The Wikipedia Template:Infobox_biodatabase is now integrated in DBPedia
In January 2011, I started the project Template:Infobox_biodatabase. The goal of this project is the annotation of the biological databases in wikipedia using an infobox. The pages annotated with this template have now been integrated into DBpedia 3.7 and it is now possible to query the data through a SPARQL endpoint.
(Note: during the process of writing the new pages in wikipedia, a few articles have been proposed for deletion for notability reasons: I din't fight against the choise of the WP editors).
Articles in category: "Biological database"
SPARQL
List the biological databases.PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dbpedia: <http://dbpedia.org/ontology/> SELECT ?title ?uri WHERE { ?uri a dbpedia:BiologicalDatabase . OPTIONAL { ?uri dbpedia:title ?title. } } ORDER By ?uri
Result:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | title | uri | ======================================================================================================================================================================================================== | "3did"@en | <http://dbpedia.org/resource/3did> | | "ABCdb"@en | <http://dbpedia.org/resource/ABCdb> | | "AREsite"@en | <http://dbpedia.org/resource/AREsite> | | "AlloSteric Database"@en | <http://dbpedia.org/resource/ASD_%28database%29> | | "AgBase"@en | <http://dbpedia.org/resource/AgBase> | | "Allele frequency net"@en | <http://dbpedia.org/resource/Allele_frequency_net_database> | | "ASTD"@en | <http://dbpedia.org/resource/Alternative_splicing_and_transcript_diversity_database> | | "ASAP"@en | <http://dbpedia.org/resource/Alternative_splicing_annotation_project> | | "AmoebaDB"@en | <http://dbpedia.org/resource/AmoebaDB> | | "ArachnoServer"@en | <http://dbpedia.org/resource/ArachnoServer> | | "ArtadeDB"@en | <http://dbpedia.org/resource/Artade> | | "ASPicDB"@en | <http://dbpedia.org/resource/AspicDB> | | "The Autophagy Database"@en | <http://dbpedia.org/resource/Autophagy_database> | | "BGMUT"@en | <http://dbpedia.org/resource/BGMUT> | | "BISC"@en | <http://dbpedia.org/resource/BISC_%28database%29> | | "BRENDA"@en | <http://dbpedia.org/resource/BRENDA> | | "The BRENDA Tissue Ontology (BTO)"@en | <http://dbpedia.org/resource/BRENDA_tissue_ontology> | | | <http://dbpedia.org/resource/BindingDB> | | "Bio2RDF"@en | <http://dbpedia.org/resource/Bio2RDF> | | "BioGRID"@en | <http://dbpedia.org/resource/BioGRID> | | "BioModels Database"@en | <http://dbpedia.org/resource/BioModels_Database> | | "BSDB"@en | <http://dbpedia.org/resource/Biomolecule_stretching_database> | | "Bovine Genome Database"@en | <http://dbpedia.org/resource/Bovine_genome_database> | | "BriX"@en | <http://dbpedia.org/resource/Brix_%28database%29> | | "CADgene"@en | <http://dbpedia.org/resource/CADgene> | | "CATH"@en | <http://dbpedia.org/resource/CATH> | | "CLIPZ:"@en | <http://dbpedia.org/resource/CLIPZ> | | "COSMIC"@en | <http://dbpedia.org/resource/COSMIC_cancer_database> | | "CaSNP"@en | <http://dbpedia.org/resource/CaSNP> | | "CancerResource:"@en | <http://dbpedia.org/resource/CancerResource> | | "cBARBEL"@en | <http://dbpedia.org/resource/Catfish_genome_database> | | "CCDB"@en | <http://dbpedia.org/resource/Cervical_cancer_gene_database> | | | <http://dbpedia.org/resource/ChEBI> | | | <http://dbpedia.org/resource/ChEMBL> | | "ChemProt"@en | <http://dbpedia.org/resource/ChemProt> | | "ChimerDB"@en | <http://dbpedia.org/resource/ChimerDB> | | "MDS_IES_DB"@en | <http://dbpedia.org/resource/Ciliate_MDS/IES_database> | | "Ciona intestinalis protein database"@en | <http://dbpedia.org/resource/Ciona_intestinalis_protein_database> | | "ACLAME"@en | <http://dbpedia.org/resource/Classification_of_mobile_genetic_elements> | | "COMBREX: COMputational BRidges to EXperiments"@en | <http://dbpedia.org/resource/Combrex> | | "CAMERA"@en | <http://dbpedia.org/resource/Community_Cyberinfrastructure_for_Advanced_Marine_Microbial_Ecology_Research_and_Analysis> | | "CORG"@en | <http://dbpedia.org/resource/Comparative_regulatory_genomics_database> | | "CPLA"@en | <http://dbpedia.org/resource/Compendium_of_protein_lysine_acetylation> | | "Conformational dynamics data bank"@en | <http://dbpedia.org/resource/Conformational_dynamics_data_bank> | | "ConsensusPathDB"@en | <http://dbpedia.org/resource/ConsensusPathDB> | | "CDD"@en | <http://dbpedia.org/resource/Conserved_domain_database> | | "DAnCER"@en | <http://dbpedia.org/resource/DAnCER_%28database%29> | | "DBASS3 and DBASS5"@en | <http://dbpedia.org/resource/DBASS3/5> | | "DIMA"@en | <http://dbpedia.org/resource/DIMA_%28database%29> | | "DNA Data Bank of Japan"@en | <http://dbpedia.org/resource/DNA_Data_Bank_of_Japan> | | "PCDB"@en | <http://dbpedia.org/resource/Database_of_protein_conformational_diversity> | | "dbCRID"@en | <http://dbpedia.org/resource/DbCRID> | | "dbDNV"@en | <http://dbpedia.org/resource/DbDNV> | | "dbSNP"@en | <http://dbpedia.org/resource/DbSNP> | | "DiProDB: a database for dinucleotide properties."@en | <http://dbpedia.org/resource/DiProDB> | | "dictyBase"@en | <http://dbpedia.org/resource/DictyBase> | | "DOMINE"@en | <http://dbpedia.org/resource/Domine_Database> | | "DroID"@en | <http://dbpedia.org/resource/Droid_%28database%29> | | "ECRbase"@en | <http://dbpedia.org/resource/ECRbase> | | "ECgene"@en | <http://dbpedia.org/resource/ECgene> | | "EDAS."@en | <http://dbpedia.org/resource/EDAS> | | "EMAGE"@en | <http://dbpedia.org/resource/EMAGE> | | "EMDataBank.org"@en | <http://dbpedia.org/resource/EM_Data_Bank> | | "ENCODE"@en | <http://dbpedia.org/resource/ENCODE> | | "EcoCyc"@en | <http://dbpedia.org/resource/EcoCyc> | | "Effective-"@en | <http://dbpedia.org/resource/Effective_%28database%29> | | "The Ensembl genome database project."@en | <http://dbpedia.org/resource/Ensembl> | | "EID"@en | <http://dbpedia.org/resource/Exon-intron_database> | | "ExtraTrain"@en | <http://dbpedia.org/resource/ExtraTrain> | | "FANTOM"@en | <http://dbpedia.org/resource/FANTOM> | | "FINDbase"@en | <http://dbpedia.org/resource/FINDbase> | | "FREP"@en | <http://dbpedia.org/resource/FREP> | | "FishBase"@en | <http://dbpedia.org/resource/FishBase> | | "FlyFactorSurvey"@en | <http://dbpedia.org/resource/FlyFactorSurvey> | | "Full-parasites"@en | <http://dbpedia.org/resource/Full-parasites> | | "FESD"@en | <http://dbpedia.org/resource/Functional_element_SNPs_database> | | "FGDB"@en | <http://dbpedia.org/resource/Fusarium_graminearum_genome_database> | | "GISSD"@en | <http://dbpedia.org/resource/GISSD> | | "GPnotebook"@en | <http://dbpedia.org/resource/GPnotebook> | | "GPCRDB"@en | <http://dbpedia.org/resource/G_protein-coupled_receptors_database> | | "GenBank"@en | <http://dbpedia.org/resource/GenBank> | | "Genetic codes"@en | <http://dbpedia.org/resource/Genetic_codes_%28database%29> | | "GlycomeDB"@en | <http://dbpedia.org/resource/GlycomeDB> | | "GyDB of mobile genetic elements:"@en | <http://dbpedia.org/resource/Gypsy_%28database%29> | | "The H-Invitational"@en | <http://dbpedia.org/resource/H-Invitational> | | "HGNC"@en | <http://dbpedia.org/resource/HUGO_Gene_Nomenclature_Committee> | | "HitPredict"@en | <http://dbpedia.org/resource/HitPredict> | | "HOLLYWOOD"@en | <http://dbpedia.org/resource/Hollywood_%28database%29> | | "HUMHOT"@en | <http://dbpedia.org/resource/HumHot> | | "H-DBAS"@en | <http://dbpedia.org/resource/Human-transcriptome_database_for_alternative_splicing> | | "Hymenoptera Genome Database"@en | <http://dbpedia.org/resource/Hymenoptera_genome_database> | | "IGRhCellID"@en | <http://dbpedia.org/resource/IGRhCellID> | | "IUPHAR-DB."@en | <http://dbpedia.org/resource/IUPHAR_%28database%29> | | "InSatDb"@en | <http://dbpedia.org/resource/InSatDb> | | | <http://dbpedia.org/resource/Indian_Genetic_Disease_Database_%28IGDD%29> | | "InterPro"@en | <http://dbpedia.org/resource/InterPro> | | "INTERFEROME"@en | <http://dbpedia.org/resource/Interferome> | | "IKMC: International Knockout Mouse Consortium"@en | <http://dbpedia.org/resource/International_Knockout_Mouse_Consortium> | | "Intronerator"@en | <http://dbpedia.org/resource/Intronerator> | | "ISfinder"@en | <http://dbpedia.org/resource/Isfinder> | | "Islander"@en | <http://dbpedia.org/resource/Islander_%28database%29> | | "IsoBase"@en | <http://dbpedia.org/resource/IsoBase> | | "KEGG"@en | <http://dbpedia.org/resource/KEGG> | | "KUPS"@en | <http://dbpedia.org/resource/KUPS_%28database%29> | | "KaPPA-View4"@en | <http://dbpedia.org/resource/KaPPA-View4> | | "L1Base"@en | <http://dbpedia.org/resource/L1Base> | | "Laminin database"@en | <http://dbpedia.org/resource/Laminin_database> | | "LarvalBase"@en | <http://dbpedia.org/resource/LarvalBase> | | "lncRNAdb"@en | <http://dbpedia.org/resource/LncRNAdb> | | "LocDB"@en | <http://dbpedia.org/resource/LocDB> | | "mESAdb"@en | <http://dbpedia.org/resource/MESAdb> | | "MICdb"@en | <http://dbpedia.org/resource/MICdb> | | "MPromDb"@en | <http://dbpedia.org/resource/Mammalian_promoter_database> | | "MatrixDB, the extracellular matrix interaction database."@en | <http://dbpedia.org/resource/MatrixDB> | | "MetaCyc"@en | <http://dbpedia.org/resource/MetaCyc> | | "MethDB-"@en | <http://dbpedia.org/resource/MethDB> | | "miRBase"@en | <http://dbpedia.org/resource/MiRBase> | | "miRGator"@en | <http://dbpedia.org/resource/MiRGator> | | "miRTarBase"@en | <http://dbpedia.org/resource/MiRTarBase> | | "ModBase"@en | <http://dbpedia.org/resource/ModBase> | | "The Mouse Genome Database"@en | <http://dbpedia.org/resource/Mouse_Genome_Database> | | "The mouse Gene Expression Database"@en | <http://dbpedia.org/resource/Mouse_gene_expression_database> | | "MIPS"@en | <http://dbpedia.org/resource/Munich_Information_Center_for_Protein_Sequences> | | "NCBI Epigenomics"@en | <http://dbpedia.org/resource/NCBI_Epigenomics> | | "PID"@en | <http://dbpedia.org/resource/NCI-Nature_Pathway_Interaction_Database> | | "NGSmethDB"@en | <http://dbpedia.org/resource/NGSmethDB> | | "neXtProt"@en | <http://dbpedia.org/resource/NeXtProt> | | "NetPath"@en | <http://dbpedia.org/resource/Netpath> | | "NeuroLex"@en | <http://dbpedia.org/resource/NeuroLex> | | "Non-B DB"@en | <http://dbpedia.org/resource/Non-B_database> | | "NPRD"@en | <http://dbpedia.org/resource/Nucleosome_positioning_region_database> | | "OMPdb"@en | <http://dbpedia.org/resource/OMPdb> | | "TOPSAN"@en | <http://dbpedia.org/resource/Open_protein_structure_annotation_network> | | "ODB"@en | <http://dbpedia.org/resource/Operon_database> | | "OriDB"@en | <http://dbpedia.org/resource/OriDB> | | "Orientations of Proteins in Membranes"@en | <http://dbpedia.org/resource/Orientations_of_Proteins_in_Membranes_database> | | "OrthoDB"@en | <http://dbpedia.org/resource/OrthoDB> | | "OMA"@en | <http://dbpedia.org/resource/Orthologous_MAtrix> | | "P2CS"@en | <http://dbpedia.org/resource/P2CS> | | "PANDIT"@en | <http://dbpedia.org/resource/PANDIT_%28database%29> | | "PCRPi-DB"@en | <http://dbpedia.org/resource/PCRPi-DB> | | "PDBSum"@en | <http://dbpedia.org/resource/PDBsum> | | "PROSITE"@en | <http://dbpedia.org/resource/PROSITE> | | "PSORTdb"@en | <http://dbpedia.org/resource/PSORTdb> | | "ParameciumDB"@en | <http://dbpedia.org/resource/ParameciumDB> | | "Pathway Commons"@en | <http://dbpedia.org/resource/Pathway_commons> | | "Patome"@en | <http://dbpedia.org/resource/Patome> | | "PREX"@en | <http://dbpedia.org/resource/Peroxiredoxin_classification_index> | | "Pfam"@en | <http://dbpedia.org/resource/Pfam> | | "PhEVER"@en | <http://dbpedia.org/resource/PhEVER> | | "PHOSIDA"@en | <http://dbpedia.org/resource/Phosida> | | "Phospho.ELM"@en | <http://dbpedia.org/resource/Phospho.ELM> | | "Phospho3D"@en | <http://dbpedia.org/resource/Phospho3D> | | "PhylomeDB"@en | <http://dbpedia.org/resource/PhylomeDB> | | "PlasmoDB"@en | <http://dbpedia.org/resource/PlasmoDB> | | "PmiRKB"@en | <http://dbpedia.org/resource/PmiRKB> | | "PolyQ"@en | <http://dbpedia.org/resource/PolyQ_%28database%29> | | "PolymiRTS"@en | <http://dbpedia.org/resource/PolymiRTS> | | "PSSRdb"@en | <http://dbpedia.org/resource/Polymorphic_simple_sequence_repeats_database> | | "ProSAS"@en | <http://dbpedia.org/resource/ProSAS> | | "ProtCID"@en | <http://dbpedia.org/resource/ProtCID> | | "PRIDB"@en | <http://dbpedia.org/resource/Protein-RNA_interface_database> | | "The Protein Data Bank."@en | <http://dbpedia.org/resource/Protein_Data_Bank> | | "PCDDB"@en | <http://dbpedia.org/resource/Protein_circular_dichroism_data_bank> | | "Pseudogene.org"@en | <http://dbpedia.org/resource/Pseudogene_%28database%29> | | "Pseudomonas Genome Database"@en | <http://dbpedia.org/resource/Pseudomonas_genome_database> | | "PubChem"@en | <http://dbpedia.org/resource/PubChem> | | "PubMed"@en | <http://dbpedia.org/resource/PubMed> | | "REDfly"@en | <http://dbpedia.org/resource/REDfly> | | "REPAIRtoire"@en | <http://dbpedia.org/resource/REPAIRtoire> | | "RIKEN integrated database of mammals."@en | <http://dbpedia.org/resource/RIKEN_integrated_database_of_mammals> | | "RBPDB"@en | <http://dbpedia.org/resource/RNA-binding_protein_database> | | "RNA helicase database."@en | <http://dbpedia.org/resource/RNA_helicase_database> | | "RNAMDB"@en | <http://dbpedia.org/resource/RNA_modification_database> | | "Reactome: a database of reactions, pathways and biological processes."@en | <http://dbpedia.org/resource/Reactome> | | "REBASE"@en | <http://dbpedia.org/resource/Rebase_%28database%29> | | "RECODE"@en | <http://dbpedia.org/resource/Recode_%28database%29> | | "Refseq"@en | <http://dbpedia.org/resource/RefSeq> | | "RegPhos"@en | <http://dbpedia.org/resource/RegPhos> | | "RegTransBase"@en | <http://dbpedia.org/resource/RegTransBase> | | "RegulonDB"@en | <http://dbpedia.org/resource/RegulonDB> | | "RepTar"@en | <http://dbpedia.org/resource/RepTar_%28database%29> | | "RetrOryza"@en | <http://dbpedia.org/resource/RetrOryza> | | "Rfam"@en | <http://dbpedia.org/resource/Rfam> | | "S/MARt DB"@en | <http://dbpedia.org/resource/S/MARt> | | "STRING"@en | <http://dbpedia.org/resource/STRING> | | "SUPERFAMILY"@en | <http://dbpedia.org/resource/SUPERFAMILY> | | "SeaLifeBase"@en | <http://dbpedia.org/resource/SeaLifeBase> | | "SMART"@en | <http://dbpedia.org/resource/Simple_Modular_Architecture_Research_Tool> | | "SNPSTR"@en | <http://dbpedia.org/resource/Snptstr_%28database%29> | | "SPIKE"@en | <http://dbpedia.org/resource/Spike_%28database%29> | | "SpliceInfo"@en | <http://dbpedia.org/resource/SpliceInfo> | | "StarBase"@en | <http://dbpedia.org/resource/StarBase_%28database%29> | | "SCLD"@en | <http://dbpedia.org/resource/Stem_cell_lineage_database> | | "STRBase"@en | <http://dbpedia.org/resource/Strbase> | | "SAHG"@en | <http://dbpedia.org/resource/Structure_atlas_of_human_genome> | | "SuperSweet"@en | <http://dbpedia.org/resource/SuperSweet> | | "SGDB"@en | <http://dbpedia.org/resource/Synthetic_gene_database> | | "TIARA"@en | <http://dbpedia.org/resource/TIARA_%28database%29> | | "The TIGR Plant Repeat Databases"@en | <http://dbpedia.org/resource/TIGR_plant_repeat_database> | | "TIGR Plant Transcript Assemblies database."@en | <http://dbpedia.org/resource/TIGR_plant_transcript_assembly_database> | | "TMPad"@en | <http://dbpedia.org/resource/TMPad> | | "tRNADB"@en | <http://dbpedia.org/resource/TRNADB> | | "TRDB-"@en | <http://dbpedia.org/resource/Tandem_repeats_database> | | "TassDB"@en | <http://dbpedia.org/resource/TassDB> | | "TcoF-DB"@en | <http://dbpedia.org/resource/TcoF-DB> | | "ThYme"@en | <http://dbpedia.org/resource/ThYme_%28database%29> | | "TADB"@en | <http://dbpedia.org/resource/Toxin-antitoxin_database> | | "TRIP"@en | <http://dbpedia.org/resource/Transient_receptor_potential_channel-interacting_protein_database> | | "TranspoGene and microTranspoGene"@en | <http://dbpedia.org/resource/Transpogene> | | "TreeFam"@en | <http://dbpedia.org/resource/TreeFam> | | "U12DB"@en | <http://dbpedia.org/resource/U12_intron_database> | | "The UCSC Genome Browser"@en | <http://dbpedia.org/resource/UCSC_Genome_Browser> | | "UCbase & miRfunc"@en | <http://dbpedia.org/resource/UCbase> | | "UKPMC"@en | <http://dbpedia.org/resource/UK_PubMed_Central> | | "UTRdb and UTRsite"@en | <http://dbpedia.org/resource/UTRdb> | | "UTRome"@en | <http://dbpedia.org/resource/UTRome> | | "UgMicroSatdb"@en | <http://dbpedia.org/resource/UgMicroSatdb> | | "UniGene"@en | <http://dbpedia.org/resource/UniGene> | | "UniPROBE"@en | <http://dbpedia.org/resource/UniPROBE> | | "UniProt"@en | <http://dbpedia.org/resource/UniProt> | | "UniVec"@en | <http://dbpedia.org/resource/Univec> | | "VISTA Enhancer Browser"@en | <http://dbpedia.org/resource/VISTA_%28comparative_genomics%29> | | "VnD"@en | <http://dbpedia.org/resource/Variations_and_drugs_database> | | "VectorDB"@en | <http://dbpedia.org/resource/VectorDB> | | "ViralZon"@en | <http://dbpedia.org/resource/ViralZone> | | "VKCDB"@en | <http://dbpedia.org/resource/Voltage-gated_potassium_channel_database> | | "WebGeSTer DB"@en | <http://dbpedia.org/resource/WebGeSTer> | | "WormBase"@en | <http://dbpedia.org/resource/WormBase> | | "YPA"@en | <http://dbpedia.org/resource/Yeast_promoter_atlas> | | "YEASTRACT"@en | <http://dbpedia.org/resource/Yeastract> | | | <http://dbpedia.org/resource/ZINC_database> | | "ZFIN"@en | <http://dbpedia.org/resource/Zebrafish_Information_Network> | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List the biological databases in the category "Systems Biology"
SPARQL
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dbpedia: <http://dbpedia.org/ontology/> SELECT ?title ?description ?uri WHERE { ?uri a dbpedia:BiologicalDatabase . ?uri <http://purl.org/dc/terms/subject> <http://dbpedia.org/resource/Category:Systems_biology> . OPTIONAL { ?uri <http://dbpedia.org/property/title> ?title. } OPTIONAL { ?uri <http://dbpedia.org/property/description> ?description . } } ORDER By ?title
Results:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | title | description | uri | ====================================================================================================================================================================================================================================== | "BISC"@en | "Protein–protein interaction database linking structural biology with functional genomics"@en | <http://dbpedia.org/resource/BISC_%28database%29> | | "BioGRID"@en | "interaction data."@en | <http://dbpedia.org/resource/BioGRID> | | "BioModels Database"@en | "A database for storing, exchanging and retrieving published quantitative models of biological interest."@en | <http://dbpedia.org/resource/BioModels_Database> | | "ChemProt"@en | "disease chemical biology database."@en | <http://dbpedia.org/resource/ChemProt> | | "ConsensusPathDB"@en | "human functional interaction networks."@en | <http://dbpedia.org/resource/ConsensusPathDB> | | "DIMA"@en | "predicted and known interactions between protein domains"@en | <http://dbpedia.org/resource/DIMA_%28database%29> | | "HitPredict"@en | "quality assessed protein-protein interactions in nine species."@en | <http://dbpedia.org/resource/HitPredict> | | "KEGG"@en | "The KEGG resource for deciphering the genome."@en | <http://dbpedia.org/resource/KEGG> | | "KUPS"@en | "datasets of interacting and non-interacting protein pairs with associated attributions."@en | <http://dbpedia.org/resource/KUPS_%28database%29> | | "PID"@en | "Pathway Interaction Database."@en | <http://dbpedia.org/resource/NCI-Nature_Pathway_Interaction_Database> | | "Pathway Commons"@en | "biological pathways."@en | <http://dbpedia.org/resource/Pathway_commons> | | "ProtCID"@en | "interactions of homologous proteins in multiple crystal forms."@en | <http://dbpedia.org/resource/ProtCID> | | "REPAIRtoire"@en | <http://dbpedia.org/resource/DNA_repair> | <http://dbpedia.org/resource/REPAIRtoire> | | "REPAIRtoire"@en | <http://dbpedia.org/resource/Systems_biology> | <http://dbpedia.org/resource/REPAIRtoire> | | "SPIKE"@en | "highly curated human signaling pathways."@en | <http://dbpedia.org/resource/Spike_%28database%29> | | "STRING"@en | "Search Tool for the Retrieval of Interacting Genes/Proteins"@en | <http://dbpedia.org/resource/STRING> | | "3"^^<http://www.w3.org/2001/XMLSchema#int> | "identification and classification of domain-based interactions of known three-dimensional structure."@en | <http://dbpedia.org/resource/3did> | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
list the databases available at the NCBI
Sparql query
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dbpedia: <http://dbpedia.org/ontology/> SELECT ?title ?description ?uri WHERE { ?uri a <http://dbpedia.org/ontology/BiologicalDatabase> . ?uri <http://dbpedia.org/property/center> <http://dbpedia.org/resource/National_Center_for_Biotechnology_Information> . OPTIONAL { ?uri <http://dbpedia.org/property/title> ?title . } OPTIONAL { ?uri <http://dbpedia.org/property/description> ?description . } } ORDER BY ?title
Result:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | title | description | uri | ======================================================================================================================================================================================================== | "BGMUT"@en | "database of variations in the genes that encode antigens of blood group systems"@en | <http://dbpedia.org/resource/BGMUT> | | "CDD"@en | "Conserved Domain Database for the functional annotation of proteins."@en | <http://dbpedia.org/resource/Conserved_domain_database> | | "GenBank"@en | "Nucleotide sequences for more than 300 000 organisms with supporting bibliographic and biological annotation."@en | <http://dbpedia.org/resource/GenBank> | | "NCBI Epigenomics"@en | "epigenomic data sets."@en | <http://dbpedia.org/resource/NCBI_Epigenomics> | | "Refseq"@en | "curated non-redundant sequence database of genomes."@en | <http://dbpedia.org/resource/RefSeq> | | "UniGene"@en | <http://dbpedia.org/resource/Transcriptome> | <http://dbpedia.org/resource/UniGene> | | "dbSNP"@en | <http://dbpedia.org/resource/Database> | <http://dbpedia.org/resource/DbSNP> | | "dbSNP"@en | <http://dbpedia.org/resource/Single-nucleotide_polymorphism> | <http://dbpedia.org/resource/DbSNP> | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
List the biological databases having a SPARQL endpoint
SPARQL query
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?uri ?endpoint WHERE { ?uri a <http://dbpedia.org/ontology/BiologicalDatabase> . ?uri <http://dbpedia.org/property/sparql> ?endpoint . }
Result:
------------------------------------------------------------------------------------ | uri | endpoint | ==================================================================================== | <http://dbpedia.org/resource/ChEBI> | <http://chebi.bio2rdf.org> | | <http://dbpedia.org/resource/ChEMBL> | <http://rdf.farmbio.uu.se/chembl/snorql/> | ------------------------------------------------------------------------------------That's It, Pierre
1 comment:
I wanted to create an entry called "cas9 genome editing" on Wikipedia, but I saw those unfamiliar with the template and gave up. After reading your article, I can finish the entry again.
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