Enum: SpecimenPreparationMethodEnum

Methods for preparing and preserving biological specimens for analysis. Sourced from NF-OSI metadata dictionary and Human Cell Atlas standards.

URI: valuesets:SpecimenPreparationMethodEnum

Permissible Values

Value	Meaning	Description	Embedding	Fixative	Manufacturer	Method	Preservation	Preservative	Purpose	Temperature	Viability
FFPE	NCIT:C143028	Formalin-fixed, paraffin-embedded tissue preservation	paraffin	formalin
FORMALIN_FIXED		Tissue fixed with formalin without paraffin embedding		formalin
CRYOPRESERVED	NCIT:C16475	Specimen preserved by freezing with cryoprotectant								ultra-low
VIABLY_FROZEN		Specimen frozen while maintaining cell viability									preserved
FLASH_FROZEN		Rapid freezing to preserve molecular integrity				rapid freezing
FRESH_COLLECTED		Freshly collected specimen without preservation					none
OCT_EMBEDDED		Tissue embedded in optimal cutting temperature compound	OCT compound						cryosectioning
RNALATER		Storage in reagent that stabilizes and protects cellular RNA			Thermo Fisher				RNA stabilization
ETHANOL_PRESERVED		Specimen preserved in ethanol						ethanol
METHANOL_FIXED		Specimen fixed with methanol		methanol
ACETONE_FIXED		Specimen fixed with acetone		acetone
PAXgene_FIXED		Tissue fixed using PAXgene tissue system							RNA and DNA preservation
DRIED		Air-dried or desiccated specimen
LYOPHILIZED	NCIT:C28150	Freeze-dried specimen

Slots

Name	Description
specimen_preparation_method	Method used to prepare/preserve specimen

See Also

• https://nf-osi.github.io/nf-metadata-dictionary/
• https://data.humancellatlas.org/

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: SpecimenPreparationMethodEnum
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Methods for preparing and preserving biological specimens for analysis.
  Sourced from NF-OSI metadata dictionary and Human Cell Atlas standards.
title: Specimen Preparation Methods
from_schema: https://w3id.org/linkml/valuesets
see_also:
- https://nf-osi.github.io/nf-metadata-dictionary/
- https://data.humancellatlas.org/
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  FFPE:
    text: FFPE
    description: Formalin-fixed, paraffin-embedded tissue preservation
    meaning: NCIT:C143028
    annotations:
      fixative:
        tag: fixative
        value: formalin
      embedding:
        tag: embedding
        value: paraffin
    aliases:
    - Formalin-fixed paraffin-embedded
    - formalin-fixed, paraffin-embedded
    - FFPE Tissue Block
  FORMALIN_FIXED:
    text: FORMALIN_FIXED
    description: Tissue fixed with formalin without paraffin embedding
    annotations:
      fixative:
        tag: fixative
        value: formalin
    aliases:
    - formalin-fixed
  CRYOPRESERVED:
    text: CRYOPRESERVED
    description: Specimen preserved by freezing with cryoprotectant
    meaning: NCIT:C16475
    annotations:
      temperature:
        tag: temperature
        value: ultra-low
    aliases:
    - Cryopreserved
    - Cryopreservation
  VIABLY_FROZEN:
    text: VIABLY_FROZEN
    description: Specimen frozen while maintaining cell viability
    annotations:
      viability:
        tag: viability
        value: preserved
    aliases:
    - Viably frozen
  FLASH_FROZEN:
    text: FLASH_FROZEN
    description: Rapid freezing to preserve molecular integrity
    annotations:
      method:
        tag: method
        value: rapid freezing
    aliases:
    - Flash frozen
    - snap frozen
  FRESH_COLLECTED:
    text: FRESH_COLLECTED
    description: Freshly collected specimen without preservation
    annotations:
      preservation:
        tag: preservation
        value: none
    aliases:
    - Fresh collected
    - fresh
  OCT_EMBEDDED:
    text: OCT_EMBEDDED
    description: Tissue embedded in optimal cutting temperature compound
    annotations:
      embedding:
        tag: embedding
        value: OCT compound
      purpose:
        tag: purpose
        value: cryosectioning
    aliases:
    - OCT
    - OCT embedded
  RNALATER:
    text: RNALATER
    description: Storage in reagent that stabilizes and protects cellular RNA
    annotations:
      purpose:
        tag: purpose
        value: RNA stabilization
      manufacturer:
        tag: manufacturer
        value: Thermo Fisher
    aliases:
    - RNAlater
  ETHANOL_PRESERVED:
    text: ETHANOL_PRESERVED
    description: Specimen preserved in ethanol
    annotations:
      preservative:
        tag: preservative
        value: ethanol
    aliases:
    - ethanol
  METHANOL_FIXED:
    text: METHANOL_FIXED
    description: Specimen fixed with methanol
    annotations:
      fixative:
        tag: fixative
        value: methanol
    aliases:
    - methanol
  ACETONE_FIXED:
    text: ACETONE_FIXED
    description: Specimen fixed with acetone
    annotations:
      fixative:
        tag: fixative
        value: acetone
  PAXgene_FIXED:
    text: PAXgene_FIXED
    description: Tissue fixed using PAXgene tissue system
    annotations:
      purpose:
        tag: purpose
        value: RNA and DNA preservation
  DRIED:
    text: DRIED
    description: Air-dried or desiccated specimen
    aliases:
    - air-dried
  LYOPHILIZED:
    text: LYOPHILIZED
    description: Freeze-dried specimen
    meaning: NCIT:C28150
    aliases:
    - freeze-dried
    - lyophilization
    - Freeze-Drying