Class: Emsl (EmslInterface)
emsl dh_interface
URI: nmdc_sub_schema:EmslInterface
classDiagram
class EmslInterface
DhMultiviewCommonColumnsMixin <|-- EmslInterface
DhInterface <|-- EmslInterface
EmslInterface : analysis_type
EmslInterface --|> AnalysisTypeEnum : analysis_type
EmslInterface : emsl_store_temp
EmslInterface : project_id
EmslInterface : replicate_number
EmslInterface : samp_name
EmslInterface : sample_shipped
EmslInterface : sample_type
EmslInterface --|> SampleTypeEnum : sample_type
EmslInterface : source_mat_id
EmslInterface : technical_reps
Inheritance
- DhInterface
- EmslInterface [ DhMultiviewCommonColumnsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
emsl_store_temp | 1..1 Float |
The temperature at which the sample should be stored upon delivery to EMSL | direct |
project_id | 1..1 String |
Proposal IDs or names associated with dataset | direct |
replicate_number | 0..1 recommended Integer |
If sending biological replicates, indicate the rep number here | direct |
sample_shipped | 1..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... | direct |
sample_type | 1..1 SampleTypeEnum |
Type of sample being submitted | direct |
technical_reps | 0..1 recommended Integer |
If sending technical replicates of the same sample, indicate the replicate co... | direct |
emsl_store_temp | 1..1 Float |
The temperature at which the sample should be stored upon delivery to EMSL | direct |
project_id | 1..1 String |
Proposal IDs or names associated with dataset | direct |
replicate_number | 0..1 recommended Integer |
If sending biological replicates, indicate the rep number here | direct |
sample_shipped | 1..1 String |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... | direct |
sample_type | 1..1 SampleTypeEnum |
Type of sample being submitted | direct |
technical_reps | 0..1 recommended Integer |
If sending technical replicates of the same sample, indicate the replicate co... | direct |
analysis_type | 1..* AnalysisTypeEnum |
Select all the data types associated or available for this biosample | DhMultiviewCommonColumnsMixin |
samp_name | 1..1 String |
A local identifier or name that for the material sample collected | DhMultiviewCommonColumnsMixin |
source_mat_id | 0..1 String |
A globally unique identifier assigned to the biological sample | DhMultiviewCommonColumnsMixin |
Usages
used by | used in | type | used |
---|---|---|---|
SampleData | emsl_data | range | EmslInterface |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | EMSL |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:EmslInterface |
native | nmdc_sub_schema:EmslInterface |
LinkML Source
Direct
name: EmslInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: EMSL
description: emsl dh_interface
title: Emsl
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- emsl_store_temp
- project_id
- replicate_number
- sample_shipped
- sample_type
- technical_reps
- emsl_store_temp
- project_id
- replicate_number
- sample_shipped
- sample_type
- technical_reps
slot_usage:
emsl_store_temp:
name: emsl_store_temp
description: The temperature at which the sample should be stored upon delivery
to EMSL
title: EMSL sample storage temperature, deg. C
todos:
- add 'see_alsos' with link to NEXUS info
comments:
- Enter a temperature in celsius. Numeric portion only.
examples:
- value: '-80'
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{float}'
owner: Biosample
domain_of:
- EmslInterface
slot_group: emsl_section
range: float
required: true
recommended: false
project_id:
name: project_id
description: Proposal IDs or names associated with dataset
title: project ID
from_schema: https://w3id.org/nmdc/nmdc
rank: 1
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
replicate_number:
name: replicate_number
description: If sending biological replicates, indicate the rep number here.
title: replicate number
comments:
- This will guide staff in ensuring your samples are blocked & randomized correctly
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{integer}'
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
sample_shipped:
name: sample_shipped
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample sent to EMSL.
title: sample shipped amount
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: 15 g
- value: 100 uL
- value: 5 mL
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
sample_type:
name: sample_type
description: Type of sample being submitted
title: sample type
comments:
- This can vary from 'environmental package' if the sample is an extraction.
examples:
- value: water extracted soil
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: SampleTypeEnum
required: true
recommended: false
technical_reps:
name: technical_reps
description: If sending technical replicates of the same sample, indicate the
replicate count.
title: number technical replicate
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{integer}'
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
Induced
name: EmslInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: EMSL
description: emsl dh_interface
title: Emsl
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
emsl_store_temp:
name: emsl_store_temp
description: The temperature at which the sample should be stored upon delivery
to EMSL
title: EMSL sample storage temperature, deg. C
todos:
- add 'see_alsos' with link to NEXUS info
comments:
- Enter a temperature in celsius. Numeric portion only.
examples:
- value: '-80'
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{float}'
owner: Biosample
domain_of:
- EmslInterface
slot_group: emsl_section
range: float
required: true
recommended: false
project_id:
name: project_id
description: Proposal IDs or names associated with dataset
title: project ID
from_schema: https://w3id.org/nmdc/nmdc
rank: 1
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
replicate_number:
name: replicate_number
description: If sending biological replicates, indicate the rep number here.
title: replicate number
comments:
- This will guide staff in ensuring your samples are blocked & randomized correctly
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{integer}'
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
sample_shipped:
name: sample_shipped
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample sent to EMSL.
title: sample shipped amount
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: 15 g
- value: 100 uL
- value: 5 mL
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{float} {unit}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
sample_type:
name: sample_type
description: Type of sample being submitted
title: sample type
comments:
- This can vary from 'environmental package' if the sample is an extraction.
examples:
- value: water extracted soil
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: SampleTypeEnum
required: true
recommended: false
technical_reps:
name: technical_reps
description: If sending technical replicates of the same sample, indicate the
replicate count.
title: number technical replicate
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{integer}'
owner: Biosample
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
attributes:
emsl_store_temp:
name: emsl_store_temp
description: The temperature at which the sample should be stored upon delivery
to EMSL
title: EMSL sample storage temperature, deg. C
todos:
- add 'see_alsos' with link to NEXUS info
comments:
- Enter a temperature in celsius. Numeric portion only.
examples:
- value: '-80'
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{float}'
alias: emsl_store_temp
owner: EmslInterface
domain_of:
- EmslInterface
slot_group: emsl_section
range: float
required: true
recommended: false
project_id:
name: project_id
description: Proposal IDs or names associated with dataset
title: project ID
from_schema: https://w3id.org/nmdc/nmdc
rank: 1
string_serialization: '{text}'
multivalued: false
alias: project_id
owner: EmslInterface
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
replicate_number:
name: replicate_number
description: If sending biological replicates, indicate the rep number here.
title: replicate number
comments:
- This will guide staff in ensuring your samples are blocked & randomized correctly
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{integer}'
alias: replicate_number
owner: EmslInterface
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
sample_shipped:
name: sample_shipped
description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
sample sent to EMSL.
title: sample shipped amount
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: 15 g
- value: 100 uL
- value: 5 mL
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{float} {unit}'
multivalued: false
alias: sample_shipped
owner: EmslInterface
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: string
required: true
recommended: false
pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$
sample_type:
name: sample_type
description: Type of sample being submitted
title: sample type
comments:
- This can vary from 'environmental package' if the sample is an extraction.
examples:
- value: water extracted soil
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
alias: sample_type
owner: EmslInterface
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: SampleTypeEnum
required: true
recommended: false
technical_reps:
name: technical_reps
description: If sending technical replicates of the same sample, indicate the
replicate count.
title: number technical replicate
comments:
- This field is only required when completing metadata for samples being submitted
to EMSL for analyses.
examples:
- value: '2'
from_schema: https://w3id.org/nmdc/nmdc
rank: 5
string_serialization: '{integer}'
alias: technical_reps
owner: EmslInterface
domain_of:
- Biosample
- EmslInterface
slot_group: emsl_section
range: integer
recommended: true
analysis_type:
name: analysis_type
description: Select all the data types associated or available for this biosample
title: analysis/data type
examples:
- value: metagenomics; metabolomics; proteomics
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- MIxS:investigation_type
rank: 3
multivalued: true
alias: analysis_type
owner: EmslInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: AnalysisTypeEnum
required: true
recommended: false
samp_name:
name: samp_name
annotations:
expected_value:
tag: expected_value
value: text
description: A local identifier or name that for the material sample collected.
Refers to the original material collected or to any derived sub-samples.
title: sample name
comments:
- It can have any format, but we suggest that you make it concise, unique and
consistent within your lab, and as informative as possible.
examples:
- value: Rock core CB1178(5-6) from NSW
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- sample name
rank: 1
is_a: investigation field
string_serialization: '{text}'
slot_uri: MIXS:0001107
multivalued: false
identifier: true
alias: samp_name
owner: EmslInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
required: true
source_mat_id:
name: source_mat_id
description: A globally unique identifier assigned to the biological sample.
title: source material identifier
todos:
- Currently, the comments say to use UUIDs. However, if we implement assigning
NMDC identifiers with the minter we dont need to require a GUID. It can be an
optional field to fill out only if they already have a resolvable ID.
- Currently, the comments say to use UUIDs. However, if we implement assigning
NMDC identifiers with the minter we dont need to require a GUID. It can be an
optional field to fill out only if they already have a resolvable ID.
notes:
- The source material IS the Globally Unique ID
comments:
- Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
IDs enable linking to derived analytes and subsamples. If you have not assigned
FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
- Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),
NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These
IDs enable linking to derived analytes and subsamples. If you have not assigned
FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).
examples:
- value: IGSN:AU1243
- value: UUID:24f1467a-40f4-11ed-b878-0242ac120002
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
is_a: nucleic acid sequence source field
string_serialization: '{text}:{text}'
slot_uri: MIXS:0000026
multivalued: false
alias: source_mat_id
owner: EmslInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'