Class: microbial mat_biofilm MIMARKS specimen

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

URI: mixs.vocab:MicrobialMatBiofilmMIMARKSSpecimen

Parents

• is_a: MicrobialMatBiofilm - microbial mat/biofilm

Uses Checklist

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

Attributes

Inherited from microbial mat_biofilm:

• 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
• microbial mat_biofilm➞depth _0..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
• microbial mat_biofilm➞elev _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞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
• microbial mat_biofilm➞alkalinity _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞alkyl_diethers _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞aminopept_act _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞ammonium _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞bacteria_carb_prod _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞biomass _0..*
  • Range: String
• microbial mat_biofilm➞bishomohopanol _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞bromide _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞calcium _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞carb_nitro_ratio _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞chem_administration _0..*
  • Range: String
• microbial mat_biofilm➞chloride _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞chlorophyll _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diether_lipids _0..*
  • Range: String
• microbial mat_biofilm➞diss_carb_dioxide _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diss_hydrogen _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diss_inorg_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diss_org_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diss_org_nitro _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞diss_oxygen _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞glucosidase_act _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞magnesium _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞mean_frict_vel _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞mean_peak_frict_vel _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞methane _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞misc_param _0..*
  • Range: String
• microbial mat_biofilm➞n_alkanes _0..*
  • Range: String
• microbial mat_biofilm➞nitrate _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞nitrite _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞nitro _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞org_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞org_matter _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞org_nitro _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞organism_count _0..*
  • Range: organism_count_enum
• microbial mat_biofilm➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• microbial mat_biofilm➞ph _0..1
  • Range: Double
• microbial mat_biofilm➞part_org_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞perturbation _0..*
  • Range: String
• microbial mat_biofilm➞petroleum_hydrocarb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞phaeopigments _0..*
  • Range: String
• microbial mat_biofilm➞phosphate _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞phosplipid_fatt_acid _0..*
  • Range: String
• microbial mat_biofilm➞potassium _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞pressure _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞redox_potential _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞salinity _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞samp_store_dur _0..1
  • Range: String
• microbial mat_biofilm➞samp_store_loc _0..1
  • Range: String
• microbial mat_biofilm➞samp_store_temp _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞silicate _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞sodium _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞sulfate _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞sulfide _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞tot_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞tot_nitro_content _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞tot_org_carb _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞turbidity _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞water_content _0..1
  • Range: QuantityValue
• microbial mat_biofilm➞samp_name _1..1
  • Range: String
• microbial mat_biofilm➞project_name _1..1
  • Range: String
• microbial mat_biofilm➞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