Class: JGI MT (JgiMtInterface)

name: JgiMtInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: JGI MT
description: jgi_mt dh_interface
title: JGI MT
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- nuc_acid_absorb1
- nuc_acid_absorb2
- nuc_acid_concentration
- cont_type
- cont_well
- container_name
- dnase
- rna_isolate_meth
- jgi_samp_id
- jgi_sample_format
- jgi_sample_name
- jgi_seq_project
- jgi_seq_project_name
- jgi_sample_volume
- rna_isolate_meth
slot_usage:
  cont_type:
    name: cont_type
    slot_group: jgi_metatranscriptomics_section
  cont_well:
    name: cont_well
    slot_group: jgi_metatranscriptomics_section
  container_name:
    name: container_name
    slot_group: jgi_metatranscriptomics_section
  dnase:
    name: dnase
    slot_group: jgi_metatranscriptomics_section
  jgi_samp_id:
    name: jgi_samp_id
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_format:
    name: jgi_sample_format
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_name:
    name: jgi_sample_name
    slot_group: jgi_metatranscriptomics_section
  jgi_seq_project:
    name: jgi_seq_project
    slot_group: jgi_metatranscriptomics_section
  jgi_seq_project_name:
    name: jgi_seq_project_name
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_volume:
    name: jgi_sample_volume
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_absorb1:
    name: nuc_acid_absorb1
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_absorb2:
    name: nuc_acid_absorb2
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_concentration:
    name: nuc_acid_concentration
    slot_group: jgi_metatranscriptomics_section
  rna_isolate_meth:
    name: rna_isolate_meth
    description: Describe the method/protocol/kit used to extract DNA/RNA.
    title: RNA isolation method
    examples:
    - value: phenol/chloroform extraction
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - Sample Isolation Method
    rank: 16
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    recommended: false
    multivalued: false
  oxy_stat_samp:
    name: oxy_stat_samp
    range: OxyStatSampEnum
rules:
- preconditions:
    slot_conditions:
      cont_well:
        name: cont_well
        pattern: .+
  postconditions:
    slot_conditions:
      cont_type:
        name: cont_type
        equals_string: plate
  description: If a well is specified, the container type must be a plate.
  title: well_requires_plate
- preconditions:
    slot_conditions:
      cont_type:
        name: cont_type
        equals_string: plate
  postconditions:
    slot_conditions:
      cont_well:
        name: cont_well
        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
  description: If a plate is specified, a well must be specified according to the
    pattern.
  title: plate_requires_well

name: JgiMtInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: JGI MT
description: jgi_mt dh_interface
title: JGI MT
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
  cont_type:
    name: cont_type
    slot_group: jgi_metatranscriptomics_section
  cont_well:
    name: cont_well
    slot_group: jgi_metatranscriptomics_section
  container_name:
    name: container_name
    slot_group: jgi_metatranscriptomics_section
  dnase:
    name: dnase
    slot_group: jgi_metatranscriptomics_section
  jgi_samp_id:
    name: jgi_samp_id
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_format:
    name: jgi_sample_format
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_name:
    name: jgi_sample_name
    slot_group: jgi_metatranscriptomics_section
  jgi_seq_project:
    name: jgi_seq_project
    slot_group: jgi_metatranscriptomics_section
  jgi_seq_project_name:
    name: jgi_seq_project_name
    slot_group: jgi_metatranscriptomics_section
  jgi_sample_volume:
    name: jgi_sample_volume
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_absorb1:
    name: nuc_acid_absorb1
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_absorb2:
    name: nuc_acid_absorb2
    slot_group: jgi_metatranscriptomics_section
  nuc_acid_concentration:
    name: nuc_acid_concentration
    slot_group: jgi_metatranscriptomics_section
  rna_isolate_meth:
    name: rna_isolate_meth
    description: Describe the method/protocol/kit used to extract DNA/RNA.
    title: RNA isolation method
    examples:
    - value: phenol/chloroform extraction
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - Sample Isolation Method
    rank: 16
    string_serialization: '{text}'
    owner: Biosample
    domain_of:
    - Biosample
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    recommended: false
    multivalued: false
  oxy_stat_samp:
    name: oxy_stat_samp
    range: OxyStatSampEnum
attributes:
  nuc_acid_absorb1:
    name: nuc_acid_absorb1
    description: 260/280 measurement of nucleic acid sample purity
    title: nucleic acid absorbance 260/280
    comments:
    - Recommended value is between 1 and 3.
    examples:
    - value: '2.02'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_absorb1
    - rna_absorb1
    rank: 7
    alias: nuc_acid_absorb1
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: float
    recommended: true
  nuc_acid_absorb2:
    name: nuc_acid_absorb2
    description: 260/230 measurement of nucleic acid sample purity
    title: nucleic acid absorbance 260/230
    comments:
    - Recommended value is between 1 and 3.
    examples:
    - value: '2.02'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_absorb2
    - nuc_acid_absorb2
    rank: 8
    alias: nuc_acid_absorb2
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: float
    recommended: true
  nuc_acid_concentration:
    name: nuc_acid_concentration
    title: nucleic acid concentration in ng/ul
    comments:
    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using
      a fluorometric method. Acceptable values are 0-2000.
    examples:
    - value: '100'
    from_schema: https://example.com/nmdc_submission_schema
    see_also:
    - nmdc:nucleic_acid_concentration
    aliases:
    - dna_concentration
    - rna_concentration
    rank: 5
    alias: nuc_acid_concentration
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: float
    required: true
    minimum_value: 0
    maximum_value: 2000
  cont_type:
    name: cont_type
    description: Tube or plate (96-well)
    title: JGI container type
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_cont_type
    - rna_cont_type
    rank: 10
    alias: cont_type
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: JgiContTypeEnum
    required: true
  cont_well:
    name: cont_well
    title: plate position
    comments:
    - Required when 'plate' is selected for container type.
    - Leave blank if the sample will be shipped in a tube.
    - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not
      pass validation.
    - Fill plate in column-wise format. B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).
    examples:
    - value: B2
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_cont_well
    - rna_cont_well
    rank: 11
    string_serialization: '{96 well plate pos}'
    alias: cont_well
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    recommended: true
    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
  container_name:
    name: container_name
    title: container name
    comments:
    - Must be unique across all tubes and plates, and <20 characters.
    - All samples in a plate should have the same plate name.
    examples:
    - value: Pond_MT_041618
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_container_id
    - rna_container_id
    rank: 9
    string_serialization: '{text < 20 characters}'
    alias: container_name
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    pattern: ^[-_.a-zA-Z0-9]{1,20}$
  dnase:
    name: dnase
    title: DNase treatment
    comments:
    - Note DNase treatment is required for all RNA samples.
    examples:
    - value: 'no'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_dnase
    - dnase_rna
    rank: 13
    alias: dnase
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: YesNoEnum
    required: true
  rna_isolate_meth:
    name: rna_isolate_meth
    description: Describe the method/protocol/kit used to extract DNA/RNA.
    title: RNA isolation method
    examples:
    - value: phenol/chloroform extraction
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - Sample Isolation Method
    rank: 16
    string_serialization: '{text}'
    alias: rna_isolate_meth
    owner: JgiMtInterface
    domain_of:
    - Biosample
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    recommended: false
    multivalued: false
  jgi_samp_id:
    name: jgi_samp_id
    title: JGI sample ID
    comments:
    - Do not edit these values. A template will be provided by NMDC in which these
      values have been pre-filled.
    examples:
    - value: '187654'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_samp_id
    - rna_samp_id
    rank: 3
    alias: jgi_samp_id
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    multivalued: false
  jgi_sample_format:
    name: jgi_sample_format
    description: Solution in which the JGI sample has been suspended
    title: JGI sample format
    examples:
    - value: Water
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_sample_format
    - rna_sample_format
    rank: 12
    alias: jgi_sample_format
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: JGISampleFormatEnum
    required: true
  jgi_sample_name:
    name: jgi_sample_name
    description: Give the JGI sample a name that is meaningful to you. Sample names
      must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
    title: JGI sample name
    examples:
    - value: JGI_pond_041618
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_sample_name
    - rna_sample_name
    rank: 4
    alias: jgi_sample_name
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    multivalued: false
    pattern: ^[-_.a-zA-Z0-9]*$
  jgi_seq_project:
    name: jgi_seq_project
    title: JGI seq project ID
    comments:
    - Do not edit these values. A template will be provided by NMDC in which these
      values have been pre-filled.
    examples:
    - value: '1191234'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - Seq Project ID
    - dna_seq_project
    - rna_seq_project
    rank: 1
    alias: jgi_seq_project
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: float
    required: true
  jgi_seq_project_name:
    name: jgi_seq_project_name
    title: JGI seq project name
    comments:
    - Do not edit these values. A template will be provided by NMDC in which these
      values have been pre-filled.
    examples:
    - value: JGI Pond metagenomics
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_seq_project_name
    - rna_seq_project_name
    rank: 2
    alias: jgi_seq_project_name
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: string
    required: true
    multivalued: false
  jgi_sample_volume:
    name: jgi_sample_volume
    title: JGI sample volume in ul
    comments:
    - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This
      form accepts values < 25, but JGI may refuse to process them unless permission
      has been granted by a project manager
    examples:
    - value: '25'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - dna_volume
    - rna_volume
    rank: 6
    alias: jgi_sample_volume
    owner: JgiMtInterface
    domain_of:
    - JgiMgInterface
    - JgiMgLrInterface
    - JgiMtInterface
    slot_group: jgi_metatranscriptomics_section
    range: float
    required: true
    minimum_value: 0
    maximum_value: 1000
  analysis_type:
    name: analysis_type
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    comments:
    - MIxS:investigation_type was included as a `see_also` but that term doesn't resolve
      any more
    examples:
    - value: metagenomics; metabolomics; metaproteomics
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 3
    alias: analysis_type
    owner: JgiMtInterface
    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: JgiMtInterface
    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: JgiMtInterface
    domain_of:
    - Biosample
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    multivalued: false
    pattern: '[^\:\n\r]+\:[^\:\n\r]+'
rules:
- preconditions:
    slot_conditions:
      cont_well:
        name: cont_well
        pattern: .+
  postconditions:
    slot_conditions:
      cont_type:
        name: cont_type
        equals_string: plate
  description: If a well is specified, the container type must be a plate.
  title: well_requires_plate
- preconditions:
    slot_conditions:
      cont_type:
        name: cont_type
        equals_string: plate
  postconditions:
    slot_conditions:
      cont_well:
        name: cont_well
        pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
  description: If a plate is specified, a well must be specified according to the
    pattern.
  title: plate_requires_well