Class: wastewater_sludge

wastewater/sludge

URI: mixs.vocab:WastewaterSludge

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Children

  • WastewaterSludgeMIGSBacteria - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge
  • WastewaterSludgeMIGSEukaryote - Combinatorial checklist Minimal Information about a Genome Sequence: eukaryote with environmental package wastewater_sludge
  • WastewaterSludgeMIGSOrg - Combinatorial checklist Minimal Information about a Genome Sequence: org with environmental package wastewater_sludge
  • WastewaterSludgeMIGSPlant - Combinatorial checklist Minimal Information about a Genome Sequence: plant with environmental package wastewater_sludge
  • WastewaterSludgeMIGSVirus - Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package wastewater_sludge
  • WastewaterSludgeMIMAG - Combinatorial checklist Minimum Information About a Metagenome-Assembled Genome with environmental package wastewater_sludge
  • WastewaterSludgeMIMARKSSpecimen - Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package wastewater_sludge
  • WastewaterSludgeMIMARKSSurvey - Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package wastewater_sludge
  • WastewaterSludgeMIMS - Combinatorial checklist Metagenome or Environmental with environmental package wastewater_sludge
  • WastewaterSludgeMISAG - Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package wastewater_sludge
  • WastewaterSludgeMIUVIG - Combinatorial checklist Minimum Information About an Uncultivated Virus Genome with environmental package wastewater_sludge

Referenced by Class

Attributes

Own

  • lat_lon 0..1
    • 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
    • Range: String
    • Example: 50.586825 6.408977 None
  • wastewater_sludge➞depth 0..1
    • 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.
    • Range: QuantityValue
    • Example: 10 meter None
  • alt 0..1
    • 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
    • Range: QuantityValue
    • Example: 100 meter None
  • elev 0..1
    • 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.
    • Range: QuantityValue
    • Example: 100 meter None
  • wastewater_sludge➞temp 0..1
    • Description: Temperature of the sample at the time of sampling.
    • Range: QuantityValue
    • Example: 25 degree Celsius None
  • geo_loc_name 0..1
    • 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)
    • Range: String
    • Example: USA: Maryland, Bethesda None
  • collection_date 0..1
    • 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
    • Range: Date
    • Example: 2018-05-11T10:00:00+01:00; 2018-05-11 None
  • env_broad_scale 0..1
    • 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
    • Range: String
    • Example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean None
  • env_local_scale 0..1
    • 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.
    • Range: String
    • Example: litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. None
  • env_medium 0..1
    • 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).
    • Range: String
    • Example: soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005] None
  • wastewater_sludge➞alkalinity 0..1
    • Description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
    • Range: QuantityValue
    • Example: 50 milligram per liter None
  • wastewater_sludge➞biochem_oxygen_dem 0..1
    • 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
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞chem_administration 0..*
    • 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
    • Range: String
    • Example: agar [CHEBI:2509];2018-05-11T20:00Z None
  • wastewater_sludge➞chem_oxygen_dem 0..1
    • 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
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞efficiency_percent 0..1
    • Description: Percentage of volatile solids removed from the anaerobic digestor
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞emulsions 0..*
    • Description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
    • Range: String
    • Example: None
  • wastewater_sludge➞gaseous_substances 0..*
    • Description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
    • Range: String
    • Example: None
  • wastewater_sludge➞indust_eff_percent 0..1
    • Description: Percentage of industrial effluents received by wastewater treatment plant
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞inorg_particles 0..*
    • Description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
    • Range: String
    • Example: None
  • wastewater_sludge➞misc_param 0..*
    • Description: Any other measurement performed or parameter collected, that is not listed here
    • Range: String
    • Example: Bicarbonate ion concentration;2075 micromole per kilogram None
  • wastewater_sludge➞nitrate 0..1
    • Description: Concentration of nitrate in the sample
    • Range: QuantityValue
    • Example: 65 micromole per liter None
  • wastewater_sludge➞org_particles 0..*
    • Description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.
    • Range: String
    • Example: None
  • wastewater_sludge➞organism_count 0..*
    • 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)
    • Range: organism_count_enum
    • Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
  • wastewater_sludge➞oxy_stat_samp 0..1
    • Description: Oxygenation status of sample
    • Range: oxy_stat_samp_enum
    • Example: aerobic None
  • wastewater_sludge➞ph 0..1
    • Description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
    • Range: Double
    • Example: 7.2 None
  • wastewater_sludge➞perturbation 0..*
    • 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
    • Range: String
    • Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None
  • wastewater_sludge➞phosphate 0..1
    • Description: Concentration of phosphate
    • Range: QuantityValue
    • Example: 0.7 micromole per liter None
  • wastewater_sludge➞pre_treatment 0..1
    • Description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater
    • Range: String
    • Example: None
  • wastewater_sludge➞primary_treatment 0..1
    • 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
    • Range: String
    • Example: None
  • wastewater_sludge➞reactor_type 0..1
    • 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
    • Range: String
    • Example: None
  • wastewater_sludge➞samp_salinity 0..1
    • Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater
    • Range: QuantityValue
    • Example: 1 milligram per liter None
  • wastewater_sludge➞salinity 0..1
    • 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.
    • Range: QuantityValue
    • Example: 25 practical salinity unit None
  • wastewater_sludge➞samp_store_dur 0..1
    • Description: Duration for which the sample was stored
    • Range: String
    • Example: P1Y6M None
  • wastewater_sludge➞samp_store_loc 0..1
    • Description: Location at which sample was stored, usually name of a specific freezer/room
    • Range: String
    • Example: Freezer no:5 None
  • wastewater_sludge➞samp_store_temp 0..1
    • Description: Temperature at which sample was stored, e.g. -80 degree Celsius
    • Range: QuantityValue
    • Example: -80 degree Celsius None
  • wastewater_sludge➞secondary_treatment 0..1
    • Description: The process for substantially degrading the biological content of the sewage
    • Range: String
    • Example: None
  • wastewater_sludge➞sewage_type 0..1
    • Description: Type of wastewater treatment plant as municipial or industrial
    • Range: String
    • Example: None
  • wastewater_sludge➞sludge_retent_time 0..1
    • Description: The time activated sludge remains in reactor
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞sodium 0..1
    • Description: Sodium concentration in the sample
    • Range: QuantityValue
    • Example: 10.5 milligram per liter None
  • wastewater_sludge➞soluble_inorg_mat 0..*
    • Description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
    • Range: String
    • Example: None
  • wastewater_sludge➞soluble_org_mat 0..*
    • Description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.
    • Range: String
    • Example: None
  • wastewater_sludge➞suspend_solids 0..*
    • Description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
    • Range: String
    • Example: None
  • wastewater_sludge➞tertiary_treatment 0..1
    • Description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
    • Range: String
    • Example: None
  • wastewater_sludge➞tot_nitro 0..1
    • 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
    • Range: QuantityValue
    • Example: 50 micromole per liter None
  • wastewater_sludge➞tot_phosphate 0..1
    • Description: Total amount or concentration of phosphate
    • Range: QuantityValue
    • Example: None
  • wastewater_sludge➞wastewater_type 0..1
    • Description: The origin of wastewater such as human waste, rainfall, storm drains, etc.
    • Range: String
    • Example: None
  • wastewater_sludge➞samp_name 1..1
    • 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.
    • Range: String
    • Example: ISDsoil1 None
  • wastewater_sludge➞project_name 1..1
    • Description: Name of the project within which the sequencing was organized
    • Range: String
    • Example: Forest soil metagenome None
  • wastewater_sludge➞samp_vol_we_dna_ext 0..1
    • 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).
    • Range: QuantityValue
    • Example: 1500 milliliter None