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Class: Dh Mutliview Common Columns (DhMultiviewCommonColumnsMixin)

Mixin with DhMutliviewCommon Columns

URI: nmdc_sub_schema:DhMultiviewCommonColumnsMixin

classDiagram class DhMultiviewCommonColumnsMixin click DhMultiviewCommonColumnsMixin href "../DhMultiviewCommonColumnsMixin" DhMultiviewCommonColumnsMixin <|-- AirInterface click AirInterface href "../AirInterface" DhMultiviewCommonColumnsMixin <|-- BiofilmInterface click BiofilmInterface href "../BiofilmInterface" DhMultiviewCommonColumnsMixin <|-- BuiltEnvInterface click BuiltEnvInterface href "../BuiltEnvInterface" DhMultiviewCommonColumnsMixin <|-- EmslInterface click EmslInterface href "../EmslInterface" DhMultiviewCommonColumnsMixin <|-- HcrCoresInterface click HcrCoresInterface href "../HcrCoresInterface" DhMultiviewCommonColumnsMixin <|-- HcrFluidsSwabsInterface click HcrFluidsSwabsInterface href "../HcrFluidsSwabsInterface" DhMultiviewCommonColumnsMixin <|-- HostAssociatedInterface click HostAssociatedInterface href "../HostAssociatedInterface" DhMultiviewCommonColumnsMixin <|-- JgiMgInterface click JgiMgInterface href "../JgiMgInterface" DhMultiviewCommonColumnsMixin <|-- JgiMgLrInterface click JgiMgLrInterface href "../JgiMgLrInterface" DhMultiviewCommonColumnsMixin <|-- JgiMtInterface click JgiMtInterface href "../JgiMtInterface" DhMultiviewCommonColumnsMixin <|-- MiscEnvsInterface click MiscEnvsInterface href "../MiscEnvsInterface" DhMultiviewCommonColumnsMixin <|-- PlantAssociatedInterface click PlantAssociatedInterface href "../PlantAssociatedInterface" DhMultiviewCommonColumnsMixin <|-- SedimentInterface click SedimentInterface href "../SedimentInterface" DhMultiviewCommonColumnsMixin <|-- SoilInterface click SoilInterface href "../SoilInterface" DhMultiviewCommonColumnsMixin <|-- WastewaterSludgeInterface click WastewaterSludgeInterface href "../WastewaterSludgeInterface" DhMultiviewCommonColumnsMixin <|-- WaterInterface click WaterInterface href "../WaterInterface" DhMultiviewCommonColumnsMixin : analysis_type DhMultiviewCommonColumnsMixin --> "1..*" AnalysisTypeEnum : analysis_type click AnalysisTypeEnum href "../AnalysisTypeEnum" DhMultiviewCommonColumnsMixin : samp_name DhMultiviewCommonColumnsMixin : source_mat_id

Slots

Name Cardinality and Range Description Inheritance
analysis_type 1..*
AnalysisTypeEnum		 Select all the data types associated or available for this biosample direct
samp_name 1
String		 A local identifier or name that for the material sample collected direct
source_mat_id 0..1
String		 A globally unique identifier assigned to the biological sample direct

Mixin Usage

mixed into description
AirInterface air dh_interface
BiofilmInterface biofilm dh_interface
BuiltEnvInterface built_env dh_interface
EmslInterface emsl dh_interface
HcrCoresInterface hcr_cores dh_interface
HcrFluidsSwabsInterface hcr_fluids_swabs dh_interface
HostAssociatedInterface host_associated dh_interface
JgiMgInterface Metadata for samples sent to JGI for standard metagenome sequencing
JgiMgLrInterface Metadata for samples sent to JGI for long read metagenome sequecning
JgiMtInterface jgi_mt dh_interface
MiscEnvsInterface misc_envs dh_interface
PlantAssociatedInterface plant_associated dh_interface
SedimentInterface sediment dh_interface
SoilInterface soil dh_interface
WastewaterSludgeInterface wastewater_sludge dh_interface
WaterInterface water dh_interface

Identifier and Mapping Information

Schema Source

  • from schema: https://example.com/nmdc_submission_schema

Mappings

Mapping Type Mapped Value
self nmdc_sub_schema:DhMultiviewCommonColumnsMixin
native nmdc_sub_schema:DhMultiviewCommonColumnsMixin

LinkML Source

Direct

name: DhMultiviewCommonColumnsMixin
description: Mixin with DhMutliviewCommon Columns
title: Dh Mutliview Common Columns
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slots:
- analysis_type
- samp_name
- source_mat_id
slot_usage:
  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
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    recommended: false
    multivalued: true
  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
    identifier: true
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
  source_mat_id:
    name: source_mat_id
    annotations:
      expected_value:
        tag: expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    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
    aliases:
    - source material identifiers
    rank: 2
    is_a: nucleic acid sequence source field
    string_serialization: '{text}:{text}'
    slot_uri: MIXS:0000026
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  oxy_stat_samp:
    name: oxy_stat_samp
    range: OxyStatSampEnum

Induced

name: DhMultiviewCommonColumnsMixin
description: Mixin with DhMutliviewCommon Columns
title: Dh Mutliview Common Columns
from_schema: https://example.com/nmdc_submission_schema
mixin: true
slot_usage:
  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
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    recommended: false
    multivalued: true
  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
    identifier: true
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
  source_mat_id:
    name: source_mat_id
    annotations:
      expected_value:
        tag: expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    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
    aliases:
    - source material identifiers
    rank: 2
    is_a: nucleic acid sequence source field
    string_serialization: '{text}:{text}'
    slot_uri: MIXS:0000026
    owner: Biosample
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
  oxy_stat_samp:
    name: oxy_stat_samp
    range: OxyStatSampEnum
attributes:
  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
    alias: analysis_type
    owner: DhMultiviewCommonColumnsMixin
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    recommended: false
    multivalued: true
  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
    identifier: true
    alias: samp_name
    owner: DhMultiviewCommonColumnsMixin
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true
    multivalued: false
  source_mat_id:
    name: source_mat_id
    annotations:
      expected_value:
        tag: expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    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
    aliases:
    - source material identifiers
    rank: 2
    is_a: nucleic acid sequence source field
    string_serialization: '{text}:{text}'
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: DhMultiviewCommonColumnsMixin
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'