Class: sediment

sediment

URI: mixs.vocab:Sediment

Children

• SedimentME - Combinatorial checklist Metagenome or Environmental with environmental package sediment
• SedimentMIGSBacteria - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment
• SedimentMIGSEukaryote - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package sediment
• SedimentMIGSOrg - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package sediment
• SedimentMIGSPlant - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package sediment
• SedimentMIGSVirus - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package sediment
• SedimentMIMAG - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package sediment
• SedimentMIMARKSSpecimen - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment
• SedimentMIMARKSSurvey - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package sediment
• SedimentMISAG - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package sediment
• SedimentMIUVIG - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package sediment

Referenced by Package

Attributes

Own

• lat_lon _0..1
  • Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
  • Range: String
  • Example: 50.586825 6.408977 None
• sediment➞depth _1..1
  • Range: QuantityValue
• alt _0..1
  • Description: 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
  • Range: QuantityValue
  • Example: 100 meter None
• sediment➞elev _0..1
  • Range: QuantityValue
• sediment➞temp _0..1
  • Range: QuantityValue
• geo_loc_name _0..1
  • Description: 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)
  • Range: String
  • Example: USA: Maryland, Bethesda None
• collection_date _0..1
  • Description: 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
  • Range: Date
  • Example: 2018-05-11T10:00:00+01:00; 2018-05-11 None
• env_broad_scale _0..1
  • Description: 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
  • Range: String
  • Example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean None
• env_local_scale _0..1
  • Description: 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
  • Range: String
  • Example: litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. None
• env_medium _0..1
  • Description: 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).
  • Range: String
  • Example: soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005] None
• sediment➞alkalinity _0..1
  • Range: QuantityValue
• sediment➞alkyl_diethers _0..1
  • Range: QuantityValue
• sediment➞aminopept_act _0..1
  • Range: QuantityValue
• sediment➞ammonium _0..1
  • Range: QuantityValue
• sediment➞bacteria_carb_prod _0..1
  • Range: QuantityValue
• sediment➞biomass _0..*
  • Range: String
• sediment➞bishomohopanol _0..1
  • Range: QuantityValue
• sediment➞bromide _0..1
  • Range: QuantityValue
• sediment➞calcium _0..1
  • Range: QuantityValue
• sediment➞carb_nitro_ratio _0..1
  • Range: QuantityValue
• sediment➞chem_administration _0..*
  • Range: String
• sediment➞chloride _0..1
  • Range: QuantityValue
• sediment➞chlorophyll _0..1
  • Range: QuantityValue
• sediment➞density _0..1
  • Range: QuantityValue
• sediment➞diether_lipids _0..*
  • Range: String
• sediment➞diss_carb_dioxide _0..1
  • Range: QuantityValue
• sediment➞diss_hydrogen _0..1
  • Range: QuantityValue
• sediment➞diss_inorg_carb _0..1
  • Range: QuantityValue
• sediment➞diss_org_carb _0..1
  • Range: QuantityValue
• sediment➞diss_org_nitro _0..1
  • Range: QuantityValue
• sediment➞diss_oxygen _0..1
  • Range: QuantityValue
• sediment➞glucosidase_act _0..1
  • Range: QuantityValue
• sediment➞magnesium _0..1
  • Range: QuantityValue
• sediment➞mean_frict_vel _0..1
  • Range: QuantityValue
• sediment➞mean_peak_frict_vel _0..1
  • Range: QuantityValue
• sediment➞methane _0..1
  • Range: QuantityValue
• sediment➞misc_param _0..*
  • Range: String
• sediment➞n_alkanes _0..*
  • Range: String
• sediment➞nitrate _0..1
  • Range: QuantityValue
• sediment➞nitrite _0..1
  • Range: QuantityValue
• sediment➞nitro _0..1
  • Range: QuantityValue
• sediment➞org_carb _0..1
  • Range: QuantityValue
• sediment➞org_matter _0..1
  • Range: QuantityValue
• sediment➞org_nitro _0..1
  • Range: QuantityValue
• sediment➞organism_count _0..*
  • Range: organism_count_enum
• sediment➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• sediment➞ph _0..1
  • Range: Double
• sediment➞particle_class _0..*
  • Range: String
• sediment➞part_org_carb _0..1
  • Range: QuantityValue
• sediment➞perturbation _0..*
  • Range: String
• sediment➞petroleum_hydrocarb _0..1
  • Range: QuantityValue
• sediment➞phaeopigments _0..*
  • Range: String
• sediment➞phosphate _0..1
  • Range: QuantityValue
• sediment➞phosplipid_fatt_acid _0..*
  • Range: String
• sediment➞porosity _0..1
  • Range: String
• sediment➞potassium _0..1
  • Range: QuantityValue
• sediment➞pressure _0..1
  • Range: QuantityValue
• sediment➞redox_potential _0..1
  • Range: QuantityValue
• sediment➞salinity _0..1
  • Range: QuantityValue
• sediment➞samp_store_dur _0..1
  • Range: String
• sediment➞samp_store_loc _0..1
  • Range: String
• sediment➞samp_store_temp _0..1
  • Range: QuantityValue
• sediment➞sediment_type _0..1
  • Range: sediment_type_enum
• sediment➞silicate _0..1
  • Range: QuantityValue
• sediment➞sodium _0..1
  • Range: QuantityValue
• sediment➞sulfate _0..1
  • Range: QuantityValue
• sediment➞sulfide _0..1
  • Range: QuantityValue
• sediment➞tidal_stage _0..1
  • Range: tidal_stage_enum
• sediment➞tot_carb _0..1
  • Range: QuantityValue
• sediment➞tot_depth_water_col _0..1
  • Range: QuantityValue
• sediment➞tot_nitro_content _0..1
  • Range: QuantityValue
• sediment➞tot_org_carb _0..1
  • Range: QuantityValue
• sediment➞turbidity _0..1
  • Range: QuantityValue
• sediment➞water_content _0..1
  • Range: QuantityValue
• sediment➞samp_name _1..1
  • Range: String
• sediment➞project_name _1..1
  • Range: String
• sediment➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue