Combination: MimagAir
MIxS data that complies with the Mimag checklist and the Air Extension
Inheritance
Terms
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... | Air, Mimag |
| size_frac | 0..1 String |
Filtering pore size used in sample preparation | Mimag |
| lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... | Mimag |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | Mimag |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Mimag |
| lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project | Mimag |
| contam_screen_input | 0..1 CONTAMSCREENINPUTENUM |
The type of sequence data used as input | Mimag |
| mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | Mimag |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | Mimag |
| temp | 0..1 recommended String |
Temperature of the sample at the time of sampling | Air, Mimag |
| compl_score | 1..1 String |
Completeness score is typically based on either the fraction of markers found... | Mimag |
| trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG | Mimag |
| mag_cov_software | 0..1 MAGCOVSOFTWAREENUM |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... | Mimag |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Mimag |
| samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | Mimag |
| alt | 1..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | Air, Mimag |
| bin_param | 1..1 BINPARAMENUM |
The parameters that have been applied during the extraction of genomes from m... | Mimag |
| bin_software | 1..1 String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... | Mimag |
| source_mat_id | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | Mimag |
| samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | Air, Mimag |
| lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library | Mimag |
| rel_to_oxygen | 0..1 RELTOOXYGENENUM |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... | Mimag |
| reassembly_bin | 0..1 Boolean |
Has an assembly been performed on a genome bin extracted from a metagenomic a... | Mimag |
| decontam_software | 0..1 String |
Tool(s) used in contamination screening | Mimag |
| samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample | Mimag |
| number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | Mimag |
| trna_ext_software | 0..1 String |
Tools used for tRNA identification | Mimag |
| lib_layout | 0..1 recommended LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | Mimag |
| contam_screen_param | 0..1 String |
Specific parameters used in the decontamination sofware, such as reference da... | Mimag |
| assembly_qual | 1..1 String |
The assembly quality category is based on sets of criteria outlined for each ... | Mimag |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | Mimag |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | Air, Mimag |
| lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries | Mimag |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | Mimag |
| neg_cont_type | 0..1 recommended NEGCONTTYPEENUM |
The substance or equipment used as a negative control in an investigation | Mimag |
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | Mimag |
| tax_ident | 1..1 TAXIDENTENUM |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | Mimag |
| contam_score | 1..1 Float |
The contamination score is based on the fraction of single-copy genes that ar... | Mimag |
| annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... | Mimag |
| x16s_recover_software | 0..1 String |
Tools used for 16S rRNA gene extraction | Mimag |
| x16s_recover | 0..1 Boolean |
Can a 16S gene be recovered from the submitted SAG or MAG? | Mimag |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | Mimag |
| feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc | Mimag |
| compl_software | 1..1 String |
Tools used for completion estimate, i | Mimag |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... | Mimag |
| samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... | Mimag |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | Mimag |
| depth | 0..1 recommended String |
The vertical distance below local surface | Mimag |
| samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample | Mimag |
| compl_appr | 0..1 COMPLAPPRENUM |
The approach used to determine the completeness of a given genomic assembly, ... | Mimag |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | Mimag |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | Mimag |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | Mimag |
| collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... | Mimag |
| seq_meth | 1..1 String |
Sequencing machine used | Mimag |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | Mimag |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | Air, Mimag |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | Mimag |
| tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... | Mimag |
| experimental_factor | 0..* recommended String |
Variable aspects of an experiment design that can be used to describe an expe... | Mimag |
| associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | Mimag |
| sop | 0..* recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | Mimag |
| barometric_press | 0..1 String |
Force per unit area exerted against a surface by the weight of air above that... | Air |
| carb_dioxide | 0..1 String |
Carbon dioxide (gas) amount or concentration at the time of sampling | Air |
| carb_monoxide | 0..1 String |
Carbon monoxide (gas) amount or concentration at the time of sampling | Air |
| chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... | Air |
| humidity | 0..1 String |
Amount of water vapour in the air, at the time of sampling | Air |
| methane | 0..1 String |
Methane (gas) amount or concentration at the time of sampling | Air |
| organism_count | 0..* String |
Total cell count of any organism (or group of organisms) per gram, volume or ... | Air |
| oxygen | 0..1 String |
Oxygen (gas) amount or concentration at the time of sampling | Air |
| oxy_stat_samp | 0..1 OXYSTATSAMPENUM |
Oxygenation status of sample | Air |
| perturbation | 0..* String |
Type of perturbation, e | Air |
| pollutants | 0..* String |
Pollutant types and, amount or concentrations measured at the time of samplin... | Air |
| air_PM_concen | 0..* String |
Concentration of substances that remain suspended in the air, and comprise mi... | Air |
| salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample | Air |
| samp_store_dur | 0..1 String |
Duration for which the sample was stored | Air |
| samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | Air |
| samp_store_temp | 0..1 String |
Temperature at which sample was stored, e | Air |
| solar_irradiance | 0..* String |
The amount of solar energy that arrives at a specific area of a surface durin... | Air |
| ventilation_rate | 0..1 String |
Ventilation rate of the system in the sampled premises | Air |
| ventilation_type | 0..* String |
Ventilation system used in the sampled premises | Air |
| volatile_org_comp | 0..* String |
Concentration of carbon-based chemicals that easily evaporate at room tempera... | Air |
| wind_direction | 0..1 String |
Wind direction is the direction from which a wind originates | Air |
| wind_speed | 0..1 String |
speed of wind measured at the time of sampling | Air |
| misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... | Air |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/mixs-6-2-rc
LinkML Source
Direct
name: MimagAir
description: MIxS data that complies with the Mimag checklist and the Air Extension
title: Mimag combined with Air
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: Air
mixins:
- Mimag
class_uri: MIXS:0010011_0016000
Induced
name: MimagAir
description: MIxS data that complies with the Mimag checklist and the Air Extension
title: Mimag combined with Air
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: Air
mixins:
- Mimag
attributes:
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
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
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- sample
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
size_frac:
name: size_frac
description: Filtering pore size used in sample preparation
title: size fraction selected
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: MimagAir
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
lib_screen:
name: lib_screen
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
ref_db:
name: ref_db
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
nucl_acid_amp:
name: nucl_acid_amp
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
title: nucleic acid amplification
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
contam_screen_input:
name: contam_screen_input
description: The type of sequence data used as input
title: contamination screening input
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000005
multivalued: false
alias: contam_screen_input
owner: MimagAir
domain_of:
- Mimag
- Misag
range: CONTAM_SCREEN_INPUT_ENUM
required: false
recommended: false
mid:
name: mid
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
title: multiplex identifiers
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000047
multivalued: false
alias: mid
owner: MimagAir
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^[ACGTRKSYMWBHDVN]+$
structured_pattern:
syntax: ^{ambiguous_nucleotides}$
interpolated: true
partial_match: true
assembly_name:
name: assembly_name
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
temp:
name: temp
description: Temperature of the sample at the time of sampling
title: temperature
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
compl_score:
name: compl_score
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: true
trnas:
name: trnas
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer}'
slot_uri: MIXS:0000067
multivalued: false
alias: trnas
owner: MimagAir
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
mag_cov_software:
name: mag_cov_software
description: Tool(s) used to determine the genome coverage if coverage is used
as a binning parameter in the extraction of genomes from metagenomic datasets
title: MAG coverage software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000080
multivalued: false
alias: mag_cov_software
owner: MimagAir
domain_of:
- Mimag
- Miuvig
range: MAG_COV_SOFTWARE_ENUM
required: false
recommended: false
nucl_acid_ext:
name: nucl_acid_ext
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
title: nucleic acid extraction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
alt:
name: alt
description: 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
title: altitude
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
range: string
required: true
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
bin_param:
name: bin_param
description: The parameters that have been applied during the extraction of genomes
from metagenomic datasets
title: binning parameters
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000077
alias: bin_param
owner: MimagAir
domain_of:
- Mimag
- Miuvig
range: BIN_PARAM_ENUM
required: true
bin_software:
name: bin_software
description: Tool(s) used for the extraction of genomes from metagenomic datasets,
where possible include a product ID (PID) of the tool(s) used
title: binning software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
multivalued: false
alias: bin_software
owner: MimagAir
domain_of:
- Mimag
- Miuvig
range: string
required: true
source_mat_id:
name: source_mat_id
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)
title: source material identifiers
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: true
alias: source_mat_id
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
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)'
title: sample volume or weight for DNA extraction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
rel_to_oxygen:
name: rel_to_oxygen
description: Is this organism an aerobe, anaerobe? Please note that aerobic and
anaerobic are valid descriptors for microbial environments
title: relationship to oxygen
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000015
multivalued: false
alias: rel_to_oxygen
owner: MimagAir
domain_of:
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
range: REL_TO_OXYGEN_ENUM
required: false
recommended: false
reassembly_bin:
name: reassembly_bin
description: Has an assembly been performed on a genome bin extracted from a metagenomic
assembly?
title: reassembly post binning
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000079
multivalued: false
alias: reassembly_bin
owner: MimagAir
domain_of:
- Mimag
- Miuvig
range: boolean
required: false
recommended: false
decontam_software:
name: decontam_software
description: Tool(s) used in contamination screening
title: decontamination software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[checkm/refinem|anvi''o|prodege|bbtools:decontaminate.sh|acdc|combination]'
slot_uri: MIXS:0000074
multivalued: false
alias: decontam_software
owner: MimagAir
domain_of:
- Mimag
- Misag
range: string
required: false
recommended: false
samp_collect_device:
name: samp_collect_device
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)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collect_device
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: false
recommended: false
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000068
multivalued: false
alias: trna_ext_software
owner: MimagAir
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
recommended: true
contam_screen_param:
name: contam_screen_param
description: Specific parameters used in the decontamination sofware, such as
reference database, coverage, and kmers. Combinations of these parameters may
also be used, i.e. kmer and coverage, or reference database and kmer
title: contamination screening parameters
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[ref db|kmer|coverage|combination];{text|integer}'
slot_uri: MIXS:0000073
multivalued: false
alias: contam_screen_param
owner: MimagAir
domain_of:
- Mimag
- Misag
range: string
required: false
recommended: false
assembly_qual:
name: assembly_qual
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'
title: assembly quality
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
draft genome|Low-quality draft genome|Genome fragment(s)]'
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- project
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
lib_vector:
name: lib_vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- type
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NEG_CONT_TYPE_ENUM
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000053
alias: tax_ident
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TAX_IDENT_ENUM
required: true
contam_score:
name: contam_score
description: 'The contamination score is based on the fraction of single-copy
genes that are observed more than once in a query genome. The following scores
are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
deposited into any of the public databases'
title: contamination score
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000072
multivalued: false
alias: contam_score
owner: MimagAir
domain_of:
- Mimag
- Misag
range: float
required: true
annot:
name: annot
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
title: annotation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
x16s_recover_software:
name: x16s_recover_software
description: Tools used for 16S rRNA gene extraction
title: 16S recovery software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000066
multivalued: false
alias: x16s_recover_software
owner: MimagAir
domain_of:
- Mimag
- Misag
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
x16s_recover:
name: x16s_recover
description: Can a 16S gene be recovered from the submitted SAG or MAG?
title: 16S recovered
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000065
multivalued: false
alias: x16s_recover
owner: MimagAir
domain_of:
- Mimag
- Misag
range: boolean
required: false
recommended: false
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
compl_software:
name: compl_software
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: true
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
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'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- context
- environmental
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
samp_mat_process:
name: samp_mat_process
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
title: sample material processing
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
depth:
name: depth
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collect_method
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
compl_appr:
name: compl_appr
description: The approach used to determine the completeness of a given genomic
assembly, which would typically make use of a set of conserved marker genes
or a closely related reference genome. For UViG completeness, include reference
genome or group used, and contig feature suggesting a complete genome
title: completeness approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000071
alias: compl_appr
owner: MimagAir
domain_of:
- Mimag
- Misag
- Miuvig
range: COMPL_APPR_ENUM
required: false
recommended: false
env_medium:
name: env_medium
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)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- environmental
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_taxon_id:
name: samp_taxon_id
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
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
geo_loc_name:
name: geo_loc_name
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)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- geographic
- location
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
collection_date:
name: collection_date
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'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- date
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
seq_meth:
name: seq_meth
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)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- method
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
annotations:
Expected_value:
tag: Expected_value
value: decimal degrees, limit to 8 decimal points
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
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- geographic
- location
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
elev:
name: elev
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
title: elevation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
env_broad_scale:
name: env_broad_scale
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'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- context
- environmental
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
experimental_factor:
name: experimental_factor
description: Variable aspects of an experiment design that 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)
title: experimental factor
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
multivalued: true
alias: experimental_factor
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
multivalued: true
alias: associated_resource
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sop:
name: sop
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: true
alias: sop
owner: MimagAir
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
barometric_press:
name: barometric_press
annotations:
Preferred_unit:
tag: Preferred_unit
value: millibar
description: Force per unit area exerted against a surface by the weight of air
above that surface
title: barometric pressure
examples:
- value: 5 millibar
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- pressure
slot_uri: MIXS:0000096
multivalued: false
alias: barometric_press
owner: MimagAir
domain_of:
- Air
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
carb_dioxide:
name: carb_dioxide
description: Carbon dioxide (gas) amount or concentration at the time of sampling
title: carbon dioxide
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000097
multivalued: false
alias: carb_dioxide
owner: MimagAir
domain_of:
- Air
- BuiltEnvironment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
carb_monoxide:
name: carb_monoxide
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, parts per million
description: Carbon monoxide (gas) amount or concentration at the time of sampling
title: carbon monoxide
examples:
- value: 0.1 parts per million
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- carbon
slot_uri: MIXS:0000098
multivalued: false
alias: carb_monoxide
owner: MimagAir
domain_of:
- Air
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
chem_administration:
name: chem_administration
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
multivalued: true
alias: chem_administration
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
humidity:
name: humidity
description: Amount of water vapour in the air, at the time of sampling
title: humidity
examples:
- value: 25 gram per cubic meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000100
multivalued: false
alias: humidity
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
methane:
name: methane
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 1800 parts per billion
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000101
multivalued: false
alias: methane
owner: MimagAir
domain_of:
- Air
- MicrobialMatBiofilm
- Sediment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
organism_count:
name: organism_count
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)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
multivalued: true
alias: organism_count
owner: MimagAir
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
oxygen:
name: oxygen
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per liter, parts per million
description: Oxygen (gas) amount or concentration at the time of sampling
title: oxygen
examples:
- value: 600 parts per million
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- oxygen
slot_uri: MIXS:0000104
multivalued: false
alias: oxygen
owner: MimagAir
domain_of:
- Air
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000753
multivalued: false
alias: oxy_stat_samp
owner: MimagAir
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OXY_STAT_SAMP_ENUM
required: false
recommended: false
perturbation:
name: perturbation
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: true
alias: perturbation
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pollutants:
name: pollutants
annotations:
Expected_value:
tag: Expected_value
value: pollutant name;measurement value
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter, microgram per cubic meter
description: Pollutant types and, amount or concentrations measured at the time
of sampling; can report multiple pollutants by entering numeric values preceded
by name of pollutant
title: pollutants
examples:
- value: lead;0.15 microgram per cubic meter
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000107
multivalued: true
alias: pollutants
owner: MimagAir
domain_of:
- Air
range: string
required: false
recommended: false
air_PM_concen:
name: air_PM_concen
description: Concentration of substances that remain suspended in the air, and
comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can
report multiple PM's by entering numeric values preceded by name of PM
title: air particulate matter concentration
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000108
multivalued: true
alias: air_PM_concen
owner: MimagAir
domain_of:
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
salinity:
name: salinity
annotations:
Preferred_unit:
tag: Preferred_unit
value: practical salinity unit, percentage
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- salinity
slot_uri: MIXS:0000183
multivalued: false
alias: salinity
owner: MimagAir
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000116
multivalued: false
alias: samp_store_dur
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_store_loc:
name: samp_store_loc
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
alias: samp_store_loc
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
multivalued: false
alias: samp_store_temp
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
solar_irradiance:
name: solar_irradiance
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilowatts per square meter per day, ergs per square centimeter per
second
description: The amount of solar energy that arrives at a specific area of a surface
during a specific time interval
title: solar irradiance
examples:
- value: 1.36 kilowatts per square meter per day
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000112
multivalued: true
alias: solar_irradiance
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
ventilation_rate:
name: ventilation_rate
annotations:
Preferred_unit:
tag: Preferred_unit
value: cubic meter per minute, liters per second
description: Ventilation rate of the system in the sampled premises
title: ventilation rate
examples:
- value: 750 cubic meter per minute
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- rate
slot_uri: MIXS:0000114
multivalued: false
alias: ventilation_rate
owner: MimagAir
domain_of:
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
ventilation_type:
name: ventilation_type
description: Ventilation system used in the sampled premises
title: ventilation type
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000756
multivalued: true
alias: ventilation_type
owner: MimagAir
domain_of:
- Air
- BuiltEnvironment
- FoodFarmEnvironment
range: string
required: false
recommended: false
volatile_org_comp:
name: volatile_org_comp
annotations:
Expected_value:
tag: Expected_value
value: volatile organic compound name;measurement value
Preferred_unit:
tag: Preferred_unit
value: microgram per cubic meter, parts per million, nanogram per liter
description: Concentration of carbon-based chemicals that easily evaporate at
room temperature; can report multiple volatile organic compounds by entering
numeric values preceded by name of compound
title: volatile organic compounds
examples:
- value: formaldehyde;500 nanogram per liter
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- organic
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000115
multivalued: true
alias: volatile_org_comp
owner: MimagAir
domain_of:
- Air
range: string
required: false
recommended: false
wind_direction:
name: wind_direction
description: Wind direction is the direction from which a wind originates
title: wind direction
examples:
- value: Northwest
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000757
multivalued: false
alias: wind_direction
owner: MimagAir
domain_of:
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
wind_speed:
name: wind_speed
description: speed of wind measured at the time of sampling
title: wind speed
examples:
- value: 21 kilometer per hour
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000118
multivalued: false
alias: wind_speed
owner: MimagAir
domain_of:
- Air
- FoodFarmEnvironment
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: true
alias: misc_param
owner: MimagAir
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
class_uri: MIXS:0010011_0016000