Class: miscellaneous natural or artificial environment MIMARKS specimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package miscellaneous natural or artificial environment

URI: mixs.vocab:MiscellaneousNaturalOrArtificialEnvironmentMIMARKSSpecimen

Parents

• is_a: MiscellaneousNaturalOrArtificialEnvironment - miscellaneous natural or artificial environment

Uses Checklist

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

Attributes

Inherited from miscellaneous natural or artificial environment:

• 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
• miscellaneous natural or artificial environment➞depth _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞alt _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞elev _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞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
• miscellaneous natural or artificial environment➞alkalinity _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞ammonium _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞biomass _0..*
  • Range: String
• miscellaneous natural or artificial environment➞bromide _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞calcium _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞chem_administration _0..*
  • Range: String
• miscellaneous natural or artificial environment➞chloride _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞chlorophyll _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞density _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞diether_lipids _0..*
  • Range: String
• miscellaneous natural or artificial environment➞diss_carb_dioxide _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞diss_hydrogen _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞diss_inorg_carb _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞diss_org_nitro _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞diss_oxygen _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞misc_param _0..*
  • Range: String
• miscellaneous natural or artificial environment➞nitrate _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞nitrite _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞nitro _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞org_carb _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞org_matter _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞org_nitro _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞organism_count _0..*
  • Range: organism_count_enum
• miscellaneous natural or artificial environment➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• miscellaneous natural or artificial environment➞ph _0..1
  • Range: Double
• miscellaneous natural or artificial environment➞perturbation _0..*
  • Range: String
• miscellaneous natural or artificial environment➞phosphate _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞phosplipid_fatt_acid _0..*
  • Range: String
• miscellaneous natural or artificial environment➞potassium _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞pressure _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞salinity _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞samp_store_dur _0..1
  • Range: String
• miscellaneous natural or artificial environment➞samp_store_loc _0..1
  • Range: String
• miscellaneous natural or artificial environment➞samp_store_temp _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞silicate _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞sodium _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞sulfate _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞sulfide _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞water_current _0..1
  • Range: QuantityValue
• miscellaneous natural or artificial environment➞samp_name _1..1
  • Range: String
• miscellaneous natural or artificial environment➞project_name _1..1
  • Range: String
• miscellaneous natural or artificial environment➞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