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Slot: fecal contamination value (fecal_contamination_value)

The measured amount of the indicator named in fecal_contamination_indicator, as a concentration in the wastewater.

URI: nmdc:fecal_contamination_value

Applicable Classes

Name Description Modifies Slot
Biosample Biological source material which can be characterized by an experiment. no

Properties

Examples

A crAssphage concentration reported as gene copies per liter of wastewater.

type: "nmdc:QuantityValue"
has_raw_value: "1.92E+08 copies/L wastewater"
has_numeric_value: 192000000
has_unit: "{copies}/L"

Comments

  • Store copies per liter, milliliter or gram. A cycle threshold reported instead of a concentration does not fit these units; keep it in misc_param.

See Also

Identifier and Mapping Information

Annotations

property value
storage_units {copies}/L

Schema Source

Mappings

Mapping Type Mapped Value
related GENEPIO:0100815, GENEPIO:0100816, NCBI_BIOSAMPLE_ATTRIBUTE:ww_endog_control_1_conc
close NCBI_BIOSAMPLE_ATTRIBUTE:fecal_contamination_value

LinkML Source

name: fecal_contamination_value
annotations:
  storage_units:
    tag: storage_units
    value: '{copies}/L|{copies}/mL|{copies}/g'
description: The measured amount of the indicator named in fecal_contamination_indicator,
  as a concentration in the wastewater.
title: fecal contamination value
notes:
- 'PHA4GE Wastewater Contextual Data Specification 4.4.4: related match to fecal contamination
  value (GENEPIO:0100815) and fecal contamination unit (GENEPIO:0100816); one QuantityValue
  here is split across PHA4GE value and unit fields.'
- 'NCBI BioSample: close match to the fecal_contamination_value attribute of the PHA4GE.wwsurv.1.0
  package (value and unit in one string); related match to the ww_endog_control_1_conc
  attribute of the SARS-CoV-2.wwsurv.1.0 package, whose unit sits in ww_endog_control_1_units.'
comments:
- Store copies per liter, milliliter or gram. A cycle threshold reported instead of
  a concentration does not fit these units; keep it in misc_param.
examples:
- description: A crAssphage concentration reported as gene copies per liter of wastewater.
  object:
    type: nmdc:QuantityValue
    has_raw_value: 1.92E+08 copies/L wastewater
    has_numeric_value: 192000000
    has_unit: '{copies}/L'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/pha4ge/wastewater-contextual-data-specification/releases/tag/v4.4.4
- https://github.com/cidgoh/pathogen-genomics-package/blob/PGPv5.6.5/templates/wastewater/schema.yaml
close_mappings:
- NCBI_BIOSAMPLE_ATTRIBUTE:fecal_contamination_value
related_mappings:
- GENEPIO:0100815
- GENEPIO:0100816
- NCBI_BIOSAMPLE_ATTRIBUTE:ww_endog_control_1_conc
rank: 1000
domain_of:
- Biosample
range: QuantityValue