Class: built environment MIGS bacteria

Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package built environment

URI: mixs.vocab:BuiltEnvironmentMIGSBacteria

Parents

• is_a: BuiltEnvironment - built environment

Uses Checklist

• mixin: MIGSBacteria - Minimal Information about a Genome Sequence: cultured bacteria/archaea

Attributes

Inherited from built 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
• depth _0..1
  • Description: The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
  • Range: QuantityValue
  • Example: 10 meter None
• 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
• elev _0..1
  • Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.
  • Range: QuantityValue
  • Example: 100 meter 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
• built environment➞surf_material _0..1
  • Range: surf_material_enum
• built environment➞surf_air_cont _0..*
  • Range: surf_air_cont_enum
• built environment➞rel_air_humidity _1..1
  • Range: QuantityValue
• built environment➞abs_air_humidity _1..1
  • Range: QuantityValue
• built environment➞surf_humidity _0..1
  • Range: QuantityValue
• built environment➞temp _1..1
  • Range: QuantityValue
• built environment➞surf_temp _0..1
  • Range: QuantityValue
• built environment➞surf_moisture_ph _0..1
  • Range: Double
• built environment➞build_occup_type _1..*
  • Range: build_occup_type_enum
• built environment➞surf_moisture _0..1
  • Range: QuantityValue
• built environment➞dew_point _0..1
  • Range: QuantityValue
• built environment➞carb_dioxide _1..1
  • Range: QuantityValue
• built environment➞ventilation_type _1..1
  • Range: String
• built environment➞organism_count _1..*
  • Range: organism_count_enum
• built environment➞indoor_space _1..1
  • Range: indoor_space_enum
• built environment➞indoor_surf _0..1
  • Range: indoor_surf_enum
• built environment➞filter_type _1..*
  • Range: filter_type_enum
• built environment➞heat_cool_type _1..*
  • Range: heat_cool_type_enum
• built environment➞substructure_type _0..*
  • Range: substructure_type_enum
• built environment➞building_setting _1..1
  • Range: building_setting_enum
• built environment➞light_type _1..*
  • Range: light_type_enum
• built environment➞samp_sort_meth _0..*
  • Range: String
• built environment➞space_typ_state _1..1
  • Range: String
• built environment➞typ_occup_density _1..1
  • Range: Double
• built environment➞occup_samp _1..1
  • Range: Integer
• built environment➞occup_density_samp _1..1
  • Range: Double
• built environment➞address _0..1
  • Range: String
• built environment➞adj_room _0..1
  • Range: String
• built environment➞aero_struc _0..1
  • Range: String
• built environment➞amount_light _0..1
  • Range: QuantityValue
• built environment➞arch_struc _0..1
  • Range: arch_struc_enum
• built environment➞avg_occup _0..1
  • Range: Double
• built environment➞avg_dew_point _0..1
  • Range: QuantityValue
• built environment➞avg_temp _0..1
  • Range: QuantityValue
• built environment➞bathroom_count _0..1
  • Range: Integer
• built environment➞bedroom_count _0..1
  • Range: Integer
• built environment➞built_struc_age _0..1
  • Range: QuantityValue
• built environment➞built_struc_set _0..1
  • Range: String
• built environment➞built_struc_type _0..1
  • Range: String
• built environment➞ceil_area _0..1
  • Range: QuantityValue
• built environment➞ceil_cond _0..1
  • Range: ceil_cond_enum
• built environment➞ceil_finish_mat _0..1
  • Range: ceil_finish_mat_enum
• built environment➞ceil_water_mold _0..1
  • Range: String
• built environment➞ceil_struc _0..1
  • Range: String
• built environment➞ceil_texture _0..1
  • Range: ceil_texture_enum
• built environment➞ceil_thermal_mass _0..1
  • Range: QuantityValue
• built environment➞ceil_type _0..1
  • Range: ceil_type_enum
• built environment➞cool_syst_id _0..1
  • Range: Integer
• built environment➞date_last_rain _0..1
  • Range: Date
• built environment➞build_docs _0..1
  • Range: build_docs_enum
• built environment➞door_size _0..1
  • Range: QuantityValue
• built environment➞door_cond _0..1
  • Range: door_cond_enum
• built environment➞door_direct _0..1
  • Range: door_direct_enum
• built environment➞door_loc _0..1
  • Range: door_loc_enum
• built environment➞door_mat _0..1
  • Range: door_mat_enum
• built environment➞door_move _0..1
  • Range: door_move_enum
• built environment➞door_water_mold _0..1
  • Range: String
• built environment➞door_type _0..1
  • Range: door_type_enum
• built environment➞door_comp_type _0..1
  • Range: door_comp_type_enum
• built environment➞door_type_metal _0..1
  • Range: door_type_metal_enum
• built environment➞door_type_wood _0..1
  • Range: door_type_wood_enum
• built environment➞drawings _0..1
  • Range: drawings_enum
• built environment➞elevator _0..1
  • Range: Integer
• built environment➞escalator _0..1
  • Range: Integer
• built environment➞exp_duct _0..1
  • Range: QuantityValue
• built environment➞exp_pipe _0..1
  • Range: Integer
• built environment➞ext_door _0..1
  • Range: Integer
• built environment➞fireplace_type _0..1
  • Range: String
• built environment➞floor_age _0..1
  • Range: QuantityValue
• built environment➞floor_area _0..1
  • Range: QuantityValue
• built environment➞floor_cond _0..1
  • Range: floor_cond_enum
• built environment➞floor_count _0..1
  • Range: Integer
• built environment➞floor_finish_mat _0..1
  • Range: floor_finish_mat_enum
• built environment➞floor_water_mold _0..1
  • Range: floor_water_mold_enum
• built environment➞floor_struc _0..1
  • Range: floor_struc_enum
• built environment➞floor_thermal_mass _0..1
  • Range: QuantityValue
• built environment➞freq_clean _0..1
  • Range: freq_clean_enum
• built environment➞freq_cook _0..1
  • Range: Integer
• built environment➞furniture _0..1
  • Range: furniture_enum
• built environment➞gender_restroom _0..1
  • Range: gender_restroom_enum
• built environment➞hall_count _0..1
  • Range: Integer
• built environment➞handidness _0..1
  • Range: handidness_enum
• built environment➞heat_deliv_loc _0..1
  • Range: heat_deliv_loc_enum
• built environment➞heat_sys_deliv_meth _0..1
  • Range: String
• built environment➞heat_system_id _0..1
  • Range: Integer
• built environment➞height_carper_fiber _0..1
  • Range: QuantityValue
• built environment➞inside_lux _0..1
  • Range: QuantityValue
• built environment➞int_wall_cond _0..1
  • Range: int_wall_cond_enum
• built environment➞last_clean _0..1
  • Range: Date
• built environment➞max_occup _0..1
  • Range: Integer
• built environment➞mech_struc _0..1
  • Range: mech_struc_enum
• built environment➞number_plants _0..1
  • Range: Integer
• built environment➞number_pets _0..1
  • Range: Integer
• built environment➞number_resident _0..1
  • Range: Integer
• built environment➞occup_document _0..1
  • Range: occup_document_enum
• built environment➞ext_wall_orient _0..1
  • Range: ext_wall_orient_enum
• built environment➞ext_window_orient _0..1
  • Range: ext_window_orient_enum
• built environment➞rel_humidity_out _0..1
  • Range: QuantityValue
• built environment➞pres_animal_insect _0..1
  • Range: pres_animal_insect_enum
• built environment➞quad_pos _0..1
  • Range: quad_pos_enum
• built environment➞rel_samp_loc _0..1
  • Range: rel_samp_loc_enum
• built environment➞room_air_exch_rate _0..1
  • Range: QuantityValue
• built environment➞room_architec_elem _0..1
  • Range: String
• built environment➞room_condt _0..1
  • Range: room_condt_enum
• built environment➞room_count _0..1
  • Range: Integer
• built environment➞room_dim _0..1
  • Range: String
• built environment➞room_door_dist _0..1
  • Range: String
• built environment➞room_loc _0..1
  • Range: room_loc_enum
• built environment➞room_moist_dam_hist _0..1
  • Range: Integer
• built environment➞room_net_area _0..1
  • Range: String
• built environment➞room_occup _0..1
  • Range: Integer
• built environment➞room_samp_pos _0..1
  • Range: room_samp_pos_enum
• built environment➞room_type _0..1
  • Range: room_type_enum
• built environment➞room_vol _0..1
  • Range: String
• built environment➞room_window_count _0..1
  • Range: Integer
• built environment➞room_connected _0..1
  • Range: room_connected_enum
• built environment➞room_hallway _0..1
  • Range: String
• built environment➞room_door_share _0..1
  • Range: String
• built environment➞room_wall_share _0..1
  • Range: String
• built environment➞samp_weather _0..1
  • Range: samp_weather_enum
• built environment➞samp_floor _0..1
  • Range: samp_floor_enum
• built environment➞samp_room_id _0..1
  • Range: Integer
• built environment➞samp_time_out _0..1
  • Range: Double
• built environment➞season _0..1
  • Range: String
• built environment➞season_use _0..1
  • Range: season_use_enum
• built environment➞shading_device_cond _0..1
  • Range: shading_device_cond_enum
• built environment➞shading_device_loc _0..1
  • Range: String
• built environment➞shading_device_mat _0..1
  • Range: String
• built environment➞shad_dev_water_mold _0..1
  • Range: String
• built environment➞shading_device_type _0..1
  • Range: shading_device_type_enum
• built environment➞specific_humidity _0..1
  • Range: QuantityValue
• built environment➞specific _0..1
  • Range: specific_enum
• built environment➞temp_out _0..1
  • Range: QuantityValue
• built environment➞train_line _0..1
  • Range: train_line_enum
• built environment➞train_stat_loc _0..1
  • Range: train_stat_loc_enum
• built environment➞train_stop_loc _0..1
  • Range: train_stop_loc_enum
• built environment➞vis_media _0..1
  • Range: vis_media_enum
• built environment➞wall_area _0..1
  • Range: QuantityValue
• built environment➞wall_const_type _0..1
  • Range: wall_const_type_enum
• built environment➞wall_finish_mat _0..1
  • Range: wall_finish_mat_enum
• built environment➞wall_height _0..1
  • Range: QuantityValue
• built environment➞wall_loc _0..1
  • Range: wall_loc_enum
• built environment➞wall_water_mold _0..1
  • Range: String
• built environment➞wall_surf_treatment _0..1
  • Range: wall_surf_treatment_enum
• built environment➞wall_texture _0..1
  • Range: wall_texture_enum
• built environment➞wall_thermal_mass _0..1
  • Range: QuantityValue
• built environment➞water_feat_size _0..1
  • Range: QuantityValue
• built environment➞water_feat_type _0..1
  • Range: water_feat_type_enum
• built environment➞weekday _0..1
  • Range: weekday_enum
• built environment➞window_size _0..1
  • Range: String
• built environment➞window_cond _0..1
  • Range: window_cond_enum
• built environment➞window_cover _0..1
  • Range: window_cover_enum
• built environment➞window_horiz_pos _0..1
  • Range: window_horiz_pos_enum
• built environment➞window_loc _0..1
  • Range: window_loc_enum
• built environment➞window_mat _0..1
  • Range: window_mat_enum
• built environment➞window_open_freq _0..1
  • Range: Integer
• built environment➞window_water_mold _0..1
  • Range: String
• built environment➞window_status _0..1
  • Range: String
• built environment➞window_type _0..1
  • Range: window_type_enum
• built environment➞window_vert_pos _0..1
  • Range: window_vert_pos_enum
• built environment➞samp_name _1..1
  • Range: String
• built environment➞project_name _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_taxon_id _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞experimental_factor _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞env_package _0..1
  • Range: env_package_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞subspecf_gen_lin _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞num_replicons _1..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞extrachrom_elements _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞estimated_size _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_biomaterial _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞source_mat_id _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞pathogenicity _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞biotic_relationship _0..1
  • Range: biotic_relationship_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞specific_host _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞host_spec_range _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞health_disease_stat _0..1
  • Range: health_disease_stat_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞host_disease_stat _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞trophic_level _0..1
  • Range: trophic_level_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞encoded_traits _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞isol_growth_condt _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_collec_device _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_collec_method _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_mat_process _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_size _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_vector _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_screen _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞adapters _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞seq_meth _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_ident _0..1
  • Range: tax_ident_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_qual _1..1
  • Range: assembly_qual_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_name _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_software _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞annot _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞number_contig _1..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞feat_pred _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_db _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sim_search_meth _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_class _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_score _0..1
  • Range: compl_score_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_software _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞associated resource _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sop _0..1
  • Range: String