Class: Miuvig
Minimum Information About an Uncultivated Virus Genome
URI: MIXS:0010012
Inheritance
- Checklist
- Miuvig
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | direct |
| assembly_qual | 1..1 String |
The assembly quality category is based on sets of criteria outlined for each ... | direct |
| samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... | direct |
| estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing | direct |
| host_disease_stat | 0..1 recommended String |
List of diseases with which the host has been diagnosed; can include multiple... | direct |
| alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | direct |
| host_spec_range | 0..* String |
The range and diversity of host species that an organism is capable of infect... | direct |
| feat_pred | 0..1 recommended String |
Method used to predict UViGs features such as ORFs, integration site, etc | direct |
| compl_software | 0..1 String |
Tools used for completion estimate, i | direct |
| neg_cont_type | 0..1 recommended NEGCONTTYPEENUM |
The substance or equipment used as a negative control in an investigation | direct |
| samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... | direct |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | direct |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | direct |
| tax_class | 0..1 recommended String |
Method used for taxonomic classification, along with reference database used,... | direct |
| specific_host | 0..1 String |
Report the host's taxonomic name and/or NCBI taxonomy ID | direct |
| source_mat_id | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | direct |
| lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project | direct |
| samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample | direct |
| size_frac | 0..1 recommended String |
Filtering pore size used in sample preparation | direct |
| virus_enrich_appr | 1..1 VIRUSENRICHAPPRENUM |
List of approaches used to enrich the sample for viruses, if any | direct |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | direct |
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | direct |
| trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG | direct |
| samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample | direct |
| biotic_relationship | 0..1 BIOTICRELATIONSHIPENUM |
Description of relationship(s) between the subject organism and other organis... | direct |
| annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... | direct |
| sim_search_meth | 0..1 recommended String |
Tool used to compare ORFs with database, along with version and cutoffs used | direct |
| number_contig | 1..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | direct |
| collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... | direct |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | direct |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | direct |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | direct |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | direct |
| lib_layout | 0..1 recommended LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | direct |
| tax_ident | 0..1 TAXIDENTENUM |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | direct |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | direct |
| pathogenicity | 0..1 String |
To what is the entity pathogenic | direct |
| compl_appr | 0..1 recommended COMPLAPPRENUM |
The approach used to determine the completeness of a given genomic assembly, ... | direct |
| samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
| lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library | direct |
| seq_meth | 1..1 String |
Sequencing machine used | direct |
| temp | 0..1 recommended String |
Temperature of the sample at the time of sampling | direct |
| experimental_factor | 0..* recommended String |
Variable aspects of an experiment design that can be used to describe an expe... | direct |
| lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries | direct |
| samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | direct |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | direct |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... | direct |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | direct |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | direct |
| compl_score | 0..1 recommended String |
Completeness score is typically based on either the fraction of markers found... | direct |
| source_uvig | 1..1 String |
Type of dataset from which the UViG was obtained | direct |
| ref_db | 0..1 recommended String |
List of database(s) used for ORF annotation, along with version number and re... | direct |
| trna_ext_software | 0..1 String |
Tools used for tRNA identification | direct |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | direct |
| depth | 0..1 recommended String |
The vertical distance below local surface | direct |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | direct |
| lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... | direct |
| sort_tech | 0..1 recommended SORTTECHENUM |
Method used to sort/isolate cells or particles of interest | direct |
| sc_lysis_approach | 0..1 recommended SCLYSISAPPROACHENUM |
Method used to free DNA from interior of the cell(s) or particle(s) | direct |
| sc_lysis_method | 0..1 recommended String |
Name of the kit or standard protocol used for cell(s) or particle(s) lysis | direct |
| wga_amp_appr | 0..1 recommended WGAAMPAPPRENUM |
Method used to amplify genomic DNA in preparation for sequencing | direct |
| wga_amp_kit | 0..1 recommended String |
Kit used to amplify genomic DNA in preparation for sequencing | direct |
| bin_param | 0..1 recommended BINPARAMENUM |
The parameters that have been applied during the extraction of genomes from m... | direct |
| bin_software | 0..1 recommended String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... | direct |
| reassembly_bin | 0..1 recommended Boolean |
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 | 1..1 String |
Tool(s) used for the identification of UViG as a viral genome, software or pr... | direct |
| pred_genome_type | 1..1 String |
Type of genome predicted for the UViG | direct |
| pred_genome_struc | 1..1 PREDGENOMESTRUCENUM |
Expected structure of the viral genome | direct |
| detec_type | 1..1 String |
Type of UViG detection | direct |
| otu_class_appr | 0..1 recommended String |
Cutoffs and approach used when clustering species-level OTUs | direct |
| otu_seq_comp_appr | 0..1 recommended String |
Tool and thresholds used to compare sequences when computing "species-level" ... | direct |
| otu_db | 0..1 recommended String |
Reference database (i | direct |
| host_pred_appr | 0..1 recommended HOSTPREDAPPRENUM |
Tool or approach used for host prediction | direct |
| host_pred_est_acc | 0..1 recommended String |
For each tool or approach used for host prediction, estimated false discovery... | direct |
| associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | direct |
| sop | 0..* recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | direct |
Mixin Usage
| mixed into | description |
|---|---|
Aliases
- miuvig
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:0010012 |
| native | mixs_6_2_rc:Miuvig |
LinkML Source
Direct
name: Miuvig
description: Minimum Information About an Uncultivated Virus Genome
title: Minimum Information About an Uncultivated Virus Genome
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
aliases:
- miuvig
is_a: Checklist
mixin: true
slots:
- mid
- assembly_qual
- samp_name
- estimated_size
- host_disease_stat
- alt
- host_spec_range
- feat_pred
- compl_software
- neg_cont_type
- samp_mat_process
- elev
- assembly_name
- tax_class
- specific_host
- source_mat_id
- lib_size
- samp_collect_device
- size_frac
- virus_enrich_appr
- adapters
- assembly_software
- trnas
- samp_collect_method
- biotic_relationship
- annot
- sim_search_meth
- number_contig
- collection_date
- geo_loc_name
- ref_biomaterial
- nucl_acid_amp
- samp_taxon_id
- lib_layout
- tax_ident
- env_medium
- pathogenicity
- compl_appr
- samp_size
- lib_reads_seqd
- seq_meth
- temp
- experimental_factor
- lib_vector
- samp_vol_we_dna_ext
- pos_cont_type
- env_local_scale
- env_broad_scale
- nucl_acid_ext
- compl_score
- source_uvig
- ref_db
- trna_ext_software
- lat_lon
- depth
- project_name
- lib_screen
- sort_tech
- sc_lysis_approach
- sc_lysis_method
- 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:
adapters:
name: adapters
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
alt:
name: alt
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
recommended: true
annot:
name: annot
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
assembly_name:
name: assembly_name
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
assembly_qual:
name: assembly_qual
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
required: true
assembly_software:
name: assembly_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: true
bin_param:
name: bin_param
domain_of:
- Mimag
- Miuvig
recommended: true
bin_software:
name: bin_software
domain_of:
- Mimag
- Miuvig
recommended: true
biotic_relationship:
name: biotic_relationship
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
required: false
recommended: false
compl_appr:
name: compl_appr
domain_of:
- Mimag
- Misag
- Miuvig
recommended: true
compl_score:
name: compl_score
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
recommended: true
compl_software:
name: compl_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
depth:
name: depth
examples:
- value: 10 meter
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
recommended: true
detec_type:
name: detec_type
domain_of:
- Miuvig
required: true
elev:
name: elev
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
recommended: true
estimated_size:
name: estimated_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
required: false
recommended: false
experimental_factor:
name: experimental_factor
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
feat_pred:
name: feat_pred
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
host_disease_stat:
name: host_disease_stat
examples:
- value: rabies [DOID:11260]
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
recommended: true
host_pred_appr:
name: host_pred_appr
domain_of:
- Miuvig
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
domain_of:
- Miuvig
recommended: true
host_spec_range:
name: host_spec_range
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
lib_layout:
name: lib_layout
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_screen:
name: lib_screen
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_size:
name: lib_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_vector:
name: lib_vector
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
mag_cov_software:
name: mag_cov_software
domain_of:
- Mimag
- Miuvig
required: false
recommended: false
mid:
name: mid
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
nucl_acid_ext:
name: nucl_acid_ext
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
number_contig:
name: number_contig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: true
otu_class_appr:
name: otu_class_appr
domain_of:
- Miuvig
recommended: true
otu_db:
name: otu_db
domain_of:
- Miuvig
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
domain_of:
- Miuvig
recommended: true
pathogenicity:
name: pathogenicity
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
pred_genome_struc:
name: pred_genome_struc
domain_of:
- Miuvig
required: true
pred_genome_type:
name: pred_genome_type
domain_of:
- Miuvig
required: true
reassembly_bin:
name: reassembly_bin
domain_of:
- Mimag
- Miuvig
recommended: true
ref_biomaterial:
name: ref_biomaterial
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
ref_db:
name: ref_db
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
samp_collect_device:
name: samp_collect_device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_collect_method:
name: samp_collect_method
examples:
- value: swabbing
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_mat_process:
name: samp_mat_process
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
samp_size:
name: samp_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
required: false
recommended: false
sc_lysis_approach:
name: sc_lysis_approach
domain_of:
- Misag
- Miuvig
recommended: true
sc_lysis_method:
name: sc_lysis_method
domain_of:
- Misag
- Miuvig
recommended: true
sim_search_meth:
name: sim_search_meth
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
size_frac:
name: size_frac
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
recommended: true
sop:
name: sop
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
sort_tech:
name: sort_tech
domain_of:
- Misag
- Miuvig
recommended: true
source_mat_id:
name: source_mat_id
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
recommended: true
source_uvig:
name: source_uvig
domain_of:
- Miuvig
required: true
specific_host:
name: specific_host
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
tax_class:
name: tax_class
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
tax_ident:
name: tax_ident
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
temp:
name: temp
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
recommended: true
trna_ext_software:
name: trna_ext_software
domain_of:
- Mimag
- Misag
- Miuvig
required: false
recommended: false
trnas:
name: trnas
domain_of:
- Mimag
- Misag
- Miuvig
required: false
recommended: false
vir_ident_software:
name: vir_ident_software
domain_of:
- Miuvig
required: true
virus_enrich_appr:
name: virus_enrich_appr
domain_of:
- MigsVi
- Miuvig
required: true
wga_amp_appr:
name: wga_amp_appr
domain_of:
- Misag
- Miuvig
recommended: true
wga_amp_kit:
name: wga_amp_kit
domain_of:
- Misag
- Miuvig
recommended: true
class_uri: MIXS:0010012
Induced
name: Miuvig
description: Minimum Information About an Uncultivated Virus Genome
title: Minimum Information About an Uncultivated Virus Genome
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
aliases:
- miuvig
is_a: Checklist
mixin: true
slot_usage:
adapters:
name: adapters
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
alt:
name: alt
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
recommended: true
annot:
name: annot
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
assembly_name:
name: assembly_name
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
assembly_qual:
name: assembly_qual
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
required: true
assembly_software:
name: assembly_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: true
bin_param:
name: bin_param
domain_of:
- Mimag
- Miuvig
recommended: true
bin_software:
name: bin_software
domain_of:
- Mimag
- Miuvig
recommended: true
biotic_relationship:
name: biotic_relationship
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
required: false
recommended: false
compl_appr:
name: compl_appr
domain_of:
- Mimag
- Misag
- Miuvig
recommended: true
compl_score:
name: compl_score
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
recommended: true
compl_software:
name: compl_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
depth:
name: depth
examples:
- value: 10 meter
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
recommended: true
detec_type:
name: detec_type
domain_of:
- Miuvig
required: true
elev:
name: elev
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
recommended: true
estimated_size:
name: estimated_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
required: false
recommended: false
experimental_factor:
name: experimental_factor
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
feat_pred:
name: feat_pred
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
host_disease_stat:
name: host_disease_stat
examples:
- value: rabies [DOID:11260]
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
recommended: true
host_pred_appr:
name: host_pred_appr
domain_of:
- Miuvig
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
domain_of:
- Miuvig
recommended: true
host_spec_range:
name: host_spec_range
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
lib_layout:
name: lib_layout
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_screen:
name: lib_screen
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_size:
name: lib_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
lib_vector:
name: lib_vector
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
mag_cov_software:
name: mag_cov_software
domain_of:
- Mimag
- Miuvig
required: false
recommended: false
mid:
name: mid
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
nucl_acid_ext:
name: nucl_acid_ext
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
number_contig:
name: number_contig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: true
otu_class_appr:
name: otu_class_appr
domain_of:
- Miuvig
recommended: true
otu_db:
name: otu_db
domain_of:
- Miuvig
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
domain_of:
- Miuvig
recommended: true
pathogenicity:
name: pathogenicity
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
pred_genome_struc:
name: pred_genome_struc
domain_of:
- Miuvig
required: true
pred_genome_type:
name: pred_genome_type
domain_of:
- Miuvig
required: true
reassembly_bin:
name: reassembly_bin
domain_of:
- Mimag
- Miuvig
recommended: true
ref_biomaterial:
name: ref_biomaterial
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
ref_db:
name: ref_db
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
samp_collect_device:
name: samp_collect_device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_collect_method:
name: samp_collect_method
examples:
- value: swabbing
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_mat_process:
name: samp_mat_process
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
samp_size:
name: samp_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
required: false
recommended: false
sc_lysis_approach:
name: sc_lysis_approach
domain_of:
- Misag
- Miuvig
recommended: true
sc_lysis_method:
name: sc_lysis_method
domain_of:
- Misag
- Miuvig
recommended: true
sim_search_meth:
name: sim_search_meth
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
size_frac:
name: size_frac
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
recommended: true
sop:
name: sop
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
recommended: true
sort_tech:
name: sort_tech
domain_of:
- Misag
- Miuvig
recommended: true
source_mat_id:
name: source_mat_id
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
recommended: true
source_uvig:
name: source_uvig
domain_of:
- Miuvig
required: true
specific_host:
name: specific_host
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
required: false
recommended: false
tax_class:
name: tax_class
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
recommended: true
tax_ident:
name: tax_ident
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
temp:
name: temp
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
recommended: true
trna_ext_software:
name: trna_ext_software
domain_of:
- Mimag
- Misag
- Miuvig
required: false
recommended: false
trnas:
name: trnas
domain_of:
- Mimag
- Misag
- Miuvig
required: false
recommended: false
vir_ident_software:
name: vir_ident_software
domain_of:
- Miuvig
required: true
virus_enrich_appr:
name: virus_enrich_appr
domain_of:
- MigsVi
- Miuvig
required: true
wga_amp_appr:
name: wga_amp_appr
domain_of:
- Misag
- Miuvig
recommended: true
wga_amp_kit:
name: wga_amp_kit
domain_of:
- Misag
- Miuvig
recommended: true
attributes:
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000047
multivalued: false
alias: mid
owner: Miuvig
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^[ACGTRKSYMWBHDVN]+$
structured_pattern:
syntax: ^{ambiguous_nucleotides}$
interpolated: true
partial_match: true
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
review of assembly other than reporting of standard assembly statistics. Low
Quality Draft:Many fragments with little to no review of assembly other than
reporting of standard assembly statistics. Assembly statistics include, but
are not limited to total assembly size, number of contigs, contig N50/L50, and
maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
per replicon without gaps or ambiguities, with extensive manual review and editing
to annotate putative gene functions and transcriptional units. High-quality
draft genome: One or multiple fragments, totaling 90% of the expected genome
or replicon sequence or predicted complete. Genome fragment(s): One or multiple
fragments, totalling < 90% of the expected genome or replicon sequence, or for
which no genome size could be estimated'
title: assembly quality
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
draft genome|Low-quality draft genome|Genome fragment(s)]'
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
multivalued: false
alias: estimated_size
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
required: false
recommended: false
host_disease_stat:
name: host_disease_stat
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: rabies [DOID:11260]
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
multivalued: false
alias: host_disease_stat
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
recommended: true
alt:
name: alt
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- HostAssociated
- MiscellaneousNaturalOrArtificialEnvironment
- SymbiontAssociated
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{integer}'
slot_uri: MIXS:0000030
multivalued: true
alias: host_spec_range
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: false
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
compl_software:
name: compl_software
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NEG_CONT_TYPE_ENUM
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
elev:
name: elev
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
assembly_name:
name: assembly_name
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
specific_host:
name: specific_host
description: Report the host's taxonomic name and/or NCBI taxonomy ID
title: host scientific name
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
multivalued: false
alias: specific_host
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: true
alias: source_mat_id
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
samp_collect_device:
name: samp_collect_device
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collect_device
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
size_frac:
name: size_frac
description: Filtering pore size used in sample preparation
title: size fraction selected
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: Miuvig
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000036
alias: virus_enrich_appr
owner: Miuvig
domain_of:
- MigsVi
- Miuvig
range: VIRUS_ENRICH_APPR_ENUM
required: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
trnas:
name: trnas
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{integer}'
slot_uri: MIXS:0000067
multivalued: false
alias: trnas
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collect_method
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000028
multivalued: false
alias: biotic_relationship
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BIOTIC_RELATIONSHIP_ENUM
required: false
recommended: false
annot:
name: annot
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
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
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
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)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
recommended: true
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000053
alias: tax_ident
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TAX_IDENT_ENUM
required: false
recommended: false
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
pathogenicity:
name: pathogenicity
description: To what is the entity pathogenic
title: known pathogenicity
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000027
multivalued: false
alias: pathogenicity
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000071
alias: compl_appr
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: COMPL_APPR_ENUM
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
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
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
temp:
name: temp
description: Temperature of the sample at the time of sampling
title: temperature
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
experimental_factor:
name: experimental_factor
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
multivalued: true
alias: experimental_factor
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
lib_vector:
name: lib_vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: 'Report the entity or entities which are in the sample or specimen
s local vicinity and which you believe have significant causal influences on
your sample or specimen. We recommend using EnvO terms which are of smaller
spatial grain than your entry for env_broad_scale. Terms, such as anatomical
sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
UBERON) are accepted in this field. EnvO documentation about how to use the
field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
compl_score:
name: compl_score
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
recommended: true
source_uvig:
name: source_uvig
description: Type of dataset from which the UViG was obtained
title: source of UViGs
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome
(virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral
fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial
single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial
genome|other]'
slot_uri: MIXS:0000035
multivalued: false
alias: source_uvig
owner: Miuvig
domain_of:
- Miuvig
range: string
required: true
ref_db:
name: ref_db
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000068
multivalued: false
alias: trna_ext_software
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
annotations:
Expected_value:
tag: Expected_value
value: decimal degrees, limit to 8 decimal points
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
depth:
name: depth
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
lib_screen:
name: lib_screen
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sort_tech:
name: sort_tech
description: Method used to sort/isolate cells or particles of interest
title: sorting technology
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000075
multivalued: false
alias: sort_tech
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: SORT_TECH_ENUM
recommended: true
sc_lysis_approach:
name: sc_lysis_approach
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000076
multivalued: false
alias: sc_lysis_approach
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: SC_LYSIS_APPROACH_ENUM
recommended: true
sc_lysis_method:
name: sc_lysis_method
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000054
multivalued: false
alias: sc_lysis_method
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000055
multivalued: false
alias: wga_amp_appr
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: WGA_AMP_APPR_ENUM
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{text}'
slot_uri: MIXS:0000006
multivalued: false
alias: wga_amp_kit
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000077
alias: bin_param
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
multivalued: false
alias: bin_software
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000079
multivalued: false
alias: reassembly_bin
owner: Miuvig
domain_of:
- Mimag
- Miuvig
range: boolean
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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000080
multivalued: false
alias: mag_cov_software
owner: Miuvig
domain_of:
- Mimag
- Miuvig
range: MAG_COV_SOFTWARE_ENUM
required: false
recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000081
multivalued: false
alias: vir_ident_software
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]'
slot_uri: MIXS:0000082
multivalued: false
alias: pred_genome_type
owner: Miuvig
domain_of:
- Miuvig
range: string
required: true
pred_genome_struc:
name: pred_genome_struc
description: Expected structure of the viral genome
title: predicted genome structure
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000083
multivalued: false
alias: pred_genome_struc
owner: Miuvig
domain_of:
- Miuvig
range: PRED_GENOME_STRUC_ENUM
required: true
detec_type:
name: detec_type
description: Type of UViG detection
title: detection type
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '[independent sequence (UViG)|provirus (UpViG)]'
slot_uri: MIXS:0000084
multivalued: false
alias: detec_type
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}'
slot_uri: MIXS:0000085
multivalued: false
alias: otu_class_appr
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000086
multivalued: false
alias: otu_seq_comp_appr
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{database};{version}'
slot_uri: MIXS:0000087
multivalued: false
alias: otu_db
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000088
multivalued: false
alias: host_pred_appr
owner: Miuvig
domain_of:
- 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000089
multivalued: false
alias: host_pred_est_acc
owner: Miuvig
domain_of:
- Miuvig
range: string
recommended: true
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
multivalued: true
alias: associated_resource
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sop:
name: sop
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: true
alias: sop
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
class_uri: MIXS:0010012