Class: Symbiont-associatedMIMAG
Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package symbiont-associated
URI: MIXS:Symbiont-associatedMIMAG
Inheritance
- Symbiont-associated
- Symbiont-associatedMIMAG [ MIMAG]
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| samp_name | 1..1 String |
A local identifier or name that for the material sample used for extracting n... | MIMAG |
| samp_taxon_id | 1..1 String |
NCBI taxon id of the sample | MIMAG |
| project_name | 1..1 String |
Name of the project within which the sequencing was organized | MIMAG |
| experimental_factor | 0..1 recommended String |
Experimental factors are essentially the variable aspects of an experiment de... | MIMAG |
| lat_lon | 1..1 String |
The geographical origin of the sample as defined by latitude and longitude | MIMAG, Symbiont-associated |
| geo_loc_name | 1..1 String |
The geographical origin of the sample as defined by the country or sea name f... | MIMAG, Symbiont-associated |
| collection_date | 1..1 Date |
The time of sampling, either as an instance (single point in time) or interva... | MIMAG, Symbiont-associated |
| neg_cont_type | 0..1 recommended NegContTypeEnum |
The substance or equipment used as a negative control in an investigation | MIMAG |
| pos_cont_type | 0..1 recommended String |
The substance, mixture, product, or apparatus used to verify that a process w... | MIMAG |
| env_broad_scale | 1..1 String |
Report the major environmental system the sample or specimen came from | MIMAG, Symbiont-associated |
| env_local_scale | 1..1 String |
Report the entity or entities which are in the sample or specimen’s local vic... | MIMAG, Symbiont-associated |
| env_medium | 1..1 String |
Report the environmental material(s) immediately surrounding the sample or sp... | MIMAG, Symbiont-associated |
| ref_biomaterial | 0..1 String |
Primary publication if isolated before genome publication; otherwise, primary... | MIMAG |
| source_mat_id | 0..1 recommended String |
A unique identifier assigned to a material sample (as defined by http://rs | MIMAG |
| rel_to_oxygen | 0..1 RelToOxygenEnum |
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... | MIMAG |
| samp_collec_device | 0..1 recommended String |
The device used to collect an environmental sample | MIMAG |
| samp_collec_method | 0..1 recommended String |
The method employed for collecting the sample | MIMAG |
| samp_mat_process | 0..1 recommended String |
A brief description of any processing applied to the sample during or after r... | MIMAG |
| size_frac | 0..1 String |
Filtering pore size used in sample preparation | MIMAG |
| samp_size | 0..1 recommended QuantityValue |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... | MIMAG |
| samp_vol_we_dna_ext | 0..1 QuantityValue |
Volume (ml) or mass (g) of total collected sample processed for DNA extractio... | MIMAG |
| nucl_acid_ext | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | MIMAG |
| nucl_acid_amp | 0..1 recommended String |
A link to a literature reference, electronic resource or a standard operating... | MIMAG |
| lib_size | 0..1 recommended Integer |
Total number of clones in the library prepared for the project | MIMAG |
| lib_reads_seqd | 0..1 recommended Integer |
Total number of clones sequenced from the library | MIMAG |
| lib_layout | 0..1 recommended LibLayoutEnum |
Specify whether to expect single, paired, or other configuration of reads | MIMAG |
| lib_vector | 0..1 recommended String |
Cloning vector type(s) used in construction of libraries | MIMAG |
| lib_screen | 0..1 recommended String |
Specific enrichment or screening methods applied before and/or after creating... | MIMAG |
| mid | 0..1 recommended String |
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... | MIMAG |
| adapters | 0..1 recommended String |
Adapters provide priming sequences for both amplification and sequencing of t... | MIMAG |
| seq_meth | 1..1 String |
Sequencing machine used | MIMAG |
| tax_ident | 1..1 TaxIdentEnum |
The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | MIMAG |
| assembly_qual | 1..1 AssemblyQualEnum |
The assembly quality category is based on sets of criteria outlined for each ... | MIMAG |
| assembly_name | 0..1 recommended String |
Name/version of the assembly provided by the submitter that is used in the ge... | MIMAG |
| assembly_software | 1..1 String |
Tool(s) used for assembly, including version number and parameters | MIMAG |
| annot | 0..1 String |
Tool used for annotation, or for cases where annotation was provided by a com... | MIMAG |
| number_contig | 0..1 Integer |
Total number of contigs in the cleaned/submitted assembly that makes up a giv... | MIMAG |
| feat_pred | 0..1 String |
Method used to predict UViGs features such as ORFs, integration site, etc | MIMAG |
| ref_db | 0..1 String |
List of database(s) used for ORF annotation, along with version number and re... | MIMAG |
| sim_search_meth | 0..1 String |
Tool used to compare ORFs with database, along with version and cutoffs used | MIMAG |
| tax_class | 0..1 String |
Method used for taxonomic classification, along with reference database used,... | MIMAG |
| x_16s_recover | 0..1 String |
Can a 16S gene be recovered from the submitted SAG or MAG? | MIMAG |
| x_16s_recover_software | 0..1 String |
Tools used for 16S rRNA gene extraction | MIMAG |
| trnas | 0..1 Integer |
The total number of tRNAs identified from the SAG or MAG | MIMAG |
| trna_ext_software | 0..1 String |
Tools used for tRNA identification | MIMAG |
| compl_score | 1..1 String |
Completeness score is typically based on either the fraction of markers found... | MIMAG |
| compl_software | 1..1 String |
Tools used for completion estimate, i | MIMAG |
| compl_appr | 0..1 ComplApprEnum |
The approach used to determine the completeness of a given genomic assembly, ... | MIMAG |
| contam_score | 1..1 String |
The contamination score is based on the fraction of single-copy genes that ar... | MIMAG |
| contam_screen_input | 0..1 String |
The type of sequence data used as input | MIMAG |
| contam_screen_param | 0..1 String |
Specific parameters used in the decontamination sofware, such as reference da... | MIMAG |
| decontam_software | 0..1 DecontamSoftwareEnum |
Tool(s) used in contamination screening | MIMAG |
| bin_param | 1..1 BinParamEnum |
The parameters that have been applied during the extraction of genomes from m... | MIMAG |
| bin_software | 1..1 String |
Tool(s) used for the extraction of genomes from metagenomic datasets, where p... | MIMAG |
| reassembly_bin | 0..1 String |
Has an assembly been performed on a genome bin extracted from a metagenomic a... | MIMAG |
| mag_cov_software | 0..1 MagCovSoftwareEnum |
Tool(s) used to determine the genome coverage if coverage is used as a binnin... | MIMAG |
| associated_resource | 0..1 recommended String |
A related resource that is referenced, cited, or otherwise associated to the ... | MIMAG |
| sop | 0..1 recommended String |
Standard operating procedures used in assembly and/or annotation of genomes, ... | MIMAG |
| depth | 0..1 QuantityValue |
The vertical distance below local surface, e | Symbiont-associated |
| alt | 0..1 QuantityValue |
Altitude is a term used to identify heights of objects such as airplanes, spa... | Symbiont-associated |
| elev | 0..1 QuantityValue |
Elevation of the sampling site is its height above a fixed reference point, m... | Symbiont-associated |
| temp | 0..1 QuantityValue |
Temperature of the sample at the time of sampling | Symbiont-associated |
| sample_name | 1..1 String |
Sample Name is a name that you choose for the sample | Symbiont-associated |
| host_subject_id | 0..1 String |
A unique identifier by which each subject can be referred to, de-identified | Symbiont-associated |
| host_common_name | 0..1 String |
Common name of the host | Symbiont-associated |
| host_taxid | 0..1 String |
NCBI taxon id of the host, e | Symbiont-associated |
| host_dependence | 1..1 String |
Type of host dependence for the symbiotic host organism to its host | Symbiont-associated |
| type_of_symbiosis | 0..1 TypeOfSymbiosisEnum |
Type of biological interaction established between the symbiotic host organis... | Symbiont-associated |
| sym_life_cycle_type | 1..1 String |
Type of life cycle of the symbiotic host species (the thing being sampled) | Symbiont-associated |
| host_life_stage | 1..1 String |
Description of life stage of host | Symbiont-associated |
| host_age | 0..1 QuantityValue |
Age of host at the time of sampling; relevant scale depends on species and st... | Symbiont-associated |
| host_sex | 0..1 HostSexEnum |
Gender or physical sex of the host | Symbiont-associated |
| mode_transmission | 0..1 ModeTransmissionEnum |
The process through which the symbiotic host organism entered the host from w... | Symbiont-associated |
| route_transmission | 0..1 RouteTransmissionEnum |
Description of path taken by the symbiotic host organism being sampled in ord... | Symbiont-associated |
| host_body_habitat | 0..1 String |
Original body habitat where the sample was obtained from | Symbiont-associated |
| host_body_site | 0..1 String |
Name of body site where the sample was obtained from, such as a specific orga... | Symbiont-associated |
| host_body_product | 0..1 String |
Substance produced by the body, e | Symbiont-associated |
| host_tot_mass | 0..1 QuantityValue |
Total mass of the host at collection, the unit depends on host | Symbiont-associated |
| host_height | 0..1 QuantityValue |
The height of subject | Symbiont-associated |
| host_length | 0..1 QuantityValue |
The length of subject | Symbiont-associated |
| host_growth_cond | 0..1 String |
Literature reference giving growth conditions of the host | Symbiont-associated |
| host_substrate | 0..1 String |
The growth substrate of the host | Symbiont-associated |
| host_family_relationship | 0..1 String |
Relationships to other hosts in the same study; can include multiple relation... | Symbiont-associated |
| host_infra_specific_name | 0..1 String |
Taxonomic information about the host below subspecies level | Symbiont-associated |
| host_infra_specific_rank | 0..1 String |
Taxonomic rank information about the host below subspecies level, such as var... | Symbiont-associated |
| host_genotype | 0..1 String |
Observed genotype | Symbiont-associated |
| host_phenotype | 0..1 String |
Phenotype of human or other host | Symbiont-associated |
| host_dry_mass | 0..1 QuantityValue |
Measurement of dry mass | Symbiont-associated |
| host_color | 0..1 String |
The color of host | Symbiont-associated |
| host_shape | 0..1 String |
Morphological shape of host | Symbiont-associated |
| gravidity | 0..1 String |
Whether or not subject is gravid, and if yes date due or date post-conception... | Symbiont-associated |
| host_number | 0..1 String |
Number of symbiotic host individuals pooled at the time of collection | Symbiont-associated |
| host_symbiont | 0..* String |
The taxonomic name of the organism(s) found living in mutualistic, commensali... | Symbiont-associated |
| host_specificity | 0..1 HostSpecificityEnum |
Level of specificity of symbiont-host interaction: e | Symbiont-associated |
| symbiont_host_role | 0..1 SymbiontHostRoleEnum |
Role of the host in the life cycle of the symbiotic organism | Symbiont-associated |
| host_cellular_loc | 0..1 HostCellularLocEnum |
The localization of the symbiotic host organism within the host from which it... | Symbiont-associated |
| association_duration | 0..1 QuantityValue |
Time spent in host of the symbiotic organism at the time of sampling; relevan... | Symbiont-associated |
| host_of_host_coinf | 0..1 String |
The taxonomic name of any coinfecting organism observed in a symbiotic relati... | Symbiont-associated |
| host_of_host_name | 0..1 String |
Common name of the host of the symbiotic host organism | Symbiont-associated |
| host_of_host_env_loc | 0..* String |
For a symbiotic host organism the local anatomical environment within its hos... | Symbiont-associated |
| host_of_host_env_med | 0..1 String |
Report the environmental material(s) immediately surrounding the symbiotic ho... | Symbiont-associated |
| host_of_host_taxid | 0..1 Integer |
NCBI taxon id of the host of the symbiotic host organism | Symbiont-associated |
| host_of_host_sub_id | 0..1 String |
A unique identifier by which each host of the symbiotic host organism subject... | Symbiont-associated |
| host_of_host_disease | 0..* String |
List of diseases with which the host of the symbiotic host organism has been ... | Symbiont-associated |
| host_of_host_fam_rel | 0..* String |
Familial relationship of the host of the symbiotic host organisms to other ho... | Symbiont-associated |
| host_of_host_infname | 0..1 String |
Taxonomic name information of the host of the symbiotic host organism below s... | Symbiont-associated |
| host_of_host_infrank | 0..1 String |
Taxonomic rank information about the host of the symbiotic host organism belo... | Symbiont-associated |
| host_of_host_geno | 0..1 String |
Observed genotype of the host of the symbiotic host organism | Symbiont-associated |
| host_of_host_pheno | 0..1 String |
Phenotype of the host of the symbiotic host organism | Symbiont-associated |
| host_of_host_gravid | 0..1 String |
Whether or not the host of the symbiotic host organism is gravid, and if yes ... | Symbiont-associated |
| host_of_host_totmass | 0..1 QuantityValue |
Total mass of the host of the symbiotic host organism at collection, the unit... | Symbiont-associated |
| chem_administration | 0..* String |
List of chemical compounds administered to the host or site where sampling oc... | Symbiont-associated |
| perturbation | 0..* String |
Type of perturbation, e | Symbiont-associated |
| samp_salinity | 0..1 QuantityValue |
Salinity is the total concentration of all dissolved salts in a liquid or sol... | Symbiont-associated |
| oxy_stat_samp | 0..1 OxyStatSampEnum |
Oxygenation status of sample | Symbiont-associated |
| organism_count | 0..* OrganismCountEnum |
Total cell count of any organism (or group of organisms) per gram, volume or ... | Symbiont-associated |
| samp_store_temp | 0..1 QuantityValue |
Temperature at which sample was stored, e | Symbiont-associated |
| samp_store_dur | 0..1 String |
Duration for which the sample was stored | Symbiont-associated |
| samp_store_loc | 0..1 String |
Location at which sample was stored, usually name of a specific freezer/room | Symbiont-associated |
| samp_store_sol | 0..1 String |
Solution within which sample was stored, if any | Symbiont-associated |
| misc_param | 0..* String |
Any other measurement performed or parameter collected, that is not listed he... | Symbiont-associated |
Identifier and Mapping Information
Schema Source
- from schema: http://w3id.org/mixs
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:Symbiont-associatedMIMAG |
| native | MIXS:Symbiont-associatedMIMAG |
LinkML Source
Direct
name: symbiont-associated MIMAG
description: Combinatorial checklist Minimum Information About a Metagenome-Assembled
Genome with environmental package symbiont-associated
from_schema: http://w3id.org/mixs
is_a: symbiont-associated
mixins:
- MIMAG
Induced
name: symbiont-associated MIMAG
description: Combinatorial checklist Minimum Information About a Metagenome-Assembled
Genome with environmental package symbiont-associated
from_schema: http://w3id.org/mixs
is_a: symbiont-associated
mixins:
- MIMAG
attributes:
samp_name:
name: samp_name
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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0001107
multivalued: false
alias: samp_name
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text} [NCBI:txid]'
slot_uri: MIXS:0001320
multivalued: false
alias: samp_taxon_id
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
project_name:
name: project_name
description: Name of the project within which the sequencing was organized
title: project name
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0000092
multivalued: false
alias: project_name
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
experimental_factor:
name: experimental_factor
description: Experimental factors are essentially the variable aspects of an experiment
design which 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). For
a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
title: experimental factor
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000008
multivalued: false
alias: experimental_factor
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
lat_lon:
name: lat_lon
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
multivalued: false
alias: lat_lon
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: true
geo_loc_name:
name: geo_loc_name
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{term}: {term}, {text}'
slot_uri: MIXS:0000010
multivalued: false
alias: geo_loc_name
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- 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
from_schema: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000011
multivalued: false
alias: collection_date
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: date
required: true
neg_cont_type:
name: neg_cont_type
description: The substance or equipment used as a negative control in an investigation
title: negative control type
from_schema: http://w3id.org/mixs
is_a: investigation field
slot_uri: MIXS:0001321
multivalued: false
alias: neg_cont_type
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: neg_cont_type_enum
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
from_schema: http://w3id.org/mixs
is_a: investigation field
string_serialization: '{term} or {text}'
slot_uri: MIXS:0001322
multivalued: false
alias: pos_cont_type
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
multivalued: false
alias: env_broad_scale
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: true
env_local_scale:
name: env_local_scale
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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
multivalued: false
alias: env_local_scale
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
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
from_schema: http://w3id.org/mixs
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000014
multivalued: false
alias: env_medium
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
- built environment
- air
- agriculture
range: string
required: true
ref_biomaterial:
name: ref_biomaterial
description: Primary publication if isolated before genome publication; otherwise,
primary genome report.
title: reference for biomaterial
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000025
multivalued: false
alias: ref_biomaterial
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
source_mat_id:
name: source_mat_id
description: A unique identifier assigned to a material sample (as defined by
http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
digital record of a material sample) used for extracting nucleic acids, and
subsequent sequencing. The identifier can refer either to the original material
collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
/bio_material, or /culture_collection may or may not share the same value as
the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
sampled tissue with the same identifier. However, the /culture_collection qualifier
may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
would refer to an identifier from some derived culture from which the nucleic
acids were extracted (e.g. xatc123 or ark:/2154/R2).
title: source material identifiers
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000026
multivalued: false
alias: source_mat_id
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
recommended: true
rel_to_oxygen:
name: rel_to_oxygen
description: Is this organism an aerobe, anaerobe? Please note that aerobic and
anaerobic are valid descriptors for microbial environments
title: relationship to oxygen
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000015
multivalued: false
alias: rel_to_oxygen
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS bacteria
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
range: rel_to_oxygen_enum
required: false
samp_collec_device:
name: samp_collec_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
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000002
multivalued: false
alias: samp_collec_device
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
samp_collec_method:
name: samp_collec_method
description: The method employed for collecting the sample.
title: sample collection method
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0001225
multivalued: false
alias: samp_collec_method
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{text}'
slot_uri: MIXS:0000016
multivalued: false
alias: samp_mat_process
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
size_frac:
name: size_frac
description: Filtering pore size used in sample preparation
title: size fraction selected
from_schema: http://w3id.org/mixs
is_a: nucleic acid sequence source field
string_serialization: '{float}-{float} {unit}'
slot_uri: MIXS:0000017
multivalued: false
alias: size_frac
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000001
multivalued: false
alias: samp_size
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: quantity value
recommended: true
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: http://w3id.org/mixs
is_a: nucleic acid sequence source field
slot_uri: MIXS:0000111
multivalued: false
alias: samp_vol_we_dna_ext
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: quantity value
required: false
nucl_acid_ext:
name: nucl_acid_ext
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the material separation to recover
the nucleic acid fraction from a sample
title: nucleic acid extraction
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000037
multivalued: false
alias: nucl_acid_ext
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
nucl_acid_amp:
name: nucl_acid_amp
description: A link to a literature reference, electronic resource or a standard
operating procedure (SOP), that describes the enzymatic amplification (PCR,
TMA, NASBA) of specific nucleic acids
title: nucleic acid amplification
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000038
multivalued: false
alias: nucl_acid_amp
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000039
multivalued: false
alias: lib_size
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: integer
recommended: true
lib_reads_seqd:
name: lib_reads_seqd
description: Total number of clones sequenced from the library
title: library reads sequenced
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000040
multivalued: false
alias: lib_reads_seqd
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: integer
recommended: true
lib_layout:
name: lib_layout
description: Specify whether to expect single, paired, or other configuration
of reads
title: library layout
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000041
multivalued: false
alias: lib_layout
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: lib_layout_enum
recommended: true
lib_vector:
name: lib_vector
description: Cloning vector type(s) used in construction of libraries
title: library vector
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000042
multivalued: false
alias: lib_vector
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000043
multivalued: false
alias: lib_screen
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{dna}'
slot_uri: MIXS:0000047
multivalued: false
alias: mid
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{dna};{dna}'
slot_uri: MIXS:0000048
multivalued: false
alias: adapters
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: 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
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0000050
multivalued: false
alias: seq_meth
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000053
multivalued: false
alias: tax_ident
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: tax_ident_enum
required: 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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000056
multivalued: false
alias: assembly_qual
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: assembly_qual_enum
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text} {text}'
slot_uri: MIXS:0000057
multivalued: false
alias: assembly_name
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
assembly_software:
name: assembly_software
description: Tool(s) used for assembly, including version number and parameters
title: assembly software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000058
multivalued: false
alias: assembly_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000059
multivalued: false
alias: annot
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
number_contig:
name: number_contig
description: Total number of contigs in the cleaned/submitted assembly that makes
up a given genome, SAG, MAG, or UViG
title: number of contigs
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000060
multivalued: false
alias: number_contig
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: integer
required: false
feat_pred:
name: feat_pred
description: Method used to predict UViGs features such as ORFs, integration site,
etc.
title: feature prediction
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000061
multivalued: false
alias: feat_pred
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
ref_db:
name: ref_db
description: List of database(s) used for ORF annotation, along with version number
and reference to website or publication
title: reference database(s)
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{database};{version};{reference}'
slot_uri: MIXS:0000062
multivalued: false
alias: ref_db
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
sim_search_meth:
name: sim_search_meth
description: Tool used to compare ORFs with database, along with version and cutoffs
used
title: similarity search method
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000063
multivalued: false
alias: sim_search_meth
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{text}'
slot_uri: MIXS:0000064
multivalued: false
alias: tax_class
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
x_16s_recover:
name: x_16s_recover
description: Can a 16S gene be recovered from the submitted SAG or MAG?
title: 16S recovered
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{boolean}'
slot_uri: MIXS:0000065
multivalued: false
alias: x_16s_recover
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: string
required: false
x_16s_recover_software:
name: x_16s_recover_software
description: Tools used for 16S rRNA gene extraction
title: 16S recovery software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000066
multivalued: false
alias: x_16s_recover_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: string
required: false
trnas:
name: trnas
description: The total number of tRNAs identified from the SAG or MAG
title: number of standard tRNAs extracted
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000067
multivalued: false
alias: trnas
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: integer
required: false
trna_ext_software:
name: trna_ext_software
description: Tools used for tRNA identification
title: tRNA extraction software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version};{parameters}'
slot_uri: MIXS:0000068
multivalued: false
alias: trna_ext_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000069
multivalued: false
alias: compl_score
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: string
required: true
pattern: ^(high|med|low);(0|([0-9]{1,2})|100)%$
compl_software:
name: compl_software
description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
title: completeness software
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version}'
slot_uri: MIXS:0000070
multivalued: false
alias: compl_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MISAG
- MIMAG
- MIUVIG
range: string
required: 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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000071
multivalued: false
alias: compl_appr
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
- MIUVIG
range: compl_appr_enum
required: false
contam_score:
name: contam_score
description: 'The contamination score is based on the fraction of single-copy
genes that are observed more than once in a query genome. The following scores
are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low
Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be
deposited into any of the public databases'
title: contamination score
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{float} percentage'
slot_uri: MIXS:0000072
multivalued: false
alias: contam_score
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: string
required: true
contam_screen_input:
name: contam_screen_input
description: The type of sequence data used as input
title: contamination screening input
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '[reads| contigs]'
slot_uri: MIXS:0000005
multivalued: false
alias: contam_screen_input
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: string
required: false
contam_screen_param:
name: contam_screen_param
description: Specific parameters used in the decontamination sofware, such as
reference database, coverage, and kmers. Combinations of these parameters may
also be used, i.e. kmer and coverage, or reference database and kmer
title: contamination screening parameters
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000073
multivalued: false
alias: contam_screen_param
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: string
required: false
pattern: ^(ref db|kmer|coverage|combination);.+
decontam_software:
name: decontam_software
description: Tool(s) used in contamination screening
title: decontamination software
from_schema: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000074
multivalued: false
alias: decontam_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MISAG
- MIMAG
range: decontam_software_enum
required: false
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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000077
multivalued: false
alias: bin_param
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMAG
- MIUVIG
range: bin_param_enum
required: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{software};{version}{PID}'
slot_uri: MIXS:0000078
multivalued: false
alias: bin_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMAG
- MIUVIG
range: string
required: 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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{boolean}'
slot_uri: MIXS:0000079
multivalued: false
alias: reassembly_bin
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMAG
- MIUVIG
range: string
required: false
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: http://w3id.org/mixs
is_a: sequencing field
slot_uri: MIXS:0000080
multivalued: false
alias: mag_cov_software
owner: symbiont-associated MIMAG
domain_of:
- core
- MIMAG
- MIUVIG
range: mag_cov_software_enum
required: false
associated resource:
name: associated resource
description: A related resource that is referenced, cited, or otherwise associated
to the sequence.
title: relevant electronic resources
from_schema: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID} | {DOI} | {URL}'
slot_uri: MIXS:0000091
multivalued: false
alias: associated_resource
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
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: http://w3id.org/mixs
is_a: sequencing field
string_serialization: '{PMID}|{DOI}|{URL}'
slot_uri: MIXS:0000090
multivalued: false
alias: sop
owner: symbiont-associated MIMAG
domain_of:
- core
- MIGS eukaryote
- MIGS bacteria
- MIGS plant
- MIGS virus
- MIGS org
- MIMS
- MIMARKS specimen
- MIMARKS survey
- MISAG
- MIMAG
- MIUVIG
range: string
recommended: true
depth:
name: depth
description: The vertical distance below local surface, e.g. 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
from_schema: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000018
multivalued: false
alias: depth
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- built environment
- air
- agriculture
range: quantity value
required: false
alt:
name: alt
description: Altitude is a term used to identify 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: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000094
multivalued: false
alias: alt
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- built environment
- air
- agriculture
range: quantity value
required: false
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: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000093
multivalued: false
alias: elev
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- built environment
- air
- agriculture
range: quantity value
required: false
temp:
name: temp
description: Temperature of the sample at the time of sampling.
title: temperature
from_schema: http://w3id.org/mixs
is_a: environment field
slot_uri: MIXS:0000113
multivalued: false
alias: temp
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- core
- built environment
- air
- agriculture
range: quantity value
required: false
sample_name:
name: sample_name
description: Sample Name is a name that you choose for the sample. It can have
any format, but we suggest that you make it concise, unique and consistent within
your lab, and as informative as possible. Every Sample Name from a single Submitter
must be unique.
title: sample name
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001107
multivalued: false
alias: sample_name
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000861
multivalued: false
alias: host_subject_id
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
range: string
required: false
host_common_name:
name: host_common_name
description: Common name of the host.
title: host common name
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000248
multivalued: false
alias: host_common_name
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- host-associated
- agriculture
range: string
required: false
host_taxid:
name: host_taxid
description: NCBI taxon id of the host, e.g. 9606
title: host taxid
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{NCBI taxid}'
slot_uri: MIXS:0000250
multivalued: false
alias: host_taxid
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- host-associated
- food-farm environment
- agriculture
range: string
required: false
host_dependence:
name: host_dependence
description: Type of host dependence for the symbiotic host organism to its host.
title: host dependence
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '[facultative|obligate]'
slot_uri: MIXS:0001315
multivalued: false
alias: host_dependence
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: true
type_of_symbiosis:
name: type_of_symbiosis
description: Type of biological interaction established between the symbiotic
host organism being sampled and its respective host
title: type of symbiosis
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001307
multivalued: false
alias: type_of_symbiosis
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: type_of_symbiosis_enum
required: false
sym_life_cycle_type:
name: sym_life_cycle_type
description: Type of life cycle of the symbiotic host species (the thing being
sampled). Simple life cycles occur within a single host, complex ones within
multiple different hosts over the course of their normal life cycle.
title: symbiotic host organism life cycle type
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '[complex life cycle | simple life cycle]'
slot_uri: MIXS:0001300
multivalued: false
alias: sym_life_cycle_type
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: true
host_life_stage:
name: host_life_stage
description: Description of life stage of host
title: host life stage
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000251
multivalued: false
alias: host_life_stage
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- host-associated
- agriculture
range: string
required: true
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
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000255
multivalued: false
alias: host_age
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- agriculture
range: quantity value
required: false
host_sex:
name: host_sex
description: Gender or physical sex of the host.
title: host sex
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000811
multivalued: false
alias: host_sex
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
range: host_sex_enum
required: false
mode_transmission:
name: mode_transmission
description: The process through which the symbiotic host organism entered the
host from which it was sampled.
title: mode of transmission
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001312
multivalued: false
alias: mode_transmission
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: mode_transmission_enum
required: false
route_transmission:
name: route_transmission
description: Description of path taken by the symbiotic host organism being sampled
in order to establish a symbiotic relationship with the host (with which it
was observed at the time of sampling) via a mode of transmission (specified
in mode_transmission).
title: route of transmission
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001316
multivalued: false
alias: route_transmission
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: route_transmission_enum
required: false
host_body_habitat:
name: host_body_habitat
description: Original body habitat where the sample was obtained from
title: host body habitat
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000866
multivalued: false
alias: host_body_habitat
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: 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...). For foundational model of anatomy ontology
(fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,
please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
title: host body site
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000867
multivalued: false
alias: host_body_site
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
range: string
required: false
host_body_product:
name: host_body_product
description: Substance produced by the body, e.g. Stool, mucus, where the sample
was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy
ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma
or https://www.ebi.ac.uk/ols/ontologies/uberon
title: host body product
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000888
multivalued: false
alias: host_body_product
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
range: string
required: 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
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000263
multivalued: false
alias: host_tot_mass
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- agriculture
range: quantity value
required: false
host_height:
name: host_height
description: The height of subject
title: host height
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000264
multivalued: false
alias: host_height
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- agriculture
range: quantity value
required: false
host_length:
name: host_length
description: The length of subject
title: host length
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000256
multivalued: false
alias: host_length
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- host-associated
- food-farm environment
- agriculture
range: quantity value
required: false
host_growth_cond:
name: host_growth_cond
description: Literature reference giving growth conditions of the host
title: host growth conditions
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{PMID}|{DOI}|{URL}|{text}'
slot_uri: MIXS:0000871
multivalued: false
alias: host_growth_cond
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: false
host_substrate:
name: host_substrate
description: The growth substrate of the host.
title: host substrate
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000252
multivalued: false
alias: host_substrate
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: false
host_family_relationship:
name: host_family_relationship
description: Relationships to other hosts in the same study; can include multiple
relationships.
title: host family relationship
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text};{text}'
slot_uri: MIXS:0000872
multivalued: false
alias: host_family_relationship
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_infra_specific_name:
name: host_infra_specific_name
description: Taxonomic information about the host below subspecies level.
title: host infra-specific name
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000253
multivalued: false
alias: host_infra_specific_name
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_infra_specific_rank:
name: host_infra_specific_rank
description: Taxonomic rank information about the host below subspecies level,
such as variety, form, rank etc.
title: host infra-specific rank
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000254
multivalued: false
alias: host_infra_specific_rank
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_genotype:
name: host_genotype
description: Observed genotype
title: host genotype
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000365
multivalued: false
alias: host_genotype
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- agriculture
range: string
required: false
host_phenotype:
name: host_phenotype
description: Phenotype of human or other host. For phenotypic quality ontology
(pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
title: host phenotype
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000874
multivalued: false
alias: host_phenotype
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- agriculture
range: string
required: false
host_dry_mass:
name: host_dry_mass
description: Measurement of dry mass
title: host dry mass
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000257
multivalued: false
alias: host_dry_mass
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- host-associated
- food-farm environment
- agriculture
range: quantity value
required: false
host_color:
name: host_color
description: The color of host
title: host color
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000260
multivalued: false
alias: host_color
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: false
host_shape:
name: host_shape
description: Morphological shape of host
title: host shape
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000261
multivalued: false
alias: host_shape
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: false
gravidity:
name: gravidity
description: Whether or not subject is gravid, and if yes date due or date post-conception,
specifying which is used
title: gravidity
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0000875
multivalued: false
alias: gravidity
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- host-associated
range: string
required: false
host_number:
name: host_number
description: Number of symbiotic host individuals pooled at the time of collection.
title: host number individual
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{float} m'
slot_uri: MIXS:0001305
multivalued: false
alias: host_number
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: 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.
title: observed host symbionts
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001298
multivalued: true
alias: host_symbiont
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- plant-associated
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- agriculture
range: string
required: false
host_specificity:
name: host_specificity
description: 'Level of specificity of symbiont-host interaction: e.g. generalist
(symbiont able to establish associations with distantly related hosts) or species-specific.'
title: host specificity
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001308
multivalued: false
alias: host_specificity
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: host_specificity_enum
required: false
symbiont_host_role:
name: symbiont_host_role
description: Role of the host in the life cycle of the symbiotic organism.
title: host of the symbiont role
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001303
multivalued: false
alias: symbiont_host_role
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: symbiont_host_role_enum
required: false
host_cellular_loc:
name: host_cellular_loc
description: 'The localization of the symbiotic host organism within the host
from which it was sampled: e.g. intracellular if the symbiotic host organism
is localized within the cells or extracellular if the symbiotic host organism
is localized outside of cells.'
title: host cellular location
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001313
multivalued: false
alias: host_cellular_loc
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: host_cellular_loc_enum
required: false
association_duration:
name: association_duration
description: Time spent in host of the symbiotic organism at the time of sampling;
relevant scale depends on symbiotic organism and study.
title: duration of association with the host
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001299
multivalued: false
alias: association_duration
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: quantity value
required: false
host_of_host_coinf:
name: host_of_host_coinf
description: The taxonomic name of any coinfecting organism observed in a symbiotic
relationship with the host of the sampled host organism. e.g. where a sample
collected from a host trematode species (A) which was collected from a host_of_host
fish (B) that was also infected with a nematode (C), the value here would be
(C) the nematode {species name} or {common name}. Multiple co-infecting species
may be added in a comma-separated list. For listing symbiotic organisms associated
with the host (A) use the term Observed host symbiont.
title: observed coinfecting organisms in host of host
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001310
multivalued: false
alias: host_of_host_coinf
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_name:
name: host_of_host_name
description: Common name of the host of the symbiotic host organism.
title: host of the symbiotic host common name
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001324
multivalued: false
alias: host_of_host_name
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_env_loc:
name: host_of_host_env_loc
description: For a symbiotic host organism the local anatomical environment within
its host may have causal influences. Report the anatomical entity(s) which are
in the direct environment of the symbiotic host organism being sampled and which
you believe have significant causal influences on your sample or specimen. For
example, if the symbiotic host organism being sampled is an intestinal worm,
its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/).
title: host of the symbiotic host local environmental context
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0001325
multivalued: true
alias: host_of_host_env_loc
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_env_med:
name: host_of_host_env_med
description: 'Report the environmental material(s) immediately surrounding the
symbiotic host organism at the time of sampling. This usually will be a tissue
or substance type from the host, but may be another material if the symbiont
is external to the host. We recommend using classes from the UBERON ontology,
but subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483)
may also be used. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
. Terms from other OBO ontologies are permissible as long as they reference
mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
(e.g. intestines, heart).MIxS . Terms from other OBO ontologies are permissible
as long as they reference mass/volume nouns (e.g. air, water, blood) and not
discrete, countable entities (e.g. intestines, heart).'
title: host of the symbiotic host environemental medium
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0001326
multivalued: false
alias: host_of_host_env_med
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_taxid:
name: host_of_host_taxid
description: NCBI taxon id of the host of the symbiotic host organism.
title: host of the symbiotic host taxon id
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001306
multivalued: false
alias: host_of_host_taxid
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: integer
required: false
host_of_host_sub_id:
name: host_of_host_sub_id
description: 'A unique identifier by which each host of the symbiotic host organism
subject can be referred to, de-identified, e.g. #H14.'
title: host of the symbiotic host subject id
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001327
multivalued: false
alias: host_of_host_sub_id
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_disease:
name: host_of_host_disease
description: List of diseases with which the host of the symbiotic host organism
has been diagnosed; can include multiple diagnoses. The value of the field depends
on host; for humans the terms should be chosen from the DO (Human Disease Ontology)
at https://www.disease-ontology.org, non-human host diseases are free text.
title: host of the symbiotic host disease status
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]}|{text}'
slot_uri: MIXS:0001319
multivalued: true
alias: host_of_host_disease
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_fam_rel:
name: host_of_host_fam_rel
description: Familial relationship of the host of the symbiotic host organisms
to other hosts of symbiotic host organism in the same study; can include multiple
relationships.
title: host of the symbiotic host family relationship
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text};{text}'
slot_uri: MIXS:0001328
multivalued: true
alias: host_of_host_fam_rel
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_infname:
name: host_of_host_infname
description: Taxonomic name information of the host of the symbiotic host organism
below subspecies level.
title: host of the symbiotic host infra-specific name
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001329
multivalued: false
alias: host_of_host_infname
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_infrank:
name: host_of_host_infrank
description: Taxonomic rank information about the host of the symbiotic host organism
below subspecies level, such as variety, form, rank etc.
title: host of the symbiotic host infra-specific rank
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001330
multivalued: false
alias: host_of_host_infrank
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_geno:
name: host_of_host_geno
description: Observed genotype of the host of the symbiotic host organism.
title: host of the symbiotic host genotype
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001331
multivalued: false
alias: host_of_host_geno
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_pheno:
name: host_of_host_pheno
description: Phenotype of the host of the symbiotic host organism. For phenotypic
quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato.
title: host of the symbiotic host phenotype
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{term}'
slot_uri: MIXS:0001332
multivalued: false
alias: host_of_host_pheno
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_gravid:
name: host_of_host_gravid
description: Whether or not the host of the symbiotic host organism is gravid,
and if yes date due or date post-conception, specifying which is used.
title: host of the symbiotic host gravidity
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{boolean};{timestamp}'
slot_uri: MIXS:0001333
multivalued: false
alias: host_of_host_gravid
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
host_of_host_totmass:
name: host_of_host_totmass
description: Total mass of the host of the symbiotic host organism at collection,
the unit depends on the host.
title: host of the symbiotic host total mass
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0001334
multivalued: false
alias: host_of_host_totmass
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: quantity value
required: 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: http://w3id.org/mixs
is_a: core field
string_serialization: '{termLabel} {[termID]};{timestamp}'
slot_uri: MIXS:0000751
multivalued: true
alias: chem_administration
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-farm environment
- air
- agriculture
range: string
required: false
perturbation:
name: perturbation
description: Type of perturbation, e.g. chemical administration, physical disturbance,
etc., coupled with perturbation regimen including how many times the perturbation
was repeated, how long each perturbation lasted, and the start and end time
of the entire perturbation period; can include multiple perturbation types
title: perturbation
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text};{Rn/start_time/end_time/duration}'
slot_uri: MIXS:0000754
multivalued: true
alias: perturbation
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-farm environment
- food-animal and animal feed
- air
- agriculture
range: string
required: false
samp_salinity:
name: samp_salinity
description: Salinity is the total concentration of all dissolved salts in a liquid
or solid (in the form of an extract obtained by centrifugation) 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: sample salinity
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000109
multivalued: false
alias: samp_salinity
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
- human-vaginal
range: quantity value
required: false
oxy_stat_samp:
name: oxy_stat_samp
description: Oxygenation status of sample
title: oxygenation status of sample
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000753
multivalued: false
alias: oxy_stat_samp
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- air
- agriculture
range: oxy_stat_samp_enum
required: 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
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000103
multivalued: true
alias: organism_count
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- built environment
- air
- agriculture
range: organism_count_enum
required: false
samp_store_temp:
name: samp_store_temp
description: Temperature at which sample was stored, e.g. -80 degree Celsius
title: sample storage temperature
from_schema: http://w3id.org/mixs
is_a: core field
slot_uri: MIXS:0000110
multivalued: false
alias: samp_store_temp
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- air
range: quantity value
required: false
samp_store_dur:
name: samp_store_dur
description: Duration for which the sample was stored
title: sample storage duration
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{duration}'
slot_uri: MIXS:0000116
multivalued: false
alias: samp_store_dur
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- air
- agriculture
range: string
required: false
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: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000755
multivalued: false
alias: samp_store_loc
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- air
- agriculture
range: string
required: false
samp_store_sol:
name: samp_store_sol
description: Solution within which sample was stored, if any.
title: sample storage solution
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0001317
multivalued: false
alias: samp_store_sol
owner: symbiont-associated MIMAG
domain_of:
- symbiont-associated
range: string
required: false
misc_param:
name: misc_param
description: Any other measurement performed or parameter collected, that is not
listed here
title: miscellaneous parameter
from_schema: http://w3id.org/mixs
is_a: core field
string_serialization: '{text};{float} {unit}'
slot_uri: MIXS:0000752
multivalued: true
alias: misc_param
owner: symbiont-associated MIMAG
domain_of:
- water
- wastewater_sludge
- symbiont-associated
- soil
- sediment
- plant-associated
- miscellaneous natural or artificial environment
- microbial mat_biofilm
- hydrocarbon resources-fluids_swabs
- hydrocarbon resources-cores
- human-vaginal
- human-skin
- human-oral
- human-gut
- human-associated
- host-associated
- food-human foods
- food-food production facility
- food-farm environment
- food-animal and animal feed
- air
- agriculture
range: string
required: false