Class: MicrobialMatBiofilmMIGSEukaryote

Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package microbial mat_biofilm

URI: MIXS:MicrobialMatBiofilmMIGSEukaryote

Inheritance

• MicrobialMatBiofilm
  • MicrobialMatBiofilmMIGSEukaryote [ MIGSEukaryote]

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...	MIGSEukaryote
samp_taxon_id	1..1 String	NCBI taxon id of the sample	MIGSEukaryote
project_name	1..1 String	Name of the project within which the sequencing was organized	MIGSEukaryote
experimental_factor	0..1 String	Experimental factors are essentially the variable aspects of an experiment de...	MIGSEukaryote
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	MIGSEukaryote, MicrobialMatBiofilm
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	MIGSEukaryote, MicrobialMatBiofilm
collection_date	1..1 Date	The time of sampling, either as an instance (single point in time) or interva...	MIGSEukaryote, MicrobialMatBiofilm
neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation	MIGSEukaryote
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	MIGSEukaryote
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	MIGSEukaryote, MicrobialMatBiofilm
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen’s local vic...	MIGSEukaryote, MicrobialMatBiofilm
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	MIGSEukaryote, MicrobialMatBiofilm
subspecf_gen_lin	0..1 recommended String	Information about the genetic distinctness of the sequenced organism below th...	MIGSEukaryote
ploidy	0..1 String	The ploidy level of the genome (e	MIGSEukaryote
num_replicons	0..1 Integer	Reports the number of replicons in a nuclear genome of eukaryotes, in the gen...	MIGSEukaryote
extrachrom_elements	0..1 Integer	Do plasmids exist of significant phenotypic consequence (e	MIGSEukaryote
estimated_size	0..1 String	The estimated size of the genome prior to sequencing	MIGSEukaryote
ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...	MIGSEukaryote
source_mat_id	0..1 recommended String	A unique identifier assigned to a material sample (as defined by http://rs	MIGSEukaryote
pathogenicity	0..1 recommended String	To what is the entity pathogenic	MIGSEukaryote
biotic_relationship	0..1 BioticRelationshipEnum	Description of relationship(s) between the subject organism and other organis...	MIGSEukaryote
specific_host	0..1 String	Report the host's taxonomic name and/or NCBI taxonomy ID	MIGSEukaryote
host_spec_range	0..1 Integer	The range and diversity of host species that an organism is capable of infect...	MIGSEukaryote
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	MIGSEukaryote
trophic_level	0..1 recommended TrophicLevelEnum	Trophic levels are the feeding position in a food chain	MIGSEukaryote
propagation	0..1 recommended String	The type of reproduction from the parent stock	MIGSEukaryote
isol_growth_condt	1..1 String	Publication reference in the form of pubmed ID (pmid), digital object identif...	MIGSEukaryote
samp_collec_device	0..1 String	The device used to collect an environmental sample	MIGSEukaryote
samp_collec_method	0..1 String	The method employed for collecting the sample	MIGSEukaryote
samp_mat_process	0..1 String	A brief description of any processing applied to the sample during or after r...	MIGSEukaryote
samp_size	0..1 QuantityValue	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	MIGSEukaryote
samp_vol_we_dna_ext	0..1 QuantityValue	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	MIGSEukaryote
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MIGSEukaryote
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MIGSEukaryote
lib_size	0..1 Integer	Total number of clones in the library prepared for the project	MIGSEukaryote
lib_reads_seqd	0..1 Integer	Total number of clones sequenced from the library	MIGSEukaryote
lib_layout	0..1 LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads	MIGSEukaryote
lib_vector	0..1 String	Cloning vector type(s) used in construction of libraries	MIGSEukaryote
lib_screen	0..1 String	Specific enrichment or screening methods applied before and/or after creating...	MIGSEukaryote
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	MIGSEukaryote
seq_meth	1..1 String	Sequencing machine used	MIGSEukaryote
tax_ident	0..1 recommended TaxIdentEnum	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG	MIGSEukaryote
assembly_qual	1..1 AssemblyQualEnum	The assembly quality category is based on sets of criteria outlined for each ...	MIGSEukaryote
assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...	MIGSEukaryote
assembly_software	1..1 String	Tool(s) used for assembly, including version number and parameters	MIGSEukaryote
annot	0..1 recommended String	Tool used for annotation, or for cases where annotation was provided by a com...	MIGSEukaryote
number_contig	1..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...	MIGSEukaryote
feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc	MIGSEukaryote
ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...	MIGSEukaryote
sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used	MIGSEukaryote
tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...	MIGSEukaryote
compl_score	0..1 String	Completeness score is typically based on either the fraction of markers found...	MIGSEukaryote
compl_software	0..1 String	Tools used for completion estimate, i	MIGSEukaryote
associated_resource	0..1 recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	MIGSEukaryote
sop	0..1 recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	MIGSEukaryote
depth	0..1 QuantityValue	The vertical distance below local surface, e	MicrobialMatBiofilm
alt	0..1 QuantityValue	Altitude is a term used to identify heights of objects such as airplanes, spa...	MicrobialMatBiofilm
elev	0..1 QuantityValue	Elevation of the sampling site is its height above a fixed reference point, m...	MicrobialMatBiofilm
temp	0..1 QuantityValue	Temperature of the sample at the time of sampling	MicrobialMatBiofilm
alkalinity	0..1 QuantityValue	Alkalinity, the ability of a solution to neutralize acids to the equivalence ...	MicrobialMatBiofilm
alkyl_diethers	0..1 QuantityValue	Concentration of alkyl diethers	MicrobialMatBiofilm
aminopept_act	0..1 QuantityValue	Measurement of aminopeptidase activity	MicrobialMatBiofilm
ammonium	0..1 QuantityValue	Concentration of ammonium in the sample	MicrobialMatBiofilm
bacteria_carb_prod	0..1 QuantityValue	Measurement of bacterial carbon production	MicrobialMatBiofilm
biomass	0..* String	Amount of biomass; should include the name for the part of biomass measured, ...	MicrobialMatBiofilm
bishomohopanol	0..1 QuantityValue	Concentration of bishomohopanol	MicrobialMatBiofilm
bromide	0..1 QuantityValue	Concentration of bromide	MicrobialMatBiofilm
calcium	0..1 QuantityValue	Concentration of calcium in the sample	MicrobialMatBiofilm
carb_nitro_ratio	0..1 QuantityValue	Ratio of amount or concentrations of carbon to nitrogen	MicrobialMatBiofilm
chem_administration	0..* String	List of chemical compounds administered to the host or site where sampling oc...	MicrobialMatBiofilm
chloride	0..1 QuantityValue	Concentration of chloride in the sample	MicrobialMatBiofilm
chlorophyll	0..1 QuantityValue	Concentration of chlorophyll	MicrobialMatBiofilm
diether_lipids	0..* String	Concentration of diether lipids; can include multiple types of diether lipids	MicrobialMatBiofilm
diss_carb_dioxide	0..1 QuantityValue	Concentration of dissolved carbon dioxide in the sample or liquid portion of ...	MicrobialMatBiofilm
diss_hydrogen	0..1 QuantityValue	Concentration of dissolved hydrogen	MicrobialMatBiofilm
diss_inorg_carb	0..1 QuantityValue	Dissolved inorganic carbon concentration in the sample, typically measured af...	MicrobialMatBiofilm
diss_org_carb	0..1 QuantityValue	Concentration of dissolved organic carbon in the sample, liquid portion of th...	MicrobialMatBiofilm
diss_org_nitro	0..1 QuantityValue	Dissolved organic nitrogen concentration measured as; total dissolved nitroge...	MicrobialMatBiofilm
diss_oxygen	0..1 QuantityValue	Concentration of dissolved oxygen	MicrobialMatBiofilm
glucosidase_act	0..1 QuantityValue	Measurement of glucosidase activity	MicrobialMatBiofilm
magnesium	0..1 QuantityValue	Concentration of magnesium in the sample	MicrobialMatBiofilm
mean_frict_vel	0..1 QuantityValue	Measurement of mean friction velocity	MicrobialMatBiofilm
mean_peak_frict_vel	0..1 QuantityValue	Measurement of mean peak friction velocity	MicrobialMatBiofilm
methane	0..1 QuantityValue	Methane (gas) amount or concentration at the time of sampling	MicrobialMatBiofilm
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	MicrobialMatBiofilm
n_alkanes	0..* String	Concentration of n-alkanes; can include multiple n-alkanes	MicrobialMatBiofilm
nitrate	0..1 QuantityValue	Concentration of nitrate in the sample	MicrobialMatBiofilm
nitrite	0..1 QuantityValue	Concentration of nitrite in the sample	MicrobialMatBiofilm
nitro	0..1 QuantityValue	Concentration of nitrogen (total)	MicrobialMatBiofilm
org_carb	0..1 QuantityValue	Concentration of organic carbon	MicrobialMatBiofilm
org_matter	0..1 QuantityValue	Concentration of organic matter	MicrobialMatBiofilm
org_nitro	0..1 QuantityValue	Concentration of organic nitrogen	MicrobialMatBiofilm
organism_count	0..* OrganismCountEnum	Total cell count of any organism (or group of organisms) per gram, volume or ...	MicrobialMatBiofilm
oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample	MicrobialMatBiofilm
ph	0..1 Double	Ph measurement of the sample, or liquid portion of sample, or aqueous phase o...	MicrobialMatBiofilm
part_org_carb	0..1 QuantityValue	Concentration of particulate organic carbon	MicrobialMatBiofilm
perturbation	0..* String	Type of perturbation, e	MicrobialMatBiofilm
petroleum_hydrocarb	0..1 QuantityValue	Concentration of petroleum hydrocarbon	MicrobialMatBiofilm
phaeopigments	0..* String	Concentration of phaeopigments; can include multiple phaeopigments	MicrobialMatBiofilm
phosphate	0..1 QuantityValue	Concentration of phosphate	MicrobialMatBiofilm
phosplipid_fatt_acid	0..* String	Concentration of phospholipid fatty acids; can include multiple values	MicrobialMatBiofilm
potassium	0..1 QuantityValue	Concentration of potassium in the sample	MicrobialMatBiofilm
pressure	0..1 QuantityValue	Pressure to which the sample is subject to, in atmospheres	MicrobialMatBiofilm
redox_potential	0..1 QuantityValue	Redox potential, measured relative to a hydrogen cell, indicating oxidation o...	MicrobialMatBiofilm
salinity	0..1 QuantityValue	The total concentration of all dissolved salts in a liquid or solid sample	MicrobialMatBiofilm
samp_store_dur	0..1 String	Duration for which the sample was stored	MicrobialMatBiofilm
samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room	MicrobialMatBiofilm
samp_store_temp	0..1 QuantityValue	Temperature at which sample was stored, e	MicrobialMatBiofilm
silicate	0..1 QuantityValue	Concentration of silicate	MicrobialMatBiofilm
sodium	0..1 QuantityValue	Sodium concentration in the sample	MicrobialMatBiofilm
sulfate	0..1 QuantityValue	Concentration of sulfate in the sample	MicrobialMatBiofilm
sulfide	0..1 QuantityValue	Concentration of sulfide in the sample	MicrobialMatBiofilm
tot_carb	0..1 QuantityValue	Total carbon content	MicrobialMatBiofilm
tot_nitro_content	0..1 QuantityValue	Total nitrogen content of the sample	MicrobialMatBiofilm
tot_org_carb	0..1 QuantityValue	Definition for soil: total organic carbon content of the soil, definition oth...	MicrobialMatBiofilm
turbidity	0..1 QuantityValue	Measure of the amount of cloudiness or haziness in water caused by individual...	MicrobialMatBiofilm
water_content	0..1 QuantityValue	Water content measurement	MicrobialMatBiofilm

Identifier and Mapping Information

Schema Source

• from schema: http://w3id.org/mixs

Mappings

Mapping Type	Mapped Value
self	MIXS:MicrobialMatBiofilmMIGSEukaryote
native	MIXS:MicrobialMatBiofilmMIGSEukaryote

LinkML Source

Direct

name: microbial mat_biofilm MIGS eukaryote
description: 'Combinatorial checklist Minimal Information about a Genome Sequence:
  eukaryote with environmental package microbial mat_biofilm'
from_schema: http://w3id.org/mixs
is_a: microbial mat_biofilm
mixins:
- MIGS eukaryote

Induced

name: microbial mat_biofilm MIGS eukaryote
description: 'Combinatorial checklist Minimal Information about a Genome Sequence:
  eukaryote with environmental package microbial mat_biofilm'
from_schema: http://w3id.org/mixs
is_a: microbial mat_biofilm
mixins:
- MIGS eukaryote
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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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
  subspecf_gen_lin:
    name: subspecf_gen_lin
    description: Information about the genetic distinctness of the sequenced organism
      below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any
      relevant genetic typing schemes like Group I plasmid. Subspecies should not
      be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: subspecific genetic lineage
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    multivalued: false
    alias: subspecf_gen_lin
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMARKS survey
    range: string
    recommended: true
  ploidy:
    name: ploidy
    description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid,
      triploid, tetraploid). It has implications for the downstream study of duplicated
      gene and regions of the genomes (and perhaps for difficulties in assembly).
      For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic
      Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer
      to http://purl.bioontology.org/ontology/PATO
    title: ploidy
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000021
    multivalued: false
    alias: ploidy
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    range: string
    required: false
  num_replicons:
    name: num_replicons
    description: Reports the number of replicons in a nuclear genome of eukaryotes,
      in the genome of a bacterium or archaea or the number of segments in a segmented
      virus. Always applied to the haploid chromosome count of a eukaryote
    title: number of replicons
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000022
    multivalued: false
    alias: num_replicons
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS virus
    range: integer
    required: false
  extrachrom_elements:
    name: extrachrom_elements
    description: Do plasmids exist of significant phenotypic consequence (e.g. ones
      that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
      (borrelia has 15+ plasmids)
    title: extrachromosomal elements
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000023
    multivalued: false
    alias: extrachrom_elements
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS org
    - MIMARKS survey
    range: integer
    required: false
  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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{integer} bp'
    slot_uri: MIXS:0000024
    multivalued: false
    alias: estimated_size
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIUVIG
    range: string
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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
  pathogenicity:
    name: pathogenicity
    description: To what is the entity pathogenic
    title: known pathogenicity
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000027
    multivalued: false
    alias: pathogenicity
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS virus
    - MIUVIG
    range: string
    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: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    multivalued: false
    alias: biotic_relationship
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS virus
    - MIMARKS survey
    - MIUVIG
    range: biotic_relationship_enum
    required: false
  specific_host:
    name: specific_host
    description: Report the host's taxonomic name and/or NCBI taxonomy ID.
    title: host scientific name
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}|{NCBI taxid}'
    slot_uri: MIXS:0000029
    multivalued: false
    alias: specific_host
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIUVIG
    range: string
    required: false
  host_spec_range:
    name: host_spec_range
    description: The range and diversity of host species that an organism is capable
      of infecting, defined by NCBI taxonomy identifier.
    title: host specificity or range
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000030
    multivalued: false
    alias: host_spec_range
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIUVIG
    range: integer
    required: 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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000031
    multivalued: false
    alias: host_disease_stat
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS virus
    - MIUVIG
    range: string
    required: false
  trophic_level:
    name: trophic_level
    description: Trophic levels are the feeding position in a food chain. Microbes
      can be a range of producers (e.g. chemolithotroph)
    title: trophic level
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000032
    multivalued: false
    alias: trophic_level
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIMARKS survey
    range: trophic_level_enum
    recommended: true
  propagation:
    name: propagation
    description: 'The type of reproduction from the parent stock. Values for this
      field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately
      lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual.'
    title: propagation
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000033
    multivalued: false
    alias: propagation
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS plant
    - MIGS virus
    range: string
    recommended: true
  isol_growth_condt:
    name: isol_growth_condt
    description: Publication reference in the form of pubmed ID (pmid), digital object
      identifier (doi) or url for isolation and growth condition specifications of
      the organism/material
    title: isolation and growth condition
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000003
    multivalued: false
    alias: isol_growth_condt
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMARKS survey
    range: string
    required: true
  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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: lib_layout_enum
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: tax_ident_enum
    recommended: 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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: 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: http://w3id.org/mixs
    is_a: sequencing field
    slot_uri: MIXS:0000060
    multivalued: false
    alias: number_contig
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MISAG
    - MIMAG
    - MIUVIG
    range: integer
    required: true
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - 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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    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: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    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
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - altitude
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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
  alkalinity:
    name: alkalinity
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000421
    multivalued: false
    alias: alkalinity
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  alkyl_diethers:
    name: alkyl_diethers
    description: Concentration of alkyl diethers
    title: alkyl diethers
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000490
    multivalued: false
    alias: alkyl_diethers
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  aminopept_act:
    name: aminopept_act
    description: Measurement of aminopeptidase activity
    title: aminopeptidase activity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000172
    multivalued: false
    alias: aminopept_act
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  ammonium:
    name: ammonium
    description: Concentration of ammonium in the sample
    title: ammonium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000427
    multivalued: false
    alias: ammonium
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  bacteria_carb_prod:
    name: bacteria_carb_prod
    description: Measurement of bacterial carbon production
    title: bacterial carbon production
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000173
    multivalued: false
    alias: bacteria_carb_prod
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  biomass:
    name: biomass
    description: Amount of biomass; should include the name for the part of biomass
      measured, e.g. Microbial, total. Can include multiple measurements
    title: biomass
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000174
    multivalued: true
    alias: biomass
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: string
    required: false
  bishomohopanol:
    name: bishomohopanol
    description: Concentration of bishomohopanol
    title: bishomohopanol
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000175
    multivalued: false
    alias: bishomohopanol
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  bromide:
    name: bromide
    description: Concentration of bromide
    title: bromide
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000176
    multivalued: false
    alias: bromide
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  calcium:
    name: calcium
    description: Concentration of calcium in the sample
    title: calcium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000432
    multivalued: false
    alias: calcium
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  carb_nitro_ratio:
    name: carb_nitro_ratio
    description: Ratio of amount or concentrations of carbon to nitrogen
    title: carbon/nitrogen ratio
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000310
    multivalued: false
    alias: carb_nitro_ratio
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    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: microbial mat_biofilm MIGS eukaryote
    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
  chloride:
    name: chloride
    description: Concentration of chloride in the sample
    title: chloride
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000429
    multivalued: false
    alias: chloride
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  chlorophyll:
    name: chlorophyll
    description: Concentration of chlorophyll
    title: chlorophyll
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000177
    multivalued: false
    alias: chlorophyll
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  diether_lipids:
    name: diether_lipids
    description: Concentration of diether lipids; can include multiple types of diether
      lipids
    title: diether lipids
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000178
    multivalued: true
    alias: diether_lipids
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: string
    required: false
  diss_carb_dioxide:
    name: diss_carb_dioxide
    description: Concentration of dissolved carbon dioxide in the sample or liquid
      portion of the sample
    title: dissolved carbon dioxide
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000436
    multivalued: false
    alias: diss_carb_dioxide
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  diss_hydrogen:
    name: diss_hydrogen
    description: Concentration of dissolved hydrogen
    title: dissolved hydrogen
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000179
    multivalued: false
    alias: diss_hydrogen
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  diss_inorg_carb:
    name: diss_inorg_carb
    description: Dissolved inorganic carbon concentration in the sample, typically
      measured after filtering the sample using a 0.45 micrometer filter
    title: dissolved inorganic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000434
    multivalued: false
    alias: diss_inorg_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  diss_org_carb:
    name: diss_org_carb
    description: Concentration of dissolved organic carbon in the sample, liquid portion
      of the sample, or aqueous phase of the fluid
    title: dissolved organic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000433
    multivalued: false
    alias: diss_org_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  diss_org_nitro:
    name: diss_org_nitro
    description: Dissolved organic nitrogen concentration measured as; total dissolved
      nitrogen - NH4 - NO3 - NO2
    title: dissolved organic nitrogen
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000162
    multivalued: false
    alias: diss_org_nitro
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  diss_oxygen:
    name: diss_oxygen
    description: Concentration of dissolved oxygen
    title: dissolved oxygen
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000119
    multivalued: false
    alias: diss_oxygen
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  glucosidase_act:
    name: glucosidase_act
    description: Measurement of glucosidase activity
    title: glucosidase activity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000137
    multivalued: false
    alias: glucosidase_act
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  magnesium:
    name: magnesium
    description: Concentration of magnesium in the sample
    title: magnesium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000431
    multivalued: false
    alias: magnesium
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  mean_frict_vel:
    name: mean_frict_vel
    description: Measurement of mean friction velocity
    title: mean friction velocity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000498
    multivalued: false
    alias: mean_frict_vel
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  mean_peak_frict_vel:
    name: mean_peak_frict_vel
    description: Measurement of mean peak friction velocity
    title: mean peak friction velocity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000502
    multivalued: false
    alias: mean_peak_frict_vel
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  methane:
    name: methane
    description: Methane (gas) amount or concentration at the time of sampling
    title: methane
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000101
    multivalued: false
    alias: methane
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - sediment
    - microbial mat_biofilm
    - air
    range: quantity value
    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: microbial mat_biofilm MIGS eukaryote
    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
  n_alkanes:
    name: n_alkanes
    description: Concentration of n-alkanes; can include multiple n-alkanes
    title: n-alkanes
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000503
    multivalued: true
    alias: n_alkanes
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: string
    required: false
  nitrate:
    name: nitrate
    description: Concentration of nitrate in the sample
    title: nitrate
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000425
    multivalued: false
    alias: nitrate
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  nitrite:
    name: nitrite
    description: Concentration of nitrite in the sample
    title: nitrite
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000426
    multivalued: false
    alias: nitrite
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  nitro:
    name: nitro
    description: Concentration of nitrogen (total)
    title: nitrogen
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000504
    multivalued: false
    alias: nitro
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  org_carb:
    name: org_carb
    description: Concentration of organic carbon
    title: organic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000508
    multivalued: false
    alias: org_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  org_matter:
    name: org_matter
    description: Concentration of organic matter
    title: organic matter
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000204
    multivalued: false
    alias: org_matter
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - soil
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  org_nitro:
    name: org_nitro
    description: Concentration of organic nitrogen
    title: organic nitrogen
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000205
    multivalued: false
    alias: org_nitro
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - soil
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    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: microbial mat_biofilm MIGS eukaryote
    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
  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: microbial mat_biofilm MIGS eukaryote
    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
  ph:
    name: ph
    description: Ph measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001001
    multivalued: false
    alias: ph
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - soil
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - food-farm environment
    range: double
    required: false
  part_org_carb:
    name: part_org_carb
    description: Concentration of particulate organic carbon
    title: particulate organic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000515
    multivalued: false
    alias: part_org_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    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: microbial mat_biofilm MIGS eukaryote
    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
  petroleum_hydrocarb:
    name: petroleum_hydrocarb
    description: Concentration of petroleum hydrocarbon
    title: petroleum hydrocarbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000516
    multivalued: false
    alias: petroleum_hydrocarb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  phaeopigments:
    name: phaeopigments
    description: Concentration of phaeopigments; can include multiple phaeopigments
    title: phaeopigments
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000180
    multivalued: true
    alias: phaeopigments
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: string
    required: false
  phosphate:
    name: phosphate
    description: Concentration of phosphate
    title: phosphate
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000505
    multivalued: false
    alias: phosphate
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  phosplipid_fatt_acid:
    name: phosplipid_fatt_acid
    description: Concentration of phospholipid fatty acids; can include multiple values
    title: phospholipid fatty acid
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000181
    multivalued: true
    alias: phosplipid_fatt_acid
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: string
    required: false
  potassium:
    name: potassium
    description: Concentration of potassium in the sample
    title: potassium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000430
    multivalued: false
    alias: potassium
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  pressure:
    name: pressure
    description: Pressure to which the sample is subject to, in atmospheres
    title: pressure
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000412
    multivalued: false
    alias: pressure
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  redox_potential:
    name: redox_potential
    description: Redox potential, measured relative to a hydrogen cell, indicating
      oxidation or reduction potential
    title: redox potential
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000182
    multivalued: false
    alias: redox_potential
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  salinity:
    name: salinity
    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
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - 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-farm environment
    - 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: microbial mat_biofilm MIGS eukaryote
    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: microbial mat_biofilm MIGS eukaryote
    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_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: microbial mat_biofilm MIGS eukaryote
    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
  silicate:
    name: silicate
    description: Concentration of silicate
    title: silicate
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000184
    multivalued: false
    alias: silicate
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    range: quantity value
    required: false
  sodium:
    name: sodium
    description: Sodium concentration in the sample
    title: sodium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000428
    multivalued: false
    alias: sodium
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - wastewater_sludge
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  sulfate:
    name: sulfate
    description: Concentration of sulfate in the sample
    title: sulfate
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000423
    multivalued: false
    alias: sulfate
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  sulfide:
    name: sulfide
    description: Concentration of sulfide in the sample
    title: sulfide
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000424
    multivalued: false
    alias: sulfide
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    range: quantity value
    required: false
  tot_carb:
    name: tot_carb
    description: Total carbon content
    title: total carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000525
    multivalued: false
    alias: tot_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false
  tot_nitro_content:
    name: tot_nitro_content
    description: Total nitrogen content of the sample
    title: total nitrogen content
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000530
    multivalued: false
    alias: tot_nitro_content
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - soil
    - sediment
    - microbial mat_biofilm
    - food-farm environment
    range: quantity value
    required: false
  tot_org_carb:
    name: tot_org_carb
    description: 'Definition for soil: total organic carbon content of the soil, definition
      otherwise: total organic carbon content'
    title: total organic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000533
    multivalued: false
    alias: tot_org_carb
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - soil
    - sediment
    - microbial mat_biofilm
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  turbidity:
    name: turbidity
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000191
    multivalued: false
    alias: turbidity
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - water
    - sediment
    - microbial mat_biofilm
    - food-farm environment
    range: quantity value
    required: false
  water_content:
    name: water_content
    description: Water content measurement
    title: water content
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000185
    multivalued: false
    alias: water_content
    owner: microbial mat_biofilm MIGS eukaryote
    domain_of:
    - soil
    - sediment
    - microbial mat_biofilm
    range: quantity value
    required: false