Class: built environment MIMS
Combinatorial checklist Metagenome or Environmental with environmental package built environment
URI: mixs.vocab:BuiltEnvironmentMIMS
Parents
- is_a: BuiltEnvironment - built environment
Uses Mixin
- mixin: MIMS - Metagenome or Environmental
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
- Description: Surface materials at the point of sampling
- Range: surf_material_enum
- Example: wood None
- built environment➞surf_air_cont 0..*
- Description: Contaminant identified on surface
- Range: surf_air_cont_enum
- Example: radon None
- built environment➞rel_air_humidity 1..1
- Description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
- Range: QuantityValue
- Example: 80% None
- built environment➞abs_air_humidity 1..1
- Description: Actual mass of water vapor - mh20 - present in the air water vapor mixture
- Range: QuantityValue
- Example: 9 gram per gram None
- built environment➞surf_humidity 0..1
- Description: Surfaces: water activity as a function of air and material moisture
- Range: QuantityValue
- Example: 10% None
- built environment➞temp 1..1
- Description: Temperature of the sample at the time of sampling.
- Range: QuantityValue
- Example: 25 degree Celsius None
- built environment➞surf_temp 0..1
- Description: Temperature of the surface at the time of sampling
- Range: QuantityValue
- Example: 15 degree Celsius None
- built environment➞surf_moisture_ph 0..1
- Description: ph measurement of surface
- Range: Double
- Example: 7 None
- built environment➞build_occup_type 1..*
- Description: The primary function for which a building or discrete part of a building is intended to be used
- Range: build_occup_type_enum
- Example: market None
- built environment➞surf_moisture 0..1
- Description: Water held on a surface
- Range: QuantityValue
- Example: 0.01 gram per square meter None
- built environment➞dew_point 0..1
- Description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
- Range: QuantityValue
- Example: 22 degree Celsius None
- built environment➞carb_dioxide 1..1
- Description: Carbon dioxide (gas) amount or concentration at the time of sampling
- Range: QuantityValue
- Example: 410 parts per million None
- built environment➞ventilation_type 1..1
- Description: Ventilation system used in the sampled premises
- Range: String
- Example: Operable windows None
- built environment➞organism_count 1..*
- Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
- Range: organism_count_enum
- Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
- built environment➞indoor_space 1..1
- Description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used
- Range: indoor_space_enum
- Example: foyer None
- built environment➞indoor_surf 0..1
- Description: Type of indoor surface
- Range: indoor_surf_enum
- Example: wall None
- built environment➞filter_type 1..*
- Description: A device which removes solid particulates or airborne molecular contaminants
- Range: filter_type_enum
- Example: HEPA None
- built environment➞heat_cool_type 1..*
- Description: Methods of conditioning or heating a room or building
- Range: heat_cool_type_enum
- Example: heat pump None
- built environment➞substructure_type 0..*
- Description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
- Range: substructure_type_enum
- Example: basement None
- built environment➞building_setting 1..1
- Description: A location (geography) where a building is set
- Range: building_setting_enum
- Example: rural None
- built environment➞light_type 1..*
- Description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
- Range: light_type_enum
- Example: desk lamp None
- built environment➞samp_sort_meth 0..*
- Description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.
- Range: String
- Example: None
- built environment➞space_typ_state 1..1
- Description: Customary or normal state of the space
- Range: String
- Example: typically occupied None
- built environment➞typ_occup_density 1..1
- Description: Customary or normal density of occupants
- Range: Double
- Example: 25 None
- built environment➞occup_samp 1..1
- Description: Number of occupants present at time of sample within the given space
- Range: Integer
- Example: 10 None
- built environment➞occup_density_samp 1..1
- Description: Average number of occupants at time of sampling per square footage
- Range: Double
- Example: None
- built environment➞address 0..1
- Description: The street name and building number where the sampling occurred.
- Range: String
- Example: None
- built environment➞adj_room 0..1
- Description: List of rooms (room number, room name) immediately adjacent to the sampling room
- Range: String
- Example: None
- built environment➞aero_struc 0..1
- Description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
- Range: String
- Example: plane None
- built environment➞amount_light 0..1
- Description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area
- Range: QuantityValue
- Example: None
- built environment➞arch_struc 0..1
- Description: An architectural structure is a human-made, free-standing, immobile outdoor construction
- Range: arch_struc_enum
- Example: shed None
- built environment➞avg_occup 0..1
- Description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.
- Range: Double
- Example: 2 None
- built environment➞avg_dew_point 0..1
- Description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
- Range: QuantityValue
- Example: 25.5 degree Celsius None
- built environment➞avg_temp 0..1
- Description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
- Range: QuantityValue
- Example: 12.5 degree Celsius None
- built environment➞bathroom_count 0..1
- Description: The number of bathrooms in the building
- Range: Integer
- Example: 1 None
- built environment➞bedroom_count 0..1
- Description: The number of bedrooms in the building
- Range: Integer
- Example: 2 None
- built environment➞built_struc_age 0..1
- Description: The age of the built structure since construction
- Range: QuantityValue
- Example: 15 None
- built environment➞built_struc_set 0..1
- Description: The characterization of the location of the built structure as high or low human density
- Range: String
- Example: rural None
- built environment➞built_struc_type 0..1
- Description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
- Range: String
- Example: None
- built environment➞ceil_area 0..1
- Description: The area of the ceiling space within the room
- Range: QuantityValue
- Example: 25 square meter None
- built environment➞ceil_cond 0..1
- Description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
- Range: ceil_cond_enum
- Example: damaged None
- built environment➞ceil_finish_mat 0..1
- Description: The type of material used to finish a ceiling
- Range: ceil_finish_mat_enum
- Example: stucco None
- built environment➞ceil_water_mold 0..1
- Description: Signs of the presence of mold or mildew on the ceiling
- Range: String
- Example: presence of mold visible None
- built environment➞ceil_struc 0..1
- Description: The construction format of the ceiling
- Range: String
- Example: concrete None
- built environment➞ceil_texture 0..1
- Description: The feel, appearance, or consistency of a ceiling surface
- Range: ceil_texture_enum
- Example: popcorn None
- built environment➞ceil_thermal_mass 0..1
- Description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
- Range: QuantityValue
- Example: None
- built environment➞ceil_type 0..1
- Description: The type of ceiling according to the ceiling's appearance or construction
- Range: ceil_type_enum
- Example: coffered None
- built environment➞cool_syst_id 0..1
- Description: The cooling system identifier
- Range: Integer
- Example: 12345 None
- built environment➞date_last_rain 0..1
- Description: The date of the last time it rained
- Range: Date
- Example: 2018-05-11:T14:30Z None
- built environment➞build_docs 0..1
- Description: The building design, construction and operation documents
- Range: build_docs_enum
- Example: maintenance plans None
- built environment➞door_size 0..1
- Description: The size of the door
- Range: QuantityValue
- Example: 2.5 square meter None
- built environment➞door_cond 0..1
- Description: The phsical condition of the door
- Range: door_cond_enum
- Example: new None
- built environment➞door_direct 0..1
- Description: The direction the door opens
- Range: door_direct_enum
- Example: inward None
- built environment➞door_loc 0..1
- Description: The relative location of the door in the room
- Range: door_loc_enum
- Example: north None
- built environment➞door_mat 0..1
- Description: The material the door is composed of
- Range: door_mat_enum
- Example: wood None
- built environment➞door_move 0..1
- Description: The type of movement of the door
- Range: door_move_enum
- Example: swinging None
- built environment➞door_water_mold 0..1
- Description: Signs of the presence of mold or mildew on a door
- Range: String
- Example: presence of mold visible None
- built environment➞door_type 0..1
- Description: The type of door material
- Range: door_type_enum
- Example: wooden None
- built environment➞door_comp_type 0..1
- Description: The composite type of the door
- Range: door_comp_type_enum
- Example: revolving None
- built environment➞door_type_metal 0..1
- Description: The type of metal door
- Range: door_type_metal_enum
- Example: hollow None
- built environment➞door_type_wood 0..1
- Description: The type of wood door
- Range: door_type_wood_enum
- Example: battened None
- built environment➞drawings 0..1
- Description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
- Range: drawings_enum
- Example: sketch None
- built environment➞elevator 0..1
- Description: The number of elevators within the built structure
- Range: Integer
- Example: 2 None
- built environment➞escalator 0..1
- Description: The number of escalators within the built structure
- Range: Integer
- Example: 4 None
- built environment➞exp_duct 0..1
- Description: The amount of exposed ductwork in the room
- Range: QuantityValue
- Example: None
- built environment➞exp_pipe 0..1
- Description: The number of exposed pipes in the room
- Range: Integer
- Example: None
- built environment➞ext_door 0..1
- Description: The number of exterior doors in the built structure
- Range: Integer
- Example: None
- built environment➞fireplace_type 0..1
- Description: A firebox with chimney
- Range: String
- Example: wood burning None
- built environment➞floor_age 0..1
- Description: The time period since installment of the carpet or flooring
- Range: QuantityValue
- Example: None
- built environment➞floor_area 0..1
- Description: The area of the floor space within the room
- Range: QuantityValue
- Example: None
- built environment➞floor_cond 0..1
- Description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
- Range: floor_cond_enum
- Example: new None
- built environment➞floor_count 0..1
- Description: The number of floors in the building, including basements and mechanical penthouse
- Range: Integer
- Example: None
- built environment➞floor_finish_mat 0..1
- Description: The floor covering type; the finished surface that is walked on
- Range: floor_finish_mat_enum
- Example: carpet None
- built environment➞floor_water_mold 0..1
- Description: Signs of the presence of mold or mildew in a room
- Range: floor_water_mold_enum
- Example: ceiling discoloration None
- built environment➞floor_struc 0..1
- Description: Refers to the structural elements and subfloor upon which the finish flooring is installed
- Range: floor_struc_enum
- Example: concrete None
- built environment➞floor_thermal_mass 0..1
- Description: The ability of the floor to provide inertia against temperature fluctuations
- Range: QuantityValue
- Example: None
- built environment➞freq_clean 0..1
- Description: The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
- Range: freq_clean_enum
- Example: None
- built environment➞freq_cook 0..1
- Description: The number of times a meal is cooked per week
- Range: Integer
- Example: None
- built environment➞furniture 0..1
- Description: The types of furniture present in the sampled room
- Range: furniture_enum
- Example: chair None
- built environment➞gender_restroom 0..1
- Description: The gender type of the restroom
- Range: gender_restroom_enum
- Example: male None
- built environment➞hall_count 0..1
- Description: The total count of hallways and cooridors in the built structure
- Range: Integer
- Example: None
- built environment➞handidness 0..1
- Description: The handidness of the individual sampled
- Range: handidness_enum
- Example: right handedness None
- built environment➞heat_deliv_loc 0..1
- Description: The location of heat delivery within the room
- Range: heat_deliv_loc_enum
- Example: north None
- built environment➞heat_sys_deliv_meth 0..1
- Description: The method by which the heat is delivered through the system
- Range: String
- Example: radiant None
- built environment➞heat_system_id 0..1
- Description: The heating system identifier
- Range: Integer
- Example: None
- built environment➞height_carper_fiber 0..1
- Description: The average carpet fiber height in the indoor environment
- Range: QuantityValue
- Example: None
- built environment➞inside_lux 0..1
- Description: The recorded value at sampling time (power density)
- Range: QuantityValue
- Example: None
- built environment➞int_wall_cond 0..1
- Description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
- Range: int_wall_cond_enum
- Example: damaged None
- built environment➞last_clean 0..1
- Description: The last time the floor was cleaned (swept, mopped, vacuumed)
- Range: Date
- Example: 2018-05-11:T14:30Z None
- built environment➞max_occup 0..1
- Description: The maximum amount of people allowed in the indoor environment
- Range: Integer
- Example: None
- built environment➞mech_struc 0..1
- Description: mechanical structure: a moving structure
- Range: mech_struc_enum
- Example: elevator None
- built environment➞number_plants 0..1
- Description: The number of plant(s) in the sampling space
- Range: Integer
- Example: None
- built environment➞number_pets 0..1
- Description: The number of pets residing in the sampled space
- Range: Integer
- Example: None
- built environment➞number_resident 0..1
- Description: The number of individuals currently occupying in the sampling location
- Range: Integer
- Example: None
- built environment➞occup_document 0..1
- Description: The type of documentation of occupancy
- Range: occup_document_enum
- Example: estimate None
- built environment➞ext_wall_orient 0..1
- Description: The orientation of the exterior wall
- Range: ext_wall_orient_enum
- Example: northwest None
- built environment➞ext_window_orient 0..1
- Description: The compass direction the exterior window of the room is facing
- Range: ext_window_orient_enum
- Example: southwest None
- built environment➞rel_humidity_out 0..1
- Description: The recorded outside relative humidity value at the time of sampling
- Range: QuantityValue
- Example: 12 per kilogram of air None
- built environment➞pres_animal_insect 0..1
- Description: The type and number of animals or insects present in the sampling space.
- Range: pres_animal_insect_enum
- Example: cat;5 None
- built environment➞quad_pos 0..1
- Description: The quadrant position of the sampling room within the building
- Range: quad_pos_enum
- Example: West side None
- built environment➞rel_samp_loc 0..1
- Description: The sampling location within the train car
- Range: rel_samp_loc_enum
- Example: center of car None
- built environment➞room_air_exch_rate 0..1
- Description: The rate at which outside air replaces indoor air in a given space
- Range: QuantityValue
- Example: None
- built environment➞room_architec_elem 0..1
- Description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure
- Range: String
- Example: None
- built environment➞room_condt 0..1
- Description: The condition of the room at the time of sampling
- Range: room_condt_enum
- Example: new None
- built environment➞room_count 0..1
- Description: The total count of rooms in the built structure including all room types
- Range: Integer
- Example: None
- built environment➞room_dim 0..1
- Description: The length, width and height of sampling room
- Range: String
- Example: None
- built environment➞room_door_dist 0..1
- Description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms
- Range: String
- Example: None
- built environment➞room_loc 0..1
- Description: The position of the room within the building
- Range: room_loc_enum
- Example: interior room None
- built environment➞room_moist_dam_hist 0..1
- Description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
- Range: Integer
- Example: None
- built environment➞room_net_area 0..1
- Description: The net floor area of sampling room. Net area excludes wall thicknesses
- Range: String
- Example: None
- built environment➞room_occup 0..1
- Description: Count of room occupancy at time of sampling
- Range: Integer
- Example: None
- built environment➞room_samp_pos 0..1
- Description: The horizontal sampling position in the room relative to architectural elements
- Range: room_samp_pos_enum
- Example: south corner None
- built environment➞room_type 0..1
- Description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure
- Range: room_type_enum
- Example: bathroom None
- built environment➞room_vol 0..1
- Description: Volume of sampling room
- Range: String
- Example: None
- built environment➞room_window_count 0..1
- Description: Number of windows in the room
- Range: Integer
- Example: None
- built environment➞room_connected 0..1
- Description: List of rooms connected to the sampling room by a doorway
- Range: room_connected_enum
- Example: office None
- built environment➞room_hallway 0..1
- Description: List of room(s) (room number, room name) located in the same hallway as sampling room
- Range: String
- Example: None
- built environment➞room_door_share 0..1
- Description: List of room(s) (room number, room name) sharing a door with the sampling room
- Range: String
- Example: None
- built environment➞room_wall_share 0..1
- Description: List of room(s) (room number, room name) sharing a wall with the sampling room
- Range: String
- Example: None
- built environment➞samp_weather 0..1
- Description: The weather on the sampling day
- Range: samp_weather_enum
- Example: foggy None
- built environment➞samp_floor 0..1
- Description: The floor of the building, where the sampling room is located
- Range: samp_floor_enum
- Example: 4th floor None
- built environment➞samp_room_id 0..1
- Description: Sampling room number. This ID should be consistent with the designations on the building floor plans
- Range: Integer
- Example: None
- built environment➞samp_time_out 0..1
- Description: The recent and long term history of outside sampling
- Range: Double
- Example: None
- built environment➞season 0..1
- Description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
- Range: String
- Example: autumn [NCIT:C94733] None
- built environment➞season_use 0..1
- Description: The seasons the space is occupied
- Range: season_use_enum
- Example: Winter None
- built environment➞shading_device_cond 0..1
- Description: The physical condition of the shading device at the time of sampling
- Range: shading_device_cond_enum
- Example: new None
- built environment➞shading_device_loc 0..1
- Description: The location of the shading device in relation to the built structure
- Range: String
- Example: exterior None
- built environment➞shading_device_mat 0..1
- Description: The material the shading device is composed of
- Range: String
- Example: None
- built environment➞shad_dev_water_mold 0..1
- Description: Signs of the presence of mold or mildew on the shading device
- Range: String
- Example: no presence of mold visible None
- built environment➞shading_device_type 0..1
- Description: The type of shading device
- Range: shading_device_type_enum
- Example: slatted aluminum awning None
- built environment➞specific_humidity 0..1
- Description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.
- Range: QuantityValue
- Example: 15 per kilogram of air None
- built environment➞specific 0..1
- Description: The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
- Range: specific_enum
- Example: construction None
- built environment➞temp_out 0..1
- Description: The recorded temperature value at sampling time outside
- Range: QuantityValue
- Example: 5 degree Celsius None
- built environment➞train_line 0..1
- Description: The subway line name
- Range: train_line_enum
- Example: red None
- built environment➞train_stat_loc 0..1
- Description: The train station collection location
- Range: train_stat_loc_enum
- Example: forest hills None
- built environment➞train_stop_loc 0..1
- Description: The train stop collection location
- Range: train_stop_loc_enum
- Example: end None
- built environment➞vis_media 0..1
- Description: The building visual media
- Range: vis_media_enum
- Example: 3D scans None
- built environment➞wall_area 0..1
- Description: The total area of the sampled room's walls
- Range: QuantityValue
- Example: None
- built environment➞wall_const_type 0..1
- Description: The building class of the wall defined by the composition of the building elements and fire-resistance rating.
- Range: wall_const_type_enum
- Example: fire resistive None
- built environment➞wall_finish_mat 0..1
- Description: The material utilized to finish the outer most layer of the wall
- Range: wall_finish_mat_enum
- Example: wood None
- built environment➞wall_height 0..1
- Description: The average height of the walls in the sampled room
- Range: QuantityValue
- Example: None
- built environment➞wall_loc 0..1
- Description: The relative location of the wall within the room
- Range: wall_loc_enum
- Example: north None
- built environment➞wall_water_mold 0..1
- Description: Signs of the presence of mold or mildew on a wall
- Range: String
- Example: no presence of mold visible None
- built environment➞wall_surf_treatment 0..1
- Description: The surface treatment of interior wall
- Range: wall_surf_treatment_enum
- Example: paneling None
- built environment➞wall_texture 0..1
- Description: The feel, appearance, or consistency of a wall surface
- Range: wall_texture_enum
- Example: popcorn None
- built environment➞wall_thermal_mass 0..1
- Description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
- Range: QuantityValue
- Example: None
- built environment➞water_feat_size 0..1
- Description: The size of the water feature
- Range: QuantityValue
- Example: None
- built environment➞water_feat_type 0..1
- Description: The type of water feature present within the building being sampled
- Range: water_feat_type_enum
- Example: stream None
- built environment➞weekday 0..1
- Description: The day of the week when sampling occurred
- Range: weekday_enum
- Example: Sunday None
- built environment➞window_size 0..1
- Description: The window's length and width
- Range: String
- Example: None
- built environment➞window_cond 0..1
- Description: The physical condition of the window at the time of sampling
- Range: window_cond_enum
- Example: rupture None
- built environment➞window_cover 0..1
- Description: The type of window covering
- Range: window_cover_enum
- Example: curtains None
- built environment➞window_horiz_pos 0..1
- Description: The horizontal position of the window on the wall
- Range: window_horiz_pos_enum
- Example: middle None
- built environment➞window_loc 0..1
- Description: The relative location of the window within the room
- Range: window_loc_enum
- Example: west None
- built environment➞window_mat 0..1
- Description: The type of material used to finish a window
- Range: window_mat_enum
- Example: wood None
- built environment➞window_open_freq 0..1
- Description: The number of times windows are opened per week
- Range: Integer
- Example: None
- built environment➞window_water_mold 0..1
- Description: Signs of the presence of mold or mildew on the window.
- Range: String
- Example: no presence of mold visible None
- built environment➞window_status 0..1
- Description: Defines whether the windows were open or closed during environmental testing
- Range: String
- Example: open None
- built environment➞window_type 0..1
- Description: The type of windows
- Range: window_type_enum
- Example: fixed window None
- built environment➞window_vert_pos 0..1
- Description: The vertical position of the window on the wall
- Range: window_vert_pos_enum
- Example: middle None
- built environment➞samp_name 1..1
- Description: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.
- Range: String
- Example: ISDsoil1 None
- built environment➞project_name 1..1
- Description: Name of the project within which the sequencing was organized
- Range: String
- Example: Forest soil metagenome None
Mixed in from MIMS:
- MIMS➞submitted_to_insdc 1..1
- Description: Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases
- Range: String
- Example: yes None
Mixed in from MIMS:
- MIMS➞investigation_type 1..1
- Description: Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome
- Range: investigation_type_enum
- Example: metagenome None
Mixed in from MIMS:
- MIMS➞samp_taxon_id 1..1
- Description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome’ for mock community/positive controls, or 'blank sample' for negative controls.
- Range: String
- Example: Gut Metagenome [NCBI:txid749906] None
Mixed in from MIMS:
- MIMS➞experimental_factor 0..1
- Description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
- Range: String
- Example: time series design [EFO:EFO_0001779] None
Mixed in from MIMS:
- MIMS➞neg_cont_type 0..1
- Description: The substance or equipment used as a negative control in an investigation
- Range: neg_cont_type_enum
- Example: None
Mixed in from MIMS:
- MIMS➞pos_cont_type 0..1
- Description: The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.
- Range: String
- Example: None
Mixed in from MIMS:
- MIMS➞env_package 0..1
- Description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
- Range: env_package_enum
- Example: soil None
Mixed in from MIMS:
- MIMS➞ref_biomaterial 0..1
- Description: Primary publication if isolated before genome publication; otherwise, primary genome report.
- Range: String
- Example: doi:10.1016/j.syapm.2018.01.009 None
Mixed in from MIMS:
- MIMS➞source_mat_id 0..1
- Description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
- Range: String
- Example: MPI012345 None
Mixed in from MIMS:
- MIMS➞rel_to_oxygen 0..1
- Description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
- Range: rel_to_oxygen_enum
- Example: aerobe None
Mixed in from MIMS:
- MIMS➞samp_collec_device 0..1
- Description: The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
- Range: String
- Example: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] None
Mixed in from MIMS:
- MIMS➞samp_collec_method 0..1
- Description: The method employed for collecting the sample.
- Range: String
- Example: swabbing None
Mixed in from MIMS:
- MIMS➞samp_mat_process 0..1
- Description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.
- Range: String
- Example: filtering of seawater, storing samples in ethanol None
Mixed in from MIMS:
- MIMS➞size_frac 0..1
- Description: Filtering pore size used in sample preparation
- Range: String
- Example: 0-0.22 micrometer None
Mixed in from MIMS:
- MIMS➞samp_size 0..1
- Description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
- Range: QuantityValue
- Example: 5 liter None
Mixed in from MIMS:
- MIMS➞samp_vol_we_dna_ext 0..1
- Description: Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
- Range: QuantityValue
- Example: 1500 milliliter None
Mixed in from MIMS:
- MIMS➞nucl_acid_ext 0..1
- Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
- Range: String
- Example: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf None
Mixed in from MIMS:
- MIMS➞nucl_acid_amp 0..1
- Description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
- Range: String
- Example: https://phylogenomics.me/protocols/16s-pcr-protocol/ None
Mixed in from MIMS:
- MIMS➞lib_size 0..1
- Description: Total number of clones in the library prepared for the project
- Range: Integer
- Example: 50 None
Mixed in from MIMS:
- MIMS➞lib_reads_seqd 0..1
- Description: Total number of clones sequenced from the library
- Range: Integer
- Example: 20 None
Mixed in from MIMS:
- MIMS➞lib_layout 0..1
- Description: Specify whether to expect single, paired, or other configuration of reads
- Range: lib_layout_enum
- Example: paired None
Mixed in from MIMS:
- MIMS➞lib_vector 0..1
- Description: Cloning vector type(s) used in construction of libraries
- Range: String
- Example: Bacteriophage P1 None
Mixed in from MIMS:
- MIMS➞lib_screen 0..1
- Description: Specific enrichment or screening methods applied before and/or after creating libraries
- Range: String
- Example: enriched, screened, normalized None
Mixed in from MIMS:
- MIMS➞mid 0..1
- Description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
- Range: String
- Example: GTGAATAT None
Mixed in from MIMS:
- MIMS➞adapters 0..1
- Description: Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
- Range: String
- Example: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT None
Mixed in from MIMS:
- MIMS➞seq_meth 1..1
- Description: Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
- Range: String
- Example: 454 Genome Sequencer FLX [OBI:0000702] None
Mixed in from MIMS:
- MIMS➞assembly_qual 0..1
- Description: The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated
- Range: assembly_qual_enum
- Example: High-quality draft genome None
Mixed in from MIMS:
- MIMS➞assembly_name 0..1
- Description: Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
- Range: String
- Example: HuRef, JCVI_ISG_i3_1.0 None
Mixed in from MIMS:
- MIMS➞assembly_software 0..1
- Description: Tool(s) used for assembly, including version number and parameters
- Range: String
- Example: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise None
Mixed in from MIMS:
- MIMS➞annot 0..1
- Description: Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
- Range: String
- Example: prokka None
Mixed in from MIMS:
- MIMS➞number_contig 0..1
- Description: Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG
- Range: Integer
- Example: 40 None
Mixed in from MIMS:
- MIMS➞feat_pred 0..1
- Description: Method used to predict UViGs features such as ORFs, integration site, etc.
- Range: String
- Example: Prodigal;2.6.3;default parameters None
Mixed in from MIMS:
- MIMS➞ref_db 0..1
- Description: List of database(s) used for ORF annotation, along with version number and reference to website or publication
- Range: String
- Example: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975 None
Mixed in from MIMS:
- MIMS➞sim_search_meth 0..1
- Description: Tool used to compare ORFs with database, along with version and cutoffs used
- Range: String
- Example: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score None
Mixed in from MIMS:
- MIMS➞tax_class 0..1
- Description: Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes
- Range: String
- Example: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) None
Mixed in from MIMS:
- MIMS➞associated resource 0..1
- Description: A related resource that is referenced, cited, or otherwise associated to the sequence.
- Range: String
- Example: http://www.earthmicrobiome.org/ None