Class: JGI MG (JgiMgInterface)
Metadata for samples sent to JGI for standard metagenome sequencing
URI: nmdc_sub_schema:JgiMgInterface
classDiagram
class JgiMgInterface
DhMultiviewCommonColumnsMixin <|-- JgiMgInterface
DhInterface <|-- JgiMgInterface
JgiMgInterface : analysis_type
JgiMgInterface --|> AnalysisTypeEnum : analysis_type
JgiMgInterface : dna_absorb1
JgiMgInterface : dna_absorb2
JgiMgInterface : dna_concentration
JgiMgInterface : dna_cont_type
JgiMgInterface --|> JgiContTypeEnum : dna_cont_type
JgiMgInterface : dna_cont_well
JgiMgInterface : dna_container_id
JgiMgInterface : dna_dnase
JgiMgInterface --|> YesNoEnum : dna_dnase
JgiMgInterface : dna_isolate_meth
JgiMgInterface : dna_project_contact
JgiMgInterface : dna_samp_id
JgiMgInterface : dna_sample_format
JgiMgInterface --|> DNASampleFormatEnum : dna_sample_format
JgiMgInterface : dna_sample_name
JgiMgInterface : dna_seq_project
JgiMgInterface : dna_seq_project_name
JgiMgInterface : dna_seq_project_pi
JgiMgInterface : dna_volume
JgiMgInterface : proposal_dna
JgiMgInterface : samp_name
JgiMgInterface : source_mat_id
Inheritance
- DhInterface
- JgiMgInterface [ DhMultiviewCommonColumnsMixin]
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
dna_absorb1 | 0..1 recommended Float |
260/280 measurement of DNA sample purity | direct |
dna_absorb2 | 0..1 recommended Float |
260/230 measurement of DNA sample purity | direct |
dna_concentration | 1..1 Float |
direct | |
dna_cont_type | 1..1 JgiContTypeEnum |
Tube or plate (96-well) | direct |
dna_cont_well | 0..1 recommended String |
direct | |
dna_container_id | 1..1 String |
direct | |
dna_dnase | 1..1 YesNoEnum |
direct | |
dna_isolate_meth | 1..1 String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
dna_project_contact | 1..1 String |
direct | |
dna_samp_id | 1..1 String |
direct | |
dna_sample_format | 1..1 DNASampleFormatEnum |
Solution in which the DNA sample has been suspended | direct |
dna_sample_name | 1..1 String |
Give the DNA sample a name that is meaningful to you | direct |
dna_seq_project | 1..1 String |
direct | |
dna_seq_project_name | 1..1 String |
direct | |
dna_seq_project_pi | 1..1 String |
direct | |
dna_volume | 1..1 Float |
direct | |
proposal_dna | 1..1 String |
direct | |
dna_absorb1 | 0..1 recommended Float |
260/280 measurement of DNA sample purity | direct |
dna_absorb2 | 0..1 recommended Float |
260/230 measurement of DNA sample purity | direct |
dna_concentration | 1..1 Float |
direct | |
dna_cont_type | 1..1 JgiContTypeEnum |
Tube or plate (96-well) | direct |
dna_cont_well | 0..1 recommended String |
direct | |
dna_container_id | 1..1 String |
direct | |
dna_dnase | 1..1 YesNoEnum |
direct | |
dna_isolate_meth | 1..1 String |
Describe the method/protocol/kit used to extract DNA/RNA | direct |
dna_project_contact | 1..1 String |
direct | |
dna_samp_id | 1..1 String |
direct | |
dna_sample_format | 1..1 DNASampleFormatEnum |
Solution in which the DNA sample has been suspended | direct |
dna_sample_name | 1..1 String |
Give the DNA sample a name that is meaningful to you | direct |
dna_seq_project | 1..1 String |
direct | |
dna_seq_project_name | 1..1 String |
direct | |
dna_seq_project_pi | 1..1 String |
direct | |
dna_volume | 1..1 Float |
direct | |
proposal_dna | 1..1 String |
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_mg_data | range | JgiMgInterface |
Identifier and Mapping Information
Annotations
property | value |
---|---|
excel_worksheet_name | JGI MG |
Schema Source
- from schema: https://example.com/nmdc_submission_schema
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc_sub_schema:JgiMgInterface |
native | nmdc_sub_schema:JgiMgInterface |
LinkML Source
Direct
name: JgiMgInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: JGI MG
description: Metadata for samples sent to JGI for standard metagenome sequencing
title: JGI MG
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- dna_absorb1
- dna_absorb2
- dna_concentration
- dna_cont_type
- dna_cont_well
- dna_container_id
- dna_dnase
- dna_isolate_meth
- dna_project_contact
- dna_samp_id
- dna_sample_format
- dna_sample_name
- dna_seq_project
- dna_seq_project_name
- dna_seq_project_pi
- dna_volume
- proposal_dna
- dna_absorb1
- dna_absorb2
- dna_concentration
- dna_cont_type
- dna_cont_well
- dna_container_id
- dna_dnase
- dna_isolate_meth
- dna_project_contact
- dna_samp_id
- dna_sample_format
- dna_sample_name
- dna_seq_project
- dna_seq_project_name
- dna_seq_project_pi
- dna_volume
- proposal_dna
slot_usage:
dna_absorb1:
name: dna_absorb1
description: 260/280 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_absorb2:
name: dna_absorb2
description: 260/230 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_concentration:
name: dna_concentration
title: DNA 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
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
dna_cont_type:
name: dna_cont_type
description: Tube or plate (96-well)
title: DNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: JgiContTypeEnum
required: true
recommended: false
dna_cont_well:
name: dna_cont_well
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
dna_container_id:
name: dna_container_id
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
dna_dnase:
name: dna_dnase
title: DNase treatment DNA
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
rank: 13
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: YesNoEnum
required: true
recommended: false
dna_isolate_meth:
name: dna_isolate_meth
description: Describe the method/protocol/kit used to extract DNA/RNA.
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_project_contact:
name: dna_project_contact
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_samp_id:
name: dna_samp_id
title: DNA sample ID
todos:
- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't
have two identifiers. How to force uniqueness? Moot because that column will
be prefilled?
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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_sample_format:
name: dna_sample_format
description: Solution in which the DNA sample has been suspended
title: DNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: DNASampleFormatEnum
required: true
recommended: false
dna_sample_name:
name: dna_sample_name
description: Give the DNA 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: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project:
name: dna_seq_project
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_name:
name: dna_seq_project_name
title: DNA 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://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_pi:
name: dna_seq_project_pi
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_volume:
name: dna_volume
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
proposal_dna:
name: proposal_dna
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
rules:
- preconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: .+
postconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: dna_well_requires_plate
- preconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: DNA 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: dna_plate_requires_well
Induced
name: JgiMgInterface
annotations:
excel_worksheet_name:
tag: excel_worksheet_name
value: JGI MG
description: Metadata for samples sent to JGI for standard metagenome sequencing
title: JGI MG
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
dna_absorb1:
name: dna_absorb1
description: 260/280 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_absorb2:
name: dna_absorb2
description: 260/230 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_concentration:
name: dna_concentration
title: DNA 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
owner: Biosample
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
dna_cont_type:
name: dna_cont_type
description: Tube or plate (96-well)
title: DNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: JgiContTypeEnum
required: true
recommended: false
dna_cont_well:
name: dna_cont_well
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
dna_container_id:
name: dna_container_id
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
dna_dnase:
name: dna_dnase
title: DNase treatment DNA
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
rank: 13
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: YesNoEnum
required: true
recommended: false
dna_isolate_meth:
name: dna_isolate_meth
description: Describe the method/protocol/kit used to extract DNA/RNA.
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_project_contact:
name: dna_project_contact
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_samp_id:
name: dna_samp_id
title: DNA sample ID
todos:
- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't
have two identifiers. How to force uniqueness? Moot because that column will
be prefilled?
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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_sample_format:
name: dna_sample_format
description: Solution in which the DNA sample has been suspended
title: DNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: DNASampleFormatEnum
required: true
recommended: false
dna_sample_name:
name: dna_sample_name
description: Give the DNA 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: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project:
name: dna_seq_project
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_name:
name: dna_seq_project_name
title: DNA 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://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
owner: Biosample
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_pi:
name: dna_seq_project_pi
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_volume:
name: dna_volume
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
proposal_dna:
name: proposal_dna
title: DNA 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
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
oxy_stat_samp:
name: oxy_stat_samp
range: OxyStatSampEnum
attributes:
dna_absorb1:
name: dna_absorb1
description: 260/280 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
alias: dna_absorb1
owner: JgiMgInterface
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_absorb2:
name: dna_absorb2
description: 260/230 measurement of DNA sample purity
title: DNA 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
domain: ProcessedSample
alias: dna_absorb2
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
recommended: true
dna_concentration:
name: dna_concentration
title: DNA 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
alias: dna_concentration
owner: JgiMgInterface
domain_of:
- Biosample
- ProcessedSample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 2000
dna_cont_type:
name: dna_cont_type
description: Tube or plate (96-well)
title: DNA container type
examples:
- value: plate
from_schema: https://w3id.org/nmdc/nmdc
rank: 10
alias: dna_cont_type
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: JgiContTypeEnum
required: true
recommended: false
dna_cont_well:
name: dna_cont_well
title: DNA 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: dna_cont_well
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
recommended: true
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
dna_container_id:
name: dna_container_id
title: DNA 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: dna_container_id
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
pattern: ^.{1,20}$
dna_dnase:
name: dna_dnase
title: DNase treatment DNA
comments:
- Note DNase treatment is required for all RNA samples.
examples:
- value: 'no'
from_schema: https://w3id.org/nmdc/nmdc
rank: 13
alias: dna_dnase
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: YesNoEnum
required: true
recommended: false
dna_isolate_meth:
name: dna_isolate_meth
description: Describe the method/protocol/kit used to extract DNA/RNA.
title: DNA 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: dna_isolate_meth
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_project_contact:
name: dna_project_contact
title: DNA 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: dna_project_contact
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_samp_id:
name: dna_samp_id
title: DNA sample ID
todos:
- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't
have two identifiers. How to force uniqueness? Moot because that column will
be prefilled?
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: dna_samp_id
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_sample_format:
name: dna_sample_format
description: Solution in which the DNA sample has been suspended
title: DNA sample format
examples:
- value: Water
from_schema: https://w3id.org/nmdc/nmdc
rank: 12
alias: dna_sample_format
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: DNASampleFormatEnum
required: true
recommended: false
dna_sample_name:
name: dna_sample_name
description: Give the DNA 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: DNA sample name
examples:
- value: JGI_pond_041618
from_schema: https://w3id.org/nmdc/nmdc
rank: 4
string_serialization: '{text}'
multivalued: false
alias: dna_sample_name
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project:
name: dna_seq_project
title: DNA 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: dna_seq_project
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_name:
name: dna_seq_project_name
title: DNA 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://w3id.org/nmdc/nmdc
rank: 2
string_serialization: '{text}'
multivalued: false
alias: dna_seq_project_name
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_seq_project_pi:
name: dna_seq_project_pi
title: DNA 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: dna_seq_project_pi
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
dna_volume:
name: dna_volume
title: DNA 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: dna_volume
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: float
required: true
recommended: false
minimum_value: 0
maximum_value: 1000
proposal_dna:
name: proposal_dna
title: DNA 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_dna
owner: JgiMgInterface
domain_of:
- Biosample
- JgiMgInterface
- JgiMgLrInterface
slot_group: jgi_metagenomics_section
range: string
required: true
recommended: false
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: JgiMgInterface
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: JgiMgInterface
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: JgiMgInterface
domain_of:
- Biosample
- DhMultiviewCommonColumnsMixin
slot_group: sample_id_section
range: string
pattern: '[^\:\n\r]+\:[^\:\n\r]+'
rules:
- preconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: .+
postconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't
have any value for their plate position.
title: dna_well_requires_plate
- preconditions:
slot_conditions:
dna_cont_type:
name: dna_cont_type
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
name: dna_cont_well
pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
description: DNA 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: dna_plate_requires_well