Class: JGI MT (JgiMtInterface)
jgi_mt dh_interface
URI: nmdc_sub_schema:JgiMtInterface
classDiagram
class JgiMtInterface
DhMultiviewCommonColumnsMixin <|-- JgiMtInterface
DhInterface <|-- JgiMtInterface
JgiMtInterface : analysis_type
JgiMtInterface --|> AnalysisTypeEnum : analysis_type
JgiMtInterface : dnase_rna
JgiMtInterface --|> YesNoEnum : dnase_rna
JgiMtInterface : proposal_rna
JgiMtInterface : rna_absorb1
JgiMtInterface : rna_absorb2
JgiMtInterface : rna_concentration
JgiMtInterface : rna_cont_type
JgiMtInterface --|> JgiContTypeEnum : rna_cont_type
JgiMtInterface : rna_cont_well
JgiMtInterface : rna_container_id
JgiMtInterface : rna_isolate_meth
JgiMtInterface : rna_project_contact
JgiMtInterface : rna_samp_id
JgiMtInterface : rna_sample_format
JgiMtInterface --|> RNASampleFormatEnum : rna_sample_format
JgiMtInterface : rna_sample_name
JgiMtInterface : rna_seq_project
JgiMtInterface : rna_seq_project_name
JgiMtInterface : rna_seq_project_pi
JgiMtInterface : rna_volume
JgiMtInterface : samp_name
JgiMtInterface : source_mat_id
Inheritance
- DhInterface
- JgiMtInterface [ DhMultiviewCommonColumnsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
dnase_rna | 1..1 YesNoEnum |
direct | |
proposal_rna | 1..1 String |
direct | |
rna_absorb1 | 0..1 recommended Float |
260/280 measurement of RNA sample purity | direct |
rna_absorb2 | 0..1 recommended Float |
260/230 measurement of RNA sample purity | direct |
rna_concentration | 1..1 Float |
direct | |
rna_cont_type | 1..1 JgiContTypeEnum |
Tube or plate (96-well) | direct |
rna_cont_well | 0..1 recommended String |
direct | |
rna_container_id | 1..1 String |
direct | |
rna_isolate_meth | 1..1 String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
rna_project_contact | 1..1 String |
direct | |
rna_samp_id | 1..1 String |
direct | |
rna_sample_format | 1..1 RNASampleFormatEnum |
Solution in which the RNA sample has been suspended | direct |
rna_sample_name | 1..1 String |
Give the RNA sample a name that is meaningful to you | direct |
rna_seq_project | 1..1 String |
direct | |
rna_seq_project_name | 1..1 String |
direct | |
rna_seq_project_pi | 1..1 String |
direct | |
rna_volume | 1..1 Float |
direct | |
dnase_rna | 1..1 YesNoEnum |
direct | |
proposal_rna | 1..1 String |
direct | |
rna_absorb1 | 0..1 recommended Float |
260/280 measurement of RNA sample purity | direct |
rna_absorb2 | 0..1 recommended Float |
260/230 measurement of RNA sample purity | direct |
rna_concentration | 1..1 Float |
direct | |
rna_cont_type | 1..1 JgiContTypeEnum |
Tube or plate (96-well) | direct |
rna_cont_well | 0..1 recommended String |
direct | |
rna_container_id | 1..1 String |
direct | |
rna_isolate_meth | 1..1 String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
rna_project_contact | 1..1 String |
direct | |
rna_samp_id | 1..1 String |
direct | |
rna_sample_format | 1..1 RNASampleFormatEnum |
Solution in which the RNA sample has been suspended | direct |
rna_sample_name | 1..1 String |
Give the RNA sample a name that is meaningful to you | direct |
rna_seq_project | 1..1 String |
direct | |
rna_seq_project_name | 1..1 String |
direct | |
rna_seq_project_pi | 1..1 String |
direct | |
rna_volume | 1..1 Float |
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 | jgi_mt_data | range | JgiMtInterface |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | JGI MT |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:JgiMtInterface |
native | nmdc_sub_schema:JgiMtInterface |
LinkML Source
Direct
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:
- dnase_rna
- proposal_rna
- rna_absorb1
- rna_absorb2
- rna_concentration
- rna_cont_type
- rna_cont_well
- rna_container_id
- rna_isolate_meth
- rna_project_contact
- rna_samp_id
- rna_sample_format
- rna_sample_name
- rna_seq_project
- rna_seq_project_name
- rna_seq_project_pi
- rna_volume
- dnase_rna
- proposal_rna
- rna_absorb1
- rna_absorb2
- rna_concentration
- rna_cont_type
- rna_cont_well
- rna_container_id
- rna_isolate_meth
- rna_project_contact
- rna_samp_id
- rna_sample_format
- rna_sample_name
- rna_seq_project
- rna_seq_project_name
- rna_seq_project_pi
- rna_volume
slot_usage:
dnase_rna:
name: dnase_rna
title: DNase treated
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Was Sample DNAse treated?
rank: 13
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: YesNoEnum
required: true
recommended: false
proposal_rna:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 19
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_absorb1:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_absorb2:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_concentration:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- nmdc:nucleic_acid_concentration
rank: 5
string_serialization: '{float}'
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
rna_cont_type:
name: rna_cont_type
description: Tube or plate (96-well)
title: RNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: JgiContTypeEnum
required: true
recommended: false
rna_cont_well:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 11
string_serialization: '{96 well plate pos}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
rna_container_id:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 9
string_serialization: '{text < 20 characters}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
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}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_project_contact:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 18
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_samp_id:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_sample_format:
name: rna_sample_format
description: Solution in which the RNA sample has been suspended
title: RNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: RNASampleFormatEnum
required: true
recommended: false
rna_sample_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
rna_seq_project:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Seq Project ID
rank: 1
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_pi:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 17
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_volume:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{float}'
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
rules:
- preconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: .+
postconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: rna_well_requires_plate
- preconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: RNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: rna_plate_requires_well
Induced
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:
dnase_rna:
name: dnase_rna
title: DNase treated
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Was Sample DNAse treated?
rank: 13
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: YesNoEnum
required: true
recommended: false
proposal_rna:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 19
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_absorb1:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_absorb2:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_concentration:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- nmdc:nucleic_acid_concentration
rank: 5
string_serialization: '{float}'
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
rna_cont_type:
name: rna_cont_type
description: Tube or plate (96-well)
title: RNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: JgiContTypeEnum
required: true
recommended: false
rna_cont_well:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 11
string_serialization: '{96 well plate pos}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
rna_container_id:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 9
string_serialization: '{text < 20 characters}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
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}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_project_contact:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 18
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_samp_id:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_sample_format:
name: rna_sample_format
description: Solution in which the RNA sample has been suspended
title: RNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: RNASampleFormatEnum
required: true
recommended: false
rna_sample_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
rna_seq_project:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Seq Project ID
rank: 1
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_pi:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 17
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_volume:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{float}'
owner: Biosample
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
attributes:
dnase_rna:
name: dnase_rna
title: DNase treated
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Was Sample DNAse treated?
rank: 13
alias: dnase_rna
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: YesNoEnum
required: true
recommended: false
proposal_rna:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 19
string_serialization: '{text}'
multivalued: false
alias: proposal_rna
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_absorb1:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 7
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
alias: rna_absorb1
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_absorb2:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 8
is_a: biomaterial_purity
string_serialization: '{float}'
domain: ProcessedSample
alias: rna_absorb2
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
recommended: true
rna_concentration:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- nmdc:nucleic_acid_concentration
rank: 5
string_serialization: '{float}'
alias: rna_concentration
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
rna_cont_type:
name: rna_cont_type
description: Tube or plate (96-well)
title: RNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
alias: rna_cont_type
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: JgiContTypeEnum
required: true
recommended: false
rna_cont_well:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 11
string_serialization: '{96 well plate pos}'
multivalued: false
alias: rna_cont_well
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
rna_container_id:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 9
string_serialization: '{text < 20 characters}'
multivalued: false
alias: rna_container_id
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
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}'
multivalued: false
alias: rna_isolate_meth
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_project_contact:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 18
string_serialization: '{text}'
multivalued: false
alias: rna_project_contact
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_samp_id:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 3
string_serialization: '{text}'
multivalued: false
alias: rna_samp_id
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_sample_format:
name: rna_sample_format
description: Solution in which the RNA sample has been suspended
title: RNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
alias: rna_sample_format
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: RNASampleFormatEnum
required: true
recommended: false
rna_sample_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
multivalued: false
alias: rna_sample_name
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
rna_seq_project:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Seq Project ID
rank: 1
string_serialization: '{text}'
multivalued: false
alias: rna_seq_project
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_name:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
alias: rna_seq_project_name
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_seq_project_pi:
name: 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
from_schema: https://w3id.org/nmdc/nmdc
rank: 17
string_serialization: '{text}'
multivalued: false
alias: rna_seq_project_pi
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: string
required: true
recommended: false
rna_volume:
name: 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'
from_schema: https://w3id.org/nmdc/nmdc
rank: 6
string_serialization: '{float}'
alias: rna_volume
owner: JgiMtInterface
domain_of:
- Biosample
- JgiMtInterface
slot_group: jgi_metatranscriptomics_section
range: float
required: true
recommended: false
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
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: JgiMtInterface
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: JgiMtInterface
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: JgiMtInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'
rules:
- preconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: .+
postconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: rna_well_requires_plate
- preconditions:
slot_conditions:
rna_cont_type:
name: rna_cont_type
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
name: rna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: RNA samples in plates must have a plate position that matches the regex.
Note the requirement for an empty string in the tube case. Waiting for value_present
validation to be added to runtime
title: rna_plate_requires_well