Class: soil MIMAG

Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package soil

URI: mixs.vocab:SoilMIMAG

Parents

• is_a: Soil - soil

Uses Checklist

• mixin: MIMAG - Minimum Information About a Metagenome-Assembled Genome

Attributes

Inherited from soil:

• 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
• soil➞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
• soil➞elev _1..1
  • Range: QuantityValue
• temp _0..1
  • Description: Temperature of the sample at the time of sampling.
  • Range: QuantityValue
  • Example: 25 degree Celsius None
• 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
• soil➞cur_land_use _0..1
  • Range: cur_land_use_enum
• soil➞cur_vegetation _0..1
  • Range: String
• soil➞cur_vegetation_meth _0..1
  • Range: String
• soil➞previous_land_use _0..1
  • Range: String
• soil➞prev_land_use_meth _0..1
  • Range: String
• soil➞crop_rotation _0..1
  • Range: String
• soil➞agrochem_addition _0..*
  • Range: String
• soil➞tillage _0..*
  • Range: tillage_enum
• soil➞fire _0..1
  • Range: Date
• soil➞flooding _0..1
  • Range: Date
• soil➞extreme_event _0..1
  • Range: Date
• soil➞horizon _0..1
  • Range: horizon_enum
• soil➞horizon_meth _0..1
  • Range: String
• soil➞sieving _0..1
  • Range: String
• soil➞water_content _0..1
  • Range: QuantityValue
• soil➞water_cont_soil_meth _0..1
  • Range: String
• soil➞pool_dna_extracts _0..1
  • Range: String
• soil➞store_cond _0..1
  • Range: String
• soil➞link_climate_info _0..1
  • Range: String
• soil➞annual_temp _0..1
  • Range: QuantityValue
• soil➞season_temp _0..1
  • Range: QuantityValue
• soil➞annual_precpt _0..1
  • Range: QuantityValue
• soil➞season_precpt _0..1
  • Range: QuantityValue
• soil➞link_class_info _0..1
  • Range: String
• soil➞fao_class _0..1
  • Range: fao_class_enum
• soil➞local_class _0..1
  • Range: String
• soil➞local_class_meth _0..1
  • Range: String
• soil➞soil_type _0..1
  • Range: String
• soil➞soil_type_meth _0..1
  • Range: String
• soil➞slope_gradient _0..1
  • Range: QuantityValue
• soil➞slope_aspect _0..1
  • Range: QuantityValue
• soil➞profile_position _0..1
  • Range: profile_position_enum
• soil➞drainage_class _0..1
  • Range: drainage_class_enum
• soil➞texture _0..1
  • Range: QuantityValue
• soil➞texture_meth _0..1
  • Range: String
• soil➞ph _0..1
  • Range: Double
• soil➞ph_meth _0..1
  • Range: String
• soil➞tot_org_carb _0..1
  • Range: QuantityValue
• soil➞tot_org_c_meth _0..1
  • Range: String
• soil➞tot_nitro_content _0..1
  • Range: QuantityValue
• soil➞tot_nitro_cont_meth _0..1
  • Range: String
• soil➞microbial_biomass _0..1
  • Range: QuantityValue
• soil➞micro_biomass_meth _0..1
  • Range: String
• soil➞link_addit_analys _0..1
  • Range: String
• soil➞extreme_salinity _0..1
  • Range: QuantityValue
• soil➞salinity_meth _0..1
  • Range: String
• soil➞heavy_metals _0..*
  • Range: String
• soil➞heavy_metals_meth _0..1
  • Range: String
• soil➞al_sat _0..1
  • Range: QuantityValue
• soil➞al_sat_meth _0..1
  • Range: String
• soil➞misc_param _0..*
  • Range: String
• soil➞samp_name _1..1
  • Range: String
• soil➞project_name _1..1
  • Range: String
• soil➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MIMAG:

• MIMAG➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MIMAG:

• MIMAG➞samp_taxon_id _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞experimental_factor _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞env_package _0..1
  • Range: env_package_enum

Mixed in from MIMAG:

• MIMAG➞ref_biomaterial _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞source_mat_id _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MIMAG:

• MIMAG➞samp_collec_device _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞samp_collec_method _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞samp_mat_process _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞size_frac _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MIMAG:

• MIMAG➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞lib_size _0..1
  • Range: Integer

Mixed in from MIMAG:

• MIMAG➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MIMAG:

• MIMAG➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MIMAG:

• MIMAG➞lib_vector _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞lib_screen _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞mid _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞adapters _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞seq_meth _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞tax_ident _1..1
  • Range: tax_ident_enum

Mixed in from MIMAG:

• MIMAG➞assembly_qual _1..1
  • Range: assembly_qual_enum

Mixed in from MIMAG:

• MIMAG➞assembly_name _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞assembly_software _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞annot _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞number_contig _0..1
  • Range: Integer

Mixed in from MIMAG:

• MIMAG➞feat_pred _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞ref_db _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞sim_search_meth _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞tax_class _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞x_16s_recover _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞trnas _0..1
  • Range: Integer

Mixed in from MIMAG:

• MIMAG➞trna_ext_software _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞compl_score _1..1
  • Range: compl_score_enum

Mixed in from MIMAG:

• MIMAG➞compl_software _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞compl_appr _0..1
  • Range: compl_appr_enum

Mixed in from MIMAG:

• MIMAG➞contam_score _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞contam_screen_input _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞contam_screen_param _0..1
  • Range: contam_screen_param_enum

Mixed in from MIMAG:

• MIMAG➞decontam_software _0..1
  • Range: decontam_software_enum

Mixed in from MIMAG:

• MIMAG➞bin_param _1..1
  • Range: bin_param_enum

Mixed in from MIMAG:

• MIMAG➞bin_software _1..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞reassembly_bin _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞mag_cov_software _0..1
  • Range: mag_cov_software_enum

Mixed in from MIMAG:

• MIMAG➞associated resource _0..1
  • Range: String

Mixed in from MIMAG:

• MIMAG➞sop _0..1
  • Range: String