Class: MIUVIG
Minimum Information About an Uncultivated Virus Genome
URI: MIXS:MIUVIG
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 |
| estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing | 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 |
| pathogenicity | 0..1 String |
To what is the entity pathogenic | direct |
| biotic_relationship | 0..1 BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... | direct |
| specific_host | 0..1 String |
Report the host's taxonomic name and/or NCBI taxonomy ID | direct |
| host_spec_range | 0..1 Integer |
The range and diversity of host species that an organism is capable of infect... | direct |
| host_disease_stat | 0..1 String |
List of diseases with which the host has been diagnosed; can include multiple... | 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 |
| source_uvig | 0..1 SourceUvigEnum |
Type of dataset from which the UViG was obtained | direct |
| virus_enrich_appr | 0..1 VirusEnrichApprEnum |
List of approaches used to enrich the sample for viruses, if any | 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 |
| tax_ident | 0..1 TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | 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 |
| trnas | 0..1 Integer |
The total number of tRNAs identified from the SAG or MAG | direct |
| trna_ext_software | 0..1 String |
Tools used for tRNA identification | direct |
| compl_score | 0..1 String |
Completeness score is typically based on either the fraction of markers found... | direct |
| compl_software | 0..1 String |
Tools used for completion estimate, i | direct |
| compl_appr | 0..1 ComplApprEnum |
The approach used to determine the completeness of a given genomic assembly, ... | direct |
| sort_tech | 0..1 SortTechEnum |
Method used to sort/isolate cells or particles of interest | direct |
| single_cell_lysis_appr | 0..1 SingleCellLysisApprEnum |
Method used to free DNA from interior of the cell(s) or particle(s) | direct |
| single_cell_lysis_prot | 0..1 String |
Name of the kit or standard protocol used for cell(s) or particle(s) lysis | direct |
| wga_amp_appr | 0..1 String |
Method used to amplify genomic DNA in preparation for sequencing | direct |
| wga_amp_kit | 0..1 String |
Kit used to amplify genomic DNA in preparation for sequencing | direct |
| bin_param | 0..1 BinParamEnum |
The parameters that have been applied during the extraction of genomes from m... | direct |
| bin_software | 0..1 String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... | direct |
| reassembly_bin | 0..1 String |
Has an assembly been performed on a genome bin extracted from a metagenomic a... | direct |
| mag_cov_software | 0..1 MagCovSoftwareEnum |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... | direct |
| vir_ident_software | 0..1 String |
Tool(s) used for the identification of UViG as a viral genome, software or pr... | direct |
| pred_genome_type | 0..1 PredGenomeTypeEnum |
Type of genome predicted for the UViG | direct |
| pred_genome_struc | 0..1 PredGenomeStrucEnum |
Expected structure of the viral genome | direct |
| detec_type | 0..1 String |
Type of UViG detection | direct |
| otu_class_appr | 0..1 String |
Cutoffs and approach used when clustering “species-level” OTUs | direct |
| otu_seq_comp_appr | 0..1 String |
Tool and thresholds used to compare sequences when computing "species-level" ... | direct |
| otu_db | 0..1 String |
Reference database (i | direct |
| host_pred_appr | 0..1 HostPredApprEnum |
Tool or approach used for host prediction | direct |
| host_pred_est_acc | 0..1 String |
For each tool or approach used for host prediction, estimated false discovery... | 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 |
|---|---|
| AirMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| BuiltEnvironmentMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Host-associatedMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Human-associatedMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Human-gutMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Human-oralMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Human-skinMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Human-vaginalMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| HydrocarbonResources-coresMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| HydrocarbonResources-fluidsSwabsMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| MicrobialMatBiofilmMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| MiscellaneousNaturalOrArtificialEnvironmentMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Plant-associatedMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| SedimentMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| SoilMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| WastewaterSludgeMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| WaterMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Symbiont-associatedMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Food-humanFoodsMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Food-animalAndAnimalFeedMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Food-foodProductionFacilityMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| Food-farmEnvironmentMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
| AgricultureMIUVIG | Combinatorial checklist Minimum Information About an Uncultivated Virus Genom... |
Aliases
- MIUVIG
Identifier and Mapping Information
Schema Source
- from schema: http://w3id.org/mixs
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:MIUVIG |
| native | MIXS:MIUVIG |
LinkML Source
Direct
name: MIUVIG
description: Minimum Information About an Uncultivated Virus Genome
from_schema: http://w3id.org/mixs
aliases:
- MIUVIG
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
- estimated_size
- ref_biomaterial
- source_mat_id
- pathogenicity
- biotic_relationship
- specific_host
- host_spec_range
- host_disease_stat
- samp_collec_device
- samp_collec_method
- samp_mat_process
- size_frac
- samp_size
- samp_vol_we_dna_ext
- source_uvig
- virus_enrich_appr
- nucl_acid_ext
- nucl_acid_amp
- lib_size
- lib_reads_seqd
- lib_layout
- lib_vector
- lib_screen
- mid
- adapters
- seq_meth
- tax_ident
- assembly_qual
- assembly_name
- assembly_software
- annot
- number_contig
- feat_pred
- ref_db
- sim_search_meth
- tax_class
- trnas
- trna_ext_software
- compl_score
- compl_software
- compl_appr
- sort_tech
- single_cell_lysis_appr
- single_cell_lysis_prot
- wga_amp_appr
- wga_amp_kit
- bin_param
- bin_software
- reassembly_bin
- mag_cov_software
- vir_ident_software
- pred_genome_type
- pred_genome_struc
- detec_type
- otu_class_appr
- otu_seq_comp_appr
- otu_db
- host_pred_appr
- host_pred_est_acc
- 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
estimated_size:
name: estimated_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIUVIG
required: false
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
pathogenicity:
name: pathogenicity
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
required: false
biotic_relationship:
name: biotic_relationship
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIMARKS survey
- MIUVIG
required: false
specific_host:
name: specific_host
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
required: false
host_spec_range:
name: host_spec_range
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
required: false
host_disease_stat:
name: host_disease_stat
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
recommended: true
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
recommended: true
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
source_uvig:
name: source_uvig
domain_of:
- core
- MIUVIG
required: true
virus_enrich_appr:
name: virus_enrich_appr
domain_of:
- core
- MIGS virus
- MIUVIG
required: true
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
tax_ident:
name: tax_ident
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
required: false
assembly_qual:
name: assembly_qual
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: 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
required: true
annot:
name: annot
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
number_contig:
name: number_contig
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: true
feat_pred:
name: feat_pred
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
ref_db:
name: ref_db
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
sim_search_meth:
name: sim_search_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
tax_class:
name: tax_class
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
trnas:
name: trnas
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
required: false
trna_ext_software:
name: trna_ext_software
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
required: false
compl_score:
name: compl_score
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
recommended: true
compl_software:
name: compl_software
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
required: false
compl_appr:
name: compl_appr
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
recommended: true
sort_tech:
name: sort_tech
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
single_cell_lysis_appr:
name: single_cell_lysis_appr
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
single_cell_lysis_prot:
name: single_cell_lysis_prot
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
wga_amp_appr:
name: wga_amp_appr
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
wga_amp_kit:
name: wga_amp_kit
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
bin_param:
name: bin_param
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
bin_software:
name: bin_software
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
reassembly_bin:
name: reassembly_bin
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
mag_cov_software:
name: mag_cov_software
domain_of:
- core
- MIMAG
- MIUVIG
required: false
vir_ident_software:
name: vir_ident_software
domain_of:
- core
- MIUVIG
required: true
pred_genome_type:
name: pred_genome_type
domain_of:
- core
- MIUVIG
required: true
pred_genome_struc:
name: pred_genome_struc
domain_of:
- core
- MIUVIG
required: true
detec_type:
name: detec_type
domain_of:
- core
- MIUVIG
required: true
otu_class_appr:
name: otu_class_appr
domain_of:
- core
- MIUVIG
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
domain_of:
- core
- MIUVIG
recommended: true
otu_db:
name: otu_db
domain_of:
- core
- MIUVIG
recommended: true
host_pred_appr:
name: host_pred_appr
domain_of:
- core
- MIUVIG
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
domain_of:
- core
- MIUVIG
recommended: true
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: MIUVIG
description: Minimum Information About an Uncultivated Virus Genome
from_schema: http://w3id.org/mixs
aliases:
- MIUVIG
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
estimated_size:
name: estimated_size
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIUVIG
required: false
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
pathogenicity:
name: pathogenicity
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
required: false
biotic_relationship:
name: biotic_relationship
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIMARKS survey
- MIUVIG
required: false
specific_host:
name: specific_host
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
required: false
host_spec_range:
name: host_spec_range
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
required: false
host_disease_stat:
name: host_disease_stat
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
recommended: true
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
recommended: true
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
source_uvig:
name: source_uvig
domain_of:
- core
- MIUVIG
required: true
virus_enrich_appr:
name: virus_enrich_appr
domain_of:
- core
- MIGS virus
- MIUVIG
required: true
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
tax_ident:
name: tax_ident
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
required: false
assembly_qual:
name: assembly_qual
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: 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
required: true
annot:
name: annot
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: false
number_contig:
name: number_contig
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
required: true
feat_pred:
name: feat_pred
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
ref_db:
name: ref_db
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
sim_search_meth:
name: sim_search_meth
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
tax_class:
name: tax_class
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
recommended: true
trnas:
name: trnas
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
required: false
trna_ext_software:
name: trna_ext_software
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
required: false
compl_score:
name: compl_score
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
recommended: true
compl_software:
name: compl_software
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
required: false
compl_appr:
name: compl_appr
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
recommended: true
sort_tech:
name: sort_tech
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
single_cell_lysis_appr:
name: single_cell_lysis_appr
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
single_cell_lysis_prot:
name: single_cell_lysis_prot
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
wga_amp_appr:
name: wga_amp_appr
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
wga_amp_kit:
name: wga_amp_kit
domain_of:
- core
- MISAG
- MIUVIG
recommended: true
bin_param:
name: bin_param
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
bin_software:
name: bin_software
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
reassembly_bin:
name: reassembly_bin
domain_of:
- core
- MIMAG
- MIUVIG
recommended: true
mag_cov_software:
name: mag_cov_software
domain_of:
- core
- MIMAG
- MIUVIG
required: false
vir_ident_software:
name: vir_ident_software
domain_of:
- core
- MIUVIG
required: true
pred_genome_type:
name: pred_genome_type
domain_of:
- core
- MIUVIG
required: true
pred_genome_struc:
name: pred_genome_struc
domain_of:
- core
- MIUVIG
required: true
detec_type:
name: detec_type
domain_of:
- core
- MIUVIG
required: true
otu_class_appr:
name: otu_class_appr
domain_of:
- core
- MIUVIG
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
domain_of:
- core
- MIUVIG
recommended: true
otu_db:
name: otu_db
domain_of:
- core
- MIUVIG
recommended: true
host_pred_appr:
name: host_pred_appr
domain_of:
- core
- MIUVIG
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
domain_of:
- core
- MIUVIG
recommended: true
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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
estimated_size:
name: estimated_size
description: The estimated size of the genome prior to sequencing. Of particular
importance in the sequencing of (eukaryotic) genome which could remain in draft
form for a long or unspecified period.
title: estimated size
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
multivalued: false
alias: estimated_size
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIUVIG
range: string
required: false
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: MIUVIG
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: MIUVIG
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
pathogenicity:
name: pathogenicity
description: To what is the entity pathogenic
title: known pathogenicity
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000027
multivalued: false
alias: pathogenicity
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
range: string
required: false
biotic_relationship:
name: biotic_relationship
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated with. E.g., parasite on species X; mutualist with
species Y. The target organism is the subject of the relationship, and the other
organism(s) is the object
title: observed biotic relationship
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000028
multivalued: false
alias: biotic_relationship
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIMARKS survey
- MIUVIG
range: biotic_relationship_enum
required: false
specific_host:
name: specific_host
description: Report the host's taxonomic name and/or NCBI taxonomy ID.
title: host scientific name
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
multivalued: false
alias: specific_host
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
range: string
required: false
host_spec_range:
name: host_spec_range
description: The range and diversity of host species that an organism is capable
of infecting, defined by NCBI taxonomy identifier.
title: host specificity or range
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000030
multivalued: false
alias: host_spec_range
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIUVIG
range: integer
required: 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
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000031
multivalued: false
alias: host_disease_stat
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS virus
- MIUVIG
range: string
recommended: true
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MIUVIG
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: MIUVIG
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
source_uvig:
name: source_uvig
description: Type of dataset from which the UViG was obtained
title: source of UViGs
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000035
multivalued: false
alias: source_uvig
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: source_uvig_enum
required: true
virus_enrich_appr:
name: virus_enrich_appr
description: List of approaches used to enrich the sample for viruses, if any
title: virus enrichment approach
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000036
multivalued: false
alias: virus_enrich_appr
owner: MIUVIG
domain_of:
- core
- MIGS virus
- MIUVIG
range: virus_enrich_appr_enum
required: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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: MIUVIG
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
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000053
multivalued: false
alias: tax_ident
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: tax_ident_enum
required: false
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
review of assembly other than reporting of standard assembly statistics. Low
Quality Draft:Many fragments with little to no review of assembly other than
reporting of standard assembly statistics. Assembly statistics include, but
are not limited to total assembly size, number of contigs, contig N50/L50, and
maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
per replicon without gaps or ambiguities, with extensive manual review and editing
to annotate putative gene functions and transcriptional units. High-quality
draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome
or replicon sequence or predicted complete. Genome fragment(s): One or multiple
fragments, totalling < 90% of the expected genome or replicon sequence, or for
which no genome size could be estimated'
title: assembly quality
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: assembly_qual_enum
required: 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: MIUVIG
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: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
annot:
name: annot
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: integer
required: 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: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
trnas:
name: trnas
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000067
multivalued: false
alias: trnas
owner: MIUVIG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: integer
required: false
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000068
multivalued: false
alias: trna_ext_software
owner: MIUVIG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
compl_score:
name: compl_score
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
pattern: ^(high|med|low);(0|([0-9]{1,2})|100)%$
compl_software:
name: compl_software
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: MIUVIG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
compl_appr:
name: compl_appr
description: The approach used to determine the completeness of a given genomic
assembly, which would typically make use of a set of conserved marker genes
or a closely related reference genome. For UViG completeness, include reference
genome or group used, and contig feature suggesting a complete genome
title: completeness approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000071
multivalued: false
alias: compl_appr
owner: MIUVIG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: compl_appr_enum
recommended: true
sort_tech:
name: sort_tech
description: Method used to sort/isolate cells or particles of interest
title: sorting technology
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000075
multivalued: false
alias: sort_tech
owner: MIUVIG
domain_of:
- core
- MISAG
- MIUVIG
range: sort_tech_enum
recommended: true
single_cell_lysis_appr:
name: single_cell_lysis_appr
description: Method used to free DNA from interior of the cell(s) or particle(s)
title: single cell or viral particle lysis approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000076
multivalued: false
alias: single_cell_lysis_appr
owner: MIUVIG
domain_of:
- core
- MISAG
- MIUVIG
range: single_cell_lysis_appr_enum
recommended: true
single_cell_lysis_prot:
name: single_cell_lysis_prot
description: Name of the kit or standard protocol used for cell(s) or particle(s)
lysis
title: single cell or viral particle lysis kit protocol
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000054
multivalued: false
alias: single_cell_lysis_prot
owner: MIUVIG
domain_of:
- core
- MISAG
- MIUVIG
range: string
recommended: true
wga_amp_appr:
name: wga_amp_appr
description: Method used to amplify genomic DNA in preparation for sequencing
title: WGA amplification approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '[pcr based|mda based]'
slot_uri: MIXS:0000055
multivalued: false
alias: wga_amp_appr
owner: MIUVIG
domain_of:
- core
- MISAG
- MIUVIG
range: string
recommended: true
wga_amp_kit:
name: wga_amp_kit
description: Kit used to amplify genomic DNA in preparation for sequencing
title: WGA amplification kit
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000006
multivalued: false
alias: wga_amp_kit
owner: MIUVIG
domain_of:
- core
- MISAG
- MIUVIG
range: string
recommended: true
bin_param:
name: bin_param
description: The parameters that have been applied during the extraction of genomes
from metagenomic datasets
title: binning parameters
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000077
multivalued: false
alias: bin_param
owner: MIUVIG
domain_of:
- core
- MIMAG
- MIUVIG
range: bin_param_enum
recommended: true
bin_software:
name: bin_software
description: Tool(s) used for the extraction of genomes from metagenomic datasets,
where possible include a product ID (PID) of the tool(s) used.
title: binning software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
multivalued: false
alias: bin_software
owner: MIUVIG
domain_of:
- core
- MIMAG
- MIUVIG
range: string
recommended: true
reassembly_bin:
name: reassembly_bin
description: Has an assembly been performed on a genome bin extracted from a metagenomic
assembly?
title: reassembly post binning
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{boolean}'
slot_uri: MIXS:0000079
multivalued: false
alias: reassembly_bin
owner: MIUVIG
domain_of:
- core
- MIMAG
- MIUVIG
range: string
recommended: true
mag_cov_software:
name: mag_cov_software
description: Tool(s) used to determine the genome coverage if coverage is used
as a binning parameter in the extraction of genomes from metagenomic datasets
title: MAG coverage software
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000080
multivalued: false
alias: mag_cov_software
owner: MIUVIG
domain_of:
- core
- MIMAG
- MIUVIG
range: mag_cov_software_enum
required: false
vir_ident_software:
name: vir_ident_software
description: Tool(s) used for the identification of UViG as a viral genome, software
or protocol name including version number, parameters, and cutoffs used
title: viral identification software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000081
multivalued: false
alias: vir_ident_software
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
required: true
pred_genome_type:
name: pred_genome_type
description: Type of genome predicted for the UViG
title: predicted genome type
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000082
multivalued: false
alias: pred_genome_type
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: pred_genome_type_enum
required: true
pred_genome_struc:
name: pred_genome_struc
description: Expected structure of the viral genome
title: predicted genome structure
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000083
multivalued: false
alias: pred_genome_struc
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: pred_genome_struc_enum
required: true
detec_type:
name: detec_type
description: Type of UViG detection
title: detection type
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '[independent sequence (UViG)|provirus (UpViG)]'
slot_uri: MIXS:0000084
multivalued: false
alias: detec_type
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
required: true
otu_class_appr:
name: otu_class_appr
description: Cutoffs and approach used when clustering “species-level” OTUs. Note
that results from standard 95% ANI / 85% AF clustering should be provided alongside
OTUS defined from another set of thresholds, even if the latter are the ones
primarily used during the analysis
title: OTU classification approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}'
slot_uri: MIXS:0000085
multivalued: false
alias: otu_class_appr
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
description: Tool and thresholds used to compare sequences when computing "species-level"
OTUs
title: OTU sequence comparison approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000086
multivalued: false
alias: otu_seq_comp_appr
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
recommended: true
otu_db:
name: otu_db
description: Reference database (i.e. sequences not generated as part of the current
study) used to cluster new genomes in "species-level" OTUs, if any
title: OTU database
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{database};{version}'
slot_uri: MIXS:0000087
multivalued: false
alias: otu_db
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
recommended: true
host_pred_appr:
name: host_pred_appr
description: Tool or approach used for host prediction
title: host prediction approach
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000088
multivalued: false
alias: host_pred_appr
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: host_pred_appr_enum
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
description: For each tool or approach used for host prediction, estimated false
discovery rates should be included, either computed de novo or from the literature
title: host prediction estimated accuracy
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000089
multivalued: false
alias: host_pred_est_acc
owner: MIUVIG
domain_of:
- core
- MIUVIG
range: string
recommended: true
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: MIUVIG
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: MIUVIG
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