Skip to content

Combination: MimarksSWastewaterSludge

MIxS data that complies with the MimarksS checklist and the WastewaterSludge Extension

Inheritance

Terms

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... MimarksS, WastewaterSludge
pcr_primers 0..1 recommended
String		 PCR primers that were used to amplify the sequence of the targeted gene, locu... MimarksS
size_frac 0..1
String		 Filtering pore size used in sample preparation MimarksS
lib_screen 0..1 recommended
String		 Specific enrichment or screening methods applied before and/or after creating... MimarksS
nucl_acid_amp 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MimarksS
lib_size 0..1 recommended
Integer		 Total number of clones in the library prepared for the project MimarksS
target_subfragment 0..1 recommended
String		 Name of subfragment of a gene or locus MimarksS
mid 0..1 recommended
String		 Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe... MimarksS
temp 0..1 recommended
String		 Temperature of the sample at the time of sampling MimarksS, WastewaterSludge
nucl_acid_ext 0..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MimarksS
samp_size 0..1 recommended
String		 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... MimarksS
alt 0..1 recommended
String		 Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba... MimarksS
source_mat_id 0..* recommended
String		 A unique identifier assigned to a material sample (as defined by http://rs MimarksS
samp_vol_we_dna_ext 0..1
String		 Volume (ml) or mass (g) of total collected sample processed for DNA extractio... MimarksS, WastewaterSludge
lib_reads_seqd 0..1 recommended
Integer		 Total number of clones sequenced from the library MimarksS
rel_to_oxygen 0..1
RELTOOXYGENENUM		 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... MimarksS
samp_collect_device 0..1 recommended
String		 The device used to collect an environmental sample MimarksS
seq_quality_check 0..1 recommended
SEQQUALITYCHECKENUM		 Indicate if the sequence has been called by automatic systems (none) or under... MimarksS
lib_layout 0..1 recommended
LIBLAYOUTENUM		 Specify whether to expect single, paired, or other configuration of reads MimarksS
env_broad_scale 1..1
String		 Report the major environmental system the sample or specimen came from MimarksS
project_name 1..1
String		 Name of the project within which the sequencing was organized MimarksS, WastewaterSludge
lib_vector 0..1 recommended
String		 Cloning vector type(s) used in construction of libraries MimarksS
adapters 0..1 recommended
String		 Adapters provide priming sequences for both amplification and sequencing of t... MimarksS
neg_cont_type 0..1 recommended
NEGCONTTYPEENUM		 The substance or equipment used as a negative control in an investigation MimarksS
assembly_software 0..1 recommended
String		 Tool(s) used for assembly, including version number and parameters MimarksS
chimera_check 0..1 recommended
String		 Tool(s) used for chimera checking, including version number and parameters, t... MimarksS
pos_cont_type 0..1 recommended
String		 The substance, mixture, product, or apparatus used to verify that a process w... MimarksS
env_local_scale 1..1
String		 Report the entity or entities which are in the sample or specimen s local vic... MimarksS
samp_mat_process 0..1 recommended
String		 A brief description of any processing applied to the sample during or after r... MimarksS
depth 0..1 recommended
String		 The vertical distance below local surface MimarksS, WastewaterSludge
samp_collect_method 0..1 recommended
String		 The method employed for collecting the sample MimarksS
env_medium 1..1
String		 Report the environmental material(s) immediately surrounding the sample or sp... MimarksS
samp_taxon_id 1..1
String		 NCBI taxon id of the sample MimarksS
geo_loc_name 1..1
String		 The geographical origin of the sample as defined by the country or sea name f... MimarksS
collection_date 1..1
Datetime		 The time of sampling, either as an instance (single point in time) or interva... MimarksS
seq_meth 1..1
String		 Sequencing machine used MimarksS
lat_lon 1..1
String		 The geographical origin of the sample as defined by latitude and longitude MimarksS
elev 0..1 recommended
String		 Elevation of the sampling site is its height above a fixed reference point, m... MimarksS
pcr_cond 0..1 recommended
String		 Description of reaction conditions and components of PCR in the form of 'init... MimarksS
experimental_factor 0..* recommended
String		 Variable aspects of an experiment design that can be used to describe an expe... MimarksS
target_gene 1..1
String		 Targeted gene or locus name for marker gene studies MimarksS
associated_resource 0..* recommended
String		 A related resource that is referenced, cited, or otherwise associated to the ... MimarksS
sop 0..* recommended
String		 Standard operating procedures used in assembly and/or annotation of genomes, ... MimarksS
alkalinity 0..1
String		 Alkalinity, the ability of a solution to neutralize acids to the equivalence ... WastewaterSludge
biochem_oxygen_dem 0..1
String		 Amount of dissolved oxygen needed by aerobic biological organisms in a body o... WastewaterSludge
chem_administration 0..*
String		 List of chemical compounds administered to the host or site where sampling oc... WastewaterSludge
chem_oxygen_dem 0..1
String		 A measure of the capacity of water to consume oxygen during the decomposition... WastewaterSludge
efficiency_percent 0..1
String		 Percentage of volatile solids removed from the anaerobic digestor WastewaterSludge
emulsions 0..*
String		 Amount or concentration of substances such as paints, adhesives, mayonnaise, ... WastewaterSludge
gaseous_substances 0..*
String		 Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... WastewaterSludge
indust_eff_percent 0..1
String		 Percentage of industrial effluents received by wastewater treatment plant WastewaterSludge
inorg_particles 0..*
String		 Concentration of particles such as sand, grit, metal particles, ceramics, etc WastewaterSludge
misc_param 0..*
String		 Any other measurement performed or parameter collected, that is not listed he... WastewaterSludge
nitrate 0..1
String		 Concentration of nitrate in the sample WastewaterSludge
org_particles 0..*
String		 Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... WastewaterSludge
organism_count 0..*
String		 Total cell count of any organism (or group of organisms) per gram, volume or ... WastewaterSludge
oxy_stat_samp 0..1
OXYSTATSAMPENUM		 Oxygenation status of sample WastewaterSludge
ph 0..1
Float		 Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... WastewaterSludge
perturbation 0..*
String		 Type of perturbation, e WastewaterSludge
phosphate 0..1
String		 Concentration of phosphate WastewaterSludge
pre_treatment 0..1
String		 The process of pre-treatment removes materials that can be easily collected f... WastewaterSludge
primary_treatment 0..1
String		 The process to produce both a generally homogeneous liquid capable of being t... WastewaterSludge
reactor_type 0..1
String		 Anaerobic digesters can be designed and engineered to operate using a number ... WastewaterSludge
salinity 0..1
String		 The total concentration of all dissolved salts in a liquid or solid sample WastewaterSludge
samp_store_dur 0..1
String		 Duration for which the sample was stored WastewaterSludge
samp_store_loc 0..1
String		 Location at which sample was stored, usually name of a specific freezer/room WastewaterSludge
samp_store_temp 0..1
String		 Temperature at which sample was stored, e WastewaterSludge
secondary_treatment 0..1
String		 The process for substantially degrading the biological content of the sewage WastewaterSludge
sewage_type 0..1
String		 Type of wastewater treatment plant as municipial or industrial WastewaterSludge
sludge_retent_time 0..1
String		 The time activated sludge remains in reactor WastewaterSludge
sodium 0..1
String		 Sodium concentration in the sample WastewaterSludge
soluble_inorg_mat 0..*
String		 Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... WastewaterSludge
soluble_org_mat 0..*
String		 Concentration of substances such as urea, fruit sugars, soluble proteins, dru... WastewaterSludge
suspend_solids 0..*
String		 Concentration of substances including a wide variety of material, such as sil... WastewaterSludge
tertiary_treatment 0..1
String		 The process providing a final treatment stage to raise the effluent quality b... WastewaterSludge
tot_nitro 0..1
String		 Total nitrogen concentration of water samples, calculated by: total nitrogen ... WastewaterSludge
tot_phosphate 0..1
String		 Total amount or concentration of phosphate WastewaterSludge
wastewater_type 0..1
String		 The origin of wastewater such as human waste, rainfall, storm drains, etc WastewaterSludge

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/mixs-6-2-rc

LinkML Source

Direct

name: MimarksSWastewaterSludge
description: MIxS data that complies with the MimarksS checklist and the WastewaterSludge
  Extension
title: MimarksS combined with WastewaterSludge
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: WastewaterSludge
mixins:
- MimarksS
class_uri: MIXS:0010008_0016013

Induced

name: MimarksSWastewaterSludge
description: MIxS data that complies with the MimarksS checklist and the WastewaterSludge
  Extension
title: MimarksS combined with WastewaterSludge
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc
is_a: WastewaterSludge
mixins:
- MimarksS
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - sample
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  size_frac:
    name: size_frac
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    multivalued: false
    alias: size_frac
    owner: MimarksSWastewaterSludge
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000047
    multivalued: false
    alias: mid
    owner: MimarksSWastewaterSludge
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling
    title: temperature
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  source_mat_id:
    name: source_mat_id
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: true
    alias: source_mat_id
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: REL_TO_OXYGEN_ENUM
    required: false
    recommended: false
  samp_collect_device:
    name: samp_collect_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  seq_quality_check:
    name: seq_quality_check
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SEQ_QUALITY_CHECK_ENUM
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LIB_LAYOUT_ENUM
    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
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - project
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences
    title: chimera check software
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    description: 'Report the entity or entities which are in the sample or specimen
      s local vicinity and which you believe have significant causal influences on
      your sample or specimen. We recommend using EnvO terms which are of smaller
      spatial grain than your entry for env_broad_scale. Terms, such as anatomical
      sites, from other OBO Library ontologies which interoperate with EnvO (e.g.
      UBERON) are accepted in this field. EnvO documentation about how to use the
      field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: local environmental context
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - context
    - environmental
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  depth:
    name: depth
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - date
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - method
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - geographic
    - location
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of PCR in the form
      of 'initial denaturation:94degC_1.5min; annealing=...'
    title: pcr conditions
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    multivalued: false
    alias: pcr_cond
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  experimental_factor:
    name: experimental_factor
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    multivalued: true
    alias: experimental_factor
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: MimarksSWastewaterSludge
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: true
    alias: sop
    owner: MimarksSWastewaterSludge
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  alkalinity:
    name: alkalinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliequivalent per liter, milligram per liter
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    examples:
    - value: 50 milligram per liter
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - alkalinity
    slot_uri: MIXS:0000421
    multivalued: false
    alias: alkalinity
    owner: MimarksSWastewaterSludge
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  biochem_oxygen_dem:
    name: biochem_oxygen_dem
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: Amount of dissolved oxygen needed by aerobic biological organisms
      in a body of water to break down organic material present in a given water sample
      at certain temperature over a specific time period
    title: biochemical oxygen demand
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - oxygen
    slot_uri: MIXS:0000653
    multivalued: false
    alias: biochem_oxygen_dem
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  chem_administration:
    name: chem_administration
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  chem_oxygen_dem:
    name: chem_oxygen_dem
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter
    description: A measure of the capacity of water to consume oxygen during the decomposition
      of organic matter and the oxidation of inorganic chemicals such as ammonia and
      nitrite
    title: chemical oxygen demand
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - oxygen
    slot_uri: MIXS:0000656
    multivalued: false
    alias: chem_oxygen_dem
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  efficiency_percent:
    name: efficiency_percent
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Percentage of volatile solids removed from the anaerobic digestor
    title: efficiency percent
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - percent
    slot_uri: MIXS:0000657
    multivalued: false
    alias: efficiency_percent
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  emulsions:
    name: emulsions
    annotations:
      Expected_value:
        tag: Expected_value
        value: emulsion name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: gram per liter
    description: Amount or concentration of substances such as paints, adhesives,
      mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion
      types
    title: emulsions
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000660
    multivalued: true
    alias: emulsions
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  gaseous_substances:
    name: gaseous_substances
    annotations:
      Expected_value:
        tag: Expected_value
        value: gaseous substance name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Amount or concentration of substances such as hydrogen sulfide, carbon
      dioxide, methane, etc.; can include multiple substances
    title: gaseous substances
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000661
    multivalued: true
    alias: gaseous_substances
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  indust_eff_percent:
    name: indust_eff_percent
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: percentage
    description: Percentage of industrial effluents received by wastewater treatment
      plant
    title: industrial effluent percent
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - percent
    slot_uri: MIXS:0000662
    multivalued: false
    alias: indust_eff_percent
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  inorg_particles:
    name: inorg_particles
    annotations:
      Expected_value:
        tag: Expected_value
        value: inorganic particle name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: mole per liter, milligram per liter
    description: Concentration of particles such as sand, grit, metal particles, ceramics,
      etc.; can include multiple particles
    title: inorganic particles
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - inorganic
    - particle
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000664
    multivalued: true
    alias: inorg_particles
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  nitrate:
    name: nitrate
    description: Concentration of nitrate in the sample
    title: nitrate
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000425
    multivalued: false
    alias: nitrate
    owner: MimarksSWastewaterSludge
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  org_particles:
    name: org_particles
    annotations:
      Expected_value:
        tag: Expected_value
        value: particle name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: gram per liter
    description: Concentration of particles such as faeces, hairs, food, vomit, paper
      fibers, plant material, humus, etc
    title: organic particles
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - organic
    - particle
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000665
    multivalued: true
    alias: org_particles
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OXY_STAT_SAMP_ENUM
    required: false
    recommended: false
  ph:
    name: ph
    description: Ph measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0001001
    multivalued: false
    alias: ph
    owner: MimarksSWastewaterSludge
    domain_of:
    - FoodFarmEnvironment
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - WastewaterSludge
    - Water
    range: float
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  phosphate:
    name: phosphate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - phosphate
    slot_uri: MIXS:0000505
    multivalued: false
    alias: phosphate
    owner: MimarksSWastewaterSludge
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pre_treatment:
    name: pre_treatment
    annotations:
      Expected_value:
        tag: Expected_value
        value: pre-treatment type
    description: The process of pre-treatment removes materials that can be easily
      collected from the raw wastewater
    title: pre-treatment
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000348
    multivalued: false
    alias: pre_treatment
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  primary_treatment:
    name: primary_treatment
    annotations:
      Expected_value:
        tag: Expected_value
        value: primary treatment type
    description: The process to produce both a generally homogeneous liquid capable
      of being treated biologically and a sludge that can be separately treated or
      processed
    title: primary treatment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - primary
    - treatment
    string_serialization: '{text}'
    slot_uri: MIXS:0000349
    multivalued: false
    alias: primary_treatment
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  reactor_type:
    name: reactor_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: reactor type name
    description: Anaerobic digesters can be designed and engineered to operate using
      a number of different process configurations, as batch or continuous, mesophilic,
      high solid or low solid, and single stage or multistage
    title: reactor type
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{text}'
    slot_uri: MIXS:0000350
    multivalued: false
    alias: reactor_type
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  salinity:
    name: salinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: practical salinity unit, percentage
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    multivalued: false
    alias: salinity
    owner: MimarksSWastewaterSludge
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: https://w3id.org/mixs-6-2-rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_store_temp
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  secondary_treatment:
    name: secondary_treatment
    annotations:
      Expected_value:
        tag: Expected_value
        value: secondary treatment type
    description: The process for substantially degrading the biological content of
      the sewage
    title: secondary treatment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - secondary
    - treatment
    string_serialization: '{text}'
    slot_uri: MIXS:0000351
    multivalued: false
    alias: secondary_treatment
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  sewage_type:
    name: sewage_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: sewage type name
    description: Type of wastewater treatment plant as municipial or industrial
    title: sewage type
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{text}'
    slot_uri: MIXS:0000215
    multivalued: false
    alias: sewage_type
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  sludge_retent_time:
    name: sludge_retent_time
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: hours
    description: The time activated sludge remains in reactor
    title: sludge retention time
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - time
    slot_uri: MIXS:0000669
    multivalued: false
    alias: sludge_retent_time
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  sodium:
    name: sodium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter, parts per million
    description: Sodium concentration in the sample
    title: sodium
    examples:
    - value: 10.5 milligram per liter
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000428
    multivalued: false
    alias: sodium
    owner: MimarksSWastewaterSludge
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  soluble_inorg_mat:
    name: soluble_inorg_mat
    annotations:
      Expected_value:
        tag: Expected_value
        value: soluble inorganic material name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
    description: Concentration of substances such as ammonia, road-salt, sea-salt,
      cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc
    title: soluble inorganic material
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - inorganic
    - material
    - soluble
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000672
    multivalued: true
    alias: soluble_inorg_mat
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  soluble_org_mat:
    name: soluble_org_mat
    annotations:
      Expected_value:
        tag: Expected_value
        value: soluble organic material name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: gram, microgram, mole per liter, gram per liter, parts per million
    description: Concentration of substances such as urea, fruit sugars, soluble proteins,
      drugs, pharmaceuticals, etc
    title: soluble organic material
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - material
    - organic
    - soluble
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000673
    multivalued: true
    alias: soluble_org_mat
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  suspend_solids:
    name: suspend_solids
    annotations:
      Expected_value:
        tag: Expected_value
        value: suspended solid name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: gram, microgram, milligram per liter, mole per liter, gram per liter,
          part per million
    description: Concentration of substances including a wide variety of material,
      such as silt, decaying plant and animal matter; can include multiple substances
    title: suspended solids
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - solids
    - suspended
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000150
    multivalued: true
    alias: suspend_solids
    owner: MimarksSWastewaterSludge
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  tertiary_treatment:
    name: tertiary_treatment
    annotations:
      Expected_value:
        tag: Expected_value
        value: tertiary treatment type
    description: The process providing a final treatment stage to raise the effluent
      quality before it is discharged to the receiving environment
    title: tertiary treatment
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - treatment
    string_serialization: '{text}'
    slot_uri: MIXS:0000352
    multivalued: false
    alias: tertiary_treatment
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
  tot_nitro:
    name: tot_nitro
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per liter, micromole per liter, milligram per liter
    description: 'Total nitrogen concentration of water samples, calculated by: total
      nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
      without filtering, reported as nitrogen'
    title: total nitrogen concentration
    examples:
    - value: 50 micromole per liter
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - concentration
    - nitrogen
    - total
    slot_uri: MIXS:0000102
    multivalued: false
    alias: tot_nitro
    owner: MimarksSWastewaterSludge
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - WastewaterSludge
    - Water
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_phosphate:
    name: tot_phosphate
    description: Total amount or concentration of phosphate
    title: total phosphate
    from_schema: https://w3id.org/mixs-6-2-rc
    slot_uri: MIXS:0000689
    multivalued: false
    alias: tot_phosphate
    owner: MimarksSWastewaterSludge
    domain_of:
    - Agriculture
    - WastewaterSludge
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  wastewater_type:
    name: wastewater_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: wastewater type name
    description: The origin of wastewater such as human waste, rainfall, storm drains,
      etc
    title: wastewater type
    from_schema: https://w3id.org/mixs-6-2-rc
    keywords:
    - type
    string_serialization: '{text}'
    slot_uri: MIXS:0000353
    multivalued: false
    alias: wastewater_type
    owner: MimarksSWastewaterSludge
    domain_of:
    - WastewaterSludge
    range: string
    required: false
    recommended: false
class_uri: MIXS:0010008_0016013