BH11.11/統合検索とRDFからの表データ生成/uniprot sparql

提供：TogoWiki

目次 1 Names and origin 1.1 Protein names 1.1.1 Recommended name 1.1.1.1 Full name 1.1.1.1.1 Short name(s) 1.1.1.1.2 EC 1.1.2 Alternative name(s) 1.1.2.1 Full name 1.1.2.1.1 Short name(s) 1.1.2.1.2 EC 1.1.2.2 Allergen 1.1.2.3 Biotech 1.1.2.4 CD_antigen 1.1.2.5 INN 1.2 Gene names 1.2.1 Name 1.2.2 Synonyms 1.2.3 Ordered Locus Names 1.2.4 ORF Names 1.3 Encoded on 1.4 Organism 1.5 Taxonomic identifier 1.6 Taxonomic lineage 1.7 Virus host 2 Protein attributes 2.1 Sequence length 2.2 Sequence status 2.3 Sequence processing 2.4 Protein existence 3 General annotation (Comments) 4 Ontologies 4.1 Keywords 4.2 Gene Ontology (GO) 5 Binary interactions 6 Alternative products 6.1 General information 6.2 Isoform-specific information 7 Sequence annotation (Features) 7.1 Molecule processing 7.2 Regions 7.3 Sites 7.4 Amino acid modifications 7.5 Natural variations 7.6 Experimental info 7.7 Secondary structure 8 Sequences 9 References 10 Web resources 11 Cross-references 11.1 2D gel databases 11.2 3D structure databases 11.3 Enzyme and pathway databases 11.4 Family and domain databases 11.5 Gene expression databases 11.6 Genome annotation databases 11.7 Ontologies 11.8 Organism-specific databases 11.9 Phylogenomic databases 11.10 Polymorphism databases 11.11 Protocols and materials databases 11.12 Proteomic databases 11.13 Protein-protein interaction databases 11.14 Protein family/group databases 11.15 PTM databases 11.16 Sequence databases 11.17 Other 12 Entry information 13 General annotation and Sequence annotation

Names and origin

Protein names

Recommended name

Full name

SELECT ?id ?recommended_name
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?recommended_name_node <http://purl.uniprot.org/core/fullName> ?recommended_name .
?id <http://purl.uniprot.org/core/recommendedName> ?recommended_name_node
}

Short name(s)

SELECT ?id ?short_name
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?recommended_name_node <http://purl.uniprot.org/core/shortName> ?short_name .
?id <http://purl.uniprot.org/core/recommendedName> ?recommended_name_node
}

EC

SELECT ?id ?ec
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?recommended_name_node <http://purl.uniprot.org/core/ecName> ?ec .
?id <http://purl.uniprot.org/core/recommendedName> ?recommended_name_node
}

Alternative name(s)

Full name

SELECT ?id ?alternative_names
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_names_node <http://purl.uniprot.org/core/fullName> ?alternative_names .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_names_node
}

Short name(s)

SELECT ?id ?short_name 
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/shortName> ?short_name .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

EC

SELECT ?id ?ec
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/ecName> ?ec .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

Allergen

SELECT ?id ?allergen
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/allergenName> ?allergen .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

Biotech

SELECT ?id ?biotech
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/biotechName> ?biotech .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

CD_antigen

SELECT ?id ?cd_antigen
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/cdAntigenName> ?cd_antigen .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

INN

SELECT ?id ?inn
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?alternative_name_node <http://purl.uniprot.org/core/internationalNonproprietaryName> ?inn .
?id <http://purl.uniprot.org/core/alternativeName> ?alternative_name_node
}

Gene names

Name

SELECT ?id ?gene_names
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?gene_names_node <http://www.w3.org/2004/02/skos/core#prefLabel> ?gene_names .
?id <http://purl.uniprot.org/core/encodedBy> ?gene_names_node
}

Synonyms

SELECT ?id ?alt_name
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?gene_names_node <http://www.w3.org/2004/02/skos/core#altLabel> ?alt_name .
?id <http://purl.uniprot.org/core/encodedBy> ?gene_names_node
}

Ordered Locus Names

SELECT ?id ?locus_name
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?encoded_by <http://purl.uniprot.org/core/locusName> ?locus_name .
?id <http://purl.uniprot.org/core/encodedBy> ?encoded_by
}

ORF Names

SELECT ?id ?orf_name
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?encoded_by <http://purl.uniprot.org/core/orfName> ?orf_name .
?id <http://purl.uniprot.org/core/encodedBy> ?encoded_by
}

Encoded on

SELECT ?id ?organelle ?label
WHERE {
?encoded_in <http://www.w3.org/2000/01/rdf-schema#label> ?label .
?encoded_in <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?organelle .
?id <http://purl.uniprot.org/core/encodedIn> ?encoded_in
}

Organism

SELECT ?id ?organism
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?taxonomy_id <http://purl.uniprot.org/core/scientificName> ?organism .
?id <http://purl.uniprot.org/core/organism> ?taxonomy_id
}

include=yes でRDFを取得した場合。オプションを付けずにRDFを取得した場合にはtaxonomy_idのみ取れる（その他の情報はtaxonomyのグラフから取る）

Taxonomic identifier

SELECT ?id ?taxonomic_identifier
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?id <http://purl.uniprot.org/core/organism> ?taxonomic_identifier
}

Taxonomic lineage

Virus host

SELECT ?id ?host
FROM <http://bh.dbcls.jp/DAV>
WHERE {
 ?taxonomy_id <http://purl.uniprot.org/core/host> ?host .
?id <http://purl.uniprot.org/core/organism> ?taxonomic_identifier
}

Protein attributes

Sequence length

SELECT ?id ?sequence
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?seq <http://www.w3.org/1999/02/22-rdf-syntax-ns#value> ?sequence .
?id <http://purl.uniprot.org/core/sequence> ?seq
FILTER regex (?id, "uniprot") 
}

で返ってくる文字列の長さ

Sequence status

SELECT ?id ?value
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?seq <http://purl.uniprot.org/core/fragment> ?value .
?id <http://purl.uniprot.org/core/sequence> ?seq
}

• if ?value == "single" then "Fragment" elsif ?value == "multiple" then "Fragments" elsif ?value == nil then "Complete"

Sequence processing

Protein existence

SELECT *
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?id <http://purl.uniprot.org/core/existence> ?existence
}

• 5 types of evidence for the existence: 'Evidence at protein level', 'Evidence at transcript level', 'Inferred from homology', 'Predicted', 'Uncertain'

General annotation (Comments)

SELECT ?id ?type ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

•  ?type からどの項目のアノテーションか判別可能

Function

SELECT ?id ?type ?function_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?function_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Function_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Catalytic activity

SELECT ?id ?catalytic_activity_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?catalytic_activity_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Catalytic_Activity_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Cofactor

SELECT ?id ?cofactor_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?cofactor_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Cofactor_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Enzyme regulation

SELECT ?id ?enzyme_regulation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?enzyme_regulation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Enzyme_Regulation_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Biophysicochemical properties

• ?type = http://purl.uniprot.org/core/Biophysicochemical_Annotation

Subunit structure

SELECT ?id ?subunit_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?subunit_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Subunit_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Pathway

SELECT ?id ?pathway_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?pathway_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Pathway_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Subcellular location

SELECT ?id ?location ?subcellular_location_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?subcellular_location_annotation_comment .
?located_in ?p ?location .
?annotation <http://purl.uniprot.org/core/locatedIn> ?located_in .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Subcellular_Location_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Tissue specificity

SELECT ?id ?tissue_specificity_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?tissue_specificity_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Tissue_Specificity_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Developmental stage

SELECT ?id ?developmental_stage_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?developmental_stage_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Developmental_Stage_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Induction

SELECT ?id ?induction_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?induction_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Induction_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Domain

SELECT ?id ?domain_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?domain_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Domain_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Post-translational modification

SELECT ?id ?ptm_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?ptm_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/PTM_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

RNA editing

• ?type = http://purl.uniprot.org/core/RNA_Editing_Annotation

Mass spectrometry

• ?type = http://purl.uniprot.org/core/Mass_Spectrometry_Annotation

Polymorphism

• ?type = http://purl.uniprot.org/core/Polymorphism_Annotation

Involvement in disease

• ?type = http://purl.uniprot.org/core/Disease_Annotation ?

Disruption phenotype

• ?type = http://purl.uniprot.org/core/Disruption_Phenotype_Annotation

Allergenic properties

• ?type = http://purl.uniprot.org/core/Allergen_Annotation ?

Toxic dose

• ?type = http://purl.uniprot.org/core/Toxic_Dose_Annotation

Biotechnological use

• ?type = http://purl.uniprot.org/core/Biotechnology_Annotation ?

Pharmaceutical use

• ?type = http://purl.uniprot.org/core/Pharmaceutical_Annotation

Miscellaneous

Sequence similarities

SELECT ?id ?similarity_annotation_comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?similarity_annotation_comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Similarity_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Caution

• ?type = http://purl.uniprot.org/core/Caution_Annotation

Sequence caution

• ?type = http://purl.uniprot.org/core/Sequence_Caution_Annotation

Ontologies

Keywords

Biological process

Cellular component

Coding sequence diversity

Developmental stage

Disease

Domain

Ligand

Molecular function

Post-translational modification

Technical term

Gene Ontology (GO)

Biological process

Cellular component

Molecular function

Binary interactions

SELECT ?id ?interact_with ?interact_entry ?num_experiments ?participant ?xeno
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?participant1 <http://www.w3.org/2000/01/rdf-schema#label> ?interact_with .
?participant1 <http://www.w3.org/2002/07/owl#sameAs> ?interact_entry .
?interaction <http://purl.uniprot.org/core/xeno> ?xeno .
?interaction <http://purl.uniprot.org/core/experiments> ?num_experiments .
?interaction <http://purl.uniprot.org/core/participant> ?participant1 .
?interaction <http://purl.uniprot.org/core/participant> ?participant .
?id <http://purl.uniprot.org/core/interaction> ?interaction
}

• with, entry, #Exp., IntAct, Notes の5項目で一セットの情報

Alternative products

General information

Isoform-specific information

Identifier

Name and synonym(s)

Description of the sequence differences

Additional comments

Sequence annotation (Features)

Molecule processing

Initiator methionine

Signal

Transit peptide

• Mitochondrion, Apicoplast, Chromoplast, Chloroplast, Cyanelle, Thylakoid, Amyloplast, Peroxisome, Glyoxysome, Hydrogenosome

Propeptide

SELECT ?id ?begin ?end ?comment ?annotation
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Propeptide_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Chain

SELECT ?id ?begin ?end ?comment ?annotation
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Chain_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Peptide

Regions

Topological domain

Transmembrane

Intramembrane

Domain

Repeat

Calcium binding

Zinc finger

DNA binding

Nucleotide binding

SELECT ?id ?begin ?end ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/NP_Binding_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Region

SELECT ?id ?begin ?end (?comment AS ?merge) 
WHERE { OPTIONAL {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Region_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation .
}}

Coiled coil

Motif

SELECT ?id ?begin ?end ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Motif_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Compositional bias

Sites

Active site

Metal binding

Binding site

Site

Amino acid modifications

Non-standard residue

Modified residue

SELECT ?id ?begin ?end ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Modified_Residue_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Lipidation

SELECT ?id ?begin ?end ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Lipidation_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Glycosylation

Disulfide bond

Cross-link

Natural variations

Alternative sequence

SELECT ?id ?begin ?end ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Alternative_Sequence_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Natural variant

Experimental info

Mutagenesis

SELECT ?id ?begin ?end ?substitution ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://purl.uniprot.org/core/substitution> ?substitution .
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Mutagenesis_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Sequence uncertainty

Sequence conflict

Non-adjacent residues

Non-terminal residue

Secondary structure

Helix

SELECT ?id ?begin ?end
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Helix_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Turn

SELECT ?id ?begin ?end
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Turn_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Beta strand

SELECT ?id ?begin ?end
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?range <http://purl.uniprot.org/core/end> ?end .
?range <http://purl.uniprot.org/core/begin> ?begin .
?annotation <http://purl.uniprot.org/core/range> ?range .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Beta_Strand_Annotation> .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

Sequences

Sequence

SELECT ?id ?sequence
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?seq <http://www.w3.org/1999/02/22-rdf-syntax-ns#value> ?sequence .
?id <http://purl.uniprot.org/core/sequence> ?seq
FILTER regex (?id, "uniprot") 
}

Length

• ↑Sequenceの結果返ってくる文字列の長さ

Mass (Da)

SELECT ?id ?mass
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?seq <http://purl.uniprot.org/core/mass> ?mass .
?id <http://purl.uniprot.org/core/sequence> ?seq
FILTER regex (?id, "uniprot") 
}

References

Number

Title

Author(s) names

Reference information

Cross-references

SELECT ?id ?o ?pmid
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?o <http://www.w3.org/2004/02/skos/core#exactMatch> ?pmid .
?id <http://purl.uniprot.org/core/citation> ?o
FILTER regex (?pmid, "pubmed")
}

http://purl.uniprot.org/pubmed/#{pmid}

Citation content (Cited for)

Sequence origin

Web resources

Cross-references

SELECT ?id ?xref_id
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?id <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?xref_id
}

http://purl.uniprot.org/#{DB_name}/#{id}

• total 145 DBs

2D gel databases

• 2DBase-Ecoli, ANU-2DPAGE, COMPLUYEAST-2DPAGE, Cornea-2DPAGE, DOSAC-COBS-2DPAGE, OGP, PHCI-2DPAGE, PMMA-2DPAGE, Rat-heart-2DPAGE, REPRODUCTION-2DPAGE, Siena-2DPAGE, SWISS-2DPAGE, UCD-2DPAGE, World-2DPAGE, Aarhus/Ghent-2DPAGE, ECO2DBASE
• 16 DBs (0 DB)

3D structure databases

• DisProt, HSSP, ModBase, PDB, PDBsum, ProteinModelPortal, SMR
• 7 DBs (2 DBs)

Enzyme and pathway databases

• BioCyc, BRENDA, ENZYME, Pathway_Interaction_DB, Reactome
• 5 DBs

Family and domain databases

• Gene3D, HAMAP, InterPro, KO, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPFAM, TIGRFAMs
• 13 DBs (13 DBs)

Gene expression databases

• ArrayExpress, Bgee, CleanEx, Genevestigator, GermOnline
• 5 DBs

Genome annotation databases

• CMR, Ensembl, EnsemblBacteria, EnsemblFungi, EnsemblMetazoa, EnsemblPlants, EnsemblProtists, GeneID, GenomeReviews, KEGG, NMPDR, TIGR, VectorBase, UCSC, PATRIC
• 15 DBs (14 DBs)

Ontologies

• GO
• 1 DB

Organism-specific databases

• AGD, ArachnoServer, CGD, ConoServer, CTD, CYGD, dictyBase, EchoBASE, EcoGene, euHCVdb, EuPathDB, FlyBase, GenAtlas, GeneCards, GeneDB_Spombe, GeneFarm, GenoList, Gramene, H-InvDB, HGNC, HPA, HUGE, LegioList, Leproma, MaizeGDB, MGI, Micado, MIM, neXtProt, Orphanet, PharmGKB, PseudoCAP, RGD, Rouge, SGD, TAIR, TubercuList, WormBase, Xenbase, ZFIN
• 40 DBs

Phylogenomic databases

• eggNOG, GeneTree, HOGENOM, HOVERGEN, InParanoid, OMA, OrthoDB, PhylomeDB, ProtClustDB
• 9 DBs

Polymorphism databases

• dbSNP (in Natural variations), DMDM
• 2 DBs (1DB)

Protocols and materials databases

• SBKB
• 1 DB (0 DB)

Proteomic databases

• PeptideAtlas, PRIDE, ProMEX
• 3 DBs (0 DB)

Protein-protein interaction databases

• DIP, IntAct, MINT, STRING
• 4 DBs (2 DBs)

Protein family/group databases

• Allergome, AraC-XylS, CAZy, GPCRDB, IMGT, MEROPS, PeroxiBase, PptaseDB, REBASE, TCDB
• 10 DBs (7 DBs)

PTM databases

• GlycoSuiteDB, PhosphoSite, PhosSite
• 3 DBs (0 DB)

Sequence databases

• EMBL/GenBank/DDBJ, IPI, PIR, RefSeq, UniGene
• 7 DBs (5 DBs)

Other

• BindingDB, DrugBank, NextBio, PMAP-CutDB, ProtoNet, SOURCE
• 6 DBs (2 DBs)

Entry information

Entry name

SELECT ?id ?entry_name
FROM <http://bh.dbcls.jp/DAV>
WHERE { ?id <http://purl.uniprot.org/core/mnemonic> ?entry_name
FILTER regex(?id, "http://purl.uniprot.org/uniprot")
}

Accession

• UniProt ID itself

Entry history

Entry status

SELECT ?id ?reviewed
FROM <http://bh.dbcls.jp/DAV>
WHERE { ?id <http://purl.uniprot.org/core/reviewed> ?reviewed
FILTER regex(?id, "http://purl.uniprot.org/uniprot")
}

• 1=reviewed, 0=unreviewed

General annotation and Sequence annotation

SELECT ?id ?type ?comment
FROM <http://bh.dbcls.jp/DAV>
WHERE {
?annotation <http://www.w3.org/2000/01/rdf-schema#comment> ?comment .
?annotation <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type .
?id <http://purl.uniprot.org/core/annotation> ?annotation
}

• typeから、どの項目のアノテーションか判別可能