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

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目次

Names and origin

Protein names

Recommended name

RecommendedName.png

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

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

Mass spectrometry

Polymorphism

Involvement in disease

Disruption phenotype

Allergenic properties

Toxic dose

Biotechnological use

Pharmaceutical use

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

Sequence caution

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