Slot: sample_isolated_from

Free-text description of the environmental or biological matrix from which the organism sample was isolated — the what it came out of (e.g. iron-rich microbial mat, leaf tissue, catalog vial). For the where (geographic / environmental site of collection) see sample_collection_site; for in-vitro growth conditions (lab maintenance, culture media, growth chambers) see sample_growth_conditions.

URI: nmdc:sample_isolated_from

Applicable Classes

Name	Description	Modifies Slot
OrganismSample	A material sample in which all cells are expected to share the same genome	no

Properties

Range: String

Examples

Value
Iron-rich microbial mat from hydrothermal vent, Naha Vents, south rift of Loihi seamount, Hawaii
Saltwater from water column off the Georgia coast, USA
DSMZ catalog vial (DSM 6125)

Comments

Routes JGI Isolate (NA) v19 form field 44 ("Sample Isolated From"). Field 45 ("Collection Site or Growth Conditions") routes to sample_collection_site or sample_growth_conditions depending on which half the submitter is reporting.
Used when no upstream Biosample carries env-triad information (e.g. culture collection orders, lab-derived samples). When a linked Biosample is available, environmental provenance belongs there. Not a typed reference — future work may add a structured slot or wrapper class for typed sample-to-sample links; see #3033 and #3054.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value

LinkML Source

name: sample_isolated_from
description: Free-text description of the environmental or biological matrix from
  which the organism sample was isolated — the *what* it came out of (e.g. iron-rich
  microbial mat, leaf tissue, catalog vial). For the *where* (geographic / environmental
  site of collection) see `sample_collection_site`; for in-vitro growth conditions
  (lab maintenance, culture media, growth chambers) see `sample_growth_conditions`.
todos:
- 'Redesign in #3054 will sharpen the boundary between this slot and the sample_collection_site
  / sample_growth_conditions siblings.'
comments:
- Routes JGI Isolate (NA) v19 form field 44 ("Sample Isolated From"). Field 45 ("Collection
  Site or Growth Conditions") routes to `sample_collection_site` or `sample_growth_conditions`
  depending on which half the submitter is reporting.
- 'Used when no upstream Biosample carries env-triad information (e.g. culture collection
  orders, lab-derived samples). When a linked Biosample is available, environmental
  provenance belongs there. Not a typed reference — future work may add a structured
  slot or wrapper class for typed sample-to-sample links; see #3033 and #3054.'
examples:
- value: Iron-rich microbial mat from hydrothermal vent, Naha Vents, south rift of
    Loihi seamount, Hawaii
  description: GOLD organism_v2 Go0000189 (Shewanella loihica PV-4, queried 2026-04-21)
- value: Saltwater from water column off the Georgia coast, USA
  description: GOLD organism_v2 Go0000514 (Ruegeria pomeroyi DSS-3, queried 2026-04-21)
- value: DSMZ catalog vial (DSM 6125)
  description: Catalog-collection origin — no environmental matrix upstream
in_subset:
- jgi_isolate
from_schema: https://w3id.org/nmdc/nmdc
structured_aliases:
- literal_form: Sample Isolated From
  predicate: EXACT_SYNONYM
  contexts:
  - https://jgi.doe.gov/isolate-submission-form/v19
rank: 1000
alias: sample_isolated_from
domain_of:
- OrganismSample
range: string