators involved in these projects.
Saccaride Id, Publication Details
Copy select distinct ?pmid ?id ?sacc
where {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?p ; glycan:published_in ?published .
?published glycan:has_pmid ?pmid .
?p a gco:Referenced_protein ; gco:has_saccharide_set ?set .
?set a gco:Saccharide_Set ; sio:is-component-part-of ?comp .
?comp a gco:Saccharide_Set_Item ; owl:sameAs ?sacc .
?sacc a glycan:Saccharide ; glycan:has_unicarbkb_id ?id .
OPTIONAL { ?p a gco:Referenced_protein ; glycan:has_protein_description ?description } .
OPTIONAL { ?p a gco:Referenced_protein ; rdfs:seeAlso ?uniprot } .
OPTIONAL { ?p rdfs:comment ?comment } .
} Get all proteins
Copy SELECT distinct ?Protein ?ReferencedProtein
WHERE {
?ReferencedProtein gco:has_protein ?Protein
}
LIMIT 25 Get Reference Compound with Publication, Species filtered by a Protein Accession
Copy SELECT distinct ?ReferencedCompound ?Pmid ?Protein ?Species
WHERE {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?Protein ; glycan:published_in ?published ; glycan:is_from_source ?Source .
?published glycan:has_pmid ?Pmid .
?Protein a gco:Referenced_protein ; gco:has_saccharide_set ?set .
?Source glycan:has_taxon ?Taxon .
?Taxon uniprot:scientificName ?Species .
FILTER regex(str(?ProteinAcc), "P07911") .
} Glycoprotein and Glycosylation Site
Copy SELECT distinct ?Region ?Protein ?pos ?Faldo
WHERE {
?Protein gco:glycosylated_at ?Region .
?Region faldo:ExactPosition ?Faldo .
?Faldo faldo:position ?pos .
FILTER regex(str(?ProteinAcc), "P07911") .
} Get unicarbkb glycan ids for structures at a location for a specific protein.
Copy SELECT distinct ?ProteinAcc ?Position ?Saccharide ?Id
WHERE {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?Protein .
?Protein gco:has_protein ?ProteinAcc .
?Protein gco:glycosylated_at ?Region .
?Protein gco:has_saccharide_set ?Set .
?Set sio:is-component-part-of ?SetItem .
?SetItem owl:sameAs ?Saccharide .
?Saccharide dcterms:identifier ?Id .
?Region faldo:ExactPosition ?Faldo .
?Faldo faldo:position ?Position .
FILTER regex(str(?ProteinAcc), "P07911") .
}
limit 10 Glycan Structures Attached to a Specific Site for P07911
List of structures attached to P07911 at position 76
Copy SELECT distinct ?ProteinAcc ?Position ?Saccharide ?Id
WHERE {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?Protein .
?Protein gco:has_protein ?ProteinAcc .
?Protein gco:has_saccharide_set ?Set .
?Set sio:is-component-part-of ?SetItem .
?SetItem owl:sameAs ?Saccharide .
?Saccharide dcterms:identifier ?Id .
?Protein gco:glycosylated_at ?Region .
?Region faldo:ExactPosition ?Faldo .
?Faldo faldo:position ?Position .
FILTER regex(str(?Position), "76") .
FILTER regex(str(?ProteinAcc), "P07911") .
} Haptoglobin - UniProt, UniCarbKB Id, GlyTouCan, Position, Amino Acid and Curation Notes
Copy select distinct ?identifer ?Position ?Id ?Toucan ?AminoAcid ?TypeAminoAcid ?Pmid
where {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?Protein ; glycan:published_in ?published ; glycan:is_from_source ?Source .
?published glycan:has_pmid ?Pmid .
?Protein a gco:Referenced_protein ; gco:has_protein ?test .
?test a gco:Glycoprotein ; rdfs:seeAlso ?uniprot2 ; dcterms:identifier ?identifer .
?Protein gco:glycosylated_at ?Region .
?Region a faldo:region ; faldo:ExactPosition ?Faldo .
?Faldo faldo:position ?Position .
?Region a faldo:region ; gco:has_saccharide_set ?Set .
?Set sio:is-component-part-of ?SetItem .
?SetItem owl:sameAs ?Saccharide .
?Saccharide dcterms:identifier ?Id .
optional { ?Saccharide glycan:has_glytoucan_id ?Toucan . }
?Faldo gco:has_amino_acid ?AminoAcid .
?AminoAcid gco:amino_acid ?TypeAminoAcid .
FILTER regex(str(?identifer), "P00738") .
}
group by ?identifer ?Position ?Id ?Toucan ?AminoAcid ?TypeAminoAcid ?Pmid Haptoglobin - Tissue
Copy
select distinct ?Label ?Source
where {
?Glyco a gco:Referenced_glycoconjugate ; gco:has_protein_part ?Protein ; glycan:published_in ?published ; glycan:is_from_source ?Source ; glycan:has_tissue ?tissue .
?tissue ?x ?related .
?related rdfs:label ?Label .
?published glycan:has_pmid ?Pmid .
?Protein a gco:Referenced_protein ; gco:has_protein ?ProteinInfo .
?ProteinInfo a gco:Glycoprotein ; rdfs:seeAlso ?uniprot2 ; dcterms:identifier ?identifer .
FILTER regex(str(?identifer), "P00738") .
}
group by ?Label ?Source Use of CAR Identifiers
A selection of Uniprot / UniCarbKb cross-refs have implemented unique CAR ids
Copy select distinct ?P ?CAR ?Region ?Position
where {
?P up:Annotation ?Anno .
?Anno gco:has_car_id ?CAR .
?CAR gco:glycosylated_at ?Region .
?Region faldo:ExactPosition ?Exact .
?Exact faldo:position ?Position .
} 