11 September 2011

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:

andrea wang said...

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.