Slot: fecal contamination indicator (fecal_contamination_indicator)

The gene, virus, bacterium or substance that was measured as an indicator of fecal contamination of the sample, for example crAssphage or pepper mild mottle virus.

URI: nmdc:fecal_contamination_indicator

Applicable Classes

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

Properties

• Range: FecalContaminationIndicatorEnum

Examples

• crAssphage

Comments

• Record the measured amount in fecal_contamination_value and the assay in fecal_contamination_method. One indicator per sample; put further indicators in misc_param.

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

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
related	NCBI_BIOSAMPLE_ATTRIBUTE:ww_endog_control_1
close	GENEPIO:0100814, NCBI_BIOSAMPLE_ATTRIBUTE:fecal_contamination_indicator

LinkML Source

name: fecal_contamination_indicator
description: The gene, virus, bacterium or substance that was measured as an indicator
  of fecal contamination of the sample, for example crAssphage or pepper mild mottle
  virus.
title: fecal contamination indicator
notes:
- 'PHA4GE Wastewater Contextual Data Specification 4.4.4: close match to fecal contamination
  indicator (GENEPIO:0100814); FecalContaminationIndicatorEnum carries the PHA4GE
  picklist.'
- 'NCBI BioSample: close match to the fecal_contamination_indicator attribute of the
  PHA4GE.wwsurv.1.0 package; related match to the ww_endog_control_1 attribute of
  the SARS-CoV-2.wwsurv.1.0 package, which records the same organisms as endogenous
  process controls.'
comments:
- Record the measured amount in fecal_contamination_value and the assay in fecal_contamination_method.
  One indicator per sample; put further indicators in misc_param.
examples:
- value: crAssphage
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:
- GENEPIO:0100814
- NCBI_BIOSAMPLE_ATTRIBUTE:fecal_contamination_indicator
related_mappings:
- NCBI_BIOSAMPLE_ATTRIBUTE:ww_endog_control_1
rank: 1000
domain_of:
- Biosample
range: FecalContaminationIndicatorEnum