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第三回LinkedData勉強会での発表資料です

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2012-01-18 第三回LinkedData勉強会@DBCLSでの発表資料です。Slide単体でわかるように発表時から若干改変しています。

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第三回LinkedData勉強会での発表資料です

  1. 1. This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.Boston Skyline: Arvind Balaraman / FreeDigitalPhotos.net,ISS: NASA,Heater: CDC, Mold: EPA, Staph: Janice Haney Carr, CDC
  2. 2. Meta-genome Meta-transcriptome Gen-ome Transcript-ome Prote-ome Gene Transcript Protein transcription translation DNA RNA Protein replication
  3. 3. ABI Roche illumina Illustration from: http://g86.dbcls.jp/~togoriv/Data from: http://www.genome.gov/sequencingcosts/
  4. 4. Ignicoccus hospitalis
  5. 5. GOLD:http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  6. 6. http://www.earthmicrobiome.org/
  7. 7. 4054 627
  8. 8. Attributes/Extra attributes Literal Taxonomy freshwater mouse gut metagenome, fish metagenome, freshwater metagenome, soil metagenomemeta Title marine metagenome GOB1A Genomic DNA sample GOB_1 Enviornmental package Soil, soil Environment (biome) terrestrial biome Environment (feature) Grassland, soil, freshwater, animal-associated habitat Environment (material) rhizosphere, feces, freshwater Habitat soybean rhizosphere soil, Biochar from Amazonian anthrosol under secondary forest Habitat Type Coastal Site_description--Other ? Amazonian soil Soil Type Bioreactor slurry, Untreated soil Biochar, clay, Stages of soiling, Rhizosphere Biochar, Type_of_Sample clay, Stages of soiling, Rhizosphere whole intestine, colon body habitat gut, mucosa 401 body site FMA:Feces body_product FMA:Feces body_site FMA:Feces env_biome ENVO:feces, biome, calcite hot spring, hot spring env_feature ENVO:feces, wastewater treatment plant, spring, Freshwater Habitat env_matter ENVO:feces, anaerobic digester sludge, Fresh Water, Underground Water environment 1 m depth of Lake Llebreta, River water, insecta-associated-habitat, marine biome, fjord, coastal water environment (biome) food production factory, Rainforest Division environment (feature) feature biotic mesoscopic physical object, arboreal habitat environment (material) material fermented food product, forest soil, anthrosol, Clay soil environmental package ? MIENS_16S, MIMARKS_16S , host-associated, water, soil envo_biome EnvO biome marine biome [ENVO:00000447] envo_feature EnvO feature marine habitat [ENVO:00000569]37 envo_material EnvO material sea water [ENVO:00002149] general_location offshore area [ENVO:00000090], Fore Reef, Cooks Bay geographic location White Oak River alphanumeric, Gulf of Mexico (MC118) alphanumeric, Storegga seep geographic location (Country) ( ) South Korea:Damyang, Yeongsan river, South Korea:Jeonnam, farm, South Korea:Naju, habitat Yeongsan river vents Alphanumeric location Top Vent Alphanumeric, Nikko Background seawater Alphanumeric oxy_stat_samp , Aerobic, aerobic plant body site Roots rel_to_oxygen , Aerobic relationship to oxygen , facultative anaerobe, anaerobic sample_type Hydrothermal fluids Alphanumeric, arch/bact biological mat from diffuse flow sample sample_type_beta water Alphanumeric substrate salt water tissue Leech crop intraluminal fluid, unopened flower buds
  9. 9. Literal No. of sample Arctic: Amundsen Gulf, Beaufort Sea 1 Kaneohe Bay, Kaneohe, Hawaii 2 Lake 227, Experimental Lakes Area, Ontario 1 Lake 239, Experimental Lakes Area, Ontario 1 Rifle DOE IFRC, Rifle Colorado 3 Arctic Ocean 1 Arctic: Permafrost Shaft 1 Arctic:Chukchi Sea 1 “Arctic:Chukchi Sea” skos:broadMatch “sea water ENVO:00002149” Argentine Sea 9 Atlantic 2 Atlantic:Equatorial 1 Atlantic:North Sea 2 Babs Cove 4 Bay of Biscay (NE Atlantic Ocean) 1 Beaufort Sea 1 Black Sea 1 Black Sea Carbonate reef alphanumeric 2 Boiling Springs Lake 2 Caroline Island site 12 1 Caroline Island site 9 1 Caroline Island wreck 1 Chesapeake bay station 858 4 Estuary 4 Guaymas Basin alphanumeric 4 Gulf of Mexico 1 Gulf of Mexico (MC118) alphanumeric 648 Irish Sea (NE Atlantic Ocean) 1 Jaco Summit 3 Key West Coral Nursery 2 Mediterranean Sea 1 Octopus Hot Spring 1 Pacific 14 Pacific Ocean 20 Pacific Ocean: Coral Sea 2 Pacific Ocean: Southern California Bight 5 Pacific: Gulf of California 4 “Pacific: Gulf of California” skos:broadMatch “sea water ENVO:00002149” Pacific: Strait of Georgia 8 Pt Loma San Diego 3 Raunefjorden 8 Saanich Inlet 1 Storegga seep enrichment alphanumeric 2 Strait of Georgia 3 White Oak River alphanumeric 2 Wreck Reef 2 Yellowstone National Park 16 near BATS 2 shark skin Caroline Island 1 shark skin Malden Island 1
  10. 10. “Pacific: Gulf of California” “Pacific: Gulf of California” skos:broadMatch “sea water ENVO:00002149”“Arctic:Chukchi Sea” “Arctic:Chukchi Sea” skos:broadMatch “sea water ENVO:00002149” http://environmentontology.org/
  11. 11. Literal No. of sample Arctic: Amundsen Gulf, Beaufort Sea 1 “Arctic: Amundsen Gulf” skos:broadMatch “sea water ENVO:00002149” Kaneohe Bay, Kaneohe, Hawaii 2 “Kaneohe Bay” skos:broadMatch “sea water ENVO:00002149” Lake 227, Experimental Lakes Area, Ontario 1 Lake 239, Experimental Lakes Area, Ontario 1 Rifle DOE IFRC, Rifle Colorado 3 Arctic Ocean 1 “Arctic Ocean” skos:broadMatch “sea water ENVO:00002149” Arctic: Permafrost Shaft 1 “Arctic: Permafrost Shaft” skos:broadMatch “sea water ENVO:00002149” Arctic:Chukchi Sea 1 “Arctic:Chukchi Sea” skos:broadMatch “sea water ENVO:00002149” Argentine Sea 9 “Argentine Sea” skos:broadMatch “sea water ENVO:00002149” Atlantic 2 “Atlantic” skos:broadMatch “sea water ENVO:00002149” Atlantic:Equatorial 1 “Atlantic:Equatorial” skos:broadMatch “sea water ENVO:00002149” Atlantic:North Sea 2 “Atlantic:North Sea” skos:broadMatch “sea water ENVO:00002149” Babs Cove 4 Bay of Biscay (NE Atlantic Ocean) 1 “Bay of Biscay (NE Atlantic Ocean)” skos:broadMatch “sea water ENVO:00002149” Beaufort Sea 1 “Beaufort Sea” skos:broadMatch “sea water ENVO:00002149” Black Sea 1 “Black Sea” skos:broadMatch “sea water ENVO:00002149” Black Sea Carbonate reef alphanumeric 2 “Black Sea Carbonate reef alphanumeric” skos:broadMatch “sea water ENVO:00002149” Boiling Springs Lake 2 Caroline Island site 12 1 Caroline Island site 9 1 Caroline Island wreck 1 Chesapeake bay station 858 4 Estuary 4 Guaymas Basin alphanumeric 4 Gulf of Mexico 1 “Gulf of Mexico” skos:broadMatch “sea water ENVO:00002149” Gulf of Mexico (MC118) alphanumeric 6 “Gulf of Mexico (MC118) alphanumeric” skos:broadMatch “sea water ENVO:00002149” Irish Sea (NE Atlantic Ocean) 1 “Irish Sea (NE Atlantic Ocean)” skos:broadMatch “sea water ENVO:00002149”48 Jaco Summit 3 Key West Coral Nursery 2 Mediterranean Sea 1 Octopus Hot Spring 1 Pacific 14 “Pacific” skos:broadMatch “sea water ENVO:00002149” Pacific Ocean 20 “Pacific Ocean” skos:broadMatch “sea water ENVO:00002149” Pacific Ocean: Coral Sea 2 “Pacific Ocean: Coral Sea” skos:broadMatch “sea water ENVO:00002149” Pacific Ocean: Southern California Bight 5 “Pacific Ocean: Southern California Bight” skos:broadMatch “sea water ENVO:00002149” Pacific: Gulf of California 4 “Pacific: Gulf of California” skos:broadMatch “sea water ENVO:00002149” Pacific: Strait of Georgia 8 “Pacific: Strait of Georgia” skos:broadMatch “sea water ENVO:00002149” Pt Loma San Diego 3 Raunefjorden 8 Saanich Inlet 1 Storegga seep enrichment alphanumeric 2 Strait of Georgia 3 “Strait of Georgia” skos:broadMatch “sea water ENVO:00002149” White Oak River alphanumeric 2 Wreck Reef 2 Yellowstone National Park 16 near BATS 2 shark skin Caroline Island 1 “Caroline Island” skos:broadMatch “sea water ENVO:00002149” shark skin Malden Island 1 “Malden Island” skos:broadMatch “sea water ENVO:00002149”
  12. 12. “Pacific: Gulf of California” “Gulf of California” skos:exactMatch “Gulf of California GAZ:00002619”“Arctic:Chukchi Sea” “Chukchi Sea” skos:exactMatch “Chukchi Sea GAZ:00008942”
  13. 13. GAZZTEER http://bioportal.bioontology.org/ontologies/1397
  14. 14. “Gulf of California” skos:exactMatch “Gulf of California GAZ:00002619”
  15. 15. Metagenome Environment Ontology (MEO) http://environmentontology.org/ Thing biome environmental feature environmental material place (ENVO:00000428) (ENVO:00002297) (ENVO:00010483) (MEO:######) habitat (ENVO:00002036) GAZETTEER http://bioportal.bioontology.org/ontologies/1397 organism-associated habitat (ENVO:00002032) plant-associated habitat animal-associated habitat NCBI (ENVO:00009001) (ENVO:00006776) Taxonomy PO FMA http://plantontology.org/ http://sig.biostr.washington.edu/projects/fm/Environment Ontology (EnvO)
  16. 16. MEOExperimental data RDF store Environmental onotology Material feature data SRA:SRS12345 Salinity MEO EnvO ENVO:00002149 Experimental data (sea water) : SRA:SRS12345 : ORG:TAX1234 Attributes Gulf of California GAZZTEER GAZ:00002619 Satellite dataTaxonomy data (Gulf of California) : : Sea surface temp. ORG:TAX1234 Gulf of California FMA PO

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