Class: MigsOrg
Minimal Information about a Genome Sequence: organelle
URI: MIXS:0010006
Inheritance
- Checklist
- MigsOrg
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| assembly_qual | 0..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 |
| alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | direct |
| isol_growth_condt | 1..1 String |
Publication reference in the form of pubmed ID (pmid), digital object identif... | direct |
| feat_pred | 0..1 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 |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | direct |
| samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... | 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 String |
Method used for taxonomic classification, along with reference database used,... | 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 Integer |
Total number of clones in the library prepared for the project | direct |
| samp_collect_device | 0..1 String |
The device used to collect an environmental sample | direct |
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | direct |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | direct |
| samp_collect_method | 0..1 String |
The method employed for collecting the sample | direct |
| annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... | direct |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | direct |
| number_contig | 0..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 LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | direct |
| tax_ident | 0..1 recommended TAXIDENTENUM |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | direct |
| extrachrom_elements | 0..1 recommended Integer |
Do plasmids exist of significant phenotypic consequence (e | direct |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | direct |
| samp_size | 0..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | direct |
| subspecf_gen_lin | 0..1 recommended String |
Information about the genetic distinctness of the sequenced organism below th... | direct |
| lib_reads_seqd | 0..1 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..* String |
Variable aspects of an experiment design that can be used to describe an expe... | direct |
| lib_vector | 0..1 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 String |
Completeness score is typically based on either the fraction of markers found... | direct |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | 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 String |
Specific enrichment or screening methods applied before and/or after creating... | 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
- migs_org
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:0010006 |
| native | mixs_6_2_rc:MigsOrg |
LinkML Source
Direct
name: MigsOrg
description: 'Minimal Information about a Genome Sequence: organelle'
title: MIGS org
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
aliases:
- migs_org
is_a: Checklist
mixin: true
slots:
- assembly_qual
- samp_name
- estimated_size
- alt
- isol_growth_condt
- feat_pred
- compl_software
- neg_cont_type
- elev
- samp_mat_process
- assembly_name
- tax_class
- source_mat_id
- lib_size
- samp_collect_device
- assembly_software
- adapters
- samp_collect_method
- annot
- sim_search_meth
- number_contig
- collection_date
- geo_loc_name
- ref_biomaterial
- nucl_acid_amp
- samp_taxon_id
- lib_layout
- tax_ident
- extrachrom_elements
- env_medium
- samp_size
- subspecf_gen_lin
- 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
- ref_db
- lat_lon
- depth
- project_name
- lib_screen
- 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
recommended: true
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: false
recommended: false
assembly_software:
name: assembly_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: true
compl_score:
name: compl_score
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
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
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
required: false
recommended: false
extrachrom_elements:
name: extrachrom_elements
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
recommended: true
feat_pred:
name: feat_pred
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
isol_growth_condt:
name: isol_growth_condt
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- Agriculture
required: true
lib_layout:
name: lib_layout
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_screen:
name: lib_screen
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_size:
name: lib_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_vector:
name: lib_vector
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
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: false
recommended: false
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
required: false
recommended: false
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
required: false
recommended: false
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
required: false
recommended: false
samp_mat_process:
name: samp_mat_process
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
samp_size:
name: samp_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
required: false
recommended: false
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
sim_search_meth:
name: sim_search_meth
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
sop:
name: sop
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
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
subspecf_gen_lin:
name: subspecf_gen_lin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
recommended: true
tax_class:
name: tax_class
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
tax_ident:
name: tax_ident
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
recommended: true
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
class_uri: MIXS:0010006
Induced
name: MigsOrg
description: 'Minimal Information about a Genome Sequence: organelle'
title: MIGS org
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
aliases:
- migs_org
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
recommended: true
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: false
recommended: false
assembly_software:
name: assembly_software
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: true
compl_score:
name: compl_score
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
required: false
recommended: false
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
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
required: false
recommended: false
extrachrom_elements:
name: extrachrom_elements
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
recommended: true
feat_pred:
name: feat_pred
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
isol_growth_condt:
name: isol_growth_condt
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- Agriculture
required: true
lib_layout:
name: lib_layout
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_reads_seqd:
name: lib_reads_seqd
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_screen:
name: lib_screen
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_size:
name: lib_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
lib_vector:
name: lib_vector
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
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: false
recommended: false
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
required: false
recommended: false
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
required: false
recommended: false
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
required: false
recommended: false
samp_mat_process:
name: samp_mat_process
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
required: false
recommended: false
samp_size:
name: samp_size
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
required: false
recommended: false
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
sim_search_meth:
name: sim_search_meth
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
sop:
name: sop
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
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
subspecf_gen_lin:
name: subspecf_gen_lin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
recommended: true
tax_class:
name: tax_class
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
required: false
recommended: false
tax_ident:
name: tax_ident
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
recommended: true
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
attributes:
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
required: false
recommended: false
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: MigsOrg
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
isol_growth_condt:
name: isol_growth_condt
description: Publication reference in the form of pubmed ID (pmid), digital object
identifier (doi) or url for isolation and growth condition specifications of
the organism/material
title: isolation and growth condition
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000003
multivalued: false
alias: isol_growth_condt
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- Agriculture
range: string
required: 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
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NEG_CONT_TYPE_ENUM
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: MigsOrg
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
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
required: false
recommended: false
samp_collect_device:
name: samp_collect_device
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collect_device
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: false
recommended: false
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: MigsOrg
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
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collect_method
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: false
recommended: false
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: false
recommended: false
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
required: false
recommended: false
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TAX_IDENT_ENUM
recommended: true
extrachrom_elements:
name: extrachrom_elements
description: Do plasmids exist of significant phenotypic consequence (e.g. ones
that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
(borrelia has 15+ plasmids)
title: extrachromosomal elements
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000023
multivalued: false
alias: extrachrom_elements
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
range: integer
recommended: true
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MigsOrg
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_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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
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
subspecf_gen_lin:
name: subspecf_gen_lin
description: Information about the genetic distinctness of the sequenced organism
below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any
relevant genetic typing schemes like Group I plasmid. Subspecies should not
be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
name and the lineage rank separated by a colon, e.g., biovar:abc123
title: subspecific genetic lineage
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0000020
multivalued: false
alias: subspecf_gen_lin
owner: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
range: string
recommended: 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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
required: false
recommended: false
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: MigsOrg
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: false
recommended: false
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
ref_db:
name: ref_db
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
from_schema: 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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
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: MigsOrg
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: MigsOrg
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
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: MigsOrg
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: MigsOrg
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
class_uri: MIXS:0010006