Combination: MimsPlantAssociated
MIxS data that complies with the Mims checklist and the PlantAssociated Extension
Inheritance
- Extension
- PlantAssociated
- MimsPlantAssociated [ Mims]
- PlantAssociated
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... | PlantAssociated, Mims |
| size_frac | 0..1 String |
Filtering pore size used in sample preparation | Mims |
| lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... | Mims |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | Mims |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Mims |
| lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project | Mims |
| mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | Mims |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | Mims |
| temp | 0..1 recommended String |
Temperature of the sample at the time of sampling | PlantAssociated, Mims |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Mims |
| samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | Mims |
| alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | Mims |
| source_mat_id | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | Mims |
| samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | PlantAssociated, Mims |
| lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library | Mims |
| rel_to_oxygen | 0..1 RELTOOXYGENENUM |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... | Mims |
| samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample | Mims |
| number_contig | 0..1 recommended Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | Mims |
| lib_layout | 0..1 recommended LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | Mims |
| assembly_qual | 0..1 recommended String |
The assembly quality category is based on sets of criteria outlined for each ... | Mims |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | Mims |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | PlantAssociated, Mims |
| lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries | Mims |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | Mims |
| neg_cont_type | 0..1 recommended NEGCONTTYPEENUM |
The substance or equipment used as a negative control in an investigation | Mims |
| assembly_software | 0..1 recommended String |
Tool(s) used for assembly, including version number and parameters | Mims |
| annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... | Mims |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | Mims |
| feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc | Mims |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... | Mims |
| samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... | Mims |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | Mims |
| depth | 0..1 recommended String |
The vertical distance below local surface | PlantAssociated, Mims |
| samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample | Mims |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | Mims |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | Mims |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | Mims |
| collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... | Mims |
| seq_meth | 1..1 String |
Sequencing machine used | Mims |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | Mims |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | PlantAssociated, Mims |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | Mims |
| tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... | Mims |
| experimental_factor | 0..* recommended String |
Variable aspects of an experiment design that can be used to describe an expe... | Mims |
| associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | Mims |
| sop | 0..* recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | Mims |
| air_temp_regm | 0..* String |
Information about treatment involving an exposure to varying temperatures; sh... | PlantAssociated |
| ances_data | 0..1 String |
Information about either pedigree or other ancestral information description ... | PlantAssociated |
| antibiotic_regm | 0..* String |
Information about treatment involving antibiotic administration; should inclu... | PlantAssociated |
| biol_stat | 0..1 String |
The level of genome modification | PlantAssociated |
| biotic_regm | 0..* String |
Information about treatment(s) involving use of biotic factors, such as bacte... | PlantAssociated |
| chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... | PlantAssociated |
| chem_mutagen | 0..* String |
Treatment involving use of mutagens; should include the name of mutagen, amou... | PlantAssociated |
| climate_environment | 0..* String |
Treatment involving an exposure to a particular climate; treatment regimen in... | PlantAssociated |
| cult_root_med | 0..1 String |
Name or reference for the hydroponic or in vitro culture rooting medium; can ... | PlantAssociated |
| fertilizer_regm | 0..* String |
Information about treatment involving the use of fertilizers; should include ... | PlantAssociated |
| fungicide_regm | 0..* String |
Information about treatment involving use of fungicides; should include the n... | PlantAssociated |
| gaseous_environment | 0..* String |
Use of conditions with differing gaseous environments; should include the nam... | PlantAssociated |
| genetic_mod | 0..1 String |
Genetic modifications of the genome of an organism, which may occur naturally... | PlantAssociated |
| gravity | 0..* String |
Information about treatment involving use of gravity factor to study various ... | PlantAssociated |
| growth_facil | 0..1 String |
Type of facility where the sampled plant was grown; controlled vocabulary: gr... | PlantAssociated |
| growth_habit | 0..1 GROWTHHABITENUM |
Characteristic shape, appearance or growth form of a plant species | PlantAssociated |
| growth_hormone_regm | 0..* String |
Information about treatment involving use of growth hormones; should include ... | PlantAssociated |
| herbicide_regm | 0..* String |
Information about treatment involving use of herbicides; information about tr... | PlantAssociated |
| host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... | PlantAssociated |
| host_common_name | 0..1 String |
Common name of the host | PlantAssociated |
| host_disease_stat | 0..1 String |
List of diseases with which the host has been diagnosed; can include multiple... | PlantAssociated |
| host_dry_mass | 0..1 String |
Measurement of dry mass | PlantAssociated |
| host_genotype | 0..1 String |
Observed genotype | PlantAssociated |
| host_height | 0..1 String |
The height of subject | PlantAssociated |
| host_subspecf_genlin | 0..* String |
Information about the genetic distinctness of the host organism below the sub... | PlantAssociated |
| host_length | 0..1 String |
The length of subject | PlantAssociated |
| host_life_stage | 0..1 String |
Description of life stage of host | PlantAssociated |
| host_phenotype | 0..1 String |
Phenotype of human or other host | PlantAssociated |
| host_taxid | 0..1 String |
NCBI taxon id of the host, e | PlantAssociated |
| host_tot_mass | 0..1 String |
Total mass of the host at collection, the unit depends on host | PlantAssociated |
| host_wet_mass | 0..1 String |
Measurement of wet mass | PlantAssociated |
| humidity_regm | 0..* String |
Information about treatment involving an exposure to varying degree of humidi... | PlantAssociated |
| light_regm | 0..1 String |
Information about treatment(s) involving exposure to light, including both li... | PlantAssociated |
| mechanical_damage | 0..* String |
Information about any mechanical damage exerted on the plant; can include mul... | PlantAssociated |
| mineral_nutr_regm | 0..* String |
Information about treatment involving the use of mineral supplements; should ... | PlantAssociated |
| misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... | PlantAssociated |
| non_min_nutr_regm | 0..* String |
Information about treatment involving the exposure of plant to non-mineral nu... | PlantAssociated |
| organism_count | 0..* String |
Total cell count of any organism (or group of organisms) per gram, volume or ... | PlantAssociated |
| oxy_stat_samp | 0..1 OXYSTATSAMPENUM |
Oxygenation status of sample | PlantAssociated |
| ph_regm | 0..* String |
Information about treatment involving exposure of plants to varying levels of... | PlantAssociated |
| perturbation | 0..* String |
Type of perturbation, e | PlantAssociated |
| pesticide_regm | 0..* String |
Information about treatment involving use of insecticides; should include the... | PlantAssociated |
| plant_growth_med | 0..1 String |
Specification of the media for growing the plants or tissue cultured samples,... | PlantAssociated |
| plant_product | 0..1 String |
Substance produced by the plant, where the sample was obtained from | PlantAssociated |
| plant_sex | 0..1 PLANTSEXENUM |
Sex of the reproductive parts on the whole plant, e | PlantAssociated |
| plant_struc | 0..1 String |
Name of plant structure the sample was obtained from; for Plant Ontology (PO)... | PlantAssociated |
| radiation_regm | 0..* String |
Information about treatment involving exposure of plant or a plant part to a ... | PlantAssociated |
| rainfall_regm | 0..* String |
Information about treatment involving an exposure to a given amount of rainfa... | PlantAssociated |
| root_cond | 0..1 String |
Relevant rooting conditions such as field plot size, sowing density, containe... | PlantAssociated |
| root_med_carbon | 0..1 String |
Source of organic carbon in the culture rooting medium; e | PlantAssociated |
| root_med_macronutr | 0..1 String |
Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... | PlantAssociated |
| root_med_micronutr | 0..1 String |
Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... | PlantAssociated |
| root_med_suppl | 0..1 String |
Organic supplements of the culture rooting medium, such as vitamins, amino ac... | PlantAssociated |
| root_med_ph | 0..1 Float |
pH measurement of the culture rooting medium; e | PlantAssociated |
| root_med_regl | 0..1 String |
Growth regulators in the culture rooting medium such as cytokinins, auxins, g... | PlantAssociated |
| root_med_solid | 0..1 String |
Specification of the solidifying agent in the culture rooting medium; e | PlantAssociated |
| salt_regm | 0..* String |
Information about treatment involving use of salts as supplement to liquid an... | PlantAssociated |
| samp_capt_status | 0..1 SAMPCAPTSTATUSENUM |
Reason for the sample | PlantAssociated |
| samp_dis_stage | 0..1 SAMPDISSTAGEENUM |
Stage of the disease at the time of sample collection, e | PlantAssociated |
| salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample | PlantAssociated |
| samp_store_dur | 0..1 String |
Duration for which the sample was stored | PlantAssociated |
| samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | PlantAssociated |
| samp_store_temp | 0..1 String |
Temperature at which sample was stored, e | PlantAssociated |
| season_environment | 0..* String |
Treatment involving an exposure to a particular season (e | PlantAssociated |
| standing_water_regm | 0..* String |
Treatment involving an exposure to standing water during a plant's life span,... | PlantAssociated |
| tiss_cult_growth_med | 0..1 String |
Description of plant tissue culture growth media used | PlantAssociated |
| water_temp_regm | 0..* String |
Information about treatment involving an exposure to water with varying degre... | PlantAssociated |
| watering_regm | 0..* String |
Information about treatment involving an exposure to watering frequencies, tr... | PlantAssociated |
| host_symbiont | 0..* String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... | PlantAssociated |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/mixs-6-2-rc
LinkML Source
Direct
name: MimsPlantAssociated
description: MIxS data that complies with the Mims checklist and the PlantAssociated
Extension
title: Mims combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: PlantAssociated
mixins:
- Mims
class_uri: MIXS:0010007_0016010
Induced
name: MimsPlantAssociated
description: MIxS data that complies with the Mims checklist and the PlantAssociated
Extension
title: Mims combined with PlantAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: PlantAssociated
mixins:
- Mims
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
domain_of:
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
range: REL_TO_OXYGEN_ENUM
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: MimsPlantAssociated
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
recommended: 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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
recommended: true
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: 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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- 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
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
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-6-2-rc
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: MimsPlantAssociated
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: MimsPlantAssociated
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
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
air_temp_regm:
name: air_temp_regm
annotations:
Expected_value:
tag: Expected_value
value: temperature value;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: meter
description: Information about treatment involving an exposure to varying temperatures;
should include the temperature, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include different temperature regimens
title: air temperature regimen
examples:
- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- air
- regimen
- temperature
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000551
multivalued: true
alias: air_temp_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
ances_data:
name: ances_data
description: Information about either pedigree or other ancestral information
description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
(meaning [(A x B) x B] x B)
title: ancestral data
examples:
- value: A/3*B
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000247
multivalued: false
alias: ances_data
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
antibiotic_regm:
name: antibiotic_regm
annotations:
Expected_value:
tag: Expected_value
value: antibiotic name;antibiotic amount;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: milligram
description: Information about treatment involving antibiotic administration;
should include the name of antibiotic, amount administered, treatment regimen
including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
antibiotic regimens
title: antibiotic regimen
examples:
- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- regimen
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000553
multivalued: true
alias: antibiotic_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
biol_stat:
name: biol_stat
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: The level of genome modification
title: biological status
examples:
- value: natural
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- status
string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal
selection|mutant]'
slot_uri: MIXS:0000858
multivalued: false
alias: biol_stat
owner: MimsPlantAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
biotic_regm:
name: biotic_regm
description: Information about treatment(s) involving use of biotic factors, such
as bacteria, viruses or fungi
title: biotic regimen
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001038
multivalued: true
alias: biotic_regm
owner: MimsPlantAssociated
domain_of:
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
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: MimsPlantAssociated
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
chem_mutagen:
name: chem_mutagen
annotations:
Expected_value:
tag: Expected_value
value: mutagen name;mutagen amount;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Treatment involving use of mutagens; should include the name of mutagen,
amount administered, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple mutagen regimens
title: chemical mutagen
examples:
- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000555
multivalued: true
alias: chem_mutagen
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
climate_environment:
name: climate_environment
description: Treatment involving an exposure to a particular climate; treatment
regimen including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
climates
title: climate environment
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001040
multivalued: true
alias: climate_environment
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
cult_root_med:
name: cult_root_med
annotations:
Expected_value:
tag: Expected_value
value: name, PMID,DOI or url
description: Name or reference for the hydroponic or in vitro culture rooting
medium; can be the name of a commonly used medium or reference to a specific
medium, e.g. Murashige and Skoog medium. If the medium has not been formally
published, use the rooting medium descriptors
title: culture rooting medium
examples:
- value: http://himedialabs.com/TD/PT158.pdf
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- culture
string_serialization: '{text}|{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0001041
multivalued: false
alias: cult_root_med
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
fertilizer_regm:
name: fertilizer_regm
annotations:
Expected_value:
tag: Expected_value
value: fertilizer name;fertilizer amount;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: Information about treatment involving the use of fertilizers; should
include the name of fertilizer, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple fertilizer
regimens
title: fertilizer regimen
examples:
- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- regimen
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000556
multivalued: true
alias: fertilizer_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
fungicide_regm:
name: fungicide_regm
description: Information about treatment involving use of fungicides; should include
the name of fungicide, amount administered, treatment regimen including how
many times the treatment was repeated, how long each treatment lasted, and the
start and end time of the entire treatment; can include multiple fungicide regimens
title: fungicide regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000557
multivalued: true
alias: fungicide_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
gaseous_environment:
name: gaseous_environment
description: Use of conditions with differing gaseous environments; should include
the name of gaseous compound, amount administered, treatment duration, interval
and total experimental duration; can include multiple gaseous environment regimens
title: gaseous environment
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000558
multivalued: true
alias: gaseous_environment
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
genetic_mod:
name: genetic_mod
annotations:
Expected_value:
tag: Expected_value
value: PMID, DOI, URL or text
description: Genetic modifications of the genome of an organism, which may occur
naturally by spontaneous mutation, or be introduced by some experimental means,
e.g. specification of a transgene or the gene knocked-out or details of transient
transfection
title: genetic modification
examples:
- value: aox1A transgenic
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000859
multivalued: false
alias: genetic_mod
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
gravity:
name: gravity
annotations:
Expected_value:
tag: Expected_value
value: gravity factor value;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: meter per square second, g
description: Information about treatment involving use of gravity factor to study
various types of responses in presence, absence or modified levels of gravity;
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple treatments
title: gravity
examples:
- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000559
multivalued: true
alias: gravity
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
growth_facil:
name: growth_facil
annotations:
Expected_value:
tag: Expected_value
value: free text or CO
description: 'Type of facility where the sampled plant was grown; controlled vocabulary:
growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively
use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'
title: growth facility
examples:
- value: Growth chamber [CO_715:0000189]
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- facility
- growth
string_serialization: '{text}|{termLabel} [{termID}]'
slot_uri: MIXS:0001043
multivalued: false
alias: growth_facil
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
growth_habit:
name: growth_habit
description: Characteristic shape, appearance or growth form of a plant species
title: growth habit
examples:
- value: spreading
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- growth
slot_uri: MIXS:0001044
multivalued: false
alias: growth_habit
owner: MimsPlantAssociated
domain_of:
- FoodFarmEnvironment
- PlantAssociated
range: GROWTH_HABIT_ENUM
required: false
recommended: false
growth_hormone_regm:
name: growth_hormone_regm
annotations:
Expected_value:
tag: Expected_value
value: growth hormone name;growth hormone amount;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: Information about treatment involving use of growth hormones; should
include the name of growth hormone, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple growth
hormone regimens
title: growth hormone regimen
examples:
- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- growth
- regimen
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000560
multivalued: true
alias: growth_hormone_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
herbicide_regm:
name: herbicide_regm
description: Information about treatment involving use of herbicides; information
about treatment involving use of growth hormones; should include the name of
herbicide, amount administered, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include multiple regimens
title: herbicide regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000561
multivalued: true
alias: herbicide_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
host_age:
name: host_age
description: Age of host at the time of sampling; relevant scale depends on species
and study, e.g. Could be seconds for amoebae or centuries for trees
title: host age
examples:
- value: 10 days
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000255
multivalued: false
alias: host_age
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_common_name:
name: host_common_name
description: Common name of the host
title: host common name
examples:
- value: rice
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000248
multivalued: false
alias: host_common_name
owner: MimsPlantAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_disease_stat:
name: host_disease_stat
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: downy mildew
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
multivalued: false
alias: host_disease_stat
owner: MimsPlantAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
required: false
recommended: false
host_dry_mass:
name: host_dry_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Measurement of dry mass
title: host dry mass
examples:
- value: 500 gram
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- dry
- host
- host.
- mass
slot_uri: MIXS:0000257
multivalued: false
alias: host_dry_mass
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
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
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
examples:
- value: Ts
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000365
multivalued: false
alias: host_genotype
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_height:
name: host_height
description: The height of subject
title: host height
examples:
- value: 1 meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000264
multivalued: false
alias: host_height
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_subspecf_genlin:
name: host_subspecf_genlin
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 host organism below
the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
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: host subspecific genetic lineage
examples:
- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
- lineage
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0001318
multivalued: true
alias: host_subspecf_genlin
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
host_length:
name: host_length
description: The length of subject
title: host length
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000256
multivalued: false
alias: host_length
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
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
host_life_stage:
name: host_life_stage
description: Description of life stage of host
title: host life stage
examples:
- value: adult
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000251
multivalued: false
alias: host_life_stage
owner: MimsPlantAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_phenotype:
name: host_phenotype
description: Phenotype of human or other host. Use terms from the phenotypic quality
ontology (pato) or the Human Phenotype Ontology (HP)
title: host phenotype
examples:
- value: seed pod; green [PATO:0000320]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
multivalued: false
alias: host_phenotype
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_taxid:
name: host_taxid
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
examples:
- value: '4530'
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{NCBI taxid}'
slot_uri: MIXS:0000250
multivalued: false
alias: host_taxid
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_tot_mass:
name: host_tot_mass
description: Total mass of the host at collection, the unit depends on host
title: host total mass
examples:
- value: 2500 gram
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000263
multivalued: false
alias: host_tot_mass
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_wet_mass:
name: host_wet_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Measurement of wet mass
title: host wet mass
examples:
- value: 1500 gram
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
- mass
- wet
slot_uri: MIXS:0000567
multivalued: false
alias: host_wet_mass
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
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
humidity_regm:
name: humidity_regm
annotations:
Expected_value:
tag: Expected_value
value: humidity value;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: gram per cubic meter
description: Information about treatment involving an exposure to varying degree
of humidity; information about treatment involving use of growth hormones; should
include amount of humidity administered, treatment regimen including how many
times the treatment was repeated, how long each treatment lasted, and the start
and end time of the entire treatment; can include multiple regimens
title: humidity regimen
examples:
- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- humidity
- regimen
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000568
multivalued: true
alias: humidity_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
light_regm:
name: light_regm
annotations:
Expected_value:
tag: Expected_value
value: exposure type;light intensity;light quality
Preferred_unit:
tag: Preferred_unit
value: lux; micrometer, nanometer, angstrom
description: Information about treatment(s) involving exposure to light, including
both light intensity and quality
title: light regimen
examples:
- value: incandescant light;10 lux;450 nanometer
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- light
- regimen
string_serialization: '{text};{float} {unit};{float} {unit}'
slot_uri: MIXS:0000569
multivalued: false
alias: light_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
mechanical_damage:
name: mechanical_damage
annotations:
Expected_value:
tag: Expected_value
value: damage type;body site
description: Information about any mechanical damage exerted on the plant; can
include multiple damages and sites
title: mechanical damage
examples:
- value: pruning;bark
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{text}'
slot_uri: MIXS:0001052
multivalued: true
alias: mechanical_damage
owner: MimsPlantAssociated
domain_of:
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
mineral_nutr_regm:
name: mineral_nutr_regm
annotations:
Expected_value:
tag: Expected_value
value: mineral nutrient name;mineral nutrient amount;treatment interval and
duration
Preferred_unit:
tag: Preferred_unit
value: gram, mole per liter, milligram per liter
description: Information about treatment involving the use of mineral supplements;
should include the name of mineral nutrient, amount administered, treatment
regimen including how many times the treatment was repeated, how long each treatment
lasted, and the start and end time of the entire treatment; can include multiple
mineral nutrient regimens
title: mineral nutrient regimen
examples:
- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- mineral
- nutrient
- regimen
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000570
multivalued: true
alias: mineral_nutr_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
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: MimsPlantAssociated
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
non_min_nutr_regm:
name: non_min_nutr_regm
description: Information about treatment involving the exposure of plant to non-mineral
nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
nutrient, amount administered, treatment regimen including how many times the
treatment was repeated, how long each treatment lasted, and the start and end
time of the entire treatment; can include multiple non-mineral nutrient regimens
title: non-mineral nutrient regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000571
multivalued: true
alias: non_min_nutr_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
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: MimsPlantAssociated
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
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: MimsPlantAssociated
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
ph_regm:
name: ph_regm
description: Information about treatment involving exposure of plants to varying
levels of ph of the growth media, treatment regimen including how many times
the treatment was repeated, how long each treatment lasted, and the start and
end time of the entire treatment; can include multiple regimen
title: pH regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001056
multivalued: true
alias: ph_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
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: MimsPlantAssociated
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
pesticide_regm:
name: pesticide_regm
description: Information about treatment involving use of insecticides; should
include the name of pesticide, amount administered, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple pesticide
regimens
title: pesticide regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000573
multivalued: true
alias: pesticide_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
plant_growth_med:
name: plant_growth_med
description: Specification of the media for growing the plants or tissue cultured
samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
vitro liquid culture medium. Recommended value is a specific value from EO:plant
growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
or other controlled vocabulary
title: plant growth medium
examples:
- value: hydroponic plant culture media [EO:0007067]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}] or [husk|other artificial liquid
medium|other artificial solid medium|peat moss|perlite|pumice|sand|soil|vermiculite|water]'
slot_uri: MIXS:0001057
multivalued: false
alias: plant_growth_med
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
plant_product:
name: plant_product
description: Substance produced by the plant, where the sample was obtained from
title: plant product
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0001058
multivalued: false
alias: plant_product
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
plant_sex:
name: plant_sex
description: Sex of the reproductive parts on the whole plant, e.g. pistillate,
staminate, monoecieous, hermaphrodite
title: plant sex
examples:
- value: Hermaphroditic
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- plant
slot_uri: MIXS:0001059
multivalued: false
alias: plant_sex
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: PLANT_SEX_ENUM
required: false
recommended: false
plant_struc:
name: plant_struc
description: Name of plant structure the sample was obtained from; for Plant Ontology
(PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
sex of it can be recorded here
title: plant structure
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001060
multivalued: false
alias: plant_struc
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
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
radiation_regm:
name: radiation_regm
annotations:
Expected_value:
tag: Expected_value
value: radiation type name;radiation amount;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: rad, gray
description: Information about treatment involving exposure of plant or a plant
part to a particular radiation regimen; should include the radiation type, amount
or intensity administered, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple radiation regimens
title: radiation regimen
examples:
- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- regimen
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000575
multivalued: true
alias: radiation_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
rainfall_regm:
name: rainfall_regm
annotations:
Expected_value:
tag: Expected_value
value: measurement value;treatment interval and duration
Preferred_unit:
tag: Preferred_unit
value: millimeter
description: Information about treatment involving an exposure to a given amount
of rainfall, treatment regimen including how many times the treatment was repeated,
how long each treatment lasted, and the start and end time of the entire treatment;
can include multiple regimens
title: rainfall regimen
examples:
- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- rain
- regimen
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000576
multivalued: true
alias: rainfall_regm
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
root_cond:
name: root_cond
description: Relevant rooting conditions such as field plot size, sowing density,
container dimensions, number of plants per container
title: rooting conditions
examples:
- value: http://himedialabs.com/TD/PT158.pdf
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- condition
slot_uri: MIXS:0001061
multivalued: false
alias: root_cond
owner: MimsPlantAssociated
domain_of:
- FoodFarmEnvironment
- PlantAssociated
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()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
root_med_carbon:
name: root_med_carbon
annotations:
Expected_value:
tag: Expected_value
value: carbon source name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Source of organic carbon in the culture rooting medium; e.g. sucrose
title: rooting medium carbon
examples:
- value: sucrose
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- carbon
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000577
multivalued: false
alias: root_med_carbon
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
root_med_macronutr:
name: root_med_macronutr
annotations:
Expected_value:
tag: Expected_value
value: macronutrient name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Measurement of the culture rooting medium macronutrients (N,P, K,
Ca, Mg, S); e.g. KH2PO4 (170 mg/L)
title: rooting medium macronutrients
examples:
- value: KH2PO4;170 milligram per liter
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- macronutrients
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000578
multivalued: false
alias: root_med_macronutr
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
root_med_micronutr:
name: root_med_micronutr
annotations:
Expected_value:
tag: Expected_value
value: micronutrient name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Measurement of the culture rooting medium micronutrients (Fe, Mn,
Zn, B, Cu, Mo); e.g. H3BO3 (6.2 mg/L)
title: rooting medium micronutrients
examples:
- value: H3BO3;6.2 milligram per liter
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- micronutrients
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000579
multivalued: false
alias: root_med_micronutr
owner: MimsPlantAssociated
domain_of:
- FoodFarmEnvironment
- PlantAssociated
range: string
required: false
recommended: false
root_med_suppl:
name: root_med_suppl
annotations:
Expected_value:
tag: Expected_value
value: supplement name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Organic supplements of the culture rooting medium, such as vitamins,
amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid
(0.5 mg/L)
title: rooting medium organic supplements
examples:
- value: nicotinic acid;0.5 milligram per liter
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- organic
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000580
multivalued: false
alias: root_med_suppl
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
root_med_ph:
name: root_med_ph
description: pH measurement of the culture rooting medium; e.g. 5.5
title: rooting medium pH
examples:
- value: '7.5'
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- ph
slot_uri: MIXS:0001062
multivalued: false
alias: root_med_ph
owner: MimsPlantAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- PlantAssociated
range: float
required: false
recommended: false
root_med_regl:
name: root_med_regl
annotations:
Expected_value:
tag: Expected_value
value: regulator name;measurement value
Preferred_unit:
tag: Preferred_unit
value: milligram per liter
description: Growth regulators in the culture rooting medium such as cytokinins,
auxins, gybberellins, abscisic acid; e.g. 0.5 mg/L NAA
title: rooting medium regulators
examples:
- value: abscisic acid;0.75 milligram per liter
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000581
multivalued: false
alias: root_med_regl
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
root_med_solid:
name: root_med_solid
description: Specification of the solidifying agent in the culture rooting medium;
e.g. agar
title: rooting medium solidifier
examples:
- value: agar
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001063
multivalued: false
alias: root_med_solid
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
range: string
required: false
recommended: false
salt_regm:
name: salt_regm
description: Information about treatment involving use of salts as supplement
to liquid and soil growth media; should include the name of salt, amount administered,
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple salt regimens
title: salt regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000582
multivalued: true
alias: salt_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
samp_capt_status:
name: samp_capt_status
description: Reason for the sample
title: sample capture status
examples:
- value: farm sample
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- sample
- status
slot_uri: MIXS:0000860
multivalued: false
alias: samp_capt_status
owner: MimsPlantAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: SAMP_CAPT_STATUS_ENUM
required: false
recommended: false
samp_dis_stage:
name: samp_dis_stage
description: Stage of the disease at the time of sample collection, e.g. inoculation,
penetration, infection, growth and reproduction, dissemination of pathogen
title: sample disease stage
examples:
- value: infection
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- disease
- sample
slot_uri: MIXS:0000249
multivalued: false
alias: samp_dis_stage
owner: MimsPlantAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: SAMP_DIS_STAGE_ENUM
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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: MimsPlantAssociated
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
season_environment:
name: season_environment
description: Treatment involving an exposure to a particular season (e.g. Winter,
summer, rabi, rainy etc.), treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment
title: seasonal environment
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001068
multivalued: true
alias: season_environment
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
standing_water_regm:
name: standing_water_regm
description: Treatment involving an exposure to standing water during a plant's
life span, types can be flood water or standing water, treatment regimen including
how many times the treatment was repeated, how long each treatment lasted, and
the start and end time of the entire treatment; can include multiple regimens
title: standing water regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0001069
multivalued: true
alias: standing_water_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
tiss_cult_growth_med:
name: tiss_cult_growth_med
description: Description of plant tissue culture growth media used
title: tissue culture growth media
examples:
- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- culture
- growth
slot_uri: MIXS:0001070
multivalued: false
alias: tiss_cult_growth_med
owner: MimsPlantAssociated
domain_of:
- PlantAssociated
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()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
water_temp_regm:
name: water_temp_regm
description: Information about treatment involving an exposure to water with varying
degree of temperature, treatment regimen including how many times the treatment
was repeated, how long each treatment lasted, and the start and end time of
the entire treatment; can include multiple regimens
title: water temperature regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000590
multivalued: true
alias: water_temp_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
watering_regm:
name: watering_regm
description: Information about treatment involving an exposure to watering frequencies,
treatment regimen including how many times the treatment was repeated, how long
each treatment lasted, and the start and end time of the entire treatment; can
include multiple regimens
title: watering regimen
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000591
multivalued: true
alias: watering_regm
owner: MimsPlantAssociated
domain_of:
- Agriculture
- PlantAssociated
range: string
required: false
recommended: false
host_symbiont:
name: host_symbiont
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
can have its own symbionts. For example, parasites may have hyperparasites (=parasites
of the parasite)
title: observed host symbionts
examples:
- value: flukeworms
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0001298
multivalued: true
alias: host_symbiont
owner: MimsPlantAssociated
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
class_uri: MIXS:0010007_0016010