3. 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

4. Meta-genome Meta-transcriptome
Gen-ome Transcript-ome Prote-ome
Gene Transcript Protein
transcription translation
DNA RNA Protein
replication

5. ABI
Roche
illumina
Illustration from: http://g86.dbcls.jp/~togoriv/
Data from: http://www.genome.gov/sequencingcosts/

6. Ignicoccus hospitalis

8. GOLD:
http://www.genomesonline.org/cgi-bin/GOLD/index.cgi

10. http://www.earthmicrobiome.org/

11. 4054 627

12. 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

13. 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 6
48
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

14. “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/

15. 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”

16. “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”

17. GAZZTEER
http://bioportal.bioontology.org/ontologies/1397

18. “Gulf of California” skos:exactMatch “Gulf of California GAZ:00002619”

19. 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)

20. MEO
Experimental 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 data
Taxonomy data
(Gulf of California)
:
: Sea surface temp.
ORG:TAX1234
Gulf of California
FMA
PO