Class: sediment MIMARKS specimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package sediment

URI: mixs.vocab:SedimentMIMARKSSpecimen

Parents

• is_a: Sediment - sediment

Uses Checklist

• mixin: MIMARKSSpecimen - Minimal Information about a Marker Specimen: specimen

Attributes

Inherited from sediment:

• 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

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_taxon_id _1..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞experimental_factor _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞env_package _0..1
  • Range: env_package_enum

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞source_mat_id _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_collec_device _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_collec_method _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_mat_process _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞size_frac _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_size _0..1
  • Range: Integer

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_vector _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_screen _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_gene _1..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_subfragment _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_primers _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞mid _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞adapters _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_cond _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_meth _1..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_quality_check _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞chimera_check _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞assembly_software _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞associated resource _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sop _0..1
  • Range: String