Slot: organism count (organism_count)

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)

URI: MIXS:0000103 Alias: organism_count

Inheritance

core_field
- organism_count

Applicable Classes

Name	Description	Modifies Slot
WaterInterface	water dh_interface	no
HostAssociatedInterface	host_associated dh_interface	no
BiofilmInterface	biofilm dh_interface	no
AirInterface	air dh_interface	no
SedimentInterface	sediment dh_interface	no
WastewaterSludgeInterface	wastewater_sludge dh_interface	no
HcrFluidsSwabsInterface	hcr_fluids_swabs dh_interface	no
HcrCoresInterface	hcr_cores dh_interface	no
BuiltEnvInterface	built_env dh_interface	no
MiscEnvsInterface	misc_envs dh_interface	no
PlantAssociatedInterface	plant_associated dh_interface	no

Properties

Range: String
Regex pattern: ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other))$

Aliases

organism count

Examples

Value
total prokaryotes;3.5e7 cells/mL;qPCR

Identifier and Mapping Information

Annotations

property	value
expected_value	organism name;measurement value;enumeration
preferred_unit	number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter
occurrence	m
storage_units	1

Schema Source

from schema: https://example.com/nmdc_submission_schema

Mappings

Mapping Type	Mapped Value
self	MIXS:0000103
native	nmdc_sub_schema:organism_count

LinkML Source

name: organism_count
annotations:
  expected_value:
    tag: expected_value
    value: organism name;measurement value;enumeration
  preferred_unit:
    tag: preferred_unit
    value: number of cells per cubic meter, number of cells per milliliter, number
      of cells per cubic centimeter
  occurrence:
    tag: occurrence
    value: m
  storage_units:
    tag: storage_units
    value: '1'
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/mL;qPCR
from_schema: https://example.com/nmdc_submission_schema
aliases:
- organism count
rank: 30
is_a: core field
slot_uri: MIXS:0000103
alias: organism_count
domain_of:
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_core_section
range: string
multivalued: false
pattern: ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
  \S+.*\S+;(qPCR|ATP|MPN|other))$