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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

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]+'