built environment

Number of host individuals inoculated for the experiment.

Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)

Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object.

To what is the entity pathogenic, for instance plant, fungi, bacteria

Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments

The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. Mandatory for MIGs of eukayotes, plasmids and viruses.

The device used to collect an environmental sample. It is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).

The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text.

Name of the project within which the sequencing was organized

The number of times a meal is cooked per week

The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO

Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote. Mandatory for MIGS of eukaryotes, bacteria, archaea and segmented virus.

Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).

The estimated size of the genome (in bp) prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. Mandatory for MIGS of eukaryotes.

Targeted gene or locus name for marker gene studies

Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA

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

Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA

Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.

A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL

Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL

The date the sample was collected with the intention of sequencing, 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 ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.

The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.

The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by the specific region name followed by the locality name.

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.

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 "broad-scale environmental context". 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.

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).

The elevation of the sampling site as measured by the vertical distance from mean sea level.

The recent and long term history of outside sampling

The recorded temperature value at sampling time outside

The train station collection location

The train stop collection location

surface materials at the point of sampling

contaminant identified on surface

type of indoor surface

a distinguishable space within a structure, the purpose for which discrete areas of a building is used

a device which removes solid particulates or airborne molecular contaminants

methods of conditioning or heating a room or building

the substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level

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

a location (geography) where a building is set

the primary function for which a building or discrete part of a building is intended to be used

customary or normal state of the space

customary or normal density of occupants

number of occupants present at time of sample within the given space

average number of occupants at time of sampling per square footage

The intentional movement of air from outside a building to the inside through forced or natural movement of air

List of room(s) (room number, room name) located in the same hallway as sampling room

The surface treatment of interior wall

The total area of the sampled room's walls

The number of elevators within the built structure

The area of the floor space within the room

The types of furniture present in the sampled room

The type of water feature present within the building being sampled

Distance between doors (meters) in the hallway between the sampling room and adjacent rooms

The main purpose or activity of the sampling room. A room is any distinguishable space within a structure

The relative location of the window within the room

The type of ceiling according to the ceiling's appearance or construction

The direction the door opens

The number of exposed pipes in the room

The average height of the walls in the sampled room

The type of metal door

The recorded value at sampling time (power density)

The amount of exposed ductwork in the room

The material the door is composed of

List of rooms (room number, room name) immediately adjacent to the sampling room

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

Signs of the presence of mold or mildew on the ceiling

Defines whether the windows were open or closed during environmental testing

The relative location of the door in the room

Signs of the presence of mold or mildew on the window.

The type of windows

The type of material used to finish a window

The horizontal position of the window on the wall

The condition of the room at the time of sampling

The window's length and width

The floor of the building, where the sampling room is located

The total count of rooms in the built structure including all room types

Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.

The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

The type of wood door

The physical condition of the door

The type of movement of the door

The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

Signs of the presence of mold or mildew in a room

The construction format of the ceiling

The feel, appearance, or consistency of a wall surface

The ability of the floor to provide inertia against temperature fluctuations

The rate at which outside air replaces indoor air in a given space

The number of bathrooms in the building

Signs of the presence of mold or mildew on the shading device

The type of window covering

The feel, appearance, or consistency of a ceiling surface

The maximum amount of people allowed in the indoor environment

The gender type of the restroom

The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas

Refers to the structural elements and subfloor upon which the finish flooring is installed

List of room(s) (room number, room name) sharing a wall with the sampling room

The material utilized to finish the outer most layer of the wall

Count of room occupancy at time of sampling

The position of the room within the building

The floor covering type; the finished surface that is walked on

Number of windows in the room

Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).

The average carpet fiber height in the indoor environment

The area of the ceiling space within the room

The method by which the heat is delivered through the system

The horizontal sampling position in the room relative to architectural elements

The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed

Signs of the presence of mold or mildew on a door

The net floor area of sampling room. Net area excludes wall thicknesses

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

List of room(s) (room number, room name) sharing a door with the sampling room

The compass direction the exterior window of the room is facing

The relative location of the wall within the room

Volume of sampling room

The composite type of the door

The number of bedrooms in the building

The building class of the wall defined by the composition of the building elements and fire-resistance rating.

Signs of the presence of mold or mildew on a wall

The physical condition of the window at the time of sampling

The number of escalators within the built structure

The cooling system identifier

The quadrant position of the sampling room within the building

The number of pets residing in the sampled space

The vertical position of the window on the wall

A firebox with chimney

The location of heat delivery within the room

The type of material used to finish a ceiling

The type of door material

The number of plant(s) in the sampling space

The time period since instalment of the carpet or flooring

List of rooms connected to the sampling room by a doorway

The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents

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.

The number of times windows are opened per week

The length, width and height of sampling room

The size of the water feature

The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.

method by which samples are sorted

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)

mechanical structure: a moving structure

The handidness of the individual sampled

The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).

list of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text

Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.

partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air

actual mass of water vapor - mh20 - present in the air water vapor mixture

surface water activity as a function of air and material moisture

temperature of the air at time of sampling

temperature of the surface at time of sampling

water held on the surface

pH measurement of surface

The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water

temperature of the sample at time of sampling

The last time the floor was cleaned (swept, mopped, vacuumed)

The number of individuals currently occupying in the sampling location

The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day

The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.

carbon dioxide (gas) amount or concentration at the time of sampling

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).

The seasons the space is occupied

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).

The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day

The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.

type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types

The substance or equipment used as a negative control in an investigation

The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.

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. E.g. time series design [EFO:EFO_0001779]

Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage

Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.

Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)

Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen.

For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter

Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.

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.

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'.

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

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

Total number of clones in the library prepared for the project

Total number of clones sequenced from the library

Library construction method used for clone libraries

Cloning vector type(s) used in construction of libraries

Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences

Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'

PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters

Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters

The date of the last time it rained

The weather on the sampling day

The unit of illuminance and luminous emittance, measuring luminous flux per unit area

The subway line name

The recorded outside relative humidity value at the time of sampling

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.

The size of the door

The building visual media

The characterization of the location of the built structure as high or low human density

A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads

The number of exterior doors in the built structure

The building design, construction and operation documents

The physical condition of the shading device at the time of sampling

The type of documentation of occupancy

The number of floors in the building, including basements and mechanical penthouse

The material the shading device is composed of

The age of the built structure since construction

The total count of hallways and corridors in the built structure

An architectural structure is a human-made, free-standing, immobile outdoor construction

The type of shading device

The location of the shading device in relation to the built structure

The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents

The street name and building number where the sampling occurred.

The unique details and component parts that, together, form the architecture of a distinguishable space within a built structure

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