Class: MiuvigHumanSkin
MIxS data that complies with the Miuvig checklist and the HumanSkin Extension
URI: MIXS:0010012_0016006
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | Miuvig |
| temp | 0..1 recommended String |
Temperature of the sample at the time of sampling | Miuvig, HumanSkin |
| assembly_qual | 1..1 String |
The assembly quality category is based on sets of criteria outlined for each ... | Miuvig |
| collection_date | 1..1 Datetime |
The time of sampling, either as an instance (single point in time) or interva... | Miuvig |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Miuvig |
| tax_ident | 0..1 TAXIDENTENUM |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | Miuvig |
| samp_vol_we_dna_ext | 0..1 String |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | Miuvig, HumanSkin |
| compl_appr | 0..1 recommended COMPLAPPRENUM |
The approach used to determine the completeness of a given genomic assembly, ... | Miuvig |
| trna_ext_software | 0..1 String |
Tools used for tRNA identification | Miuvig |
| source_mat_id | 0..* recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | Miuvig |
| tax_class | 0..1 recommended String |
Method used for taxonomic classification, along with reference database used,... | Miuvig |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | Miuvig |
| sim_search_meth | 0..1 recommended String |
Tool used to compare ORFs with database, along with version and cutoffs used | Miuvig |
| number_contig | 1..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | Miuvig |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | Miuvig |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | Miuvig, HumanSkin |
| host_spec_range | 0..* String |
The range and diversity of host species that an organism is capable of infect... | Miuvig |
| samp_collect_device | 0..1 recommended String |
The device used to collect an environmental sample | Miuvig |
| lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project | Miuvig |
| compl_score | 0..1 recommended String |
Completeness score is typically based on either the fraction of markers found... | Miuvig |
| samp_collect_method | 0..1 recommended String |
The method employed for collecting the sample | Miuvig |
| lib_layout | 0..1 recommended LIBLAYOUTENUM |
Specify whether to expect single, paired, or other configuration of reads | Miuvig |
| annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... | Miuvig |
| seq_meth | 1..1 String |
Sequencing machine used | Miuvig |
| depth | 0..1 recommended String |
The vertical distance below local surface | Miuvig |
| samp_size | 0..1 recommended String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | Miuvig |
| specific_host | 0..1 String |
Report the host's taxonomic name and/or NCBI taxonomy ID | Miuvig |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | Miuvig |
| alt | 0..1 recommended String |
Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... | Miuvig |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | Miuvig |
| size_frac | 0..1 recommended String |
Filtering pore size used in sample preparation | Miuvig |
| trnas | 0..1 String |
The total number of tRNAs identified from the SAG or MAG | Miuvig |
| feat_pred | 0..1 recommended String |
Method used to predict UViGs features such as ORFs, integration site, etc | Miuvig |
| neg_cont_type | 0..1 recommended NEGCONTTYPEENUM |
The substance or equipment used as a negative control in an investigation | Miuvig |
| biotic_relationship | 0..1 BIOTICRELATIONSHIPENUM |
Description of relationship(s) between the subject organism and other organis... | Miuvig |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen s local vic... | Miuvig |
| estimated_size | 0..1 String |
The estimated size of the genome prior to sequencing | Miuvig |
| virus_enrich_appr | 1..1 VIRUSENRICHAPPRENUM |
List of approaches used to enrich the sample for viruses, if any | Miuvig |
| samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... | Miuvig |
| experimental_factor | 0..* recommended String |
Variable aspects of an experiment design that can be used to describe an expe... | Miuvig |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | Miuvig |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | Miuvig |
| lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... | Miuvig |
| samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... | Miuvig, HumanSkin |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | Miuvig |
| lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries | Miuvig |
| ref_db | 0..1 recommended String |
List of database(s) used for ORF annotation, along with version number and re... | Miuvig |
| elev | 0..1 recommended String |
Elevation of the sampling site is its height above a fixed reference point, m... | Miuvig |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | Miuvig |
| compl_software | 0..1 String |
Tools used for completion estimate, i | Miuvig |
| host_disease_stat | 0..1 recommended String |
List of diseases with which the host has been diagnosed; can include multiple... | Miuvig, HumanSkin |
| lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library | Miuvig |
| mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | Miuvig |
| pathogenicity | 0..1 String |
To what is the entity pathogenic | Miuvig |
| source_uvig | 1..1 String |
Type of dataset from which the UViG was obtained | Miuvig |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | Miuvig |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | Miuvig |
| sort_tech | 0..1 recommended SORTTECHENUM |
Method used to sort/isolate cells or particles of interest | Miuvig |
| sc_lysis_approach | 0..1 recommended SCLYSISAPPROACHENUM |
Method used to free DNA from interior of the cell(s) or particle(s) | Miuvig |
| sc_lysis_method | 0..1 recommended String |
Name of the kit or standard protocol used for cell(s) or particle(s) lysis | Miuvig |
| wga_amp_appr | 0..1 recommended WGAAMPAPPRENUM |
Method used to amplify genomic DNA in preparation for sequencing | Miuvig |
| wga_amp_kit | 0..1 recommended String |
Kit used to amplify genomic DNA in preparation for sequencing | Miuvig |
| bin_param | 0..1 recommended BINPARAMENUM |
The parameters that have been applied during the extraction of genomes from m... | Miuvig |
| bin_software | 0..1 recommended String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... | Miuvig |
| reassembly_bin | 0..1 recommended Boolean |
Has an assembly been performed on a genome bin extracted from a metagenomic a... | Miuvig |
| mag_cov_software | 0..1 MAGCOVSOFTWAREENUM |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... | Miuvig |
| vir_ident_software | 1..1 String |
Tool(s) used for the identification of UViG as a viral genome, software or pr... | Miuvig |
| pred_genome_type | 1..1 String |
Type of genome predicted for the UViG | Miuvig |
| pred_genome_struc | 1..1 PREDGENOMESTRUCENUM |
Expected structure of the viral genome | Miuvig |
| detec_type | 1..1 String |
Type of UViG detection | Miuvig |
| otu_class_appr | 0..1 recommended String |
Cutoffs and approach used when clustering species-level OTUs | Miuvig |
| otu_seq_comp_appr | 0..1 recommended String |
Tool and thresholds used to compare sequences when computing "species-level" ... | Miuvig |
| otu_db | 0..1 recommended String |
Reference database (i | Miuvig |
| host_pred_appr | 0..1 recommended HOSTPREDAPPRENUM |
Tool or approach used for host prediction | Miuvig |
| host_pred_est_acc | 0..1 recommended String |
For each tool or approach used for host prediction, estimated false discovery... | Miuvig |
| associated_resource | 0..* recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | Miuvig |
| sop | 0..* recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | Miuvig |
| dermatology_disord | 0..* String |
History of dermatology disorders; can include multiple disorders | HumanSkin |
| time_since_last_wash | 0..1 String |
Specification of the time since last wash | HumanSkin |
| dominant_hand | 0..1 DOMINANTHANDENUM |
Dominant hand of the subject | HumanSkin |
| host_subject_id | 0..1 String |
A unique identifier by which each subject can be referred to, de-identified | HumanSkin |
| host_age | 0..1 String |
Age of host at the time of sampling; relevant scale depends on species and st... | HumanSkin |
| host_sex | 0..1 String |
Gender or physical sex of the host | HumanSkin |
| ihmc_medication_code | 0..* Integer |
Can include multiple medication codes | HumanSkin |
| chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... | HumanSkin |
| host_body_site | 0..1 String |
Name of body site where the sample was obtained from, such as a specific orga... | HumanSkin |
| host_body_product | 0..1 String |
Substance produced by the body, e | HumanSkin |
| host_tot_mass | 0..1 String |
Total mass of the host at collection, the unit depends on host | HumanSkin |
| host_height | 0..1 String |
The height of subject | HumanSkin |
| host_diet | 0..* String |
Type of diet depending on the host, for animals omnivore, herbivore etc | HumanSkin |
| host_last_meal | 0..* String |
Content of last meal and time since feeding; can include multiple values | HumanSkin |
| host_fam_rel | 0..* String |
Relationships to other hosts in the same study; can include multiple relation... | HumanSkin |
| host_genotype | 0..1 String |
Observed genotype | HumanSkin |
| host_phenotype | 0..1 String |
Phenotype of human or other host | HumanSkin |
| host_body_temp | 0..1 String |
Core body temperature of the host when sample was collected | HumanSkin |
| host_body_mass_index | 0..1 String |
Body mass index, calculated as weight/(height)squared | HumanSkin |
| ethnicity | 0..* String |
A category of people who identify with each other, usually on the basis of pr... | HumanSkin |
| host_occupation | 0..1 String |
Most frequent job performed by subject | HumanSkin |
| medic_hist_perform | 0..1 Boolean |
Whether full medical history was collected | HumanSkin |
| host_pulse | 0..1 String |
Resting pulse, measured as beats per minute | HumanSkin |
| perturbation | 0..* String |
Type of perturbation, e | HumanSkin |
| salinity | 0..1 String |
The total concentration of all dissolved salts in a liquid or solid sample | HumanSkin |
| oxy_stat_samp | 0..1 OXYSTATSAMPENUM |
Oxygenation status of sample | HumanSkin |
| organism_count | 0..* String |
Total cell count of any organism (or group of organisms) per gram, volume or ... | HumanSkin |
| samp_store_temp | 0..1 String |
Temperature at which sample was stored, e | HumanSkin |
| samp_store_dur | 0..1 String |
Duration for which the sample was stored | HumanSkin |
| samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | HumanSkin |
| host_symbiont | 0..* String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... | HumanSkin |
| misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... | HumanSkin |
Usages
| used by | used in | type | used |
|---|---|---|---|
| MixsCompliantData | miuvig_human_skin_data | range | MiuvigHumanSkin |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/mixs-6-2-rc
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:0010012_0016006 |
| native | mixs_6_2_rc:MiuvigHumanSkin |
LinkML Source
Direct
name: MiuvigHumanSkin
description: MIxS data that complies with the Miuvig checklist and the HumanSkin Extension
title: Miuvig combined with HumanSkin
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanSkin
mixins:
- Miuvig
class_uri: MIXS:0010012_0016006
Induced
name: MiuvigHumanSkin
description: MIxS data that complies with the Miuvig checklist and the HumanSkin Extension
title: Miuvig combined with HumanSkin
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: HumanSkin
mixins:
- Miuvig
attributes:
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: MiuvigHumanSkin
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
temp:
name: temp
description: Temperature of the sample at the time of sampling
title: temperature
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
assembly_qual:
name: assembly_qual
description: 'The assembly quality category is based on sets of criteria outlined
for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
contiguous sequence per replicon without gaps or ambiguities with a consensus
error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
review of assembly other than reporting of standard assembly statistics. Low
Quality Draft:Many fragments with little to no review of assembly other than
reporting of standard assembly statistics. Assembly statistics include, but
are not limited to total assembly size, number of contigs, contig N50/L50, and
maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
per replicon without gaps or ambiguities, with extensive manual review and editing
to annotate putative gene functions and transcriptional units. High-quality
draft genome: One or multiple fragments, totaling 90% of the expected genome
or replicon sequence or predicted complete. Genome fragment(s): One or multiple
fragments, totalling < 90% of the expected genome or replicon sequence, or for
which no genome size could be estimated'
title: assembly quality
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
draft genome|Low-quality draft genome|Genome fragment(s)]'
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: true
collection_date:
name: collection_date
description: 'The time of sampling, either as an instance (single point in time)
or interval. In case no exact time is available, the date/time can be right
truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
title: collection date
examples:
- value: '2013-03-25T12:42:31+01:00'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- SymbiontAssociated
range: datetime
required: true
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: MiuvigHumanSkin
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
tax_ident:
name: tax_ident
description: The phylogenetic marker(s) used to assign an organism name to the
SAG or MAG
title: taxonomic identity marker
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000053
alias: tax_ident
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: TAX_IDENT_ENUM
required: false
recommended: false
samp_vol_we_dna_ext:
name: samp_vol_we_dna_ext
description: 'Volume (ml) or mass (g) of total collected sample processed for
DNA extraction. Note: total sample collected should be entered under the term
Sample Size (MIXS:0000001)'
title: sample volume or weight for DNA extraction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
compl_appr:
name: compl_appr
description: The approach used to determine the completeness of a given genomic
assembly, which would typically make use of a set of conserved marker genes
or a closely related reference genome. For UViG completeness, include reference
genome or group used, and contig feature suggesting a complete genome
title: completeness approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000071
alias: compl_appr
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Misag
- Miuvig
range: COMPL_APPR_ENUM
recommended: true
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000068
multivalued: false
alias: trna_ext_software
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
source_mat_id:
name: source_mat_id
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2)
title: source material identifiers
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: true
alias: source_mat_id
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- SymbiontAssociated
range: string
recommended: true
tax_class:
name: tax_class
description: Method used for taxonomic classification, along with reference database
used, classification rank, and thresholds used to classify new genomes
title: taxonomic classification
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report
title: reference for biomaterial
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
required: false
recommended: false
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}$
interpolated: true
partial_match: true
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: integer
required: true
env_broad_scale:
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came
from. The system(s) identified should have a coarse spatial grain, to provide
the general environmental context of where the sampling was done (e.g. in the
desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: MiuvigHumanSkin
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
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
examples:
- value: Forest soil metagenome
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: MiuvigHumanSkin
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
host_spec_range:
name: host_spec_range
description: The range and diversity of host species that an organism is capable
of infecting, defined by NCBI taxonomy identifier
title: host specificity or range
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer}'
slot_uri: MIXS:0000030
multivalued: true
alias: host_spec_range
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: false
samp_collect_device:
name: samp_collect_device
description: The device used to collect an environmental sample. This field accepts
terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
title: sample collection device
examples:
- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collect_device
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
lib_size:
name: lib_size
description: Total number of clones in the library prepared for the project
title: library size
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
compl_score:
name: compl_score
description: 'Completeness score is typically based on either the fraction of
markers found as compared to a database or the percent of a genome found as
compared to a closely related reference genome. High Quality Draft: >90%, Medium
Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
completeness scores'
title: completeness score
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[high|med|low];{percentage}'
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
recommended: true
samp_collect_method:
name: samp_collect_method
description: The method employed for collecting the sample
title: sample collection method
examples:
- value: swabbing
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collect_method
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{PMID}|{DOI}|{URL}|{text}$
interpolated: true
partial_match: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: LIB_LAYOUT_ENUM
recommended: true
annot:
name: annot
description: Tool used for annotation, or for cases where annotation was provided
by a community jamboree or model organism database rather than by a specific
submitter
title: annotation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
required: false
recommended: false
seq_meth:
name: seq_meth
description: Sequencing machine used. Where possible the term should be taken
from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
title: sequencing method
examples:
- value: 454 Genome Sequencer FLX [OBI:0000702]
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: MiuvigHumanSkin
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
depth:
name: depth
description: The vertical distance below local surface. For sediment or soil samples
depth is measured from sediment or soil surface, respectively. Depth can be
reported as an interval for subsurface samples
title: depth
examples:
- value: 10 meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: MiuvigHumanSkin
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_size:
name: samp_size
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample collected
title: amount or size of sample collected
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
specific_host:
name: specific_host
description: Report the host's taxonomic name and/or NCBI taxonomy ID
title: host scientific name
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}|{NCBI taxid}'
slot_uri: MIXS:0000029
multivalued: false
alias: specific_host
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsPl
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: false
pos_cont_type:
name: pos_cont_type
description: The substance, mixture, product, or apparatus used to verify that
a process which is part of an investigation delivers a true positive
title: positive control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
alt:
name: alt
description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
balloons and heights of places such as atmospheric layers and clouds. It is
used to measure the height of an object which is above the earth's surface.
In this context, the altitude measurement is the vertical distance between the
earth's surface above sea level and the sampled position in the air
title: altitude
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: MiuvigHumanSkin
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
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: MiuvigHumanSkin
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
size_frac:
name: size_frac
description: Filtering pore size used in sample preparation
title: size fraction selected
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: MiuvigHumanSkin
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
range: string
recommended: true
trnas:
name: trnas
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer}'
slot_uri: MIXS:0000067
multivalued: false
alias: trnas
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc
title: feature prediction
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{software};{version};{parameters}$
interpolated: true
partial_match: true
neg_cont_type:
name: neg_cont_type
annotations:
Expected_value:
tag: Expected_value
value: enumeration or text
description: The substance or equipment used as a negative control in an investigation
title: negative control type
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: NEG_CONT_TYPE_ENUM
recommended: true
biotic_relationship:
name: biotic_relationship
description: Description of relationship(s) between the subject organism and other
organism(s) it is associated with. E.g., parasite on species X; mutualist with
species Y. The target organism is the subject of the relationship, and the other
organism(s) is the object
title: observed biotic relationship
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000028
multivalued: false
alias: biotic_relationship
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsVi
- MimarksC
- Miuvig
- Agriculture
range: BIOTIC_RELATIONSHIP_ENUM
required: false
recommended: false
env_local_scale:
name: env_local_scale
annotations:
Expected_value:
tag: Expected_value
value: Environmental entities having causal influences upon the entity at
time of sampling
description: 'Report the entity or entities which are in the sample or specimen
s local vicinity and which you believe have significant causal influences on
your sample or specimen. We recommend using EnvO terms which are of smaller
spatial grain than your entry for env_broad_scale. Terms, such as anatomical
sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
UBERON) are accepted in this field. EnvO documentation about how to use the
field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: local environmental context
examples:
- value: hillside [ENVO:01000333]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
estimated_size:
name: estimated_size
description: The estimated size of the genome prior to sequencing. Of particular
importance in the sequencing of (eukaryotic) genome which could remain in draft
form for a long or unspecified period
title: estimated size
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{integer} bp'
slot_uri: MIXS:0000024
multivalued: false
alias: estimated_size
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Miuvig
range: string
required: false
recommended: false
virus_enrich_appr:
name: virus_enrich_appr
description: List of approaches used to enrich the sample for viruses, if any
title: virus enrichment approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000036
alias: virus_enrich_appr
owner: MiuvigHumanSkin
domain_of:
- MigsVi
- Miuvig
range: VIRUS_ENRICH_APPR_ENUM
required: true
samp_mat_process:
name: samp_mat_process
description: A brief description of any processing applied to the sample during
or after retrieving the sample from environment, or a link to the relevant protocol(s)
performed
title: sample material processing
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
experimental_factor:
name: experimental_factor
description: Variable aspects of an experiment design that can be used to describe
an experiment, or set of experiments, in an increasingly detailed manner. This
field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
Ontology for Biomedical Investigations (OBI)
title: experimental factor
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000008
multivalued: true
alias: experimental_factor
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
range: string
recommended: true
pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
samp_taxon_id:
name: samp_taxon_id
description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa
sample. Use 'synthetic metagenome for mock community/positive controls, or
'blank sample' for negative controls
title: taxonomy ID of DNA sample
examples:
- value: Gut Metagenome [NCBITaxon:749906]
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: MiuvigHumanSkin
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
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: MiuvigHumanSkin
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_screen:
name: lib_screen
description: Specific enrichment or screening methods applied before and/or after
creating libraries
title: library screening strategy
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
samp_name:
name: samp_name
annotations:
Preferred_unit:
tag: Preferred_unit
value: ''
description: A local identifier or name that for the material sample used for
extracting nucleic acids, and subsequent sequencing. It can refer either to
the original material collected or to any derived sub-samples. It can have any
format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. INSDC requires every sample name from
a single Submitter to be unique. Use of a globally unique identifier for the
field source_mat_id is recommended in addition to sample_name
title: sample name
examples:
- value: ISDsoil1
in_subset:
- investigation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: MiuvigHumanSkin
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
env_medium:
name: env_medium
description: 'Report the environmental material(s) immediately surrounding the
sample or specimen at the time of sampling. We recommend using subclasses of
''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. a tree, a leaf, a table top)'
title: environmental medium
examples:
- value: bluegrass field soil [ENVO:00005789]
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: MiuvigHumanSkin
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
lib_vector:
name: lib_vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
ref_db:
name: ref_db
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
range: string
recommended: true
elev:
name: elev
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit
title: elevation
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: MiuvigHumanSkin
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
lat_lon:
name: lat_lon
annotations:
Expected_value:
tag: Expected_value
value: decimal degrees, limit to 8 decimal points
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
in_subset:
- environment
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: MiuvigHumanSkin
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
compl_software:
name: compl_software
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Misag
- Miuvig
range: string
required: false
recommended: false
host_disease_stat:
name: host_disease_stat
description: List of diseases with which the host has been diagnosed; can include
multiple diagnoses. The value of the field depends on host; for humans the terms
should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
non-human host diseases are free text
title: host disease status
examples:
- value: rabies [DOID:11260]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]|{text}'
slot_uri: MIXS:0000031
multivalued: false
alias: host_disease_stat
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
range: string
required: false
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: integer
recommended: true
mid:
name: mid
description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
used to specifically tag unique samples in a sequencing run. Sequence should
be reported in uppercase letters
title: multiplex identifiers
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000047
multivalued: false
alias: mid
owner: MiuvigHumanSkin
domain_of:
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
pattern: ^[ACGTRKSYMWBHDVN]+$
structured_pattern:
syntax: ^{ambiguous_nucleotides}$
interpolated: true
partial_match: true
pathogenicity:
name: pathogenicity
description: To what is the entity pathogenic
title: known pathogenicity
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000027
multivalued: false
alias: pathogenicity
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsVi
- Miuvig
- Agriculture
range: string
required: false
recommended: false
source_uvig:
name: source_uvig
description: Type of dataset from which the UViG was obtained
title: source of UViGs
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[metagenome (not viral targeted)|viral fraction metagenome
(virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral
fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial
single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial
genome|other]'
slot_uri: MIXS:0000035
multivalued: false
alias: source_uvig
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
required: true
assembly_name:
name: assembly_name
description: Name/version of the assembly provided by the submitter that is used
in the genome browsers and in the community
title: assembly name
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
adapters:
name: adapters
description: Adapters provide priming sequences for both amplification and sequencing
of the sample-library fragments. Both adapters should be reported; in uppercase
letters
title: adapters
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sort_tech:
name: sort_tech
description: Method used to sort/isolate cells or particles of interest
title: sorting technology
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000075
multivalued: false
alias: sort_tech
owner: MiuvigHumanSkin
domain_of:
- Misag
- Miuvig
range: SORT_TECH_ENUM
recommended: true
sc_lysis_approach:
name: sc_lysis_approach
description: Method used to free DNA from interior of the cell(s) or particle(s)
title: single cell or viral particle lysis approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000076
multivalued: false
alias: sc_lysis_approach
owner: MiuvigHumanSkin
domain_of:
- Misag
- Miuvig
range: SC_LYSIS_APPROACH_ENUM
recommended: true
sc_lysis_method:
name: sc_lysis_method
description: Name of the kit or standard protocol used for cell(s) or particle(s)
lysis
title: single cell or viral particle lysis kit protocol
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000054
multivalued: false
alias: sc_lysis_method
owner: MiuvigHumanSkin
domain_of:
- Misag
- Miuvig
range: string
recommended: true
wga_amp_appr:
name: wga_amp_appr
description: Method used to amplify genomic DNA in preparation for sequencing
title: WGA amplification approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000055
multivalued: false
alias: wga_amp_appr
owner: MiuvigHumanSkin
domain_of:
- Misag
- Miuvig
range: WGA_AMP_APPR_ENUM
recommended: true
wga_amp_kit:
name: wga_amp_kit
description: Kit used to amplify genomic DNA in preparation for sequencing
title: WGA amplification kit
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000006
multivalued: false
alias: wga_amp_kit
owner: MiuvigHumanSkin
domain_of:
- Misag
- Miuvig
range: string
recommended: true
bin_param:
name: bin_param
description: The parameters that have been applied during the extraction of genomes
from metagenomic datasets
title: binning parameters
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000077
alias: bin_param
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Miuvig
range: BIN_PARAM_ENUM
recommended: true
bin_software:
name: bin_software
description: Tool(s) used for the extraction of genomes from metagenomic datasets,
where possible include a product ID (PID) of the tool(s) used
title: binning software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
multivalued: false
alias: bin_software
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Miuvig
range: string
recommended: true
reassembly_bin:
name: reassembly_bin
description: Has an assembly been performed on a genome bin extracted from a metagenomic
assembly?
title: reassembly post binning
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000079
multivalued: false
alias: reassembly_bin
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Miuvig
range: boolean
recommended: true
mag_cov_software:
name: mag_cov_software
description: Tool(s) used to determine the genome coverage if coverage is used
as a binning parameter in the extraction of genomes from metagenomic datasets
title: MAG coverage software
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000080
multivalued: false
alias: mag_cov_software
owner: MiuvigHumanSkin
domain_of:
- Mimag
- Miuvig
range: MAG_COV_SOFTWARE_ENUM
required: false
recommended: false
vir_ident_software:
name: vir_ident_software
description: Tool(s) used for the identification of UViG as a viral genome, software
or protocol name including version number, parameters, and cutoffs used
title: viral identification software
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000081
multivalued: false
alias: vir_ident_software
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
required: true
pred_genome_type:
name: pred_genome_type
description: Type of genome predicted for the UViG
title: predicted genome type
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]'
slot_uri: MIXS:0000082
multivalued: false
alias: pred_genome_type
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
required: true
pred_genome_struc:
name: pred_genome_struc
description: Expected structure of the viral genome
title: predicted genome structure
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000083
multivalued: false
alias: pred_genome_struc
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: PRED_GENOME_STRUC_ENUM
required: true
detec_type:
name: detec_type
description: Type of UViG detection
title: detection type
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '[independent sequence (UViG)|provirus (UpViG)]'
slot_uri: MIXS:0000084
multivalued: false
alias: detec_type
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
required: true
otu_class_appr:
name: otu_class_appr
description: Cutoffs and approach used when clustering species-level OTUs. Note
that results from standard 95% ANI / 85% AF clustering should be provided alongside
OTUS defined from another set of thresholds, even if the latter are the ones
primarily used during the analysis
title: OTU classification approach
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{ANI cutoff};{AF cutoff};{clustering method}'
slot_uri: MIXS:0000085
multivalued: false
alias: otu_class_appr
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
recommended: true
otu_seq_comp_appr:
name: otu_seq_comp_appr
description: Tool and thresholds used to compare sequences when computing "species-level"
OTUs
title: OTU sequence comparison approach
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000086
multivalued: false
alias: otu_seq_comp_appr
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
recommended: true
otu_db:
name: otu_db
description: Reference database (i.e. sequences not generated as part of the current
study) used to cluster new genomes in "species-level" OTUs, if any
title: OTU database
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{database};{version}'
slot_uri: MIXS:0000087
multivalued: false
alias: otu_db
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
recommended: true
host_pred_appr:
name: host_pred_appr
description: Tool or approach used for host prediction
title: host prediction approach
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000088
multivalued: false
alias: host_pred_appr
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: HOST_PRED_APPR_ENUM
recommended: true
host_pred_est_acc:
name: host_pred_est_acc
description: For each tool or approach used for host prediction, estimated false
discovery rates should be included, either computed de novo or from the literature
title: host prediction estimated accuracy
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000089
multivalued: false
alias: host_pred_est_acc
owner: MiuvigHumanSkin
domain_of:
- Miuvig
range: string
recommended: true
associated_resource:
name: associated_resource
annotations:
Expected_value:
tag: Expected_value
value: reference to resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence
title: relevant electronic resources
examples:
- value: http://www.earthmicrobiome.org/
in_subset:
- sequencing
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000091
multivalued: true
alias: associated_resource
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
sop:
name: sop
description: Standard operating procedures used in assembly and/or annotation
of genomes, metagenomes or environmental sequences
title: relevant standard operating procedures
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: true
alias: sop
owner: MiuvigHumanSkin
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
- Agriculture
range: string
recommended: true
dermatology_disord:
name: dermatology_disord
description: History of dermatology disorders; can include multiple disorders.
The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
skin disease (https://disease-ontology.org/?id=DOID:37)
title: dermatology disorder
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000284
multivalued: true
alias: dermatology_disord
owner: MiuvigHumanSkin
domain_of:
- HumanSkin
range: string
required: false
recommended: false
time_since_last_wash:
name: time_since_last_wash
description: Specification of the time since last wash
title: time since last wash
examples:
- value: P1D
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000943
multivalued: false
alias: time_since_last_wash
owner: MiuvigHumanSkin
domain_of:
- HumanSkin
range: string
required: false
recommended: false
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
dominant_hand:
name: dominant_hand
description: Dominant hand of the subject
title: dominant hand
examples:
- value: right
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000944
multivalued: false
alias: dominant_hand
owner: MiuvigHumanSkin
domain_of:
- HumanSkin
range: DOMINANT_HAND_ENUM
required: false
recommended: false
host_subject_id:
name: host_subject_id
description: A unique identifier by which each subject can be referred to, de-identified
title: host subject id
examples:
- value: MPI123
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000861
multivalued: false
alias: host_subject_id
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_age:
name: host_age
description: Age of host at the time of sampling; relevant scale depends on species
and study, e.g. Could be seconds for amoebae or centuries for trees
title: host age
examples:
- value: 30 years
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000255
multivalued: false
alias: host_age
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_sex:
name: host_sex
annotations:
Expected_value:
tag: Expected_value
value: enumeration
description: Gender or physical sex of the host
title: host sex
comments:
- example of non-binary from Excel sheets does not match any of the enumerated
values
from_schema: https://w3id.org/mixs-6-2-rc
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: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
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-6-2-rc
slot_uri: MIXS:0000884
multivalued: true
alias: ihmc_medication_code
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: integer
required: false
recommended: false
chem_administration:
name: chem_administration
description: List of chemical compounds administered to the host or site where
sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
include multiple compounds. For chemical entities of biological interest ontology
(chebi) (v 163), http://purl.bioontology.org/ontology/chebi
title: chemical administration
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}];{timestamp}'
slot_uri: MIXS:0000751
multivalued: true
alias: chem_administration
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
host_body_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: Skin of palm of left hand [fma38303]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000867
multivalued: false
alias: host_body_site
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_body_product:
name: host_body_product
annotations:
Expected_value:
tag: Expected_value
value: FMA or UBERON
description: Substance produced by the body, e.g. Stool, mucus, where the sample
was obtained from. Use terms from the foundational model of anatomy ontology
(fma) or Uber-anatomy ontology (UBERON)
title: host body product
examples:
- value: mucus [FMA:66938]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000888
multivalued: false
alias: host_body_product
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_tot_mass:
name: host_tot_mass
description: Total mass of the host at collection, the unit depends on host
title: host total mass
examples:
- value: 65 kilogram
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000263
multivalued: false
alias: host_tot_mass
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_height:
name: host_height
description: The height of subject
title: host height
examples:
- value: 1.75 meter
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000264
multivalued: false
alias: host_height
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_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-6-2-rc
slot_uri: MIXS:0000869
multivalued: true
alias: host_diet
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
host_last_meal:
name: host_last_meal
description: Content of last meal and time since feeding; can include multiple
values
title: host last meal
examples:
- value: french fries;P5H30M
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{duration}'
slot_uri: MIXS:0000870
multivalued: true
alias: host_last_meal
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
host_fam_rel:
name: host_fam_rel
description: Relationships to other hosts in the same study; can include multiple
relationships
title: host family relationship
examples:
- value: mother;ID298
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
multivalued: true
alias: host_fam_rel
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- SymbiontAssociated
range: string
required: false
recommended: false
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
examples:
- value: ST1
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000365
multivalued: false
alias: host_genotype
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_phenotype:
name: host_phenotype
description: Phenotype of human or other host. Use terms from the phenotypic quality
ontology (pato) or the Human Phenotype Ontology (HP)
title: host phenotype
examples:
- value: Tinnitus [HP:0000360]
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{termLabel} [{termID}]'
slot_uri: MIXS:0000874
multivalued: false
alias: host_phenotype
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
host_body_temp:
name: host_body_temp
description: Core body temperature of the host when sample was collected
title: host body temperature
examples:
- value: 36.5 degree Celsius
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000274
multivalued: false
alias: host_body_temp
owner: MiuvigHumanSkin
domain_of:
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
host_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-6-2-rc
slot_uri: MIXS:0000317
multivalued: false
alias: host_body_mass_index
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
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-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000895
multivalued: true
alias: ethnicity
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
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-6-2-rc
slot_uri: MIXS:0000896
alias: host_occupation
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
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-6-2-rc
slot_uri: MIXS:0000897
multivalued: false
alias: medic_hist_perform
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: boolean
required: false
recommended: false
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-6-2-rc
slot_uri: MIXS:0000333
multivalued: false
alias: host_pulse
owner: MiuvigHumanSkin
domain_of:
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
perturbation:
name: perturbation
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: true
alias: perturbation
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
salinity:
name: salinity
annotations:
Preferred_unit:
tag: Preferred_unit
value: practical salinity unit, percentage
description: The total concentration of all dissolved salts in a liquid or solid
sample. While salinity can be measured by a complete chemical analysis, this
method is difficult and time consuming. More often, it is instead derived from
the conductivity measurement. This is known as practical salinity. These derivations
compare the specific conductance of the sample to a salinity standard such as
seawater
title: salinity
examples:
- value: 25 practical salinity unit
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000183
multivalued: false
alias: salinity
owner: MiuvigHumanSkin
domain_of:
- Air
- FoodFarmEnvironment
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000753
multivalued: false
alias: oxy_stat_samp
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: OXY_STAT_SAMP_ENUM
required: false
recommended: false
organism_count:
name: organism_count
description: 'Total cell count of any organism (or group of organisms) per gram,
volume or area of sample, should include name of organism followed by count.
The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
title: organism count
examples:
- value: total prokaryotes;3.5e7 cells per milliliter;qPCR
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
slot_uri: MIXS:0000103
multivalued: true
alias: organism_count
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- BuiltEnvironment
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
samp_store_temp:
name: samp_store_temp
annotations:
Preferred_unit:
tag: Preferred_unit
value: degree Celsius
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
examples:
- value: -80 degree Celsius
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000110
multivalued: false
alias: samp_store_temp
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
*([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
interpolated: true
partial_match: true
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored. Indicate the duration for
which the sample was stored written in ISO 8601 format
title: sample storage duration
from_schema: https://w3id.org/mixs-6-2-rc
slot_uri: MIXS:0000116
multivalued: false
alias: samp_store_dur
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
structured_pattern:
syntax: ^{duration}$
interpolated: true
partial_match: true
samp_store_loc:
name: samp_store_loc
description: Location at which sample was stored, usually name of a specific freezer/room
title: sample storage location
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
alias: samp_store_loc
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
host_symbiont:
name: host_symbiont
description: The taxonomic name of the organism(s) found living in mutualistic,
commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont
can have its own symbionts. For example, parasites may have hyperparasites (=parasites
of the parasite)
title: observed host symbionts
examples:
- value: flukeworms
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text}'
slot_uri: MIXS:0001298
multivalued: true
alias: host_symbiont
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- PlantAssociated
- SymbiontAssociated
range: string
required: false
recommended: false
misc_param:
name: misc_param
annotations:
Expected_value:
tag: Expected_value
value: parameter name;measurement value
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
examples:
- value: Bicarbonate ion concentration;2075 micromole per kilogram
from_schema: https://w3id.org/mixs-6-2-rc
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: true
alias: misc_param
owner: MiuvigHumanSkin
domain_of:
- Agriculture
- Air
- FoodAnimalAndAnimalFeed
- FoodFarmEnvironment
- FoodFoodProductionFacility
- FoodHumanFoods
- HostAssociated
- HumanAssociated
- HumanGut
- HumanOral
- HumanSkin
- HumanVaginal
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- MicrobialMatBiofilm
- MiscellaneousNaturalOrArtificialEnvironment
- PlantAssociated
- Sediment
- Soil
- SymbiontAssociated
- WastewaterSludge
- Water
range: string
required: false
recommended: false
class_uri: MIXS:0010012_0016006