55: Number of proteins with annotated binding sites for metals or metal sulfur clusters (and experimental evidence for the binding)

SELECT ?ligand ?ligandName (COUNT(DISTINCT ?protein) as ?entries) WHERE { ?protein up:annotation ?annotation . VALUES ?evs { obo:ECO_0000269 obo:ECO_0007744 } . VALUES ?chebids { CHEBI:25213 CHEBI:25214 } . ?st rdf:subject ?protein ; rdf:predicate up:annotation ; rdf:object ?annotation ; up:attribution/up:evidence ?evs . ?annotation up:ligand/rdfs:subClassOf ?ligand . ?ligand rdfs:subClassOf+ ?chebids ; rdfs:label ?ligandName . } GROUP BY ?ligand ?ligandName ORDER BY DESC(?entries)Use

56: Select Enzymes that have Ligands that have a known allosteric effect

SELECT ?protein ?ligandName ?ligandNote ?chebi WHERE { ?protein up:annotation ?annotation . ?annotation a up:Binding_Site_Annotation . ?annotation up:ligand ?ligand . ?ligand rdfs:comment ?ligandNote ; rdfs:subClassOf ?chebi ; rdfs:label ?ligandName . FILTER(REGEX(?ligandNote, "allosteric", "i")) }Use

57: Map PDB identifiers plus chains to UniProt

SELECT ?pdbId ?chain ?pdbChain ?uniprot WHERE { # A space separated list of pairs of PDB identifiers and the chain code. VALUES(?pdbId ?pdbChain) { ('6VXC' 'A') ('1BG3' 'B') } # Make an IRI out of the pdbId BIND(iri(concat('http://rdf.wwpdb.org/pdb/', ?pdbId)) AS ?pdb) # Map to UniProt entries ?uniprot rdfs:seeAlso ?pdb . ?pdb up:database <http://purl.uniprot.org/database/PDB> ; up:chainSequenceMapping ?chainSm . ?chainSm up:chain ?chainsPlusRange . # Extract the list of chains from the text representation. BIND(STRBEFORE(?chainsPlusRange, '=') AS ?chain) # Filter those that match. FILTER(CONTAINS(?chain, ?pdbChain)) }Use

58: Map UniProt to HGNC identifiers and Symbols

SELECT ?uniprot ?hgnc ?hgncSymbol WHERE { # A space separated list of UniProt primary accessions. VALUES (?acc) {('P05067') ('P00750')} BIND(iri(concat(str(uniprotkb:), ?acc)) AS ?uniprot) ?uniprot rdfs:seeAlso ?hgnc . ?hgnc up:database <http://purl.uniprot.org/database/HGNC> ; rdfs:comment ?hgncSymbol . }Use

59: Count all isoforms for a given proteome

PREFIX proteome:<http://purl.uniprot.org/proteomes/> SELECT (COUNT(DISTINCT ?sequence) AS ?allIsoforms) WHERE { ?protein up:reviewed true . ?protein up:organism taxon:9606 . ?protein up:sequence ?sequence . ?protein up:proteome/^skos:narrower proteome:UP000005640 . }Use