Checklist: Minimum Information About an Uncultivated Virus Genome (Miuvig)
Minimum Information About an Uncultivated Virus Genome
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:0000017 | size_frac | 0..1 recommended String |
Filtering pore size used in sample preparation |
| MIXS:0000043 | lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... |
| MIXS:0000035 | source_uvig | 1 String |
Type of dataset from which the UViG was obtained |
| MIXS:0000062 | ref_db | 0..1 recommended String |
List of database(s) used for ORF annotation, along with version number and re... |
| MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000039 | lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project |
| MIXS:0000047 | mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... |
| MIXS:0000057 | assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... |
| MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000069 | compl_score | 0..1 recommended String |
Completeness score is typically based on either the fraction of markers found... |
| MIXS:0000067 | trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG |
| MIXS:0000037 | nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000001 | samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
| MIXS:0000024 | estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing |
| MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:0000027 | pathogenicity | 0..1 String |
To what is the entity pathogenic |
| MIXS:0000040 | lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library |
| MIXS:0000002 | samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample |
| MIXS:0000060 | number_contig | 1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| MIXS:0000028 | biotic_relationship | 0..1 BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... |
| MIXS:0000068 | trna_ext_software | 0..1 String |
Tools used for tRNA identification |
| MIXS:0000041 | lib_layout | 0..1 recommended LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads |
| MIXS:0000056 | assembly_qual | 1 AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... |
| MIXS:0000025 | ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... |
| MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
| MIXS:0000042 | lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries |
| MIXS:0000030 | host_spec_range | * String |
The range and diversity of host species that an organism is capable of infect... |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0000036 | virus_enrich_appr | 1 VirusEnrichApprEnum |
List of approaches used to enrich the sample for viruses, if any |
| MIXS:0000048 | adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... |
| MIXS:0000058 | assembly_software | 1 String |
Tool(s) used for assembly, including version number and parameters |
| MIXS:0000053 | tax_ident | 0..1 TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG |
| MIXS:0000059 | annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000061 | feat_pred | 0..1 recommended String |
Method used to predict UViGs features such as ORFs, integration site, etc |
| MIXS:0000070 | compl_software | 0..1 String |
Tools used for completion estimate, i |
| MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000016 | samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000063 | sim_search_meth | 0..1 recommended String |
Tool used to compare ORFs with database, along with version and cutoffs used |
| MIXS:0000031 | host_disease_stat | 0..1 recommended String |
List of diseases with which the host has been diagnosed; can include multiple... |
| MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
| MIXS:0001225 | samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample |
| MIXS:0000071 | compl_appr | 0..1 recommended ComplApprEnum |
The approach used to determine the completeness of a given genomic assembly, ... |
| MIXS:0000029 | specific_host | 0..1 String |
Report the host's taxonomic name and/or NCBI taxonomy ID |
| MIXS:0000014 | env_medium | 1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
| MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
| MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
| MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
| MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000064 | tax_class | 0..1 recommended String |
Method used for taxonomic classification, along with reference database used,... |
| MIXS:0000008 | experimental_factor | * recommended String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000075 | sort_tech | 0..1 recommended SortTechEnum |
Method used to sort/isolate cells or particles of interest |
| MIXS:0000076 | sc_lysis_approach | 0..1 recommended ScLysisApproachEnum |
Method used to free DNA from interior of the cell(s) or particle(s) |
| MIXS:0000054 | sc_lysis_method | 0..1 recommended String |
Name of the kit or standard protocol used for cell(s) or particle(s) lysis |
| MIXS:0000055 | wga_amp_appr | 0..1 recommended WgaAmpApprEnum |
Method used to amplify genomic DNA in preparation for sequencing |
| MIXS:0000006 | wga_amp_kit | 0..1 recommended String |
Kit used to amplify genomic DNA in preparation for sequencing |
| MIXS:0000077 | bin_param | 0..1 recommended BinParamEnum |
The parameters that have been applied during the extraction of genomes from m... |
| MIXS:0000078 | bin_software | 0..1 recommended String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... |
| MIXS:0000079 | reassembly_bin | 0..1 recommended Boolean |
Has an assembly been performed on a genome bin extracted from a metagenomic a... |
| MIXS:0000080 | mag_cov_software | 0..1 MagCovSoftwareEnum |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... |
| MIXS:0000081 | vir_ident_software | 1 String |
Tool(s) used for the identification of UViG as a viral genome, software or pr... |
| MIXS:0000082 | pred_genome_type | 1 String |
Type of genome predicted for the UViG |
| MIXS:0000083 | pred_genome_struc | 1 PredGenomeStrucEnum |
Expected structure of the viral genome |
| MIXS:0000084 | detec_type | 1 String |
Type of UViG detection |
| MIXS:0000085 | otu_class_appr | 0..1 recommended String |
Cutoffs and approach used when clustering species-level OTUs |
| MIXS:0000086 | otu_seq_comp_appr | 0..1 recommended String |
Tool and thresholds used to compare sequences when computing "species-level" ... |
| MIXS:0000087 | otu_db | 0..1 recommended String |
Reference database (i |
| MIXS:0000088 | host_pred_appr | 0..1 recommended HostPredApprEnum |
Tool or approach used for host prediction |
| MIXS:0000089 | host_pred_est_acc | 0..1 recommended String |
For each tool or approach used for host prediction, estimated false discovery... |
| MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
Aliases
- 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
aliases:
- miuvig
is_a: Checklist
mixin: true
slots:
- samp_name
- size_frac
- lib_screen
- source_uvig
- ref_db
- nucl_acid_amp
- lib_size
- mid
- assembly_name
- temp
- compl_score
- trnas
- nucl_acid_ext
- samp_size
- alt
- estimated_size
- source_mat_id
- samp_vol_we_dna_ext
- pathogenicity
- lib_reads_seqd
- samp_collect_device
- number_contig
- biotic_relationship
- trna_ext_software
- lib_layout
- assembly_qual
- ref_biomaterial
- project_name
- lib_vector
- host_spec_range
- neg_cont_type
- virus_enrich_appr
- adapters
- assembly_software
- tax_ident
- annot
- pos_cont_type
- feat_pred
- compl_software
- env_local_scale
- samp_mat_process
- sim_search_meth
- host_disease_stat
- depth
- samp_collect_method
- compl_appr
- specific_host
- env_medium
- samp_taxon_id
- geo_loc_name
- collection_date
- seq_meth
- lat_lon
- elev
- env_broad_scale
- tax_class
- experimental_factor
- 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
recommended: true
alt:
name: alt
recommended: true
assembly_name:
name: assembly_name
recommended: true
assembly_qual:
name: assembly_qual
required: true
assembly_software:
name: assembly_software
required: true
bin_param:
name: bin_param
recommended: true
bin_software:
name: bin_software
recommended: true
compl_appr:
name: compl_appr
recommended: true
compl_score:
name: compl_score
recommended: true
depth:
name: depth
examples:
- value: 10 meter
recommended: true
detec_type:
name: detec_type
required: true
elev:
name: elev
recommended: true
experimental_factor:
name: experimental_factor
recommended: true
feat_pred:
name: feat_pred
recommended: true
host_disease_stat:
name: host_disease_stat
examples:
- value: rabies [DOID:11260]
recommended: true
host_pred_appr:
name: host_pred_appr
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
recommended: true
lib_layout:
name: lib_layout
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
recommended: true
lib_screen:
name: lib_screen
recommended: true
lib_size:
name: lib_size
recommended: true
lib_vector:
name: lib_vector
recommended: true
mid:
name: mid
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
recommended: true
nucl_acid_ext:
name: nucl_acid_ext
recommended: true
number_contig:
name: number_contig
required: true
otu_class_appr:
name: otu_class_appr
recommended: true
otu_db:
name: otu_db
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
recommended: true
pred_genome_struc:
name: pred_genome_struc
required: true
pred_genome_type:
name: pred_genome_type
required: true
reassembly_bin:
name: reassembly_bin
recommended: true
ref_db:
name: ref_db
recommended: true
samp_collect_device:
name: samp_collect_device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
recommended: true
samp_collect_method:
name: samp_collect_method
examples:
- value: swabbing
recommended: true
samp_mat_process:
name: samp_mat_process
recommended: true
samp_size:
name: samp_size
recommended: true
sc_lysis_approach:
name: sc_lysis_approach
recommended: true
sc_lysis_method:
name: sc_lysis_method
recommended: true
sim_search_meth:
name: sim_search_meth
recommended: true
size_frac:
name: size_frac
recommended: true
sop:
name: sop
recommended: true
sort_tech:
name: sort_tech
recommended: true
source_mat_id:
name: source_mat_id
recommended: true
source_uvig:
name: source_uvig
required: true
tax_class:
name: tax_class
recommended: true
temp:
name: temp
recommended: true
vir_ident_software:
name: vir_ident_software
required: true
virus_enrich_appr:
name: virus_enrich_appr
required: true
wga_amp_appr:
name: wga_amp_appr
recommended: true
wga_amp_kit:
name: wga_amp_kit
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
aliases:
- miuvig
is_a: Checklist
mixin: true
slot_usage:
adapters:
name: adapters
recommended: true
alt:
name: alt
recommended: true
assembly_name:
name: assembly_name
recommended: true
assembly_qual:
name: assembly_qual
required: true
assembly_software:
name: assembly_software
required: true
bin_param:
name: bin_param
recommended: true
bin_software:
name: bin_software
recommended: true
compl_appr:
name: compl_appr
recommended: true
compl_score:
name: compl_score
recommended: true
depth:
name: depth
examples:
- value: 10 meter
recommended: true
detec_type:
name: detec_type
required: true
elev:
name: elev
recommended: true
experimental_factor:
name: experimental_factor
recommended: true
feat_pred:
name: feat_pred
recommended: true
host_disease_stat:
name: host_disease_stat
examples:
- value: rabies [DOID:11260]
recommended: true
host_pred_appr:
name: host_pred_appr
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
recommended: true
lib_layout:
name: lib_layout
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
recommended: true
lib_screen:
name: lib_screen
recommended: true
lib_size:
name: lib_size
recommended: true
lib_vector:
name: lib_vector
recommended: true
mid:
name: mid
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
recommended: true
nucl_acid_ext:
name: nucl_acid_ext
recommended: true
number_contig:
name: number_contig
required: true
otu_class_appr:
name: otu_class_appr
recommended: true
otu_db:
name: otu_db
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
recommended: true
pred_genome_struc:
name: pred_genome_struc
required: true
pred_genome_type:
name: pred_genome_type
required: true
reassembly_bin:
name: reassembly_bin
recommended: true
ref_db:
name: ref_db
recommended: true
samp_collect_device:
name: samp_collect_device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
recommended: true
samp_collect_method:
name: samp_collect_method
examples:
- value: swabbing
recommended: true
samp_mat_process:
name: samp_mat_process
recommended: true
samp_size:
name: samp_size
recommended: true
sc_lysis_approach:
name: sc_lysis_approach
recommended: true
sc_lysis_method:
name: sc_lysis_method
recommended: true
sim_search_meth:
name: sim_search_meth
recommended: true
size_frac:
name: size_frac
recommended: true
sop:
name: sop
recommended: true
sort_tech:
name: sort_tech
recommended: true
source_mat_id:
name: source_mat_id
recommended: true
source_uvig:
name: source_uvig
required: true
tax_class:
name: tax_class
recommended: true
temp:
name: temp
recommended: true
vir_ident_software:
name: vir_ident_software
required: true
virus_enrich_appr:
name: virus_enrich_appr
required: true
wga_amp_appr:
name: wga_amp_appr
recommended: true
wga_amp_kit:
name: wga_amp_kit
recommended: true
attributes:
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001107
alias: samp_name
owner: 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
size_frac:
name: size_frac
annotations:
Expected_value:
tag: Expected_value
value: filter size value range
description: Filtering pore size used in sample preparation
title: size fraction selected
examples:
- value: 0-0.22 micrometer
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- fraction
- size
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
alias: size_frac
owner: Miuvig
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
lib_screen:
name: lib_screen
annotations:
Expected_value:
tag: Expected_value
value: screening strategy name
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
examples:
- value: enriched, screened, normalized
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000043
alias: lib_screen
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
source_uvig:
name: source_uvig
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of dataset from which the UViG was obtained
title: source of UViGs
examples:
- value: viral fraction metagenome (virome)
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- source
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
alias: source_uvig
owner: Miuvig
domain_of:
- Miuvig
range: string
required: true
ref_db:
name: ref_db
annotations:
Expected_value:
tag: Expected_value
value: names, versions, and references of databases
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
examples:
- value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
doi:10.1093/nar/gkw975
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
alias: ref_db
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- 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
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: 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
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
examples:
- value: '50'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
- size
slot_uri: MIXS:0000039
alias: lib_size
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
examples:
- value: GTGAATAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
slot_uri: MIXS:0000047
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_name:
name: assembly_name
annotations:
Expected_value:
tag: Expected_value
value: name and version of assembly
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
examples:
- value: HuRef, JCVI_ISG_i3_1.0
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
alias: assembly_name
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- temperature
slot_uri: MIXS:0000113
alias: temp
owner: 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
compl_score:
name: compl_score
annotations:
Expected_value:
tag: Expected_value
value: quality;percent completeness
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
examples:
- value: med;60%
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- score
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
alias: compl_score
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
recommended: true
trnas:
name: trnas
annotations:
Expected_value:
tag: Expected_value
value: value from 0-21
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
examples:
- value: '18'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
string_serialization: '{integer}'
slot_uri: MIXS:0000067
alias: trnas
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: string
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: 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
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- sample
- size
slot_uri: MIXS:0000001
alias: samp_size
owner: 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
alt:
name: alt
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000094
alias: alt
owner: 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
estimated_size:
name: estimated_size
annotations:
Expected_value:
tag: Expected_value
value: number of base pairs
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
examples:
- value: 300000 bp
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- size
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
alias: estimated_size
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
source_mat_id:
name: source_mat_id
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2)
title: source material identifiers
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
alias: source_mat_id
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
multivalued: true
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
alias: samp_vol_we_dna_ext
owner: 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
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
pathogenicity:
name: pathogenicity
annotations:
Expected_value:
tag: Expected_value
value: names of organisms that the entity is pathogenic to
description: To what is the entity pathogenic
title: known pathogenicity
examples:
- value: human, animal, plant, fungi, bacteria
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000027
alias: pathogenicity
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
range: string
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
examples:
- value: '20'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000040
alias: lib_reads_seqd
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
annotations:
Expected_value:
tag: Expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
examples:
- value: '40'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
slot_uri: MIXS:0000060
alias: number_contig
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: 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
examples:
- value: free living
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- observed
- relationship
slot_uri: MIXS:0000028
alias: biotic_relationship
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BioticRelationshipEnum
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
examples:
- value: infernal;v2;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000068
alias: trna_ext_software
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: string
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
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
examples:
- value: paired
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000041
alias: lib_layout
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LibLayoutEnum
recommended: true
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
it is a eukaryotic or prokaryotic genome, respectively. 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
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000056
alias: assembly_qual
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: AssemblyQualEnum
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000025
alias: ref_biomaterial
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- project
slot_uri: MIXS:0000092
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_vector:
name: lib_vector
annotations:
Expected_value:
tag: Expected_value
value: vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
examples:
- value: Bacteriophage P1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000042
alias: lib_vector
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
host_spec_range:
name: host_spec_range
annotations:
Expected_value:
tag: Expected_value
value: NCBI taxid
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
examples:
- value: '9606'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- range
string_serialization: '{integer}'
slot_uri: MIXS:0000030
alias: host_spec_range
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
multivalued: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
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
examples:
- value: filtration
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: FeCl Precipitation
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: ultracentrifugation
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
- value: DNAse
description: was filtration + FeCl Precipitation + ultracentrifugation + DNAse
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- enrichment
slot_uri: MIXS:0000036
alias: virus_enrich_appr
owner: Miuvig
domain_of:
- MigsVi
- Miuvig
range: VirusEnrichApprEnum
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
examples:
- value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000048
alias: adapters
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
structured_pattern:
syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
interpolated: true
partial_match: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
examples:
- value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000058
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
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
examples:
- value: other
description: was other <colon> rpoB gene
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
- marker
- taxon
slot_uri: MIXS:0000053
alias: tax_ident
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TaxIdentEnum
annot:
name: annot
annotations:
Expected_value:
tag: Expected_value
value: name of tool or pipeline used, or annotation source description
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
examples:
- value: prokka
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000059
alias: annot
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
examples:
- value: Prodigal;2.6.3;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- feature
- predict
slot_uri: MIXS:0000061
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
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
examples:
- value: checkm
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
alias: compl_software
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: 'Report the entity or entities which are in the sample or specimen
s local vicinity and which you believe have significant causal influences on
your sample or specimen. We recommend using EnvO terms which are of smaller
spatial grain than your entry for env_broad_scale. Terms, such as anatomical
sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
UBERON) are accepted in this field. EnvO documentation about how to use the
field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000013
alias: env_local_scale
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000063
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
host_disease_stat:
name: host_disease_stat
annotations:
Expected_value:
tag: Expected_value
value: disease name or Disease Ontology term
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]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- disease
- host
- host.
- status
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
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
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- depth
slot_uri: MIXS:0000018
alias: depth
owner: 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
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- method
- sample
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: 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
compl_appr:
name: compl_appr
annotations:
Expected_value:
tag: Expected_value
value: text
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
examples:
- value: other
description: was other <colon> UViG length compared to the average length of
reference genomes from the P22virus genus (NCBI RefSeq v83)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000071
alias: compl_appr
owner: Miuvig
domain_of:
- Mimag
- Misag
- Miuvig
range: ComplApprEnum
recommended: true
specific_host:
name: specific_host
annotations:
Expected_value:
tag: Expected_value
value: host scientific name, taxonomy ID
description: Report the host's taxonomic name and/or NCBI taxonomy ID
title: host scientific name
examples:
- value: Homo sapiens and/or 9606
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
alias: specific_host
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- environmental
slot_uri: MIXS:0000014
alias: env_medium
owner: 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
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: 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
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: 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
collection_date:
name: collection_date
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- date
slot_uri: MIXS:0000011
alias: collection_date
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000050
alias: seq_meth
owner: 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
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000009
alias: lat_lon
owner: 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
elev:
name: elev
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- elevation
slot_uri: MIXS:0000093
alias: elev
owner: 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
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: 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
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
examples:
- value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
default parameters)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- taxon
slot_uri: MIXS:0000064
alias: tax_class
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
sort_tech:
name: sort_tech
description: Method used to sort/isolate cells or particles of interest
title: sorting technology
examples:
- value: optical manipulation
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000075
alias: sort_tech
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: SortTechEnum
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
examples:
- value: enzymatic
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- particle
- single
slot_uri: MIXS:0000076
alias: sc_lysis_approach
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: ScLysisApproachEnum
recommended: true
sc_lysis_method:
name: sc_lysis_method
annotations:
Expected_value:
tag: Expected_value
value: kit, protocol name
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
examples:
- value: ambion single cell lysis kit
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- kit
- particle
- protocol
- single
slot_uri: MIXS:0000054
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
examples:
- value: mda based
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000055
alias: wga_amp_appr
owner: Miuvig
domain_of:
- Misag
- Miuvig
range: WgaAmpApprEnum
recommended: true
wga_amp_kit:
name: wga_amp_kit
annotations:
Expected_value:
tag: Expected_value
value: kit name
description: Kit used to amplify genomic DNA in preparation for sequencing
title: WGA amplification kit
examples:
- value: qiagen repli-g
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- kit
slot_uri: MIXS:0000006
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
examples:
- value: coverage
description: was 'coverage and kmer'
- value: kmer
description: was coverage and kmer
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- parameter
slot_uri: MIXS:0000077
alias: bin_param
owner: Miuvig
domain_of:
- Mimag
- Miuvig
range: BinParamEnum
recommended: true
bin_software:
name: bin_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
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
examples:
- value: MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
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
examples:
- value: 'no'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- post
slot_uri: MIXS:0000079
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
examples:
- value: bbmap
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000080
alias: mag_cov_software
owner: Miuvig
domain_of:
- Mimag
- Miuvig
range: MagCovSoftwareEnum
vir_ident_software:
name: vir_ident_software
annotations:
Expected_value:
tag: Expected_value
value: software name, version and relevant parameters
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
examples:
- value: VirSorter; 1.0.4; Virome database, category 2
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- identifier
- software
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000081
alias: vir_ident_software
owner: Miuvig
domain_of:
- Miuvig
range: string
required: true
pred_genome_type:
name: pred_genome_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of genome predicted for the UViG
title: predicted genome type
examples:
- value: dsDNA
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- predict
- type
string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]'
slot_uri: MIXS:0000082
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
examples:
- value: non-segmented
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- predict
slot_uri: MIXS:0000083
alias: pred_genome_struc
owner: Miuvig
domain_of:
- Miuvig
range: PredGenomeStrucEnum
required: true
detec_type:
name: detec_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Type of UViG detection
title: detection type
examples:
- value: independent sequence (UViG)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- type
string_serialization: '[independent sequence (UViG)|provirus (UpViG)]'
slot_uri: MIXS:0000084
alias: detec_type
owner: Miuvig
domain_of:
- Miuvig
range: string
required: true
otu_class_appr:
name: otu_class_appr
annotations:
Expected_value:
tag: Expected_value
value: cutoffs and method used
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
examples:
- value: 95% ANI;85% AF; greedy incremental clustering
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- otu
string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}'
slot_uri: MIXS:0000085
alias: otu_class_appr
owner: Miuvig
domain_of:
- Miuvig
range: string
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
annotations:
Expected_value:
tag: Expected_value
value: software name, version and relevant parameters
description: Tool and thresholds used to compare sequences when computing "species-level"
OTUs
title: OTU sequence comparison approach
examples:
- value: 'blastn;2.6.0+;e-value cutoff: 0.001'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- otu
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000086
alias: otu_seq_comp_appr
owner: Miuvig
domain_of:
- Miuvig
range: string
recommended: true
otu_db:
name: otu_db
annotations:
Expected_value:
tag: Expected_value
value: database and version
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
examples:
- value: NCBI Viral RefSeq;83
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
- otu
string_serialization: '{database};{version}'
slot_uri: MIXS:0000087
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
examples:
- value: CRISPR spacer match
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- predict
slot_uri: MIXS:0000088
alias: host_pred_appr
owner: Miuvig
domain_of:
- Miuvig
range: HostPredApprEnum
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
examples:
- value: 'CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host
genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- predict
slot_uri: MIXS:0000089
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
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
alias: associated_resource
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- procedures
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
alias: sop
owner: Miuvig
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
class_uri: MIXS:0010012