Slot: sample collection device (samp_collec_device)
The device used to collect an environmental sample. Recommended values are subclasses of specimen collection device (http://purl.obolibrary.org/obo/OBI_0002814). OBI itself contains only swab/wipe subclasses; environmental sampling devices (corers, grab samplers, passive samplers, etc.) are defined in GENEPIO under the same OBI:0002814 parent. Free-text values are accepted for backward compatibility; new submissions should prefer the form: label [PREFIX:LOCALID].
URI: MIXS:0000002 Alias: samp_collec_device
Applicable Classes
| Name | Description | Modifies Slot |
|---|---|---|
| PlantAssociatedInterface | plant_associated dh_interface | no |
| SedimentInterface | sediment dh_interface | no |
| WaterInterface | water dh_interface | no |
| BiofilmInterface | biofilm dh_interface | no |
| SoilInterface | soil dh_interface | no |
| HcrFluidsSwabsInterface | hcr_fluids_swabs dh_interface | no |
| AirInterface | air dh_interface | no |
| HostAssociatedInterface | host_associated dh_interface | no |
| WastewaterSludgeInterface | wastewater_sludge dh_interface | no |
| HcrCoresInterface | hcr_cores dh_interface | no |
| MiscEnvsInterface | misc_envs dh_interface | no |
Properties
-
Range: String
-
Recommended: True
-
Regex pattern:
^([^\[\]]+|.+ \[[A-Za-z][A-Za-z0-9_]*:[A-Za-z0-9_]+\])$
Examples
| Value |
|---|
| specimen collection swab stick [OBI:0002820] |
| PONAR grab sampler [GENEPIO:0100929] |
| trowel |
Comments
- GENEPIO's subtree of OBI:0002814 includes grouping classes such as GENEPIO:0100941 (grab sampling device), GENEPIO:0100942 (composite sampling device), GENEPIO:0100943 (core sampling device), and GENEPIO:0100948 (passive sampling device).
- ENVO has no device classes; do not use ENVO terms here.
- Existing NMDC biosamples populate this slot with free text (e.g., "corer", "Van Dorn"). New submissions are encouraged to use the form: label [PREFIX:LOCALID].
- Report dimensions and details when applicable
Identifier and Mapping Information
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | MIXS:0000002 |
| native | nmdc_sub_schema:samp_collec_device |
LinkML Source
name: samp_collec_device
description: 'The device used to collect an environmental sample. Recommended values
are subclasses of specimen collection device (http://purl.obolibrary.org/obo/OBI_0002814).
OBI itself contains only swab/wipe subclasses; environmental sampling devices (corers,
grab samplers, passive samplers, etc.) are defined in GENEPIO under the same OBI:0002814
parent. Free-text values are accepted for backward compatibility; new submissions
should prefer the form: label [PREFIX:LOCALID].'
title: sample collection device
comments:
- GENEPIO's subtree of OBI:0002814 includes grouping classes such as GENEPIO:0100941
(grab sampling device), GENEPIO:0100942 (composite sampling device), GENEPIO:0100943
(core sampling device), and GENEPIO:0100948 (passive sampling device).
- ENVO has no device classes; do not use ENVO terms here.
- 'Existing NMDC biosamples populate this slot with free text (e.g., "corer", "Van
Dorn"). New submissions are encouraged to use the form: label [PREFIX:LOCALID].'
- Report dimensions and details when applicable
examples:
- value: specimen collection swab stick [OBI:0002820]
- value: PONAR grab sampler [GENEPIO:0100929]
- value: trowel
from_schema: https://example.com/nmdc_submission_schema
rank: 14
keywords:
- device
- sample
slot_uri: MIXS:0000002
alias: samp_collec_device
domain_of:
- AirInterface
- BiofilmInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: mixs_modified_section
range: string
recommended: true
pattern: ^([^\[\]]+|.+ \[[A-Za-z][A-Za-z0-9_]*:[A-Za-z0-9_]+\])$