portal_jgi_metatranscriptomics.yaml

name: jgi_metatranscriptomics
description: This file defines terms that appear in the 'JGI-Metatranscriptomics'
  section of the NMDC sample metadata submission portal, which is implemented with
  DataHarmonizer as of Spring 2022
title: 'NMDC Schema supplement for Submission Portal: JGI-Metatranscriptomics'
id: https://w3id.org/nmdc/portal/jgi_metatranscriptomics
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  linkml: https://w3id.org/linkml/
  nmdc: https://w3id.org/nmdc/
imports:
  - portal_enums
  #  - attribute_values # for inferring that rna_absorb1 and rna_absorb2 have the QuantityValue range, which isn't useful for the submission portal but might be required for Biosample>
  - nmdc_types
default_prefix: nmdc
default_range: string
slots:
  dnase_rna:
    title: DNase treated
    comments:
      - Note DNase treatment is required for all RNA samples.
    examples:
      - value: 'no'
    aliases:
      - Was Sample DNAse treated?
    rank: 13
    slot_group: JGI-Metatranscriptomics
    range: YesNoEnum
    recommended: true
  proposal_rna:
    title: RNA proposal ID
    comments:
      - Do not edit these values. A template will be provided by NMDC in which these
        values have been pre-filled.
    examples:
      - value: '504000'
    rank: 19
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_absorb1:
    description: 260/280 measurement of RNA sample purity
    title: RNA absorbance 260/280
    comments:
      - Recommended value is between 1 and 3.
    examples:
      - value: '2.02'
    rank: 7
    #    is_a: biomaterial_purity # this makes the import chain more complex and isn't really true for the portal. which will expect a scalar (str? float?)
    string_serialization: '{float}'
    slot_group: JGI-Metatranscriptomics
    range: float
    recommended: true
  rna_absorb2:
    description: 260/230 measurement of RNA sample purity
    title: RNA absorbance 260/230
    comments:
      - Recommended value is between 1 and 3.
    examples:
      - value: '2.02'
    rank: 8
    #    is_a: biomaterial_purity # this makes the import chain more complex and isn't really true for the portal. which will expect a scalar (str? float?)
    string_serialization: '{float}'
    slot_group: JGI-Metatranscriptomics
    range: float
    recommended: true
  rna_collect_site:
    description: Provide information on the site your RNA sample was collected from
    title: RNA collection site
    examples:
      - value: untreated pond water
    rank: 15
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_concentration:
    title: RNA 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'
    see_also:
      - nmdc:nucleic_acid_concentration
    rank: 5
    string_serialization: '{float}'
    slot_group: JGI-Metatranscriptomics
    range: float
    recommended: true
    minimum_value: 0
    maximum_value: 1000
  rna_cont_type:
    description: Tube or plate (96-well)
    title: RNA container type
    examples:
      - value: plate
    rank: 10
    slot_group: JGI-Metatranscriptomics
    range: JgiContTypeEnum
    recommended: true
  rna_cont_well:
    title: RNA 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.
      - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).
    examples:
      - value: B2
    rank: 11
    string_serialization: '{96 well plate pos}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
    pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
  rna_container_id:
    title: RNA container label
    comments:
      - Must be unique across all tubes and plates, and <20 characters. All samples
        in a plate should have the same plate label.
    examples:
      - value: Pond_MT_041618
    rank: 9
    string_serialization: '{text < 20 characters}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_isolate_meth:
    description: Describe the method/protocol/kit used to extract DNA/RNA.
    title: RNA isolation method
    examples:
      - value: phenol/chloroform extraction
    aliases:
      - Sample Isolation Method
    rank: 16
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_organisms:
    description: List any organisms known or suspected to grow in co-culture, as well
      as estimated % of the organism in that culture.
    title: RNA expected organisms
    examples:
      - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
          (1%)
    rank: 14
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_project_contact:
    title: RNA seq project contact
    comments:
      - Do not edit these values. A template will be provided by NMDC in which these
        values have been pre-filled.
    examples:
      - value: John Jones
    rank: 18
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_samp_id:
    title: RNA 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'
    rank: 3
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_sample_format:
    description: Solution in which the RNA sample has been suspended
    title: RNA sample format
    examples:
      - value: Water
    rank: 12
    slot_group: JGI-Metatranscriptomics
    range: RNASampleFormatEnum
    recommended: true
  rna_sample_name:
    description: Give the RNA 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: RNA sample name
    examples:
      - value: JGI_pond_041618
    rank: 4
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
    minimum_value: 0
    maximum_value: 2000
  rna_seq_project:
    title: RNA 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'
    aliases:
      - Seq Project ID
    rank: 1
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_seq_project_pi:
    title: RNA seq project PI
    comments:
      - Do not edit these values. A template will be provided by NMDC in which these
        values have been pre-filled.
    examples:
      - value: Jane Johnson
    rank: 17
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_seq_project_name:
    title: RNA 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 metatranscriptomics
    rank: 2
    string_serialization: '{text}'
    slot_group: JGI-Metatranscriptomics
    recommended: true
  rna_volume:
    title: RNA 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'
    rank: 6
    string_serialization: '{float}'
    slot_group: JGI-Metatranscriptomics
    range: float
    recommended: true
    minimum_value: 0
    maximum_value: 1000