[esip-semantictech] seeking geo/genomic vocabularies

[Parsons, Mark]

Dear ESIP Documentation and Semantics groups,

I have an interesting vocabulary question. I’m looking for any sort of accepted vocabulary or code list that might serve as a first baseline for classifying three variables that define environmental context in understanding subsurface life :  

- env_biome — ecological habitat of the sample, e.g estuarine biome, marine hydrothermal vent biome, neritic pelagic zone biome,...
- env_feature — physical environment of the sample, a mix of geographical, geological, and climatic variables: andesitic volcano, animal carcass fall, low tide zone,...
- env_material — substrate of the sample, e.g., anaerobic mud, metamorphic rock, sea foam, …

You can see the full list of free text variables below.

The Deep Carbon Observatory is trying to assemble a benchmark “Census of Deep Life” — the genomic sequences (ATCG…) of critters beneath the surface, even 10s of km beneath the surface. It’s an interesting intersection of life and geological sciences that challenges standard classifications.

At a first level, the goal is to simply identify the critters down there. More interesting questions arise from the characterizing the environment where the microbes live which may begin to address some more functional (not just existence) questions.

I am trying to assemble a compiled dataset from a bunch of different samples around the world and am looking for anything we can begin to standardize on. Some of the GCMD keywords under geomorphic landforms/processes, geothermal dynamics, and rocks/minerals could be useful, but there’s not a really good match.

Ultimately, this will require extensive discussion with the research community, but any thoughts on past experience or places to start would be most welcome.

cheers,

-m. 





env_biome  
aquatic biome, concentration basin mediterranean sea biome, dilution basin mediterranean sea biome, epeiric sea biome, estuarine biome, freshwater biome, freshwater lake biome, freshwater river biome, Large lake biome, Large river biome, Large river delta biome, Large river headwater biome, mangrove biome, marginal sea biome, marine abyssal zone biome, marine basaltic hydrothermal vent biome, marine bathyal zone biome, marine benthic biome, marine biome, marine black smoker biome, marine cold seep biome, marine coral reef biome, marine hadal zone biome, marine hydrothermal vent biome, marine neritic benthic zone biome, marine pelagic biome, marine reef biome, marine salt marsh biome, marine sponge reef biome, marine subtidal rocky reef biome, marine ultramafic hydrothermal vent biome, marine white smoker biome, mediterranean sea biome, neritic epipelagic zone biome, neritic mesopelagic zone biome, neritic pelagic zone biome, neritic sea surface microlayer biome, ocean biome, oceanic abyssopelagic zone biome, oceanic bathypelagic zone biome, oceanic benthopelagic zone biome, oceanic epipelagic zone biome, oceanic hadal pelagic zone biome, oceanic mesopelagic zone biome, oceanic pelagic zone biome, oceanic sea surface microlayer biome, polar biome, Small lake biome, Small river biome, Temperate shelf and sea biome, Temperate upwelling biome, Tropical coral biome, Tropical upwelling biome”

env_feature
abyssal feature, abyssal plain, achondrite, active geological fault, algal bloom, along-front current, amictic lake, anaerobic sludge, anchialine cave, anchialine pool, andesitic volcano, animal carcass fall, aquatic layer, arrugado, artificial channel, artificial harbor, artificial reef, back-arc basin, backwater, bay, bed, bedding-plane cave, biofilm, black smoker, blowhole, borehole, boulder, boundary current front, brackish estuary, brackish lake, brine pool, burrow, calanque, cave, cave entrance, cave floor, cave system, cave wall, channel, chemocline, chondrite, coastal buoyancy current front, coastal inlet, coastal upwelling, coastal upwelling front, coastal water body, coastal wetland, cold monomictic lake, cold polymictic lake, cold seep, cold surface current, complex volcano, continental margin, continental rise, continental shelf, continental slope, coral reef, cove, crater lake, crevice, dacitic volcano, deep chlorophyll maximum layer, deep ocean current, delta, dimictic lake, drop stone, eastern boundary current, endorheic basin, endorheic lake, epilimnion, equatorial upwelling front, erosional cave, estuarine bulk water, estuarine front, estuary, eutrophic lake, exorheic lake, fault cave, fjord, fjord lake, freshwater lake, fumarole, geological fault, geological fracture, geological joint, guyot, hadalpelagic zone, harbor, high tide zone, highly stratified estuary, holomictic lake, hydroform, hydrographic feature, hydrothermal seep, hydrothermal vent, hypolimnion, igneous extrusion, inflationary cave, inlet, intermittent estuary, intertidal zone, inverse estuary, iron meteorite, joint-plane cave, karst cave, kelp forest, lagoon, lake, lake bed, lake inlet, lake layer, landlocked sea, lava field, lava flow, lava tunnel, layer, lentic water body, liman, limestone cave, live cave, lotic water body, low tide zone, lysocline, maelstrom, mangrove swamp, marginal ice zone front, marine abyssalpelagic zone, marine algal bloom, marine anoxic zone, marine aphotic zone, marine bathypelagic zone, marine benthic feature, marine benthic storm, marine bulk water, marine channel, marine chemocline, marine cold-water sphere, marine coral reef back reef, marine coral reef buttress zone, marine coral reef crest, marine coral reef deep fore reef, marine coral reef flat zone, marine coral reef fore reef, marine current, marine downwelling, marine hydrographic feature, marine hydrothermal plume, marine hydrothermal vent, marine hydrothermal vent chimney, marine layer, marine lysocline, marine mesopelagic zone, marine mesoscale eddy field, marine neritic zone, marine nutricline, marine oligotrophic desert, marine oxygen minimum zone, marine pelagic zone, marine photic zone, marine pockmark, marine pycnocline, marine reef, marine sponge reef, marine streamer, marine subtidal rocky reef, marine surface current, marine Taylor column, marine terrace, marine thermocline, marine warm-water sphere, marine water body, marine water mass, marine wind mixed layer, marsh, mass of biological material, meromictic lake, mesoscale marine eddy, mesoscopic physical object, mesotrophic lake, metalimnion, meteorite, microbial feature, microbial mat, microfracture, mid-ocean ridge, mid-shelf fronts, mineral deposit, moatan, monomictic lake, mud volcano, mudflat, natural harbor, nutricline, obsolete lava field, obsolete marine mesoscale eddy, ocean, ocean basin, ocean current, ocean floor, ocean strait, ocean trench, oceanic front, oceanic gyre, oceanic zone, oil seep, oil spill, oil well, oligotrophic lake, organic matter fall, outcrop, outflow cave, pelagic isohaline surface, pelagic isopycnal surface, pelagic isothermal surface, permanent marine thermocline, plant matter fall, plume front, pockmark field, polymictic lake, polynya, primary cave, pseudocrater, pycnocline, quicksand area, range of seamounts, ravine, reef, rift lake, rocky shore, sabkha, saline hydrographic feature, saline lake, saline marsh, saline wedge estuary, saline wetland, sea, sea cave, sea floor, sea grass bed, seal fall, seamount, seasonal marine thermocline, sedimentary stratum, seep, shear fracture, shelf-slope/shelf-break front, shield volcano, slightly stratified estuary, solfatara, solutional cave, somma volcano, stony meteorite, stony-iron meteorite, strait, stratovolcano, stream channel, stromatolite mat, structural basin, subglacial lake, submarine canyon, submarine volcano, subtropical convergence front, surface convergence, Taylor column, thermocline, tidal creek, tidal mixing front, tidal mudflat, tidal pool, tidal watercourse, topographic upwelling front, trench, underground lake, underground physiographic feature, undersea feature, undersea trough, upwelling, vein, vertically mixed estuary, volcanic cave, volcanic cone, volcanic feature, volcanic field, volcanic fissure, volcanic hydrographic feature, volcano, warm monomictic lake, warm polymictic lake, warm seep, warm surface current, water body, water mass, water mass front, wave-cut platform, western boundary current, wetland, whale fall, whirlpool, white smoker, wood fall				

env_material
acidic water, agricultural waste material, alkaline water, anaerobic mud, anaerobic sediment, anaerobic stream sediment, andesite, animal waste material, anoxic water, anthropogenic environmental material, arsenate treated wood, arsenic-rich mud, basalt, biofilm material, biogenous sediment, biological waste material, biosolids, bore hole water, boulder sediment, brackish water, calcareous ooze, carbon dioxide-reducing sediment, chalk, cis-dichloroethane contaminated sediment, clastic sedimentary rock, clay, clay sediment, claystone, coastal sea water, cobble sediment, colloidal sediment, contaminated sediment, contaminated sludge, contaminated water, cosmogenous sediment, dacite, dacitic lava, dolomite, drilling bore water, estuarine mud, estuarine water, eutrophic water, felsic lava, foam, fresh water, fuel oil, glass, granite, granular sediment, gravel, high-level radioactive sediment, household waste material, hydrogenous sediment, hydrothermal fluid, hypersaline water, hyperthermophilic sediment, igneous rock, inorganically contaminated sediment, intermediate lava, intertidal sediment, iron-reducing sediment, iron-reducing zone of petroleum contaminated sediment, lake bottom mud, lava, lime mudstone, limestone, mafic lava, manganese-reducing sediment, marine mucilage, marine mud, marine sediment, marine sludge, marine snow, meltwater, mesophilic sediment, mesotrophic water, metamorphic rock, microbial mat material, mineral material, mud, muddy water, mudstone, naphthalene contaminated sediment, nitrate-reducing sediment, ocean water, oil, oil field production water, oil sludge, oligotrophic water, organic material, organic waste material, organically contaminated sediment, particulate matter, pebble sediment, petroleum, petroleum contaminated sediment, planktonic material, plastic, plutonic rock, polymetallic nodule, pulp-bleaching waste water, pumice, radioactive sediment, rainwater, raw primary sludge, red clay, river water, rock, rocky sand, root matter, saline lake sediment, saline water, salt mass, salt material, sand, sandstone, sandy sediment, scoria, scum, sea foam, sea sand, sea water, secondary sludge, sediment, sedimentary rock, sewage, shale, siliceous ooze, silt, siltstone, silty sediment, slate, sludge, soil, sulphate-reducing sediment, surface water, suspended sediment, tephra, thermophilic granular sludge, thermophilic sediment, treated wood, ultramafic lava, underground water, vegetation layer, volcanic ash, volcanic rock, waste material, waste water, water, water scum, waterborne particulate matter, wood