Combination: MigsOrg combined with HumanAssociated (MigsOrgHumanAssociated)
MIxS Data that comply with the MigsOrg checklist and the HumanAssociated Extension
Composition
MigsOrg [Checklist] + HumanAssociated [Extension]
Terms
| MIXS ID | Name | Cardinality and Range | Description |
|---|---|---|---|
| MIXS:0001107 | samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... |
| MIXS:0000043 | lib_screen | 0..1 String |
Specific enrichment or screening methods applied before and/or after creating... |
| MIXS:0000062 | ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... |
| MIXS:0000038 | nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... |
| MIXS:0000039 | lib_size | 0..1 Integer |
Total number of clones in the library prepared for the project |
| MIXS:0000057 | assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... |
| MIXS:0000113 | temp | 0..1 recommended String |
Temperature of the sample at the time of sampling |
| MIXS:0000069 | compl_score | 0..1 String |
Completeness score is typically based on either the fraction of markers found... |
| 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..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 | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs |
| MIXS:0000023 | extrachrom_elements | 0..1 recommended Integer |
Do plasmids exist of significant phenotypic consequence (e |
| MIXS:0000024 | estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing |
| MIXS:0000111 | samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... |
| MIXS:0000040 | lib_reads_seqd | 0..1 Integer |
Total number of clones sequenced from the library |
| MIXS:0000002 | samp_collect_device | 0..1 String |
The device used to collect an environmental sample |
| MIXS:0000060 | number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... |
| MIXS:0000041 | lib_layout | 0..1 LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads |
| MIXS:0000056 | assembly_qual | 0..1 String |
The assembly quality category is based on sets of criteria outlined for each ... |
| MIXS:0000025 | ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... |
| MIXS:0000092 | project_name | 1..1 String |
Name of the project within which the sequencing was organized |
| MIXS:0000042 | lib_vector | 0..1 String |
Cloning vector type(s) used in construction of libraries |
| MIXS:0000048 | adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... |
| MIXS:0001321 | neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation |
| MIXS:0000058 | assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters |
| MIXS:0000053 | tax_ident | 0..1 recommended TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG |
| MIXS:0000059 | annot | 0..1 recommended String |
Tool used for annotation, or for cases where annotation was provided by a com... |
| MIXS:0001322 | pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... |
| MIXS:0000020 | subspecf_gen_lin | 0..1 recommended String |
Information about the genetic distinctness of the sequenced organism below th... |
| MIXS:0000061 | feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc |
| MIXS:0000013 | env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... |
| MIXS:0000070 | compl_software | 0..1 String |
Tools used for completion estimate, i |
| MIXS:0000016 | samp_mat_process | 0..1 String |
A brief description of any processing applied to the sample during or after r... |
| MIXS:0000063 | sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used |
| 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..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... |
| MIXS:0001320 | samp_taxon_id | 1..1 String |
NCBI taxon id of the sample |
| MIXS:0000010 | geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... |
| MIXS:0000011 | collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... |
| MIXS:0000050 | seq_meth | 1..1 String |
Sequencing machine used |
| MIXS:0000009 | lat_lon | 1..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..1 String |
Report the major environmental system the sample or specimen came from |
| MIXS:0000064 | tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... |
| MIXS:0000008 | experimental_factor | 0..* String |
Variable aspects of an experiment design that can be used to describe an expe... |
| MIXS:0000091 | associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... |
| MIXS:0000090 | sop | 0..* 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:0000255 | host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... |
| MIXS:0000811 | host_sex | 0..1 String |
Gender or physical sex of the host |
| MIXS:0000031 | host_disease_stat | 0..1 String |
List of diseases with which the host has been diagnosed; can include multiple... |
| MIXS:0000884 | ihmc_medication_code | 0..* Integer |
Can include multiple medication codes |
| MIXS:0000751 | chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... |
| 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:0000869 | host_diet | 0..* String |
Type of diet depending on the host, for animals omnivore, herbivore etc |
| MIXS:0000870 | host_last_meal | 0..* String |
Content of last meal and time since feeding; can include multiple values |
| MIXS:0000872 | host_fam_rel | 0..* String |
Relationships to other hosts in the same study; can include multiple relation... |
| MIXS:0000365 | host_genotype | 0..1 String |
Observed genotype |
| MIXS:0000874 | host_phenotype | 0..1 String |
Phenotype of human or other host |
| MIXS:0000274 | host_body_temp | 0..1 String |
Core body temperature of the host when sample was collected |
| MIXS:0000262 | smoker | 0..1 Boolean |
Specification of smoking status |
| MIXS:0000265 | host_hiv_stat | 0..1 String |
HIV status of subject, if yes HAART initiation status should also be indicate... |
| MIXS:0000894 | drug_usage | 0..* String |
Any drug used by subject and the frequency of usage; can include multiple dru... |
| MIXS:0000317 | host_body_mass_index | 0..1 String |
Body mass index, calculated as weight/(height)squared |
| MIXS:0000266 | diet_last_six_month | 0..1 String |
Specification of major diet changes in the last six months, if yes the change... |
| MIXS:0000295 | weight_loss_3_month | 0..1 String |
Specification of weight loss in the last three months, if yes should be furth... |
| MIXS:0000895 | ethnicity | 0..* String |
A category of people who identify with each other, usually on the basis of pr... |
| MIXS:0000896 | host_occupation | 0..1 String |
Most frequent job performed by subject |
| MIXS:0000267 | pet_farm_animal | 0..* String |
Specification of presence of pets or farm animals in the environment of subje... |
| MIXS:0000268 | travel_out_six_month | 0..* String |
Specification of the countries travelled in the last six months; can include ... |
| MIXS:0000326 | twin_sibling | 0..1 Boolean |
Specification of twin sibling presence |
| MIXS:0000897 | medic_hist_perform | 0..1 Boolean |
Whether full medical history was collected |
| MIXS:0000898 | study_complt_stat | 0..1 String |
Specification of study completion status, if no the reason should be specifie... |
| MIXS:0000269 | pulmonary_disord | 0..* String |
History of pulmonary disorders; can include multiple disorders |
| MIXS:0000270 | nose_throat_disord | 0..* String |
History of nose-throat disorders; can include multiple disorders, The terms ... |
| MIXS:0000271 | blood_blood_disord | 0..* String |
History of blood disorders; can include multiple disorders |
| MIXS:0000333 | host_pulse | 0..1 String |
Resting pulse, measured as beats per minute |
| MIXS:0000272 | gestation_state | 0..1 String |
Specification of the gestation state |
| MIXS:0000273 | maternal_health_stat | 0..1 String |
Specification of the maternal health status |
| MIXS:0000275 | foetal_health_stat | 0..1 String |
Specification of foetal health status, should also include abortion |
| MIXS:0000276 | amniotic_fluid_color | 0..1 String |
Specification of the color of the amniotic fluid sample |
| MIXS:0000277 | kidney_disord | 0..* String |
History of kidney disorders; can include multiple disorders |
| MIXS:0000278 | urogenit_tract_disor | 0..* String |
History of urogenital tract disorders; can include multiple disorders |
| MIXS:0000899 | urine_collect_meth | 0..1 UrineCollectMethEnum |
Specification of urine collection method |
| MIXS:0000754 | perturbation | 0..* 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 | 0..* 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:0001298 | host_symbiont | 0..* String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... |
| MIXS:0000755 | samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room |
| MIXS:0000752 | misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... |
LinkML Source
Direct
name: MigsOrgHumanAssociated
description: MIxS Data that comply with the MigsOrg checklist and the HumanAssociated
Extension
title: MigsOrg combined with HumanAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: HumanAssociated
mixins:
- MigsOrg
class_uri: MIXS:0010006_0016003
Induced
name: MigsOrgHumanAssociated
description: MIxS Data that comply with the MigsOrg checklist and the HumanAssociated
Extension
title: MigsOrg combined with HumanAssociated
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: HumanAssociated
mixins:
- MigsOrg
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: MigsOrgHumanAssociated
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
annotations:
Expected_value:
tag: Expected_value
value: screening strategy name
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
examples:
- value: enriched, screened, normalized
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
string_serialization: '{text}'
slot_uri: MIXS:0000043
alias: lib_screen
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
ref_db:
name: ref_db
annotations:
Expected_value:
tag: Expected_value
value: names, versions, and references of databases
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
examples:
- value: pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017
doi:10.1093/nar/gkw975
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- database
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
alias: ref_db
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
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
slot_uri: MIXS:0000038
alias: nucl_acid_amp
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
examples:
- value: '50'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
- size
slot_uri: MIXS:0000039
alias: lib_size
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
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
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
alias: assembly_name
owner: MigsOrgHumanAssociated
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
slot_uri: MIXS:0000113
alias: temp
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
compl_score:
name: compl_score
annotations:
Expected_value:
tag: Expected_value
value: quality;percent completeness
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
examples:
- value: med;60%
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- score
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
alias: compl_score
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000037
alias: nucl_acid_ext
owner: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000003
alias: isol_growth_condt
owner: MigsOrgHumanAssociated
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
slot_uri: MIXS:0000094
alias: alt
owner: MigsOrgHumanAssociated
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
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: true
alias: source_mat_id
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
extrachrom_elements:
name: extrachrom_elements
description: Do plasmids exist of significant phenotypic consequence (e.g. ones
that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
(borrelia has 15+ plasmids)
title: extrachromosomal elements
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000023
alias: extrachrom_elements
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MimarksC
range: integer
recommended: true
estimated_size:
name: estimated_size
annotations:
Expected_value:
tag: Expected_value
value: number of base pairs
description: The estimated size of the genome prior to sequencing. Of particular
importance in the sequencing of (eukaryotic) genome which could remain in draft
form for a long or unspecified period
title: estimated size
examples:
- value: 300000 bp
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
keywords:
- size
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
alias: estimated_size
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
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: MigsOrgHumanAssociated
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
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
examples:
- value: '20'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000040
alias: lib_reads_seqd
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
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
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
alias: samp_collect_device
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
examples:
- value: '40'
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- number
slot_uri: MIXS:0000060
alias: number_contig
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
examples:
- value: paired
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
slot_uri: MIXS:0000041
alias: lib_layout
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LibLayoutEnum
assembly_qual:
name: assembly_qual
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the large subunit (LSU) RNA,
small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether
it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many
fragments with little to no review of assembly other than reporting of standard
assembly statistics. Low Quality Draft:Many fragments with little to no review
of assembly other than reporting of standard assembly statistics. Assembly statistics
include, but are not limited to total assembly size, number of contigs, contig
N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities, with extensive
manual review and editing to annotate putative gene functions and transcriptional
units. High-quality draft genome: One or multiple fragments, totaling 90%
of the expected genome or replicon sequence or predicted complete. Genome fragment(s):
One or multiple fragments, totalling < 90% of the expected genome or replicon
sequence, or for which no genome size could be estimated'
title: assembly quality
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
draft genome|Low-quality draft genome|Genome fragment(s)]'
slot_uri: MIXS:0000056
alias: assembly_qual
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
examples:
- value: doi:10.1016/j.syapm.2018.01.009
in_subset:
- nucleic acid sequence source
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000025
alias: ref_biomaterial
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs
keywords:
- project
slot_uri: MIXS:0000092
alias: project_name
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: true
lib_vector:
name: lib_vector
annotations:
Expected_value:
tag: Expected_value
value: vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
examples:
- value: Bacteriophage P1
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- library
string_serialization: '{text}'
slot_uri: MIXS:0000042
alias: lib_vector
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
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
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
alias: adapters
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- 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
keywords:
- type
slot_uri: MIXS:0001321
alias: neg_cont_type
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NegContTypeEnum
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
slot_uri: MIXS:0000058
alias: assembly_software
owner: MigsOrgHumanAssociated
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
slot_uri: MIXS:0000053
alias: tax_ident
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TaxIdentEnum
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
string_serialization: '{text}'
slot_uri: MIXS:0000059
alias: annot
owner: MigsOrgHumanAssociated
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
keywords:
- type
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
alias: pos_cont_type
owner: MigsOrgHumanAssociated
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
string_serialization: '{rank name}:{text}'
slot_uri: MIXS:0000020
alias: subspecf_gen_lin
owner: MigsOrgHumanAssociated
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
examples:
- value: Prodigal;2.6.3;default parameters
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- feature
- predict
slot_uri: MIXS:0000061
alias: feat_pred
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
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
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000013
alias: env_local_scale
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
compl_software:
name: compl_software
annotations:
Expected_value:
tag: Expected_value
value: names and versions of software(s) used
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
examples:
- value: checkm
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- software
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
alias: compl_software
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
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: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
examples:
- value: HMMER3;3.1b2;hmmsearch, cutoff of 50 on score
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000063
alias: sim_search_meth
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
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
slot_uri: MIXS:0000018
alias: depth
owner: MigsOrgHumanAssociated
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
slot_uri: MIXS:0001225
alias: samp_collect_method
owner: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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
keywords:
- geographic
- location
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: MigsOrgHumanAssociated
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
slot_uri: MIXS:0000093
alias: elev
owner: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
examples:
- value: vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification,
default parameters)
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- classification
- taxon
slot_uri: MIXS:0000064
alias: tax_class
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
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
multivalued: true
alias: experimental_factor
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
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
keywords:
- resource
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
multivalued: true
alias: associated_resource
owner: MigsOrgHumanAssociated
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
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: true
alias: sop
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: 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: MPI123
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000861
alias: host_subject_id
owner: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
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: 30 years
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000255
alias: host_age
owner: MigsOrgHumanAssociated
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_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
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: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
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: measles [DOID:8622]
from_schema: https://w3id.org/mixs
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
alias: host_disease_stat
owner: MigsOrgHumanAssociated
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
ihmc_medication_code:
name: ihmc_medication_code
description: Can include multiple medication codes
title: IHMC medication code
examples:
- value: '810'
from_schema: https://w3id.org/mixs
keywords:
- code
slot_uri: MIXS:0000884
multivalued: true
alias: ihmc_medication_code
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: integer
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
multivalued: true
alias: chem_administration
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
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: Lung parenchyma [fma27360]
from_schema: https://w3id.org/mixs
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000867
alias: host_body_site
owner: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
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: 65 kilogram
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000263
alias: host_tot_mass
owner: MigsOrgHumanAssociated
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
description: The height of subject
title: host height
examples:
- value: 1.75 meter
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000264
alias: host_height
owner: MigsOrgHumanAssociated
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_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: high-fat
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000869
multivalued: true
alias: host_diet
owner: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
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: french fries;P5H30M
from_schema: https://w3id.org/mixs
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000870
multivalued: true
alias: host_last_meal
owner: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
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: mother;ID298
from_schema: https://w3id.org/mixs
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
multivalued: true
alias: host_fam_rel
owner: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
examples:
- value: ST1
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000365
alias: host_genotype
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
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: Tinnitus [HP:0000360]
from_schema: https://w3id.org/mixs
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
alias: host_phenotype
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
host_body_temp:
name: host_body_temp
description: Core body temperature of the host when sample was collected
title: host body temperature
examples:
- value: 36.5 degree Celsius
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000274
alias: host_body_temp
owner: MigsOrgHumanAssociated
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
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
smoker:
name: smoker
description: Specification of smoking status
title: smoker
examples:
- value: 'yes'
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000262
alias: smoker
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: boolean
host_hiv_stat:
name: host_hiv_stat
annotations:
Expected_value:
tag: Expected_value
value: HIV status;HAART initiation status
description: HIV status of subject, if yes HAART initiation status should also
be indicated as [YES or NO]
title: host HIV status
examples:
- value: yes;yes
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
- status
string_serialization: '{boolean};{boolean}'
slot_uri: MIXS:0000265
alias: host_hiv_stat
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
drug_usage:
name: drug_usage
annotations:
Expected_value:
tag: Expected_value
value: drug name;frequency
description: Any drug used by subject and the frequency of usage; can include
multiple drugs used
title: drug usage
examples:
- value: Lipitor;2/day
from_schema: https://w3id.org/mixs
keywords:
- drug
- use
string_serialization: '{text};{integer}/[year|month|week|day|hour]'
slot_uri: MIXS:0000894
multivalued: true
alias: drug_usage
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
host_body_mass_index:
name: host_body_mass_index
annotations:
Preferred_unit:
tag: Preferred_unit
value: kilogram per square meter
description: Body mass index, calculated as weight/(height)squared
title: host body-mass index
examples:
- value: 22 kilogram per square meter
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000317
alias: host_body_mass_index
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
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
diet_last_six_month:
name: diet_last_six_month
annotations:
Expected_value:
tag: Expected_value
value: diet change;current diet
description: Specification of major diet changes in the last six months, if yes
the change should be specified
title: major diet change in last six months
examples:
- value: yes;vegetarian diet
from_schema: https://w3id.org/mixs
keywords:
- diet
- months
string_serialization: '{boolean};{text}'
slot_uri: MIXS:0000266
alias: diet_last_six_month
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
weight_loss_3_month:
name: weight_loss_3_month
annotations:
Expected_value:
tag: Expected_value
value: weight loss specification;measurement value
Preferred_unit:
tag: Preferred_unit
value: kilogram, gram
description: Specification of weight loss in the last three months, if yes should
be further specified to include amount of weight loss
title: weight loss in last three months
examples:
- value: yes;5 kilogram
from_schema: https://w3id.org/mixs
keywords:
- months
- weight
string_serialization: '{boolean};{float} {unit}'
slot_uri: MIXS:0000295
alias: weight_loss_3_month
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
ethnicity:
name: ethnicity
annotations:
Expected_value:
tag: Expected_value
value: text recommend from Wikipedia list
description: A category of people who identify with each other, usually on the
basis of presumed similarities such as a common language, ancestry, history,
society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups
title: ethnicity
examples:
- value: native american
from_schema: https://w3id.org/mixs
string_serialization: '{text}'
slot_uri: MIXS:0000895
multivalued: true
alias: ethnicity
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
host_occupation:
name: host_occupation
description: Most frequent job performed by subject
title: host occupation
comments:
- Couldn't convert host_occupation with value veterinary to integer
- almost all host_occupation values in the NCBI biosample_set are strings, not
integers
examples:
- value: veterinary
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000896
alias: host_occupation
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
pet_farm_animal:
name: pet_farm_animal
annotations:
Expected_value:
tag: Expected_value
value: presence status;type of animal or pet
description: Specification of presence of pets or farm animals in the environment
of subject, if yes the animals should be specified; can include multiple animals
present
title: presence of pets or farm animals
examples:
- value: yes; 5 cats
from_schema: https://w3id.org/mixs
keywords:
- animal
- farm
- presence
string_serialization: '{boolean};{text}'
slot_uri: MIXS:0000267
multivalued: true
alias: pet_farm_animal
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
travel_out_six_month:
name: travel_out_six_month
annotations:
Expected_value:
tag: Expected_value
value: country name
description: Specification of the countries travelled in the last six months;
can include multiple travels
title: travel outside the country in last six months
from_schema: https://w3id.org/mixs
keywords:
- months
string_serialization: '{text}'
slot_uri: MIXS:0000268
multivalued: true
alias: travel_out_six_month
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
twin_sibling:
name: twin_sibling
description: Specification of twin sibling presence
title: twin sibling presence
examples:
- value: 'yes'
from_schema: https://w3id.org/mixs
keywords:
- presence
slot_uri: MIXS:0000326
alias: twin_sibling
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: boolean
medic_hist_perform:
name: medic_hist_perform
description: Whether full medical history was collected
title: medical history performed
examples:
- value: '1'
from_schema: https://w3id.org/mixs
keywords:
- history
slot_uri: MIXS:0000897
alias: medic_hist_perform
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: boolean
study_complt_stat:
name: study_complt_stat
annotations:
Expected_value:
tag: Expected_value
value: YES or NO due to (1)adverse event (2) non-compliance (3) lost to follow
up (4)other-specify
description: Specification of study completion status, if no the reason should
be specified
title: study completion status
examples:
- value: no;non-compliance
from_schema: https://w3id.org/mixs
keywords:
- status
string_serialization: '{boolean};[adverse event|non-compliance|lost to follow
up|other-specify]'
slot_uri: MIXS:0000898
alias: study_complt_stat
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
pulmonary_disord:
name: pulmonary_disord
description: History of pulmonary disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
lung disease (https://disease-ontology.org/?id=DOID:850)
title: lung/pulmonary disorder
from_schema: https://w3id.org/mixs
keywords:
- disorder
slot_uri: MIXS:0000269
multivalued: true
alias: pulmonary_disord
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
nose_throat_disord:
name: nose_throat_disord
description: History of nose-throat disorders; can include multiple disorders, The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory
tract disease (https://disease-ontology.org/?id=DOID:974)
title: nose throat disorder
from_schema: https://w3id.org/mixs
keywords:
- disorder
slot_uri: MIXS:0000270
multivalued: true
alias: nose_throat_disord
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
blood_blood_disord:
name: blood_blood_disord
description: History of blood disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
hematopoietic system disease (https://disease-ontology.org/?id=DOID:74)
title: blood/blood disorder
from_schema: https://w3id.org/mixs
keywords:
- disorder
slot_uri: MIXS:0000271
multivalued: true
alias: blood_blood_disord
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
host_pulse:
name: host_pulse
annotations:
Preferred_unit:
tag: Preferred_unit
value: beats per minute
description: Resting pulse, measured as beats per minute
title: host pulse
examples:
- value: 65 beats per minute
from_schema: https://w3id.org/mixs
keywords:
- host
- host.
slot_uri: MIXS:0000333
alias: host_pulse
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
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
gestation_state:
name: gestation_state
description: Specification of the gestation state
title: amniotic fluid/gestation state
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000272
alias: gestation_state
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
maternal_health_stat:
name: maternal_health_stat
description: Specification of the maternal health status
title: amniotic fluid/maternal health status
from_schema: https://w3id.org/mixs
keywords:
- status
slot_uri: MIXS:0000273
alias: maternal_health_stat
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
foetal_health_stat:
name: foetal_health_stat
description: Specification of foetal health status, should also include abortion
title: amniotic fluid/foetal health status
from_schema: https://w3id.org/mixs
keywords:
- status
slot_uri: MIXS:0000275
alias: foetal_health_stat
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
amniotic_fluid_color:
name: amniotic_fluid_color
description: Specification of the color of the amniotic fluid sample
title: amniotic fluid/color
from_schema: https://w3id.org/mixs
slot_uri: MIXS:0000276
alias: amniotic_fluid_color
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
kidney_disord:
name: kidney_disord
description: History of kidney disorders; can include multiple disorders. The
terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
kidney disease (https://disease-ontology.org/?id=DOID:557)
title: urine/kidney disorder
from_schema: https://w3id.org/mixs
keywords:
- disorder
slot_uri: MIXS:0000277
multivalued: true
alias: kidney_disord
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
urogenit_tract_disor:
name: urogenit_tract_disor
description: History of urogenital tract disorders; can include multiple disorders.
The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
urinary system disease (https://disease-ontology.org/?id=DOID:18)
title: urine/urogenital tract disorder
from_schema: https://w3id.org/mixs
keywords:
- disorder
slot_uri: MIXS:0000278
multivalued: true
alias: urogenit_tract_disor
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: string
urine_collect_meth:
name: urine_collect_meth
description: Specification of urine collection method
title: urine/collection method
examples:
- value: catheter
from_schema: https://w3id.org/mixs
keywords:
- method
slot_uri: MIXS:0000899
alias: urine_collect_meth
owner: MigsOrgHumanAssociated
domain_of:
- HumanAssociated
range: UrineCollectMethEnum
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
multivalued: true
alias: perturbation
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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
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
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
multivalued: true
alias: organism_count
owner: MigsOrgHumanAssociated
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
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: MigsOrgHumanAssociated
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: MigsOrgHumanAssociated
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
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
string_serialization: '{text}'
slot_uri: MIXS:0001298
multivalued: true
alias: host_symbiont
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
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
string_serialization: '{text}'
slot_uri: MIXS:0000755
alias: samp_store_loc
owner: MigsOrgHumanAssociated
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
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
multivalued: true
alias: misc_param
owner: MigsOrgHumanAssociated
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
class_uri: MIXS:0010006_0016003