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Sediment

sediment

URI: mixs.vocab:Sediment

Combinations

Slots

MIxS ID Name Multiplicity Description Pattern Info
MIXS:0000009 lat_lon 0..1 The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system None .
MIXS:0000018 depth 1..1 The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. None .
MIXS:0000094 alt 0..1 Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air None .
MIXS:0000093 elev 0..1 Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit. None .
MIXS:0000113 temp 0..1 Temperature of the sample at the time of sampling. None .
MIXS:0000010 geo_loc_name 0..1 The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ) None .
MIXS:0000011 collection_date 0..1 The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant None .
MIXS:0000012 env_broad_scale 0..1 Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS None .
MIXS:0000013 env_local_scale 0..1 Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS. None .
MIXS:0000014 env_medium 0..1 Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). None .
MIXS:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0001078 sediment_type 0..1 Information about the sediment type based on major constituents None .
MIXS:0000750 tidal_stage 0..1 Stage of tide None .
MIXS:0000116 samp_store_dur 0..1 Duration for which the sample was stored None .
MIXS:0001001 ph 0..1 Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid None .
MIXS:0000211 porosity 0..1 Porosity of deposited sediment is volume of voids divided by the total volume of sample None .
MIXS:0000421 alkalinity 0..1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate None .
MIXS:0000490 alkyl_diethers 0..1 Concentration of alkyl diethers None .
MIXS:0000172 aminopept_act 0..1 Measurement of aminopeptidase activity None .
MIXS:0000427 ammonium 0..1 Concentration of ammonium in the sample None .
MIXS:0000173 bacteria_carb_prod 0..1 Measurement of bacterial carbon production None .
MIXS:0000175 bishomohopanol 0..1 Concentration of bishomohopanol None .
MIXS:0000176 bromide 0..1 Concentration of bromide None .
MIXS:0000432 calcium 0..1 Concentration of calcium in the sample None .
MIXS:0000310 carb_nitro_ratio 0..1 Ratio of amount or concentrations of carbon to nitrogen None .
MIXS:0000429 chloride 0..1 Concentration of chloride in the sample None .
MIXS:0000177 chlorophyll 0..1 Concentration of chlorophyll None .
MIXS:0000435 density 0..1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) None .
MIXS:0000436 diss_carb_dioxide 0..1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample None .
MIXS:0000179 diss_hydrogen 0..1 Concentration of dissolved hydrogen None .
MIXS:0000434 diss_inorg_carb 0..1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter None .
MIXS:0000433 diss_org_carb 0..1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid None .
MIXS:0000162 diss_org_nitro 0..1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 None .
MIXS:0000119 diss_oxygen 0..1 Concentration of dissolved oxygen None .
MIXS:0000137 glucosidase_act 0..1 Measurement of glucosidase activity None .
MIXS:0000431 magnesium 0..1 Concentration of magnesium in the sample None .
MIXS:0000498 mean_frict_vel 0..1 Measurement of mean friction velocity None .
MIXS:0000502 mean_peak_frict_vel 0..1 Measurement of mean peak friction velocity None .
MIXS:0000101 methane 0..1 Methane (gas) amount or concentration at the time of sampling None .
MIXS:0000425 nitrate 0..1 Concentration of nitrate in the sample None .
MIXS:0000426 nitrite 0..1 Concentration of nitrite in the sample None .
MIXS:0000504 nitro 0..1 Concentration of nitrogen (total) None .
MIXS:0000508 org_carb 0..1 Concentration of organic carbon None .
MIXS:0000204 org_matter 0..1 Concentration of organic matter None .
MIXS:0000205 org_nitro 0..1 Concentration of organic nitrogen None .
MIXS:0000515 part_org_carb 0..1 Concentration of particulate organic carbon None .
MIXS:0000516 petroleum_hydrocarb 0..1 Concentration of petroleum hydrocarbon None .
MIXS:0000505 phosphate 0..1 Concentration of phosphate None .
MIXS:0000430 potassium 0..1 Concentration of potassium in the sample None .
MIXS:0000412 pressure 0..1 Pressure to which the sample is subject to, in atmospheres None .
MIXS:0000182 redox_potential 0..1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential None .
MIXS:0000183 salinity 0..1 The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. None .
MIXS:0000110 samp_store_temp 0..1 Temperature at which sample was stored, e.g. -80 degree Celsius None .
MIXS:0000184 silicate 0..1 Concentration of silicate None .
MIXS:0000428 sodium 0..1 Sodium concentration in the sample None .
MIXS:0000423 sulfate 0..1 Concentration of sulfate in the sample None .
MIXS:0000424 sulfide 0..1 Concentration of sulfide in the sample None .
MIXS:0000525 tot_carb 0..1 Total carbon content None .
MIXS:0000634 tot_depth_water_col 0..1 Measurement of total depth of water column None .
MIXS:0000530 tot_nitro_content 0..1 Total nitrogen content of the sample None .
MIXS:0000533 tot_org_carb 0..1 Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content None .
MIXS:0000191 turbidity 0..1 Measure of the amount of cloudiness or haziness in water caused by individual particles None .
MIXS:0000185 water_content 0..1 Water content measurement None .
MIXS:0000751 chem_administration 0..* List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi None .
MIXS:0000755 samp_store_loc 0..1 Location at which sample was stored, usually name of a specific freezer/room None .
MIXS:0000174 biomass 0..* Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements None .
MIXS:0000178 diether_lipids 0..* Concentration of diether lipids; can include multiple types of diether lipids None .
MIXS:0000752 misc_param 0..* Any other measurement performed or parameter collected, that is not listed here None .
MIXS:0000503 n_alkanes 0..* Concentration of n-alkanes; can include multiple n-alkanes None .
MIXS:0000206 particle_class 0..* Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values None .
MIXS:0000180 phaeopigments 0..* Concentration of phaeopigments; can include multiple phaeopigments None .
MIXS:0000181 phosplipid_fatt_acid 0..* Concentration of phospholipid fatty acids; can include multiple values None .
MIXS:0000103 organism_count 0..* Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). None .
MIXS:0000754 perturbation 0..* Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types None .

Usages

Identifier and Mapping Information