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140_disulfide_bonds_and_interchain_links: Find the disulfide bonds of human insulin (P01308), the pair of residue positions each one connects, and whether it links two different chains (e.g. the A and B chains of mature insulin) rather than two residues within the same chain

PREFIX up: <http://purl.uniprot.org/core/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?annotation (GROUP_CONCAT(STR(?position); separator="-") AS ?positions) (SAMPLE(?rawComment) AS ?interchainNote) WHERE { uniprotkb:P01308 up:annotation ?annotation . ?annotation a up:Disulfide_Bond_Annotation ; up:range ?range . # Each disulfide bond annotation has one up:range per residue it # connects; a plain xsd:int position must be coerced with STR() before # GROUP_CONCAT can aggregate it. ?range faldo:begin/faldo:position ?position . # Absence of a comment means the bond is intra-chain; a comment # mentioning "Interchain" means it links two separate chains. OPTIONAL { ?annotation rdfs:comment ?rawComment } } GROUP BY ?annotationUse

141_lipidation_sites_and_lipid_type: Find reviewed human proteins with a covalently attached lipid (e.g. palmitoylation, farnesylation, GPI-anchor) and the residue position and kind of lipid attached

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?position ?lipidationType WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Lipidation_Annotation ; rdfs:comment ?lipidationType ; up:range ?range . ?range faldo:begin/faldo:position ?position . }Use

142_cross_linked_residues: Find reviewed human proteins with a cross-linked residue (e.g. a glycyl lysine isopeptide bond formed by ubiquitin or SUMO conjugation) and the residue position and nature of the cross-link

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?position ?crossLinkType WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Cross-link_Annotation ; rdfs:comment ?crossLinkType ; up:range ?range . ?range faldo:begin/faldo:position ?position . }Use

143_protein_function_description: Retrieve the free-text function description of human tumor suppressor TP53 (P04637), as distinct from its more specific catalytic-activity, disease, or subunit annotations

PREFIX up: <http://purl.uniprot.org/core/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?functionText WHERE { uniprotkb:P04637 up:annotation ?annotation . ?annotation a up:Function_Annotation ; rdfs:comment ?functionText . }Use

144_mature_chain_after_signal_peptide_cleavage: Find reviewed human secreted proteins where the mature chain begins immediately after the signal peptide is cleaved off

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?signalPeptideEnd ?chainName ?chainBegin ?chainEnd WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?signalPeptideAnnotation , ?chainAnnotation . ?signalPeptideAnnotation a up:Signal_Peptide_Annotation ; up:range ?signalPeptideRange . ?signalPeptideRange faldo:end/faldo:position ?signalPeptideEnd . ?chainAnnotation a up:Chain_Annotation ; up:range ?chainRange . OPTIONAL { ?chainAnnotation rdfs:comment ?chainName } ?chainRange faldo:begin/faldo:position ?chainBegin ; faldo:end/faldo:position ?chainEnd . FILTER(?chainBegin = ?signalPeptideEnd + 1) }Use

145_mitochondrial_transit_peptides: Find reviewed human proteins with a transit peptide targeting them to the mitochondrion, and the extent of that transit peptide

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?destination ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Transit_Peptide_Annotation ; rdfs:comment ?destination ; up:range ?range . ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . FILTER(CONTAINS(?destination, "Mitochondrion")) }Use

146_propeptide_regions_removed_during_maturation: Find propeptide regions of reviewed human proteins that are removed during protein maturation, with their extent

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?description ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Propeptide_Annotation ; up:range ?range . OPTIONAL { ?annotation rdfs:comment ?description } ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . }Use

147_enzymes_with_kinetic_parameters: Find reviewed enzymes with reported kinetic parameters (Michaelis-Menten constant Km and/or maximal velocity Vmax) and their reported values

PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?km ?vmax WHERE { ?protein a up:Protein ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Kinetics_Annotation . OPTIONAL { ?annotation up:measuredAffinity ?km } OPTIONAL { ?annotation up:measuredActivity ?vmax } }Use

148_optimum_ph_for_enzyme_activity: Find the optimum pH reported for the activity of reviewed human enzymes

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?phDependence WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:PH_Dependence_Annotation ; rdfs:comment ?phDependence . }Use

149_optimum_temperature_for_enzyme_activity: Find the optimum temperature or thermostability reported for the activity of reviewed human enzymes

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?temperatureDependence WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Temperature_Dependence_Annotation ; rdfs:comment ?temperatureDependence . }Use

150_redox_potential_measurements: Find redox potential (E0) measurements reported for reviewed electron-transport proteins

PREFIX up: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?redoxPotential WHERE { ?protein a up:Protein ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Redox_Potential_Annotation ; rdfs:comment ?redoxPotential . }Use

151_membrane_orientation_of_subcellular_location: Find reviewed human proteins with a known membrane orientation (e.g. cytoplasmic side vs. lumenal side) for one of their subcellular locations

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> SELECT ?protein ?subcellularLocation ?orientation WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Subcellular_Location_Annotation ; up:locatedIn ?location . ?location up:cellularComponent ?component ; up:orientation ?orientationResource . ?component skos:prefLabel ?subcellularLocation . ?orientationResource skos:prefLabel ?orientation . }Use

152_topology_of_subcellular_location: Find the membrane topology (e.g. peripheral membrane protein, lipid-anchor, multi-pass membrane protein) recorded for a subcellular location of reviewed human proteins

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> SELECT ?protein ?subcellularLocation ?topology WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Subcellular_Location_Annotation ; up:locatedIn ?location . ?location up:cellularComponent ?component ; up:topology ?topologyResource . ?component skos:prefLabel ?subcellularLocation . ?topologyResource skos:prefLabel ?topology . }Use

153_protein_domain_extents: Find the extent (start and end position) of annotated protein domains on reviewed human proteins, using UniProt's own domain model rather than an InterPro/Pfam cross-reference

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?domainName ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Domain_Extent_Annotation ; rdfs:comment ?domainName ; up:range ?range . ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . }Use

154_zinc_finger_regions: Find zinc finger regions in reviewed human DNA-binding proteins, with the zinc finger type and its extent

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?zincFingerType ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Zinc_Finger_Annotation ; up:range ?range . OPTIONAL { ?annotation rdfs:comment ?zincFingerType } ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . }Use

155_coiled_coil_regions: Find coiled-coil regions annotated on reviewed human proteins and their extent

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> SELECT ?protein ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Coiled_Coil_Annotation ; up:range ?range . ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . }Use

156_compositionally_biased_regions: Find compositionally-biased (low-complexity) regions annotated on reviewed human proteins, with the kind of bias and its extent

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?bias ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:annotation ?annotation . ?annotation a up:Compositional_Bias_Annotation ; up:range ?range . OPTIONAL { ?annotation rdfs:comment ?bias } ?range faldo:begin/faldo:position ?begin ; faldo:end/faldo:position ?end . }Use

157_polymorphisms_reported_for_a_protein: Find polymorphisms reported for proteins, i.e. population sequence variation described as such rather than as a disease-causing natural variant

PREFIX up: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?protein ?polymorphism WHERE { ?protein a up:Protein ; up:annotation ?annotation . ?annotation a up:Polymorphism_Annotation ; rdfs:comment ?polymorphism . }Use

158_citation_scope_via_citation_statement: Find the citations attached to human insulin (P01308) and, for each one, the scope of what it was cited for (e.g. which disease variant, which sequence region, or which experiment it documents). UniProt records the plain triple up:citation for direct traversal, and separately reifies that same triple as an up:Citation_Statement to attach the citation's scope to the specific citation relationship rather than to the citation itself, since one citation can support several different claims about the same protein

PREFIX up: <http://purl.uniprot.org/core/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT DISTINCT ?citation ?scope WHERE { ?statement a up:Citation_Statement ; rdf:subject uniprotkb:P01308 ; rdf:predicate up:citation ; rdf:object ?citation ; up:scope ?scope . }Use

159_excluded_proteomes_and_reason: Find proteomes that have been excluded from UniProtKB and the reason they were excluded (e.g. contaminated, derived from metagenome, unverified source organism)

PREFIX up: <http://purl.uniprot.org/core/> SELECT ?proteome ?exclusionReason WHERE { ?proteome a up:Excluded_Proteome ; up:exclusionReason ?exclusionReason . }Use

160_non_reference_proteomes_and_strain: Find non-reference proteomes and the organism and strain they were sequenced from

PREFIX up: <http://purl.uniprot.org/core/> SELECT ?proteome ?organism ?strain WHERE { ?proteome a up:Non_Reference_Proteome ; up:organism ?organism . OPTIONAL { ?proteome up:strain ?strain } }Use

161_taxa_sharing_a_rank: List all taxa in UniProt's taxonomy that have the taxonomic rank "genus", using the up:Rank resource rather than matching on a rank name string

PREFIX up: <http://purl.uniprot.org/core/> SELECT ?taxon ?scientificName WHERE { ?taxon up:rank up:Taxonomic_Rank_Genus ; up:scientificName ?scientificName . }Use

162_common_taxon_of_a_uniref_cluster: Find the common taxon (the lowest taxon shared by all members) of the UniRef100 cluster that human TP53 (P04637) belongs to, and how many sequences that cluster groups together. up:commonTaxon is precomputed per UniRef cluster from its actual members, not a general-purpose lowest-common-ancestor function over two arbitrary organisms

PREFIX up: <http://purl.uniprot.org/core/> PREFIX uniref: <http://purl.uniprot.org/uniref/> SELECT ?cluster (COUNT(?member) AS ?memberCount) (SAMPLE(?rawCommonTaxonName) AS ?commonTaxonName) WHERE { BIND(uniref:UniRef100_P04637 AS ?cluster) ?cluster up:member ?member ; up:commonTaxon ?commonTaxon . ?commonTaxon up:scientificName ?rawCommonTaxonName . } GROUP BY ?clusterUse

163_canonical_isoform_does_not_need_to_be_dash_1: Find reviewed proteins whose canonical isoform does not end in -1, ordered by the highest isoform number used as the canonical sequence. UniProt's up:sequence points to whichever isoform was chosen as canonical, which is not always isoform -1

PREFIX up: <http://purl.uniprot.org/core/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?protein (?sequence AS ?canonicalIsoform) ?isoformCount WHERE { GRAPH <http://sparql.uniprot.org/uniprot> { ?protein up:reviewed true . ?protein up:sequence ?sequence . ?sequence a up:Simple_Sequence . OPTIONAL { ?sequence a up:External_Sequence . BIND(true AS ?isExternalSequence) BIND(SUBSTR(STR(?protein), STRLEN(STR(uniprotkb:))) AS ?proteinAc) FILTER(CONTAINS(STR(?sequence), ?proteinAc)) } FILTER(?isExternalSequence || !BOUND(?isExternalSequence)) } BIND(xsd:int(STRAFTER(STR(?sequence), "-")) AS ?isoformCount) } ORDER BY DESC(?isoformCount)Use

164_batch_go_annotations_from_mnemonics: Given a batch of UniProt mnemonic identifiers (Entry Names, e.g. MTMR1_HUMAN) rather than accessions, resolve each to its protein and retrieve its GO annotations in one query. This is the classic biomaRt batch-lookup pattern where a SPARQL VALUES clause replaces getBM(), and unlike biomaRt it naturally returns one row per (protein, GO term) pair instead of dropping or truncating the one-to-many result

PREFIX up: <http://purl.uniprot.org/core/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> SELECT ?mnemonic ?protein ?goTerm ?goLabel WHERE { VALUES ?mnemonic { "MTMR1_HUMAN" "P53_HUMAN" "INS_HUMAN" } ?protein up:mnemonic ?mnemonic ; up:classifiedWith ?goTerm . ?goTerm rdfs:label ?goLabel . FILTER(STRSTARTS(STR(?goTerm), STR(GO:))) }Use

165_reviewed_proteins_for_a_go_term: Given a GO term, find all reviewed human proteins annotated with it. This is the reverse direction of retrieving GO terms for a protein, matching the classic BioMart workflow of building an enrichment-analysis candidate or background gene set from a GO id filter

PREFIX up: <http://purl.uniprot.org/core/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX GO: <http://purl.obolibrary.org/obo/GO_> SELECT ?protein WHERE { # GO:0006915 is "apoptotic process" ?protein a up:Protein ; up:organism taxon:9606 ; up:reviewed true ; up:classifiedWith GO:0006915 . }Use
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