Towards Database Integration Through RDF & Linked Data

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Our slides presented at the 34th annual meeting of the Molecular Biology Society of Japan.
Note that this version has been modified to publish under a CC-BY.

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  • Towards Database Integration Through RDF & Linked Data

    1. 1. Towards DatabaseIntegration Through RDF & Linked DataYasunori Yamamoto, Shinobu Okamoto, Akinori Yonezawa Database Center For Life Science 2T18pI-5
    2. 2. NCBI Taxonomy 4,000 biomedical journals Database indexed at NLM 1994 SWISSPROT PIR PRF PDB GenBank EMBL DDBJ LANL 3442 Nucleic Acids Research, 1994, Vol. 22, No. 17 Palent 2011 http://www.ncbi.nlm.nih.gov/sites/gqueryDatabase Center for Life Science MBSJ 2011
    3. 3. Entrez Link DescriptionsDatabase Center for Life Science MBSJ 2011
    4. 4. NAR database issue 1400 1330 1300 1230 1200 1170 1078 1100 2008 2009 2010 2011 Source: Oxford University Press dullhunkDatabase Center for Life Science MBSJ 2011
    5. 5. Legacy Web TP53 Entrez Gene:7157 Ensembl:ENSG00000141510 TP53 UCSC:uc002gij.2 Vega:OTTHUMG00000162125http://en.wikipedia.org/wiki/P53 TP53 http://www.genenames.org/data/hgnc_data.php?hgnc_id=11998 Entrez Gene:7157 http://www.ncbi.nlm.nih.gov/gene/7157 Ensembl:ENSG00000141510 http://www.ensembl.org/Homo_sapiens/Gene/ Summary?g=ENSG00000141510 UCSC:uc002gij.2 http://genome.cse.ucsc.edu/cgi-bin/hgGene? org=Human&hgg_chrom=none&hgg_type= knownGene&hgg_gene=uc002gij.2 Vega:OTTHUMG00000162125 http://vega.sanger.ac.uk/Homo_sapiens/Gene/ Summary?db=core;g=OTTHUMG00000162125 Database Center for Life Science MBSJ 2011
    6. 6. Not Only For People http://dbpedia.org/resource/P53 owl:sameAs http://www4.wiwiss.fu-berlin.de/diseasome/resource/genes/TP53 foaf:page http://en.wikipedia.org/wiki/P53 dcterms:subject category:Programmed_cell_death category:Transcription_factors category:Proteins category:Apoptosis category:Tumor_suppressor_genes rdf:type owl:Thing dbpedia-owl:Protein yago:Proteins yago:TranscriptionFactors yago:TumorSuppressorGenes Resource Description Framework (RDF) Linked DataDatabase Center for Life Science MBSJ 2011
    7. 7. Open StandardDatabase Center for Life Science MBSJ 2011
    8. 8. Link Freely | Annotation Use controlled vocabularies by LinkingDatabase Center for Life Science MBSJ 2011
    9. 9. Gene Ontology Gene Product Annotation Overview an d g en e g en e a se s ntati o n of atab rese a nd d g the rep s spe cies n dar dizin acros st a utes ttrib ro d pScienceuct a http://www.geneontology.org/Database Center for Life MBSJ 2011
    10. 10. Database Center for Life Science MBSJ 2011
    11. 11. “Gulf of California” skos:exactMatch “Gulf of California GAZ:00002619” Database Center for Life Science MBSJ 2011
    12. 12. “Gulf of California” skos:exactMatch “Gulf of California GAZ:00002619” Database Center for Life Science MBSJ 2011
    13. 13. Metadata curation is an infrastructure to create and provision liked data networksExperimental data RDF store Material feature data Environmental ontology SRA:SRS12345 Salinity MeO EnvO ENVO:00002149 Experimental data (sea water) : SRA:SRS12345 : ORG:TAX1234 Attributes Gulf of California Gazetteer GAZ:00002619 Satellite dataTaxonomy data (Gulf of California) : : Sea surface temp. ORG:TAX1234 Gulf of California FMA PO Database Center for Life Science MBSJ 2011
    14. 14. Environmental ontology for Metagenome http://wiki.lifesciencedb.jp/mw/index.php/BH11.11Database Center for Life Science MBSJ 2011
    15. 15. Poster: 2P-0978

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