Combination: MigsViHostAssociated
MIxS data that complies with the MigsVi checklist and the HostAssociated Extension
Inheritance
- Extension
- HostAssociated
- MigsViHostAssociated [ MigsVi]
- HostAssociated
Terms
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... | HostAssociated, MigsVi |
| lib_screen | 0..1 String |
Specific enrichment or screening methods applied before and/or after creating... | MigsVi |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | MigsVi |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | MigsVi |
| lib_size | 0..1 Integer |
Total number of clones in the library prepared for the project | MigsVi |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | MigsVi |
| temp | 0..1 recommended String |
Temperature of the sample at the time of sampling | HostAssociated, MigsVi |
| compl_score | 0..1 String |
Completeness score is typically based on either the fraction of markers found... | MigsVi |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | MigsVi |
| samp_size | 0..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | MigsVi |
| isol_growth_condt | 1..1 String |
Publication reference in the form of pubmed ID (pmid), digital object identif... | MigsVi |
| alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | HostAssociated, MigsVi |
| source_mat_id | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | MigsVi |
| estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing | MigsVi |
| samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | HostAssociated, MigsVi |
| pathogenicity | 0..1 recommended String |
To what is the entity pathogenic | MigsVi |
| lib_reads_seqd | 0..1 Integer |
Total number of clones sequenced from the library | MigsVi |
| encoded_traits | 0..1 recommended String |
Should include key traits like antibiotic resistance or xenobiotic degradatio... | MigsVi |
| propagation | 1..1 String |
The type of reproduction from the parent stock | MigsVi |
| samp_collect_device | 0..1 String |
The device used to collect an environmental sample | MigsVi |
| number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | MigsVi |
| biotic_relationship | 0..1 BIOTICRELATIONSHIPENUM |
Description of relationship(s) between the subject organism and other organis... | MigsVi |
| num_replicons | 0..1 recommended Integer |
Reports the number of replicons in a nuclear genome of eukaryotes, in the gen... | MigsVi |
| lib_layout | 0..1 LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | MigsVi |
| assembly_qual | 0..1 String |
The assembly quality category is based on sets of criteria outlined for each ... | MigsVi |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | MigsVi |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | HostAssociated, MigsVi |
| lib_vector | 0..1 String |
Cloning vector type(s) used in construction of libraries | MigsVi |
| host_spec_range | 0..* recommended String |
The range and diversity of host species that an organism is capable of infect... | MigsVi |
| neg_cont_type | 0..1 recommended NEGCONTTYPEENUM |
The substance or equipment used as a negative control in an investigation | MigsVi |
| virus_enrich_appr | 0..1 recommended VIRUSENRICHAPPRENUM |
List of approaches used to enrich the sample for viruses, if any | MigsVi |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | MigsVi |
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | MigsVi |
| tax_ident | 0..1 recommended TAXIDENTENUM |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | MigsVi |
| annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... | MigsVi |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | MigsVi |
| subspecf_gen_lin | 0..1 recommended String |
Information about the genetic distinctness of the sequenced organism below th... | MigsVi |
| feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc | MigsVi |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... | MigsVi |
| compl_software | 0..1 String |
Tools used for completion estimate, i | MigsVi |
| samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... | MigsVi |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | MigsVi |
| host_disease_stat | 0..1 recommended String |
List of diseases with which the host has been diagnosed; can include multiple... | HostAssociated, MigsVi |
| depth | 0..1 recommended String |
The vertical distance below local surface | HostAssociated, MigsVi |
| samp_collect_method | 0..1 String |
The method employed for collecting the sample | MigsVi |
| specific_host | 0..1 recommended String |
Report the host's taxonomic name and/or NCBI taxonomy ID | MigsVi |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | MigsVi |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | MigsVi |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | MigsVi |
| collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... | MigsVi |
| seq_meth | 1..1 String |
Sequencing machine used | MigsVi |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | MigsVi |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | HostAssociated, MigsVi |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | MigsVi |
| tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... | MigsVi |
| experimental_factor | 0..* String |
Variable aspects of an experiment design that can be used to describe an expe... | MigsVi |
| associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | MigsVi |
| sop | 0..* recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | MigsVi |
| ances_data | 0..1 String |
Information about either pedigree or other ancestral information description ... | HostAssociated |
| biol_stat | 0..1 String |
The level of genome modification | HostAssociated |
| genetic_mod | 0..1 String |
Genetic modifications of the genome of an organism, which may occur naturally... | HostAssociated |
| host_common_name | 0..1 String |
Common name of the host | HostAssociated |
| samp_capt_status | 0..1 SAMPCAPTSTATUSENUM |
Reason for the sample | HostAssociated |
| samp_dis_stage | 0..1 SAMPDISSTAGEENUM |
Stage of the disease at the time of sample collection, e | HostAssociated |
| host_taxid | 0..1 String |
NCBI taxon id of the host, e | HostAssociated |
| host_subject_id | 0..1 String |
A unique identifier by which each subject can be referred to, de-identified | HostAssociated |
| host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... | HostAssociated |
| host_life_stage | 0..1 String |
Description of life stage of host | HostAssociated |
| host_sex | 0..1 String |
Gender or physical sex of the host | HostAssociated |
| chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... | HostAssociated |
| host_body_habitat | 0..1 String |
Original body habitat where the sample was obtained from | HostAssociated |
| host_body_site | 0..1 String |
Name of body site where the sample was obtained from, such as a specific orga... | HostAssociated |
| host_body_product | 0..1 String |
Substance produced by the body, e | HostAssociated |
| host_tot_mass | 0..1 String |
Total mass of the host at collection, the unit depends on host | HostAssociated |
| host_height | 0..1 String |
The height of subject | HostAssociated |
| host_length | 0..1 String |
The length of subject | HostAssociated |
| host_diet | 0..* String |
Type of diet depending on the host, for animals omnivore, herbivore etc | HostAssociated |
| host_last_meal | 0..* String |
Content of last meal and time since feeding; can include multiple values | HostAssociated |
| host_growth_cond | 0..1 String |
Literature reference giving growth conditions of the host | HostAssociated |
| host_substrate | 0..1 String |
The growth substrate of the host | HostAssociated |
| host_fam_rel | 0..* String |
Relationships to other hosts in the same study; can include multiple relation... | HostAssociated |
| host_subspecf_genlin | 0..* String |
Information about the genetic distinctness of the host organism below the sub... | HostAssociated |
| host_genotype | 0..1 String |
Observed genotype | HostAssociated |
| host_phenotype | 0..1 String |
Phenotype of human or other host | HostAssociated |
| host_body_temp | 0..1 String |
Core body temperature of the host when sample was collected | HostAssociated |
| host_dry_mass | 0..1 String |
Measurement of dry mass | HostAssociated |
| blood_press_diast | 0..1 String |
Resting diastolic blood pressure, measured as mm mercury | HostAssociated |
| blood_press_syst | 0..1 String |
Resting systolic blood pressure, measured as mm mercury | HostAssociated |
| host_color | 0..1 String |
The color of host | HostAssociated |
| host_shape | 0..1 String |
Morphological shape of host | HostAssociated |
| gravidity | 0..1 String |
Whether or not subject is gravid, and if yes date due or date post-conception... | HostAssociated |
| perturbation | 0..* String |
Type of perturbation, e | HostAssociated |
| salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample | HostAssociated |
| oxy_stat_samp | 0..1 OXYSTATSAMPENUM |
Oxygenation status of sample | HostAssociated |
| organism_count | 0..* String |
Total cell count of any organism (or group of organisms) per gram, volume or ... | HostAssociated |
| samp_store_temp | 0..1 String |
Temperature at which sample was stored, e | HostAssociated |
| samp_store_dur | 0..1 String |
Duration for which the sample was stored | HostAssociated |
| samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | HostAssociated |
| host_symbiont | 0..* String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... | HostAssociated |
| misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... | HostAssociated |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/mixs-6-2-rc
LinkML Source
Direct
name: MigsViHostAssociated
description: MIxS data that complies with the MigsVi checklist and the HostAssociated
Extension
title: MigsVi combined with HostAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HostAssociated
mixins:
- MigsVi
class_uri: MIXS:0010005_0016002
Induced
name: MigsViHostAssociated
description: MIxS data that complies with the MigsVi checklist and the HostAssociated
Extension
title: MigsVi combined with HostAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HostAssociated
mixins:
- MigsVi
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-6-2-rc
keywords:
- sample
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: MigsViHostAssociated
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
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
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
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
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
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: MigsViHostAssociated
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
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
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: 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
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: MigsViHostAssociated
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
required: false
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
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
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: MigsViHostAssociated
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MigsViHostAssociated
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
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
slot_uri: MIXS:0000003
multivalued: false
alias: isol_growth_condt
owner: MigsViHostAssociated
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
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
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: MigsViHostAssociated
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
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
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: true
alias: source_mat_id
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: 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
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
multivalued: false
alias: estimated_size
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
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
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: MigsViHostAssociated
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
pathogenicity:
name: pathogenicity
description: To what is the entity pathogenic
title: known pathogenicity
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000027
multivalued: false
alias: pathogenicity
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
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
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
required: false
recommended: false
encoded_traits:
name: encoded_traits
description: Should include key traits like antibiotic resistance or xenobiotic
degradation phenotypes for plasmids, converting genes for phage
title: encoded traits
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000034
multivalued: false
alias: encoded_traits
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsPl
- MigsVi
range: string
recommended: true
propagation:
name: propagation
description: 'The type of reproduction from the parent stock. Values for this
field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately
lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual'
title: propagation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000033
multivalued: false
alias: propagation
owner: MigsViHostAssociated
domain_of:
- MigsEu
- MigsPl
- MigsVi
range: string
required: true
samp_collect_device:
name: samp_collect_device
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collect_device
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: false
recommended: false
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: false
recommended: false
biotic_relationship:
name: biotic_relationship
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated with. E.g., parasite on species X; mutualist with
species Y. The target organism is the subject of the relationship, and the other
organism(s) is the object
title: observed biotic relationship
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000028
multivalued: false
alias: biotic_relationship
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BIOTIC_RELATIONSHIP_ENUM
required: false
recommended: false
num_replicons:
name: num_replicons
description: Reports the number of replicons in a nuclear genome of eukaryotes,
in the genome of a bacterium or archaea or the number of segments in a segmented
virus. Always applied to the haploid chromosome count of a eukaryote
title: number of replicons
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer}'
slot_uri: MIXS:0000022
alias: num_replicons
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
range: integer
recommended: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
required: false
recommended: false
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
review of assembly other than reporting of standard assembly statistics. Low
Quality Draft:Many fragments with little to no review of assembly other than
reporting of standard assembly statistics. Assembly statistics include, but
are not limited to total assembly size, number of contigs, contig N50/L50, and
maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
per replicon without gaps or ambiguities, with extensive manual review and editing
to annotate putative gene functions and transcriptional units. High-quality
draft genome: One or multiple fragments, totaling 90% of the expected genome
or replicon sequence or predicted complete. Genome fragment(s): One or multiple
fragments, totalling < 90% of the expected genome or replicon sequence, or for
which no genome size could be estimated'
title: assembly quality
from_schema: https://w3id.org/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: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
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
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: MigsViHostAssociated
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
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
keywords:
- project
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: MigsViHostAssociated
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
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
host_spec_range:
name: host_spec_range
description: The range and diversity of host species that an organism is capable
of infecting, defined by NCBI taxonomy identifier
title: host specificity or range
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer}'
slot_uri: MIXS:0000030
multivalued: true
alias: host_spec_range
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
recommended: 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-6-2-rc
keywords:
- type
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NEG_CONT_TYPE_ENUM
recommended: true
virus_enrich_appr:
name: virus_enrich_appr
description: List of approaches used to enrich the sample for viruses, if any
title: virus enrichment approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000036
alias: virus_enrich_appr
owner: MigsViHostAssociated
domain_of:
- MigsVi
- Miuvig
range: VIRUS_ENRICH_APPR_ENUM
recommended: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: MigsViHostAssociated
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000053
alias: tax_ident
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TAX_IDENT_ENUM
recommended: true
annot:
name: annot
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: 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
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0000020
multivalued: false
alias: subspecf_gen_lin
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: MigsViHostAssociated
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
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
keywords:
- context
- environmental
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: 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
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
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
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MigsViHostAssociated
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
host_disease_stat:
name: host_disease_stat
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: rabies [DOID:11260]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
multivalued: false
alias: host_disease_stat
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
required: false
recommended: 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
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: MigsViHostAssociated
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collect_method
owner: MigsViHostAssociated
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
specific_host:
name: specific_host
description: Report the host's taxonomic name and/or NCBI taxonomy ID
title: host scientific name
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
multivalued: false
alias: specific_host
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
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
keywords:
- environmental
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MigsViHostAssociated
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-6-2-rc
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: MigsViHostAssociated
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-6-2-rc
keywords:
- geographic
- location
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: MigsViHostAssociated
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-6-2-rc
keywords:
- date
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: MigsViHostAssociated
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-6-2-rc
keywords:
- method
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: MigsViHostAssociated
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
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
keywords:
- geographic
- location
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: MigsViHostAssociated
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
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
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: MigsViHostAssociated
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-6-2-rc
keywords:
- context
- environmental
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: MigsViHostAssociated
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
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
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
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
multivalued: true
alias: experimental_factor
owner: MigsViHostAssociated
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+ \[[a-zA-Z]{2,}:\d+\]$
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
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
multivalued: true
alias: associated_resource
owner: MigsViHostAssociated
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
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: true
alias: sop
owner: MigsViHostAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
ances_data:
name: ances_data
description: Information about either pedigree or other ancestral information
description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
(meaning [(A x B) x B] x B)
title: ancestral data
examples:
- value: A/3*B
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000247
multivalued: false
alias: ances_data
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
biol_stat:
name: biol_stat
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: The level of genome modification
title: biological status
examples:
- value: natural
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- status
string_serialization: '[wild|natural|semi-natural|inbred line|breeder''s line|hybrid|clonal
selection|mutant]'
slot_uri: MIXS:0000858
multivalued: false
alias: biol_stat
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
genetic_mod:
name: genetic_mod
annotations:
Expected_value:
tag: Expected_value
value: PMID, DOI, URL or text
description: Genetic modifications of the genome of an organism, which may occur
naturally by spontaneous mutation, or be introduced by some experimental means,
e.g. specification of a transgene or the gene knocked-out or details of transient
transfection
title: genetic modification
examples:
- value: aox1A transgenic
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000859
multivalued: false
alias: genetic_mod
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
host_common_name:
name: host_common_name
description: Common name of the host
title: host common name
examples:
- value: human
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000248
multivalued: false
alias: host_common_name
owner: MigsViHostAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
samp_capt_status:
name: samp_capt_status
description: Reason for the sample
title: sample capture status
examples:
- value: farm sample
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- sample
- status
slot_uri: MIXS:0000860
multivalued: false
alias: samp_capt_status
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: SAMP_CAPT_STATUS_ENUM
required: false
recommended: false
samp_dis_stage:
name: samp_dis_stage
description: Stage of the disease at the time of sample collection, e.g. inoculation,
penetration, infection, growth and reproduction, dissemination of pathogen
title: sample disease stage
examples:
- value: infection
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- disease
- sample
slot_uri: MIXS:0000249
multivalued: false
alias: samp_dis_stage
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- PlantAssociated
range: SAMP_DIS_STAGE_ENUM
required: false
recommended: false
host_taxid:
name: host_taxid
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
examples:
- value: '7955'
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{NCBI taxid}'
slot_uri: MIXS:0000250
multivalued: false
alias: host_taxid
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_subject_id:
name: host_subject_id
description: A unique identifier by which each subject can be referred to, de-identified
title: host subject id
examples:
- value: MPI123
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000861
multivalued: false
alias: host_subject_id
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_age:
name: host_age
description: Age of host at the time of sampling; relevant scale depends on species
and study, e.g. Could be seconds for amoebae or centuries for trees
title: host age
examples:
- value: 10 days
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000255
multivalued: false
alias: host_age
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_life_stage:
name: host_life_stage
description: Description of life stage of host
title: host life stage
examples:
- value: adult
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000251
multivalued: false
alias: host_life_stage
owner: MigsViHostAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_sex:
name: host_sex
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Gender or physical sex of the host
title: host sex
comments:
- example of non-binary from Excel sheets does not match any of the enumerated
values
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
string_serialization: '[female|hermaphrodite|non-binary|male|transgender|transgender
(female to male)|transgender (male to female)
|undeclared]'
slot_uri: MIXS:0000811
alias: host_sex
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
chem_administration:
name: chem_administration
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
multivalued: true
alias: chem_administration
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
host_body_habitat:
name: host_body_habitat
description: Original body habitat where the sample was obtained from
title: host body habitat
examples:
- value: nasopharynx
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000866
multivalued: false
alias: host_body_habitat
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_body_site:
name: host_body_site
description: Name of body site where the sample was obtained from, such as a specific
organ or tissue (tongue, lung etc...). Use terms from the foundational model
of anatomy ontology (fma) or the Uber-anatomy ontology (UBERON)
title: host body site
examples:
- value: gill [UBERON:0002535]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000867
multivalued: false
alias: host_body_site
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_body_product:
name: host_body_product
annotations:
Expected_value:
tag: Expected_value
value: FMA or UBERON
description: Substance produced by the body, e.g. Stool, mucus, where the sample
was obtained from. Use terms from the foundational model of anatomy ontology
(fma) or Uber-anatomy ontology (UBERON)
title: host body product
examples:
- value: mucus [FMA:66938]
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- body
- host
- host.
- product
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000888
multivalued: false
alias: host_body_product
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_tot_mass:
name: host_tot_mass
description: Total mass of the host at collection, the unit depends on host
title: host total mass
examples:
- value: 2500 gram
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000263
multivalued: false
alias: host_tot_mass
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_height:
name: host_height
description: The height of subject
title: host height
examples:
- value: 0.1 meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000264
multivalued: false
alias: host_height
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
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
host_length:
name: host_length
description: The length of subject
title: host length
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000256
multivalued: false
alias: host_length
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
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
host_diet:
name: host_diet
description: Type of diet depending on the host, for animals omnivore, herbivore
etc., for humans high-fat, meditteranean etc.; can include multiple diet types
title: host diet
examples:
- value: herbivore
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000869
multivalued: true
alias: host_diet
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
host_last_meal:
name: host_last_meal
description: Content of last meal and time since feeding; can include multiple
values
title: host last meal
examples:
- value: corn feed;P2H
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000870
multivalued: true
alias: host_last_meal
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
host_growth_cond:
name: host_growth_cond
description: Literature reference giving growth conditions of the host
title: host growth conditions
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000871
multivalued: false
alias: host_growth_cond
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
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
host_substrate:
name: host_substrate
description: The growth substrate of the host
title: host substrate
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000252
multivalued: false
alias: host_substrate
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_fam_rel:
name: host_fam_rel
description: Relationships to other hosts in the same study; can include multiple
relationships
title: host family relationship
examples:
- value: offspring;Mussel25
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
multivalued: true
alias: host_fam_rel
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_subspecf_genlin:
name: host_subspecf_genlin
annotations:
Expected_value:
tag: Expected_value
value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
e.g. serovar, biotype, ecotype, variety, cultivar
description: Information about the genetic distinctness of the host organism below
the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
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: host subspecific genetic lineage
examples:
- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
- lineage
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0001318
multivalued: true
alias: host_subspecf_genlin
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
range: string
required: false
recommended: false
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
examples:
- value: C57BL/6
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000365
multivalued: false
alias: host_genotype
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_phenotype:
name: host_phenotype
description: Phenotype of human or other host. Use terms from the phenotypic quality
ontology (pato) or the Human Phenotype Ontology (HP)
title: host phenotype
examples:
- value: elongated [PATO:0001154]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
multivalued: false
alias: host_phenotype
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_body_temp:
name: host_body_temp
description: Core body temperature of the host when sample was collected
title: host body temperature
examples:
- value: 15 degree Celsius
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000274
multivalued: false
alias: host_body_temp
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
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
host_dry_mass:
name: host_dry_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Measurement of dry mass
title: host dry mass
examples:
- value: 500 gram
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- dry
- host
- host.
- mass
slot_uri: MIXS:0000257
multivalued: false
alias: host_dry_mass
owner: MigsViHostAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
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
blood_press_diast:
name: blood_press_diast
annotations:
Preferred_unit:
tag: Preferred_unit
value: millimeter mercury
description: Resting diastolic blood pressure, measured as mm mercury
title: host blood pressure diastolic
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
- pressure
slot_uri: MIXS:0000258
multivalued: false
alias: blood_press_diast
owner: MigsViHostAssociated
domain_of:
- HostAssociated
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
blood_press_syst:
name: blood_press_syst
annotations:
Preferred_unit:
tag: Preferred_unit
value: millimeter mercury
description: Resting systolic blood pressure, measured as mm mercury
title: host blood pressure systolic
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- host
- host.
- pressure
slot_uri: MIXS:0000259
multivalued: false
alias: blood_press_syst
owner: MigsViHostAssociated
domain_of:
- HostAssociated
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
host_color:
name: host_color
description: The color of host
title: host color
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000260
multivalued: false
alias: host_color
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_shape:
name: host_shape
description: Morphological shape of host
title: host shape
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000261
multivalued: false
alias: host_shape
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
gravidity:
name: gravidity
description: Whether or not subject is gravid, and if yes date due or date post-conception,
specifying which is used
title: gravidity
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0000875
multivalued: false
alias: gravidity
owner: MigsViHostAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
perturbation:
name: perturbation
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: true
alias: perturbation
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
salinity:
name: salinity
annotations:
Preferred_unit:
tag: Preferred_unit
value: practical salinity unit, percentage
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- salinity
slot_uri: MIXS:0000183
multivalued: false
alias: salinity
owner: MigsViHostAssociated
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- 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
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000753
multivalued: false
alias: oxy_stat_samp
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OXY_STAT_SAMP_ENUM
required: false
recommended: false
organism_count:
name: organism_count
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
multivalued: true
alias: organism_count
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
multivalued: false
alias: samp_store_temp
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- 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
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000116
multivalued: false
alias: samp_store_dur
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_store_loc:
name: samp_store_loc
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
alias: samp_store_loc
owner: MigsViHostAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
host_symbiont:
name: host_symbiont
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
can have its own symbionts. For example, parasites may have hyperparasites (=parasites
of the parasite)
title: observed host symbionts
examples:
- value: flukeworms
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0001298
multivalued: true
alias: host_symbiont
owner: MigsViHostAssociated
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs-6-2-rc
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: true
alias: misc_param
owner: MigsViHostAssociated
domain_of:
- 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
class_uri: MIXS:0010005_0016002