Combination: MimarksC combined with SymbiontAssociated (MimarksCSymbiontAssociated)
MIxS Data that comply with the MimarksC checklist and the SymbiontAssociated Extension
Composition
MimarksC [Checklist] + SymbiontAssociated [Extension]
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0001107 | samp_name | 1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:0000046 | pcr_primers | 0..1 recommended String |
PCR primers that were used to amplify the sequence of the targeted gene, locu... |
| MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000045 | target_subfragment | 0..1 recommended String |
Name of subfragment of a gene or locus |
| MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000049 | pcr_cond | 0..1 recommended String |
Description of reaction conditions and components of polymerase chain reactio... |
| MIXS:0000037 | nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000001 | samp_size | 0..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... |
| MIXS:0000003 | isol_growth_condt | 1 String |
Publication reference in the form of pubmed ID (pmid), digital object identif... |
| MIXS:0000094 | alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... |
| MIXS:0000026 | source_mat_id | * recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0000023 | extrachrom_elements | 0..1 Integer |
Do plasmids exist of significant phenotypic consequence (e |
| MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:0000015 | rel_to_oxygen | 0..1 recommended RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... |
| MIXS:0000002 | samp_collect_device | 0..1 String |
The device used to collect an environmental sample |
| MIXS:0000028 | biotic_relationship | 0..1 recommended BioticRelationshipEnum |
Description of relationship(s) between the subject organism and other organis... |
| MIXS:0000051 | seq_quality_check | 0..1 recommended SeqQualityCheckEnum |
Indicate if the sequence has been called by automatic systems (none) or under... |
| MIXS:0000092 | project_name | 1 String |
Name of the project within which the sequencing was organized |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0000052 | chimera_check | 0..1 recommended String |
Tool(s) used for chimera checking, including version number and parameters, t... |
| MIXS:0000032 | trophic_level | 0..1 recommended TrophicLevelEnum |
Trophic levels are the feeding position in a food chain |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000020 | subspecf_gen_lin | 0..1 recommended String |
Information about the genetic distinctness of the sequenced organism below th... |
| MIXS:0000013 | env_local_scale | 1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000016 | samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000018 | depth | 0..1 recommended String |
The vertical distance below local surface |
| MIXS:0001225 | samp_collect_method | 0..1 String |
The method employed for collecting the sample |
| MIXS:0000014 | env_medium | 1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001320 | samp_taxon_id | 1 String |
NCBI taxon id of the sample |
| MIXS:0000010 | geo_loc_name | 1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000011 | collection_date | 1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000050 | seq_meth | 1 String |
Sequencing machine used |
| MIXS:0000009 | lat_lon | 1 String |
The geographical origin of the sample as defined by latitude and longitude |
| MIXS:0000093 | elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... |
| MIXS:0000012 | env_broad_scale | 1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000008 | experimental_factor | * String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000044 | target_gene | 1 String |
Targeted gene or locus name for marker gene studies |
| MIXS:0000091 | associated_resource | * recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:0000090 | sop | * recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... |
| MIXS:0000861 | host_subject_id | 0..1 String |
A unique identifier by which each subject can be referred to, de-identified |
| MIXS:0000248 | host_common_name | 0..1 String |
Common name of the host |
| MIXS:0000250 | host_taxid | 0..1 String |
NCBI taxon id of the host, e |
| MIXS:0001315 | host_dependence | 1 HostDependenceEnum |
Type of host dependence for the symbiotic host organism to its host |
| MIXS:0001307 | type_of_symbiosis | 0..1 recommended TypeOfSymbiosisEnum |
Type of biological interaction established between the symbiotic host organis... |
| MIXS:0001300 | sym_life_cycle_type | 1 SymLifeCycleTypeEnum |
Type of life cycle of the symbiotic host species (the thing being sampled) |
| MIXS:0000251 | host_life_stage | 1 String |
Description of life stage of host |
| MIXS:0000255 | host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... |
| MIXS:0000862 | urobiom_sex | 0..1 UrobiomSexEnum |
Physical sex of the host |
| MIXS:0001312 | mode_transmission | 0..1 recommended ModeTransmissionEnum |
The process through which the symbiotic host organism entered the host from w... |
| MIXS:0001316 | route_transmission | 0..1 RouteTransmissionEnum |
Description of path taken by the symbiotic host organism being sampled in ord... |
| MIXS:0000866 | host_body_habitat | 0..1 String |
Original body habitat where the sample was obtained from |
| MIXS:0000867 | host_body_site | 0..1 String |
Name of body site where the sample was obtained from, such as a specific orga... |
| MIXS:0000888 | host_body_product | 0..1 String |
Substance produced by the body, e |
| MIXS:0000263 | host_tot_mass | 0..1 String |
Total mass of the host at collection, the unit depends on host |
| MIXS:0000264 | host_height | 0..1 String |
The height of subject |
| MIXS:0000256 | host_length | 0..1 String |
The length of subject |
| MIXS:0000871 | host_growth_cond | 0..1 String |
Literature reference giving growth conditions of the host |
| MIXS:0000252 | host_substrate | 0..1 String |
The growth substrate of the host |
| MIXS:0000872 | host_fam_rel | * String |
Relationships to other hosts in the same study; can include multiple relation... |
| MIXS:0000253 | host_infra_spec_name | 0..1 String |
Taxonomic information about the host below subspecies level |
| MIXS:0000254 | host_infra_spec_rank | 0..1 String |
Taxonomic rank information about the host below subspecies level, such as var... |
| MIXS:0000365 | host_genotype | 0..1 String |
Observed genotype |
| MIXS:0000874 | host_phenotype | 0..1 String |
Phenotype of human or other host |
| MIXS:0000257 | host_dry_mass | 0..1 String |
Measurement of dry mass |
| MIXS:0000260 | host_color | 0..1 String |
The color of host |
| MIXS:0000261 | host_shape | 0..1 String |
Morphological shape of host |
| MIXS:0000875 | gravidity | 0..1 String |
Whether or not subject is gravid, and if yes date due or date post-conception... |
| MIXS:0001305 | host_number | 0..1 String |
Number of symbiotic host individuals pooled at the time of collection |
| MIXS:0001298 | host_symbiont | * String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... |
| MIXS:0001308 | host_specificity | 0..1 recommended HostSpecificityEnum |
Level of specificity of symbiont-host interaction: e |
| MIXS:0001303 | symbiont_host_role | 0..1 recommended SymbiontHostRoleEnum |
Role of the host in the life cycle of the symbiotic organism |
| MIXS:0001313 | host_cellular_loc | 0..1 recommended HostCellularLocEnum |
The localization of the symbiotic host organism within the host from which it... |
| MIXS:0001299 | association_duration | 0..1 String |
Time spent in host of the symbiotic organism at the time of sampling; relevan... |
| MIXS:0001310 | host_of_host_coinf | 0..1 String |
The taxonomic name of any coinfecting organism observed in a symbiotic relati... |
| MIXS:0001324 | host_of_host_name | 0..1 String |
Common name of the host of the symbiotic host organism |
| MIXS:0001325 | host_of_host_env_loc | * String |
For a symbiotic host organism the local anatomical environment within its hos... |
| MIXS:0001326 | host_of_host_env_med | 0..1 String |
Report the environmental material(s) immediately surrounding the symbiotic ho... |
| MIXS:0001306 | host_of_host_taxid | 0..1 String |
NCBI taxon id of the host of the symbiotic host organism |
| MIXS:0001327 | host_of_host_sub_id | 0..1 String |
A unique identifier by which each host of the symbiotic host organism subject... |
| MIXS:0001319 | host_of_host_disease | * String |
List of diseases with which the host of the symbiotic host organism has been ... |
| MIXS:0001328 | host_of_host_fam_rel | * String |
Familial relationship of the host of the symbiotic host organisms to other ho... |
| MIXS:0001329 | host_of_host_infname | 0..1 String |
Taxonomic name information of the host of the symbiotic host organism below s... |
| MIXS:0001330 | host_of_host_infrank | 0..1 String |
Taxonomic rank information about the host of the symbiotic host organism belo... |
| MIXS:0001331 | host_of_host_geno | 0..1 String |
Observed genotype of the host of the symbiotic host organism |
| MIXS:0001332 | host_of_host_pheno | 0..1 String |
Phenotype of the host of the symbiotic host organism |
| MIXS:0001333 | host_of_host_gravid | 0..1 String |
Whether or not the host of the symbiotic host organism is gravid, and if yes ... |
| MIXS:0001334 | host_of_host_totmass | 0..1 String |
Total mass of the host of the symbiotic host organism at collection, the unit... |
| MIXS:0000751 | chem_administration | * String |
List of chemical compounds administered to the host or site where sampling oc... |
| MIXS:0000754 | perturbation | * String |
Type of perturbation, e |
| MIXS:0000183 | salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample |
| MIXS:0000753 | oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample |
| MIXS:0000103 | organism_count | * String |
Total cell count of any organism (or group of organisms) per gram, volume or ... |
| MIXS:0000110 | samp_store_temp | 0..1 String |
Temperature at which sample was stored, e |
| MIXS:0000116 | samp_store_dur | 0..1 String |
Duration for which the sample was stored |
| MIXS:0000755 | samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room |
| MIXS:0001317 | samp_store_sol | 0..1 String |
Solution within which sample was stored, if any |
| MIXS:0000752 | misc_param | * String |
Any other measurement performed or parameter collected, that is not listed he... |
LinkML Source
Direct
name: MimarksCSymbiontAssociated
description: MIxS Data that comply with the MimarksC checklist and the SymbiontAssociated
Extension
title: MimarksC combined with SymbiontAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: SymbiontAssociated
mixins:
- MimarksC
class_uri: MIXS:0010009_0016023
Induced
name: MimarksCSymbiontAssociated
description: MIxS Data that comply with the MimarksC checklist and the SymbiontAssociated
Extension
title: MimarksC combined with SymbiontAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: SymbiontAssociated
mixins:
- MimarksC
attributes:
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- sample
slot_uri: MIXS:0001107
alias: samp_name
owner: MimarksCSymbiontAssociated
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
pcr_primers:
name: pcr_primers
annotations:
Expected_value:
tag: Expected_value
value: 'FWD: forward primer sequence;REV:reverse primer sequence'
description: PCR primers that were used to amplify the sequence of the targeted
gene, locus or subfragment. This field should contain all the primers used for
a single PCR reaction if multiple forward or reverse primers are present in
a single PCR reaction. The primer sequence should be reported in uppercase letters
title: pcr primers
examples:
- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- pcr
string_serialization: FWD:{dna};REV:{dna}
slot_uri: MIXS:0000046
alias: pcr_primers
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
examples:
- value: https://phylogenomics.me/protocols/16s-pcr-protocol/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: MimarksCSymbiontAssociated
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
target_subfragment:
name: target_subfragment
description: Name of subfragment of a gene or locus. Important to e.g. identify
special regions on marker genes like V6 on 16S rRNA
title: target subfragment
examples:
- value: V6, V9, ITS
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000045
alias: target_subfragment
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
temp:
name: temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature of the sample at the time of sampling
title: temperature
examples:
- value: 25 degree Celsius
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- temperature
slot_uri: MIXS:0000113
alias: temp
owner: MimarksCSymbiontAssociated
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
pcr_cond:
name: pcr_cond
annotations:
Expected_value:
tag: Expected_value
value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
description: Description of reaction conditions and components of polymerase chain
reaction performed during library preparation.
title: pcr conditions
examples:
- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
- value: initial denaturation:94degC_1.5min
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- condition
- pcr
string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
elongation:degrees_minutes;total cycles
slot_uri: MIXS:0000049
alias: pcr_cond
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: 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
examples:
- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
samp_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
examples:
- value: 5 liter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- sample
- size
slot_uri: MIXS:0000001
alias: samp_size
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
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
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- condition
- growth
- isolation
slot_uri: MIXS:0000003
alias: isol_growth_condt
owner: MimarksCSymbiontAssociated
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
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000094
alias: alt
owner: MimarksCSymbiontAssociated
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
annotations:
Expected_value:
tag: Expected_value
value: 'for cultures of microorganisms: identifiers for two culture collections;
for other material a unique arbitrary identifer'
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2)
title: source material identifiers
examples:
- value: MPI012345
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- identifier
- material
- source
slot_uri: MIXS:0000026
alias: source_mat_id
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
multivalued: 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
examples:
- value: '5'
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000023
alias: extrachrom_elements
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
range: integer
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
annotations:
Preferred_unit:
tag: Preferred_unit
value: milliliter, gram, milligram, square centimeter
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
examples:
- value: 1500 milliliter
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- dna
- sample
- volume
- weight
slot_uri: MIXS:0000111
alias: samp_vol_we_dna_ext
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
rel_to_oxygen:
name: rel_to_oxygen
description: Is this organism an aerobe, anaerobe? Please note that aerobic and
anaerobic are valid descriptors for microbial environments
title: relationship to oxygen
examples:
- value: aerobe
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- relationship
slot_uri: MIXS:0000015
alias: rel_to_oxygen
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
range: RelToOxygenEnum
recommended: true
samp_collect_device:
name: samp_collect_device
annotations:
Expected_value:
tag: Expected_value
value: device name
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- device
- sample
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
biotic_relationship:
name: biotic_relationship
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated with. E.g., parasite on species X; mutualist with
species Y. The target organism is the subject of the relationship, and the other
organism(s) is the object
title: observed biotic relationship
examples:
- value: free living
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- observed
- relationship
slot_uri: MIXS:0000028
alias: biotic_relationship
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BioticRelationshipEnum
recommended: true
seq_quality_check:
name: seq_quality_check
annotations:
Expected_value:
tag: Expected_value
value: none or manually edited
description: Indicate if the sequence has been called by automatic systems (none)
or undergone a manual editing procedure (e.g. by inspecting the raw data or
chromatograms). Applied only for sequences that are not submitted to SRA,ENA
or DRA
title: sequence quality check
examples:
- value: none
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
slot_uri: MIXS:0000051
alias: seq_quality_check
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: SeqQualityCheckEnum
recommended: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- project
slot_uri: MIXS:0000092
alias: project_name
owner: MimarksCSymbiontAssociated
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
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
recommended: true
chimera_check:
name: chimera_check
description: Tool(s) used for chimera checking, including version number and parameters,
to discover and remove chimeric sequences. A chimeric sequence is comprised
of two or more phylogenetically distinct parent sequences
title: chimera check software
examples:
- value: uchime;v4.1;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
slot_uri: MIXS:0000052
alias: chimera_check
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
trophic_level:
name: trophic_level
description: Trophic levels are the feeding position in a food chain. Microbes
can be a range of producers (e.g. chemolithotroph)
title: trophic level
examples:
- value: heterotroph
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- level
slot_uri: MIXS:0000032
alias: trophic_level
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MimarksC
- Agriculture
range: TrophicLevelEnum
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
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
subspecf_gen_lin:
name: subspecf_gen_lin
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 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
examples:
- value: serovar:Newport
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- lineage
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0000020
alias: subspecf_gen_lin
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- MimarksC
- FoodFoodProductionFacility
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
keywords:
- context
- environmental
slot_uri: MIXS:0000013
alias: env_local_scale
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
examples:
- value: filtering of seawater, storing samples in ethanol
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- material
- process
- sample
slot_uri: MIXS:0000016
alias: samp_mat_process
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
depth:
name: depth
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- depth
slot_uri: MIXS:0000018
alias: depth
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- method
- sample
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: 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
keywords:
- environmental
slot_uri: MIXS:0000014
alias: env_medium
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- dna
- identifier
- sample
- taxon
slot_uri: MIXS:0001320
alias: samp_taxon_id
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
structured_pattern:
syntax: ^{text} \[{NCBItaxon_id}\]$
interpolated: true
partial_match: true
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
structured_pattern:
syntax: '^{text}: {text}, {text}$'
interpolated: true
partial_match: true
collection_date:
name: collection_date
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- date
slot_uri: MIXS:0000011
alias: collection_date
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000050
alias: seq_meth
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
structured_pattern:
syntax: ^{text}|({termLabel} \[{termID}\])$
interpolated: true
partial_match: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees, limited to 8 decimal
points, and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- geographic
- location
slot_uri: MIXS:0000009
alias: lat_lon
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: string
required: true
pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
structured_pattern:
syntax: ^{lat} {lon}$
interpolated: true
partial_match: true
elev:
name: elev
annotations:
Preferred_unit:
tag: Preferred_unit
value: meter
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
examples:
- value: 100 meter
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- elevation
slot_uri: MIXS:0000093
alias: elev
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- HostAssociated
- HydrocarbonResourcesCores
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
owner: MimarksCSymbiontAssociated
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
experimental_factor:
name: experimental_factor
annotations:
Expected_value:
tag: Expected_value
value: text or EFO and/or OBI
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
examples:
- value: time series design [EFO:0001779]
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- experimental
- factor
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
alias: experimental_factor
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
multivalued: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
target_gene:
name: target_gene
description: Targeted gene or locus name for marker gene studies
title: target gene
examples:
- value: 16S rRNA, 18S rRNA, nif, amoA, rpo
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- target
slot_uri: MIXS:0000044
alias: target_gene
owner: MimarksCSymbiontAssociated
domain_of:
- MimarksC
- MimarksS
- Agriculture
range: string
required: true
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
alias: associated_resource
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
sop:
name: sop
annotations:
Expected_value:
tag: Expected_value
value: reference to SOP
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
examples:
- value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- procedures
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
alias: sop
owner: MimarksCSymbiontAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
multivalued: true
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: P14
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- identifier
slot_uri: MIXS:0000861
alias: host_subject_id
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
host_common_name:
name: host_common_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: Common name of the host
title: host common name
examples:
- value: trematode
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000248
alias: host_common_name
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
host_taxid:
name: host_taxid
annotations:
Expected_value:
tag: Expected_value
value: NCBI taxon identifier
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
examples:
- value: '395013'
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- taxon
string_serialization: '{integer}'
slot_uri: MIXS:0000250
alias: host_taxid
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
host_dependence:
name: host_dependence
description: Type of host dependence for the symbiotic host organism to its host
title: host dependence
examples:
- value: obligate
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0001315
alias: host_dependence
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: HostDependenceEnum
required: true
type_of_symbiosis:
name: type_of_symbiosis
description: Type of biological interaction established between the symbiotic
host organism being sampled and its respective host
title: type of symbiosis
examples:
- value: parasitic
from_schema: https://w3id.org/mixs
keywords:
- symbiosis
- type
slot_uri: MIXS:0001307
alias: type_of_symbiosis
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: TypeOfSymbiosisEnum
recommended: true
sym_life_cycle_type:
name: sym_life_cycle_type
annotations:
Expected_value:
tag: Expected_value
value: type of life cycle of the symbiotic organism (host of the samples)
description: Type of life cycle of the symbiotic host species (the thing being
sampled). Simple life cycles occur within a single host, complex ones within
multiple different hosts over the course of their normal life cycle
title: symbiotic host organism life cycle type
examples:
- value: complex life cycle
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- life
- organism
- symbiosis
- type
slot_uri: MIXS:0001300
alias: sym_life_cycle_type
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: SymLifeCycleTypeEnum
required: true
host_life_stage:
name: host_life_stage
annotations:
Expected_value:
tag: Expected_value
value: stage
description: Description of life stage of host
title: host life stage
examples:
- value: redia
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- life
slot_uri: MIXS:0000251
alias: host_life_stage
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
required: true
host_age:
name: host_age
annotations:
Preferred_unit:
tag: Preferred_unit
value: year, day, hour
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
from_schema: https://w3id.org/mixs
keywords:
- age
- host
- host.
slot_uri: MIXS:0000255
alias: host_age
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
urobiom_sex:
name: urobiom_sex
annotations:
Expected_value:
tag: Expected_value
value: sex of the symbiotic organism (host of the samples); enumeration
description: Physical sex of the host
title: host sex
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000862
alias: urobiom_sex
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: UrobiomSexEnum
mode_transmission:
name: mode_transmission
description: The process through which the symbiotic host organism entered the
host from which it was sampled
title: mode of transmission
examples:
- value: horizontal:castrator
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0001312
alias: mode_transmission
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: ModeTransmissionEnum
recommended: true
route_transmission:
name: route_transmission
description: Description of path taken by the symbiotic host organism being sampled
in order to establish a symbiotic relationship with the host (with which it
was observed at the time of sampling) via a mode of transmission (specified
in mode_transmission)
title: route of transmission
from_schema: https://w3id.org/mixs
keywords:
- route
slot_uri: MIXS:0001316
alias: route_transmission
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: RouteTransmissionEnum
host_body_habitat:
name: host_body_habitat
description: Original body habitat where the sample was obtained from
title: host body habitat
examples:
- value: anterior end of a tapeworm
from_schema: https://w3id.org/mixs
keywords:
- body
- habitat
- host
- host.
slot_uri: MIXS:0000866
alias: host_body_habitat
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
host_body_site:
name: host_body_site
annotations:
Expected_value:
tag: Expected_value
value: FMA or UBERON
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: scolex [UBERON:0015119]
from_schema: https://w3id.org/mixs
keywords:
- body
- host
- site
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000867
alias: host_body_site
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
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
keywords:
- body
- host
- host.
- product
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000888
alias: host_body_product
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
host_tot_mass:
name: host_tot_mass
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Total mass of the host at collection, the unit depends on host
title: host total mass
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- mass
- total
slot_uri: MIXS:0000263
alias: host_tot_mass
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_height:
name: host_height
annotations:
Preferred_unit:
tag: Preferred_unit
value: centimeter, millimeter, meter
description: The height of subject
title: host height
from_schema: https://w3id.org/mixs
keywords:
- height
- host
- host.
slot_uri: MIXS:0000264
alias: host_height
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_length:
name: host_length
annotations:
Preferred_unit:
tag: Preferred_unit
value: centimeter, millimeter, meter
description: The length of subject
title: host length
examples:
- value: 1 meter
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- length
slot_uri: MIXS:0000256
alias: host_length
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_growth_cond:
name: host_growth_cond
description: Literature reference giving growth conditions of the host
title: host growth conditions
examples:
- value: https://academic.oup.com/icesjms/article/68/2/349/617247
from_schema: https://w3id.org/mixs
keywords:
- condition
- growth
- host
- host.
slot_uri: MIXS:0000871
alias: host_growth_cond
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
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
examples:
- value: rock
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000252
alias: host_substrate
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
host_fam_rel:
name: host_fam_rel
annotations:
Expected_value:
tag: Expected_value
value: relationship type;arbitrary identifier
description: Relationships to other hosts in the same study; can include multiple
relationships
title: host family relationship
examples:
- value: clone;P15
from_schema: https://w3id.org/mixs
keywords:
- family
- host
- host.
- relationship
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
alias: host_fam_rel
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
multivalued: true
host_infra_spec_name:
name: host_infra_spec_name
description: Taxonomic information about the host below subspecies level
title: host infra-specific name
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000253
alias: host_infra_spec_name
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_infra_spec_rank:
name: host_infra_spec_rank
description: Taxonomic rank information about the host below subspecies level,
such as variety, form, rank etc
title: host infra-specific rank
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- rank
slot_uri: MIXS:0000254
alias: host_infra_spec_rank
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000365
alias: host_genotype
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
host_phenotype:
name: host_phenotype
annotations:
Expected_value:
tag: Expected_value
value: PATO or HP
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: soldier
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
alias: host_phenotype
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
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
keywords:
- dry
- host
- host.
- mass
slot_uri: MIXS:0000257
alias: host_dry_mass
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- PlantAssociated
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_color:
name: host_color
description: The color of host
title: host color
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000260
alias: host_color
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
host_shape:
name: host_shape
description: Morphological shape of host
title: host shape
examples:
- value: round
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000261
alias: host_shape
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
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
examples:
- value: yes;due date:2018-05-11
from_schema: https://w3id.org/mixs
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0000875
alias: gravidity
owner: MimarksCSymbiontAssociated
domain_of:
- HostAssociated
- SymbiontAssociated
range: string
host_number:
name: host_number
annotations:
Expected_value:
tag: Expected_value
value: count
description: Number of symbiotic host individuals pooled at the time of collection
title: host number individual
examples:
- value: '3'
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- number
string_serialization: '{float} m'
slot_uri: MIXS:0001305
alias: host_number
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_symbiont:
name: host_symbiont
annotations:
Expected_value:
tag: Expected_value
value: species name or common name
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: Paragordius varius
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- observed
- symbiosis
slot_uri: MIXS:0001298
alias: host_symbiont
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
multivalued: true
host_specificity:
name: host_specificity
description: 'Level of specificity of symbiont-host interaction: e.g. generalist
(symbiont able to establish associations with distantly related hosts) or species-specific'
title: host specificity
examples:
- value: species-specific
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0001308
alias: host_specificity
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: HostSpecificityEnum
recommended: true
symbiont_host_role:
name: symbiont_host_role
description: Role of the host in the life cycle of the symbiotic organism
title: host of the symbiont role
examples:
- value: intermediate
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
slot_uri: MIXS:0001303
alias: symbiont_host_role
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: SymbiontHostRoleEnum
recommended: true
host_cellular_loc:
name: host_cellular_loc
description: 'The localization of the symbiotic host organism within the host
from which it was sampled: e.g. intracellular if the symbiotic host organism
is localized within the cells or extracellular if the symbiotic host organism
is localized outside of cells'
title: host cellular location
examples:
- value: extracellular
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- location
slot_uri: MIXS:0001313
alias: host_cellular_loc
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: HostCellularLocEnum
recommended: true
association_duration:
name: association_duration
annotations:
Preferred_unit:
tag: Preferred_unit
value: year, day, hour
description: Time spent in host of the symbiotic organism at the time of sampling;
relevant scale depends on symbiotic organism and study
title: duration of association with the host
from_schema: https://w3id.org/mixs
keywords:
- duration
- host
- host.
- period
slot_uri: MIXS:0001299
alias: association_duration
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_of_host_coinf:
name: host_of_host_coinf
annotations:
Expected_value:
tag: Expected_value
value: species name of coinfecting organism(s)
description: The taxonomic name of any coinfecting organism observed in a symbiotic
relationship with the host of the sampled host organism. e.g. where a sample
collected from a host trematode species (A) which was collected from a host_of_host
fish (B) that was also infected with a nematode (C), the value here would be
(C) the nematode {species name} or {common name}. Multiple co-infecting species
may be added in a comma-separated list. For listing symbiotic organisms associated
with the host (A) use the term Observed host symbiont
title: observed coinfecting organisms in host of host
examples:
- value: Maritrema novaezealandense
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- observed
- organism
slot_uri: MIXS:0001310
alias: host_of_host_coinf
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_name:
name: host_of_host_name
description: Common name of the host of the symbiotic host organism
title: host of the symbiotic host common name
examples:
- value: snail
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
slot_uri: MIXS:0001324
alias: host_of_host_name
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_env_loc:
name: host_of_host_env_loc
annotations:
Expected_value:
tag: Expected_value
value: UBERON term(s), multiple values can be separated by pipes
description: For a symbiotic host organism the local anatomical environment within
its host may have causal influences. Report the anatomical entity(s) which are
in the direct environment of the symbiotic host organism being sampled and which
you believe have significant causal influences on your sample or specimen. For
example, if the symbiotic host organism being sampled is an intestinal worm,
its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/)
title: host of the symbiotic host local environmental context
examples:
- value: small intestine[uberon:0002108]
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
- host
- host.
- symbiosis
string_serialization: small intestine [UBERON:0002108]
slot_uri: MIXS:0001325
alias: host_of_host_env_loc
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
multivalued: true
host_of_host_env_med:
name: host_of_host_env_med
annotations:
Expected_value:
tag: Expected_value
value: An ontology term for a material such as a tissue type or excreted substance
description: 'Report the environmental material(s) immediately surrounding the
symbiotic host organism at the time of sampling. This usually will be a tissue
or substance type from the host, but may be another material if the symbiont
is external to the host. We recommend using classes from the UBERON ontology,
but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483)
may also be used. 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. intestines, heart).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. intestines, heart)'
title: host of the symbiotic host environemental medium
examples:
- value: feces[uberon:0001988]
from_schema: https://w3id.org/mixs
keywords:
- environmental
- host
- host.
- symbiosis
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0001326
alias: host_of_host_env_med
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_taxid:
name: host_of_host_taxid
annotations:
Expected_value:
tag: Expected_value
value: NCBI taxon identifier of the host of the symbiotic taxon organism
description: NCBI taxon id of the host of the symbiotic host organism
title: host of the symbiotic host taxon id
examples:
- value: '145637'
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- identifier
- symbiosis
- taxon
string_serialization: '{integer}'
slot_uri: MIXS:0001306
alias: host_of_host_taxid
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_sub_id:
name: host_of_host_sub_id
description: 'A unique identifier by which each host of the symbiotic host organism
subject can be referred to, de-identified, e.g. #H14'
title: host of the symbiotic host subject id
examples:
- value: H3
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- identifier
- symbiosis
slot_uri: MIXS:0001327
alias: host_of_host_sub_id
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_disease:
name: host_of_host_disease
annotations:
Expected_value:
tag: Expected_value
value: disease name or Disease Ontology term
description: List of diseases with which the host of the symbiotic host organism
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 of the symbiotic host disease status
examples:
- value: rabies [DOID:11260]
from_schema: https://w3id.org/mixs
keywords:
- disease
- host
- host.
- status
- symbiosis
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0001319
alias: host_of_host_disease
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
multivalued: true
host_of_host_fam_rel:
name: host_of_host_fam_rel
annotations:
Expected_value:
tag: Expected_value
value: relationship type;arbitrary identifier
description: Familial relationship of the host of the symbiotic host organisms
to other hosts of symbiotic host organism in the same study; can include multiple
relationships
title: host of the symbiotic host family relationship
from_schema: https://w3id.org/mixs
keywords:
- family
- host
- host.
- relationship
- symbiosis
string_serialization: '{text};{text}'
slot_uri: MIXS:0001328
alias: host_of_host_fam_rel
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
multivalued: true
host_of_host_infname:
name: host_of_host_infname
description: Taxonomic name information of the host of the symbiotic host organism
below subspecies level
title: host of the symbiotic host infra-specific name
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
slot_uri: MIXS:0001329
alias: host_of_host_infname
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_infrank:
name: host_of_host_infrank
description: Taxonomic rank information about the host of the symbiotic host organism
below subspecies level, such as variety, form, rank etc
title: host of the symbiotic host infra-specific rank
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- rank
- symbiosis
slot_uri: MIXS:0001330
alias: host_of_host_infrank
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_geno:
name: host_of_host_geno
description: Observed genotype of the host of the symbiotic host organism
title: host of the symbiotic host genotype
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
slot_uri: MIXS:0001331
alias: host_of_host_geno
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_pheno:
name: host_of_host_pheno
annotations:
Expected_value:
tag: Expected_value
value: phenotype of the host of the symbiotic organism; PATO
description: Phenotype of the host of the symbiotic host organism. For phenotypic
quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato
title: host of the symbiotic host phenotype
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
string_serialization: '{term}'
slot_uri: MIXS:0001332
alias: host_of_host_pheno
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_gravid:
name: host_of_host_gravid
annotations:
Expected_value:
tag: Expected_value
value: gravidity status;timestamp
description: Whether or not the host of the symbiotic host organism is gravid,
and if yes date due or date post-conception, specifying which is used
title: host of the symbiotic host gravidity
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- symbiosis
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0001333
alias: host_of_host_gravid
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
host_of_host_totmass:
name: host_of_host_totmass
description: Total mass of the host of the symbiotic host organism at collection,
the unit depends on the host
title: host of the symbiotic host total mass
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- mass
- symbiosis
- total
slot_uri: MIXS:0001334
alias: host_of_host_totmass
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
chem_administration:
name: chem_administration
annotations:
Expected_value:
tag: Expected_value
value: CHEBI;timestamp
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
examples:
- value: agar [CHEBI:2509];2018-05-11T20:00Z
from_schema: https://w3id.org/mixs
keywords:
- administration
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
alias: chem_administration
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
perturbation:
name: perturbation
annotations:
Expected_value:
tag: Expected_value
value: perturbation type name;perturbation interval and duration
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
examples:
- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
from_schema: https://w3id.org/mixs
keywords:
- perturbation
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
alias: perturbation
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
multivalued: true
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
keywords:
- salinity
slot_uri: MIXS:0000183
alias: salinity
owner: MimarksCSymbiontAssociated
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
examples:
- value: aerobic
from_schema: https://w3id.org/mixs
keywords:
- oxygen
- sample
- status
slot_uri: MIXS:0000753
alias: oxy_stat_samp
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OxyStatSampEnum
organism_count:
name: organism_count
annotations:
Expected_value:
tag: Expected_value
value: organism name;measurement value;enumeration
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
keywords:
- count
- organism
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
alias: organism_count
owner: MimarksCSymbiontAssociated
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
multivalued: true
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
keywords:
- sample
- storage
- temperature
slot_uri: MIXS:0000110
alias: samp_store_temp
owner: MimarksCSymbiontAssociated
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
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
examples:
- value: P1Y6M
from_schema: https://w3id.org/mixs
keywords:
- duration
- period
- sample
- storage
slot_uri: MIXS:0000116
alias: samp_store_dur
owner: MimarksCSymbiontAssociated
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
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
annotations:
Expected_value:
tag: Expected_value
value: location name
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
examples:
- value: Freezer no:5
from_schema: https://w3id.org/mixs
keywords:
- location
- sample
- storage
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: MimarksCSymbiontAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
samp_store_sol:
name: samp_store_sol
annotations:
Expected_value:
tag: Expected_value
value: solution name
description: Solution within which sample was stored, if any
title: sample storage solution
examples:
- value: 5% ethanol
from_schema: https://w3id.org/mixs
keywords:
- sample
- storage
slot_uri: MIXS:0001317
alias: samp_store_sol
owner: MimarksCSymbiontAssociated
domain_of:
- SymbiontAssociated
range: string
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
keywords:
- parameter
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
alias: misc_param
owner: MimarksCSymbiontAssociated
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
multivalued: true
class_uri: MIXS:0010009_0016023