Combination: MimarksC combined with MicrobialMatBiofilm (MimarksCMicrobialMatBiofilm)
MIxS Data that comply with the MimarksC checklist and the MicrobialMatBiofilm Extension
Composition
MimarksC [Checklist] + MicrobialMatBiofilm [Extension]
Terms
MIXS ID | Name | Cardinality and Range | Description |
---|---|---|---|
MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
MIXS:0000046 | pcr_primers | 0..1 recommended String |
PCR primers that were used to amplify the sequence of the targeted gene, locu... |
MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
MIXS:0000045 | target_subfragment | 0..1 recommended String |
Name of subfragment of a gene or locus |
MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
MIXS:0000049 | pcr_cond | 0..1 recommended String |
Description of reaction conditions and components of polymerase chain reactio... |
MIXS:0000037 | nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
MIXS:0000001 | samp_size | 0..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
MIXS:0000003 | isol_growth_condt | 1 String |
Publication reference in the form of pubmed ID (pmid), digital object identif... |
MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
MIXS:0000023 | extrachrom_elements | 0..1 Integer |
Do plasmids exist of significant phenotypic consequence (e |
MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
MIXS:0000015 | rel_to_oxygen | 0..1 recommended RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... |
MIXS:0000002 | samp_collect_device | 0..1 String |
The device used to collect an environmental sample |
MIXS:0000028 | biotic_relationship | 0..1 recommended BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... |
MIXS:0000051 | seq_quality_check | 0..1 recommended SeqQualityCheckEnum |
Indicate if the sequence has been called by automatic systems (none) or under... |
MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
MIXS:0000052 | chimera_check | 0..1 recommended String |
Tool(s) used for chimera checking, including version number and parameters, t... |
MIXS:0000032 | trophic_level | 0..1 recommended TrophicLevelEnum |
Trophic levels are the feeding position in a food chain |
MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
MIXS:0000020 | subspecf_gen_lin | 0..1 recommended String |
Information about the genetic distinctness of the sequenced organism below th... |
MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
MIXS:0000016 | samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... |
MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
MIXS:0001225 | samp_collect_method | 0..1 String |
The method employed for collecting the sample |
MIXS:0000014 | env_medium | 1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
MIXS:0000008 | experimental_factor | * String |
Variable aspects of an experiment design that can be used to describe an expe... |
MIXS:0000044 | target_gene | 1 String |
Targeted gene or locus name for marker gene studies |
MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
MIXS:0000421 | alkalinity | 0..1 String |
Alkalinity, the ability of a solution to neutralize acids to the equivalence ... |
MIXS:0000490 | alkyl_diethers | 0..1 String |
Concentration of alkyl diethers |
MIXS:0000172 | aminopept_act | 0..1 String |
Measurement of aminopeptidase activity |
MIXS:0000427 | ammonium | 0..1 String |
Concentration of ammonium in the sample |
MIXS:0000173 | bacteria_carb_prod | 0..1 String |
Measurement of bacterial carbon production |
MIXS:0000174 | biomass | * String |
Amount of biomass; should include the name for the part of biomass measured, ... |
MIXS:0000175 | bishomohopanol | 0..1 String |
Concentration of bishomohopanol |
MIXS:0000176 | bromide | 0..1 String |
Concentration of bromide |
MIXS:0000432 | calcium | 0..1 String |
Concentration of calcium in the sample |
MIXS:0000310 | carb_nitro_ratio | 0..1 Float |
Ratio of amount or concentrations of carbon to nitrogen |
MIXS:0000751 | chem_administration | * String |
List of chemical compounds administered to the host or site where sampling oc... |
MIXS:0000429 | chloride | 0..1 String |
Concentration of chloride in the sample |
MIXS:0000177 | chlorophyll | 0..1 String |
Concentration of chlorophyll |
MIXS:0000178 | diether_lipids | * String |
Concentration of diether lipids; can include multiple types of diether lipids |
MIXS:0000436 | diss_carb_dioxide | 0..1 String |
Concentration of dissolved carbon dioxide in the sample or liquid portion of ... |
MIXS:0000179 | diss_hydrogen | 0..1 String |
Concentration of dissolved hydrogen |
MIXS:0000434 | diss_inorg_carb | 0..1 String |
Dissolved inorganic carbon concentration in the sample, typically measured af... |
MIXS:0000433 | diss_org_carb | 0..1 String |
Concentration of dissolved organic carbon in the sample, liquid portion of th... |
MIXS:0000162 | diss_org_nitro | 0..1 String |
Dissolved organic nitrogen concentration measured as; total dissolved nitroge... |
MIXS:0000119 | diss_oxygen | 0..1 String |
Concentration of dissolved oxygen |
MIXS:0000137 | glucosidase_act | 0..1 String |
Measurement of glucosidase activity |
MIXS:0000431 | magnesium | 0..1 String |
Concentration of magnesium in the sample |
MIXS:0000498 | mean_frict_vel | 0..1 String |
Measurement of mean friction velocity |
MIXS:0000502 | mean_peak_frict_vel | 0..1 String |
Measurement of mean peak friction velocity |
MIXS:0000101 | methane | 0..1 String |
Methane (gas) amount or concentration at the time of sampling |
MIXS:0000752 | misc_param | * String |
Any other measurement performed or parameter collected, that is not listed he... |
MIXS:0000503 | n_alkanes | * String |
Concentration of n-alkanes; can include multiple n-alkanes |
MIXS:0000425 | nitrate | 0..1 String |
Concentration of nitrate in the sample |
MIXS:0000426 | nitrite | 0..1 String |
Concentration of nitrite in the sample |
MIXS:0000504 | nitro | 0..1 String |
Concentration of nitrogen (total) |
MIXS:0000508 | org_carb | 0..1 String |
Concentration of organic carbon |
MIXS:0000204 | org_matter | 0..1 String |
Concentration of organic matter |
MIXS:0000205 | org_nitro | 0..1 String |
Concentration of organic nitrogen |
MIXS:0000103 | organism_count | * String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
MIXS:0000753 | oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample |
MIXS:0001001 | ph | 0..1 Float |
Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... |
MIXS:0000515 | part_org_carb | 0..1 String |
Concentration of particulate organic carbon |
MIXS:0000754 | perturbation | * String |
Type of perturbation, e |
MIXS:0000516 | petroleum_hydrocarb | 0..1 String |
Concentration of petroleum hydrocarbon |
MIXS:0000180 | phaeopigments | * String |
Concentration of phaeopigments; can include multiple phaeopigments |
MIXS:0000505 | phosphate | 0..1 String |
Concentration of phosphate |
MIXS:0000181 | phosplipid_fatt_acid | * String |
Concentration of phospholipid fatty acids; can include multiple values |
MIXS:0000430 | potassium | 0..1 String |
Concentration of potassium in the sample |
MIXS:0000412 | pressure | 0..1 String |
Pressure to which the sample is subject to, in atmospheres |
MIXS:0000182 | redox_potential | 0..1 String |
Redox potential, measured relative to a hydrogen cell, indicating oxidation o... |
MIXS:0000183 | salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample |
MIXS:0000116 | samp_store_dur | 0..1 String |
Duration for which the sample was stored |
MIXS:0000755 | samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room |
MIXS:0000110 | samp_store_temp | 0..1 String |
Temperature at which sample was stored, e |
MIXS:0000184 | silicate | 0..1 String |
Concentration of silicate |
MIXS:0000428 | sodium | 0..1 String |
Sodium concentration in the sample |
MIXS:0000423 | sulfate | 0..1 String |
Concentration of sulfate in the sample |
MIXS:0000424 | sulfide | 0..1 String |
Concentration of sulfide in the sample |
MIXS:0000525 | tot_carb | 0..1 String |
Total carbon content |
MIXS:0000530 | tot_nitro_content | 0..1 String |
Total nitrogen content of the sample |
MIXS:0000533 | tot_org_carb | 0..1 String |
Total organic carbon content |
MIXS:0000191 | turbidity | 0..1 String |
Measure of the amount of cloudiness or haziness in water caused by individual... |
MIXS:0000185 | water_content | 0..1 String |
Water content measurement |
LinkML Source
Direct
name: MimarksCMicrobialMatBiofilm
description: MIxS Data that comply with the MimarksC checklist and the MicrobialMatBiofilm
Extension
title: MimarksC combined with MicrobialMatBiofilm
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: MicrobialMatBiofilm
mixins:
- MimarksC
class_uri: MIXS:0010009_0016008
Induced
name: MimarksCMicrobialMatBiofilm
description: MIxS Data that comply with the MimarksC checklist and the MicrobialMatBiofilm
Extension
title: MimarksC combined with MicrobialMatBiofilm
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: MicrobialMatBiofilm
mixins:
- MimarksC
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
keywords:
- sample
slot_uri: MIXS:0001107
alias: samp_name
owner: MimarksCMicrobialMatBiofilm
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
pcr_primers:
name: pcr_primers
annotations:
Expected_value:
tag: Expected_value
value: 'FWD: forward primer sequence;REV:reverse primer sequence'
description: 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
title: pcr primers
examples:
- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- pcr
string_serialization: FWD:{dna};REV:{dna}
slot_uri: MIXS:0000046
alias: pcr_primers
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
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
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: MimarksCMicrobialMatBiofilm
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
target_subfragment:
name: target_subfragment
description: Name of subfragment of a gene or locus. Important to e.g. identify
special regions on marker genes like V6 on 16S rRNA
title: target subfragment
examples:
- value: V6, V9, ITS
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000045
alias: target_subfragment
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- temperature
slot_uri: MIXS:0000113
alias: temp
owner: MimarksCMicrobialMatBiofilm
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
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
pcr_cond:
name: pcr_cond
annotations:
Expected_value:
tag: Expected_value
value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
description: Description of reaction conditions and components of polymerase chain
reaction performed during library preparation.
title: pcr conditions
examples:
- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
- value: initial denaturation:94degC_1.5min
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- condition
- pcr
string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
slot_uri: MIXS:0000049
alias: pcr_cond
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
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
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: MimarksCMicrobialMatBiofilm
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
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- sample
- size
slot_uri: MIXS:0000001
alias: samp_size
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
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
isol_growth_condt:
name: isol_growth_condt
description: 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
title: isolation and growth condition
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- condition
- growth
- isolation
slot_uri: MIXS:0000003
alias: isol_growth_condt
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- Agriculture
range: string
required: 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
alt:
name: alt
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
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
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000094
alias: alt
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
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
source_mat_id:
name: source_mat_id
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
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
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
alias: source_mat_id
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
multivalued: true
extrachrom_elements:
name: extrachrom_elements
description: Do plasmids exist of significant phenotypic consequence (e.g. ones
that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
(borrelia has 15+ plasmids)
title: extrachromosomal elements
examples:
- value: '5'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000023
alias: extrachrom_elements
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
range: integer
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
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
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
alias: samp_vol_we_dna_ext
owner: MimarksCMicrobialMatBiofilm
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
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
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
examples:
- value: aerobe
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- relationship
slot_uri: MIXS:0000015
alias: rel_to_oxygen
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
range: RelToOxygenEnum
recommended: true
samp_collect_device:
name: samp_collect_device
annotations:
Expected_value:
tag: Expected_value
value: device name
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]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
biotic_relationship:
name: biotic_relationship
description: 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
title: observed biotic relationship
examples:
- value: free living
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- observed
- relationship
slot_uri: MIXS:0000028
alias: biotic_relationship
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BioticRelationshipEnum
recommended: true
seq_quality_check:
name: seq_quality_check
annotations:
Expected_value:
tag: Expected_value
value: none or manually edited
description: 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,ENA
or DRA
title: sequence quality check
examples:
- value: none
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000051
alias: seq_quality_check
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: SeqQualityCheckEnum
recommended: 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
keywords:
- project
slot_uri: MIXS:0000092
alias: project_name
owner: MimarksCMicrobialMatBiofilm
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
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
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
recommended: true
chimera_check:
name: chimera_check
description: 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
title: chimera check software
examples:
- value: uchime;v4.1;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000052
alias: chimera_check
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: 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
trophic_level:
name: trophic_level
description: Trophic levels are the feeding position in a food chain. Microbes
can be a range of producers (e.g. chemolithotroph)
title: trophic level
examples:
- value: heterotroph
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- level
slot_uri: MIXS:0000032
alias: trophic_level
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MimarksC
- Agriculture
range: TrophicLevelEnum
recommended: true
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
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
subspecf_gen_lin:
name: subspecf_gen_lin
annotations:
Expected_value:
tag: Expected_value
value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
e.g. serovar, biotype, ecotype, variety, cultivar
description: 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
title: subspecific genetic lineage
examples:
- value: serovar:Newport
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- lineage
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0000020
alias: subspecf_gen_lin
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
range: string
recommended: 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
keywords:
- context
- environmental
slot_uri: MIXS:0000013
alias: env_local_scale
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: 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
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
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
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- depth
slot_uri: MIXS:0000018
alias: depth
owner: MimarksCMicrobialMatBiofilm
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
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- method
- sample
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
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
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
keywords:
- environmental
slot_uri: MIXS:0000014
alias: env_medium
owner: MimarksCMicrobialMatBiofilm
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
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: MimarksCMicrobialMatBiofilm
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
keywords:
- geographic
- location
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: MimarksCMicrobialMatBiofilm
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
keywords:
- date
slot_uri: MIXS:0000011
alias: collection_date
owner: MimarksCMicrobialMatBiofilm
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
keywords:
- method
slot_uri: MIXS:0000050
alias: seq_meth
owner: MimarksCMicrobialMatBiofilm
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
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, 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
keywords:
- geographic
- location
slot_uri: MIXS:0000009
alias: lat_lon
owner: MimarksCMicrobialMatBiofilm
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
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
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
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- elevation
slot_uri: MIXS:0000093
alias: elev
owner: MimarksCMicrobialMatBiofilm
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
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: MimarksCMicrobialMatBiofilm
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
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
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
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
target_gene:
name: target_gene
description: Targeted gene or locus name for marker gene studies
title: target gene
examples:
- value: 16S rRNA, 18S rRNA, nif, amoA, rpo
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000044
alias: target_gene
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
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
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
alias: associated_resource
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- procedures
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
alias: sop
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
alkalinity:
name: alkalinity
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliequivalent per liter, milligram per liter
description: Alkalinity, the ability of a solution to neutralize acids to the
equivalence point of carbonate or bicarbonate
title: alkalinity
examples:
- value: 50 milligram per liter
from_schema: https://w3id.org/mixs
keywords:
- alkalinity
slot_uri: MIXS:0000421
alias: alkalinity
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- WastewaterSludge
- Water
range: string
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
alkyl_diethers:
name: alkyl_diethers
description: Concentration of alkyl diethers
title: alkyl diethers
examples:
- value: 0.005 mole per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000490
alias: alkyl_diethers
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
aminopept_act:
name: aminopept_act
annotations:
Preferred_unit:
tag: Preferred_unit
value: mole per liter per hour
description: Measurement of aminopeptidase activity
title: aminopeptidase activity
examples:
- value: 0.269 mole per liter per hour
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000172
alias: aminopept_act
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
ammonium:
name: ammonium
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter, parts per million
description: Concentration of ammonium in the sample
title: ammonium
examples:
- value: 1.5 milligram per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000427
alias: ammonium
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
bacteria_carb_prod:
name: bacteria_carb_prod
description: Measurement of bacterial carbon production
title: bacterial carbon production
examples:
- value: 2.53 microgram per liter per hour
from_schema: https://w3id.org/mixs
keywords:
- carbon
- production
slot_uri: MIXS:0000173
alias: bacteria_carb_prod
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
biomass:
name: biomass
annotations:
Expected_value:
tag: Expected_value
value: biomass type;measurement value
Preferred_unit:
tag: Preferred_unit
value: ton, kilogram, gram
description: Amount of biomass; should include the name for the part of biomass
measured, e.g. Microbial, total. Can include multiple measurements
title: biomass
examples:
- value: total;20 gram
from_schema: https://w3id.org/mixs
keywords:
- biomass
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000174
alias: biomass
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
multivalued: true
bishomohopanol:
name: bishomohopanol
annotations:
Preferred_unit:
tag: Preferred_unit
value: microgram per liter, microgram per gram
description: Concentration of bishomohopanol
title: bishomohopanol
examples:
- value: 14 microgram per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000175
alias: bishomohopanol
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
bromide:
name: bromide
annotations:
Preferred_unit:
tag: Preferred_unit
value: parts per million
description: Concentration of bromide
title: bromide
examples:
- value: 0.05 parts per million
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000176
alias: bromide
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
calcium:
name: calcium
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per liter, micromole per liter, parts per million
description: Concentration of calcium in the sample
title: calcium
examples:
- value: 0.2 micromole per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000432
alias: calcium
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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_nitro_ratio:
name: carb_nitro_ratio
annotations:
Expected_value:
tag: Expected_value
value: measurement value
description: Ratio of amount or concentrations of carbon to nitrogen
title: carbon/nitrogen ratio
examples:
- value: '0.417361111'
from_schema: https://w3id.org/mixs
keywords:
- carbon
- nitrogen
- ratio
string_serialization: '{float}:{float}'
slot_uri: MIXS:0000310
alias: carb_nitro_ratio
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: float
chem_administration:
name: chem_administration
annotations:
Expected_value:
tag: Expected_value
value: CHEBI;timestamp
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
examples:
- value: agar [CHEBI:2509];2018-05-11T20:00Z
from_schema: https://w3id.org/mixs
keywords:
- administration
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
alias: chem_administration
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
chloride:
name: chloride
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per liter, parts per million
description: Concentration of chloride in the sample
title: chloride
examples:
- value: 5000 milligram per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000429
alias: chloride
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
chlorophyll:
name: chlorophyll
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per cubic meter, microgram per liter
description: Concentration of chlorophyll
title: chlorophyll
examples:
- value: 5 milligram per cubic meter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000177
alias: chlorophyll
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
diether_lipids:
name: diether_lipids
annotations:
Expected_value:
tag: Expected_value
value: diether lipid name;measurement value
Preferred_unit:
tag: Preferred_unit
value: nanogram per liter
description: Concentration of diether lipids; can include multiple types of diether
lipids
title: diether lipids
examples:
- value: 0.2 nanogram per liter
from_schema: https://w3id.org/mixs
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000178
alias: diether_lipids
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
multivalued: true
diss_carb_dioxide:
name: diss_carb_dioxide
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter
description: Concentration of dissolved carbon dioxide in the sample or liquid
portion of the sample
title: dissolved carbon dioxide
examples:
- value: 5 milligram per liter
from_schema: https://w3id.org/mixs
keywords:
- carbon
- dissolved
slot_uri: MIXS:0000436
alias: diss_carb_dioxide
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
diss_hydrogen:
name: diss_hydrogen
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: Concentration of dissolved hydrogen
title: dissolved hydrogen
examples:
- value: 0.3 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- dissolved
slot_uri: MIXS:0000179
alias: diss_hydrogen
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
diss_inorg_carb:
name: diss_inorg_carb
annotations:
Preferred_unit:
tag: Preferred_unit
value: microgram per liter, milligram per liter, parts per million
description: Dissolved inorganic carbon concentration in the sample, typically
measured after filtering the sample using a 0.45 micrometer filter
title: dissolved inorganic carbon
examples:
- value: 2059 micromole per kilogram
from_schema: https://w3id.org/mixs
keywords:
- carbon
- dissolved
- inorganic
slot_uri: MIXS:0000434
alias: diss_inorg_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
diss_org_carb:
name: diss_org_carb
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter
description: Concentration of dissolved organic carbon in the sample, liquid portion
of the sample, or aqueous phase of the fluid
title: dissolved organic carbon
examples:
- value: 197 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- carbon
- dissolved
- organic
slot_uri: MIXS:0000433
alias: diss_org_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
diss_org_nitro:
name: diss_org_nitro
description: Dissolved organic nitrogen concentration measured as; total dissolved
nitrogen - NH4 - NO3 - NO2
title: dissolved organic nitrogen
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- dissolved
- nitrogen
- organic
slot_uri: MIXS:0000162
alias: diss_org_nitro
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
diss_oxygen:
name: diss_oxygen
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per kilogram, milligram per liter
description: Concentration of dissolved oxygen
title: dissolved oxygen
examples:
- value: 175 micromole per kilogram
from_schema: https://w3id.org/mixs
keywords:
- dissolved
- oxygen
slot_uri: MIXS:0000119
alias: diss_oxygen
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
glucosidase_act:
name: glucosidase_act
annotations:
Preferred_unit:
tag: Preferred_unit
value: mol per liter per hour
description: Measurement of glucosidase activity
title: glucosidase activity
examples:
- value: 5 mol per liter per hour
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000137
alias: glucosidase_act
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
magnesium:
name: magnesium
annotations:
Preferred_unit:
tag: Preferred_unit
value: mole per liter, milligram per liter, parts per million, micromole per
kilogram
description: Concentration of magnesium in the sample
title: magnesium
examples:
- value: 52.8 micromole per kilogram
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000431
alias: magnesium
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
mean_frict_vel:
name: mean_frict_vel
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter per second
description: Measurement of mean friction velocity
title: mean friction velocity
examples:
- value: 0.5 meter per second
from_schema: https://w3id.org/mixs
keywords:
- mean
- velocity
slot_uri: MIXS:0000498
alias: mean_frict_vel
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
mean_peak_frict_vel:
name: mean_peak_frict_vel
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter per second
description: Measurement of mean peak friction velocity
title: mean peak friction velocity
examples:
- value: 1 meter per second
from_schema: https://w3id.org/mixs
keywords:
- mean
- peak
- velocity
slot_uri: MIXS:0000502
alias: mean_peak_frict_vel
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, parts per billion, parts per million
description: Methane (gas) amount or concentration at the time of sampling
title: methane
examples:
- value: 0.15 micromole per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000101
alias: methane
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Air
- MicrobialMatBiofilm
- Sediment
range: string
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
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
alias: misc_param
owner: MimarksCMicrobialMatBiofilm
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
multivalued: true
n_alkanes:
name: n_alkanes
annotations:
Expected_value:
tag: Expected_value
value: n-alkane name;measurement value
description: Concentration of n-alkanes; can include multiple n-alkanes
title: n-alkanes
examples:
- value: n-hexadecane;100 milligram per liter
from_schema: https://w3id.org/mixs
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000503
alias: n_alkanes
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
multivalued: true
nitrate:
name: nitrate
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter, parts per million
description: Concentration of nitrate in the sample
title: nitrate
examples:
- value: 65 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- nitrate
slot_uri: MIXS:0000425
alias: nitrate
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- WastewaterSludge
- Water
range: string
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
nitrite:
name: nitrite
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter, parts per million
description: Concentration of nitrite in the sample
title: nitrite
examples:
- value: 0.5 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- nitrite
slot_uri: MIXS:0000426
alias: nitrite
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
nitro:
name: nitro
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: Concentration of nitrogen (total)
title: nitrogen
examples:
- value: 4.2 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- nitrogen
slot_uri: MIXS:0000504
alias: nitro
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
org_carb:
name: org_carb
description: Concentration of organic carbon
title: organic carbon
examples:
- value: 1.5 microgram per liter
from_schema: https://w3id.org/mixs
keywords:
- carbon
- organic
slot_uri: MIXS:0000508
alias: org_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
org_matter:
name: org_matter
annotations:
Preferred_unit:
tag: Preferred_unit
value: microgram per liter
description: Concentration of organic matter
title: organic matter
examples:
- value: 1.75 milligram per cubic meter
from_schema: https://w3id.org/mixs
keywords:
- organic
slot_uri: MIXS:0000204
alias: org_matter
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Soil
- Water
range: string
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
org_nitro:
name: org_nitro
description: Concentration of organic nitrogen
title: organic nitrogen
examples:
- value: 4 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- nitrogen
- organic
slot_uri: MIXS:0000205
alias: org_nitro
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Soil
- Water
range: string
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
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
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
keywords:
- count
- organism
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
alias: organism_count
owner: MimarksCMicrobialMatBiofilm
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
multivalued: true
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- sample
- status
slot_uri: MIXS:0000753
alias: oxy_stat_samp
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OxyStatSampEnum
ph:
name: ph
description: Ph measurement of the sample, or liquid portion of sample, or aqueous
phase of the fluid
title: pH
examples:
- value: '7.2'
from_schema: https://w3id.org/mixs
keywords:
- ph
slot_uri: MIXS:0001001
alias: ph
owner: MimarksCMicrobialMatBiofilm
domain_of:
- FoodFarmEnvironment
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Soil
- WastewaterSludge
- Water
range: float
part_org_carb:
name: part_org_carb
description: Concentration of particulate organic carbon
title: particulate organic carbon
examples:
- value: 1.92 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- carbon
- organic
- particle
- particulate
slot_uri: MIXS:0000515
alias: part_org_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
perturbation:
name: perturbation
annotations:
Expected_value:
tag: Expected_value
value: perturbation type name;perturbation interval and duration
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
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- perturbation
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
alias: perturbation
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
petroleum_hydrocarb:
name: petroleum_hydrocarb
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: Concentration of petroleum hydrocarbon
title: petroleum hydrocarbon
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- hydrocarbon
- petroleum
slot_uri: MIXS:0000516
alias: petroleum_hydrocarb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
phaeopigments:
name: phaeopigments
annotations:
Expected_value:
tag: Expected_value
value: phaeopigment name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per cubic meter
description: Concentration of phaeopigments; can include multiple phaeopigments
title: phaeopigments
examples:
- value: 2.5 milligram per cubic meter
from_schema: https://w3id.org/mixs
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000180
alias: phaeopigments
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
multivalued: true
phosphate:
name: phosphate
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: Concentration of phosphate
title: phosphate
examples:
- value: 0.7 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- phosphate
slot_uri: MIXS:0000505
alias: phosphate
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- WastewaterSludge
- Water
range: string
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
phosplipid_fatt_acid:
name: phosplipid_fatt_acid
annotations:
Expected_value:
tag: Expected_value
value: phospholipid fatty acid name;measurement value
description: Concentration of phospholipid fatty acids; can include multiple values
title: phospholipid fatty acid
examples:
- value: 2.98 milligram per liter
from_schema: https://w3id.org/mixs
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000181
alias: phosplipid_fatt_acid
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
multivalued: true
potassium:
name: potassium
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per liter, parts per million
description: Concentration of potassium in the sample
title: potassium
examples:
- value: 463 milligram per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000430
alias: potassium
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
pressure:
name: pressure
annotations:
Preferred_unit:
tag: Preferred_unit
value: atmosphere
description: Pressure to which the sample is subject to, in atmospheres
title: pressure
examples:
- value: 50 atmosphere
from_schema: https://w3id.org/mixs
keywords:
- pressure
slot_uri: MIXS:0000412
alias: pressure
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
redox_potential:
name: redox_potential
annotations:
Preferred_unit:
tag: Preferred_unit
value: millivolt
description: Redox potential, measured relative to a hydrogen cell, indicating
oxidation or reduction potential
title: redox potential
examples:
- value: 300 millivolt
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000182
alias: redox_potential
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
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
keywords:
- salinity
slot_uri: MIXS:0000183
alias: salinity
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
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
examples:
- value: P1Y6M
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- sample
- storage
slot_uri: MIXS:0000116
alias: samp_store_dur
owner: MimarksCMicrobialMatBiofilm
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
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
annotations:
Expected_value:
tag: Expected_value
value: location name
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/mixs
keywords:
- location
- sample
- storage
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
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
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
alias: samp_store_temp
owner: MimarksCMicrobialMatBiofilm
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
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
silicate:
name: silicate
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter
description: Concentration of silicate
title: silicate
examples:
- value: 0.05 micromole per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000184
alias: silicate
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
sodium:
name: sodium
annotations:
Preferred_unit:
tag: Preferred_unit
value: milligram per liter, parts per million
description: Sodium concentration in the sample
title: sodium
examples:
- value: 10.5 milligram per liter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000428
alias: sodium
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- WastewaterSludge
- Water
range: string
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
sulfate:
name: sulfate
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter, parts per million
description: Concentration of sulfate in the sample
title: sulfate
examples:
- value: 5 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- sulfate
slot_uri: MIXS:0000423
alias: sulfate
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
sulfide:
name: sulfide
annotations:
Preferred_unit:
tag: Preferred_unit
value: micromole per liter, milligram per liter, parts per million
description: Concentration of sulfide in the sample
title: sulfide
examples:
- value: 2 micromole per liter
from_schema: https://w3id.org/mixs
keywords:
- sulfide
slot_uri: MIXS:0000424
alias: sulfide
owner: MimarksCMicrobialMatBiofilm
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- Sediment
- Water
range: string
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
tot_carb:
name: tot_carb
description: Total carbon content
title: total carbon
from_schema: https://w3id.org/mixs
keywords:
- carbon
- total
slot_uri: MIXS:0000525
alias: tot_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- MicrobialMatBiofilm
- Sediment
range: string
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
tot_nitro_content:
name: tot_nitro_content
description: Total nitrogen content of the sample
title: total nitrogen content
examples:
- value: 35 milligrams Nitrogen per kilogram of soil
from_schema: https://w3id.org/mixs
keywords:
- content
- nitrogen
- total
slot_uri: MIXS:0000530
alias: tot_nitro_content
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- FoodFarmEnvironment
- MicrobialMatBiofilm
- Sediment
- Soil
range: string
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
tot_org_carb:
name: tot_org_carb
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram Carbon per kilogram sample material
description: Total organic carbon content
title: total organic carbon
examples:
- value: '0.02'
from_schema: https://w3id.org/mixs
keywords:
- carbon
- organic
- total
slot_uri: MIXS:0000533
alias: tot_org_carb
owner: MimarksCMicrobialMatBiofilm
domain_of:
- Agriculture
- FoodFarmEnvironment
- MicrobialMatBiofilm
- Sediment
- Soil
range: string
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
turbidity:
name: turbidity
description: Measure of the amount of cloudiness or haziness in water caused by
individual particles
title: turbidity
examples:
- value: 0.3 nephelometric turbidity units
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000191
alias: turbidity
owner: MimarksCMicrobialMatBiofilm
domain_of:
- FoodFarmEnvironment
- MicrobialMatBiofilm
- Sediment
- Water
range: string
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
water_content:
name: water_content
annotations:
Preferred_unit:
tag: Preferred_unit
value: gram per gram or cubic centimeter per cubic centimeter
description: Water content measurement
title: water content
from_schema: https://w3id.org/mixs
keywords:
- content
- water
string_serialization: '{float} {unit}'
slot_uri: MIXS:0000185
alias: water_content
owner: MimarksCMicrobialMatBiofilm
domain_of:
- MicrobialMatBiofilm
- Sediment
- Soil
range: string
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
class_uri: MIXS:0010009_0016008