Class: MIMS
Metagenome or Environmental
URI: MIXS:MIMS
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| samp_name | 0..1 String |
A local identifier or name that for the material sample used for extracting n... | direct |
| samp_taxon_id | 0..1 String |
NCBI taxon id of the sample | direct |
| project_name | 0..1 String |
Name of the project within which the sequencing was organized | direct |
| experimental_factor | 0..1 String |
Experimental factors are essentially the variable aspects of an experiment de... | direct |
| lat_lon | 0..1 String |
The geographical origin of the sample as defined by latitude and longitude | direct |
| geo_loc_name | 0..1 String |
The geographical origin of the sample as defined by the country or sea name f... | direct |
| collection_date | 0..1 Date |
The time of sampling, either as an instance (single point in time) or interva... | direct |
| neg_cont_type | 0..1 NegContTypeEnum |
The substance or equipment used as a negative control in an investigation | direct |
| pos_cont_type | 0..1 String |
The substance, mixture, product, or apparatus used to verify that a process w... | direct |
| env_broad_scale | 0..1 String |
Report the major environmental system the sample or specimen came from | direct |
| env_local_scale | 0..1 String |
Report the entity or entities which are in the sample or specimen’s local vic... | direct |
| env_medium | 0..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | direct |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | direct |
| source_mat_id | 0..1 String |
A unique identifier assigned to a material sample (as defined by http://rs | direct |
| rel_to_oxygen | 0..1 RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... | direct |
| samp_collec_device | 0..1 String |
The device used to collect an environmental sample | direct |
| samp_collec_method | 0..1 String |
The method employed for collecting the sample | direct |
| samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... | direct |
| size_frac | 0..1 String |
Filtering pore size used in sample preparation | direct |
| samp_size | 0..1 QuantityValue |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
| samp_vol_we_dna_ext | 0..1 QuantityValue |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | direct |
| nucl_acid_ext | 0..1 String |
A link to a literature reference, electronic resource or a standard operating... | direct |
| nucl_acid_amp | 0..1 String |
A link to a literature reference, electronic resource or a standard operating... | direct |
| lib_size | 0..1 Integer |
Total number of clones in the library prepared for the project | direct |
| lib_reads_seqd | 0..1 Integer |
Total number of clones sequenced from the library | direct |
| lib_layout | 0..1 LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads | direct |
| lib_vector | 0..1 String |
Cloning vector type(s) used in construction of libraries | direct |
| lib_screen | 0..1 String |
Specific enrichment or screening methods applied before and/or after creating... | direct |
| mid | 0..1 String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | direct |
| adapters | 0..1 String |
Adapters provide priming sequences for both amplification and sequencing of t... | direct |
| seq_meth | 0..1 String |
Sequencing machine used | direct |
| assembly_qual | 0..1 AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... | direct |
| assembly_name | 0..1 String |
Name/version of the assembly provided by the submitter that is used in the ge... | direct |
| assembly_software | 0..1 String |
Tool(s) used for assembly, including version number and parameters | direct |
| annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... | direct |
| number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | direct |
| feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc | direct |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | direct |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | direct |
| tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... | direct |
| associated_resource | 0..1 String |
A related resource that is referenced, cited, or otherwise associated to the ... | direct |
| sop | 0..1 String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | direct |
Mixin Usage
| mixed into | description |
|---|---|
| AirMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| BuiltEnvironmentMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Host-associatedMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Human-associatedMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Human-gutMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Human-oralMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Human-skinMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Human-vaginalMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| HydrocarbonResources-coresMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| HydrocarbonResources-fluidsSwabsMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| MicrobialMatBiofilmMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| MiscellaneousNaturalOrArtificialEnvironmentMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Plant-associatedMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| SedimentMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| SoilMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| WastewaterSludgeMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| WaterMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Symbiont-associatedMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Food-humanFoodsMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Food-animalAndAnimalFeedMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Food-foodProductionFacilityMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| Food-farmEnvironmentMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
| AgricultureMIMS | Combinatorial checklist Metagenome or Environmental with environmental packag... |
Aliases
- MIMS
Identifier and Mapping Information
Schema Source
- from schema: http://w3id.org/mixs
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:MIMS |
| native | MIXS:MIMS |
LinkML Source
Direct
name: MIMS
description: Metagenome or Environmental
from_schema: http://w3id.org/mixs
aliases:
- MIMS
mixin: true
slots:
- samp_name
- samp_taxon_id
- project_name
- experimental_factor
- lat_lon
- geo_loc_name
- collection_date
- neg_cont_type
- pos_cont_type
- env_broad_scale
- env_local_scale
- env_medium
- ref_biomaterial
- source_mat_id
- rel_to_oxygen
- samp_collec_device
- samp_collec_method
- samp_mat_process
- size_frac
- samp_size
- samp_vol_we_dna_ext
- nucl_acid_ext
- nucl_acid_amp
- lib_size
- lib_reads_seqd
- lib_layout
- lib_vector
- lib_screen
- mid
- adapters
- seq_meth
- assembly_qual
- assembly_name
- assembly_software
- annot
- number_contig
- feat_pred
- ref_db
- sim_search_meth
- tax_class
- associated resource
- sop
slot_usage:
samp_name:
name: samp_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
samp_taxon_id:
name: samp_taxon_id
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
project_name:
name: project_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
experimental_factor:
name: experimental_factor
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
lat_lon:
name: lat_lon
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
geo_loc_name:
name: geo_loc_name
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
collection_date:
name: collection_date
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
neg_cont_type:
name: neg_cont_type
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
pos_cont_type:
name: pos_cont_type
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
env_broad_scale:
name: env_broad_scale
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
env_local_scale:
name: env_local_scale
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
env_medium:
name: env_medium
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
ref_biomaterial:
name: ref_biomaterial
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
source_mat_id:
name: source_mat_id
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
rel_to_oxygen:
name: rel_to_oxygen
domain_of:
- core
- MIGS bacteria
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
required: false
samp_collec_device:
name: samp_collec_device
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_collec_method:
name: samp_collec_method
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_mat_process:
name: samp_mat_process
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
size_frac:
name: size_frac
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
required: false
samp_size:
name: samp_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: false
nucl_acid_ext:
name: nucl_acid_ext
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_size:
name: lib_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_layout:
name: lib_layout
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_vector:
name: lib_vector
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_screen:
name: lib_screen
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
mid:
name: mid
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
adapters:
name: adapters
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
seq_meth:
name: seq_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
assembly_qual:
name: assembly_qual
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
assembly_name:
name: assembly_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
assembly_software:
name: assembly_software
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
annot:
name: annot
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
number_contig:
name: number_contig
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
feat_pred:
name: feat_pred
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
ref_db:
name: ref_db
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
sim_search_meth:
name: sim_search_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
tax_class:
name: tax_class
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
associated resource:
name: associated resource
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
sop:
name: sop
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
Induced
name: MIMS
description: Metagenome or Environmental
from_schema: http://w3id.org/mixs
aliases:
- MIMS
mixin: true
slot_usage:
samp_name:
name: samp_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
samp_taxon_id:
name: samp_taxon_id
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
project_name:
name: project_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
experimental_factor:
name: experimental_factor
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
lat_lon:
name: lat_lon
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
geo_loc_name:
name: geo_loc_name
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
collection_date:
name: collection_date
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
neg_cont_type:
name: neg_cont_type
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
pos_cont_type:
name: pos_cont_type
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
env_broad_scale:
name: env_broad_scale
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
env_local_scale:
name: env_local_scale
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
env_medium:
name: env_medium
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
required: true
ref_biomaterial:
name: ref_biomaterial
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
source_mat_id:
name: source_mat_id
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
rel_to_oxygen:
name: rel_to_oxygen
domain_of:
- core
- MIGS bacteria
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
required: false
samp_collec_device:
name: samp_collec_device
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_collec_method:
name: samp_collec_method
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_mat_process:
name: samp_mat_process
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
size_frac:
name: size_frac
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
required: false
samp_size:
name: samp_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: false
nucl_acid_ext:
name: nucl_acid_ext
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_size:
name: lib_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_layout:
name: lib_layout
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_vector:
name: lib_vector
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
lib_screen:
name: lib_screen
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
mid:
name: mid
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
adapters:
name: adapters
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
seq_meth:
name: seq_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
required: true
assembly_qual:
name: assembly_qual
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
assembly_name:
name: assembly_name
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
assembly_software:
name: assembly_software
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
recommended: true
annot:
name: annot
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
number_contig:
name: number_contig
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
feat_pred:
name: feat_pred
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
ref_db:
name: ref_db
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
sim_search_meth:
name: sim_search_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
tax_class:
name: tax_class
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
associated resource:
name: associated resource
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
sop:
name: sop
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
recommended: true
attributes:
samp_name:
name: samp_name
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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text} [NCBI:txid]'
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
experimental_factor:
name: experimental_factor
description: Experimental factors are essentially the variable aspects of an experiment
design which can be used to describe an experiment, or set of experiments, in
an increasingly detailed manner. This field accepts ontology terms from Experimental
Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
title: experimental factor
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
multivalued: false
alias: experimental_factor
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
multivalued: false
alias: lat_lon
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: 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)
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{term}: {term}, {text}'
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: date
required: true
neg_cont_type:
name: neg_cont_type
description: The substance or equipment used as a negative control in an investigation
title: negative control type
from_schema: http://w3id.org/mixs
is_a: investigation field
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: neg_cont_type_enum
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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: true
env_local_scale:
name: env_local_scale
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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MIMS
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report.
title: reference for biomaterial
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: false
alias: source_mat_id
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000015
multivalued: false
alias: rel_to_oxygen
owner: MIMS
domain_of:
- core
- MIGS bacteria
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
range: rel_to_oxygen_enum
required: false
samp_collec_device:
name: samp_collec_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
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collec_device
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
samp_collec_method:
name: samp_collec_method
description: The method employed for collecting the sample.
title: sample collection method
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collec_method
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
size_frac:
name: size_frac
description: Filtering pore size used in sample preparation
title: size fraction selected
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: MIMS
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: quantity value
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: quantity value
required: false
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: integer
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- 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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: lib_layout_enum
recommended: true
lib_vector:
name: lib_vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
lib_screen:
name: lib_screen
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{dna}'
slot_uri: MIXS:0000047
multivalued: false
alias: mid
owner: MIMS
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: assembly_qual_enum
recommended: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: integer
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
associated resource:
name: associated resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence.
title: relevant electronic resources
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID} | {DOI} | {URL}'
slot_uri: MIXS:0000091
multivalued: false
alias: associated_resource
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: false
alias: sop
owner: MIMS
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true