Class: MetagenomeAssembly
A workflow execution activity that converts sequencing reads into an assembled metagenome.
classDiagram
class MetagenomeAssembly
click MetagenomeAssembly href "../MetagenomeAssembly"
WorkflowExecutionActivity <|-- MetagenomeAssembly
click WorkflowExecutionActivity href "../WorkflowExecutionActivity"
MetagenomeAssembly : asm_score
MetagenomeAssembly : contig_bp
MetagenomeAssembly : contigs
MetagenomeAssembly : ctg_l50
MetagenomeAssembly : ctg_l90
MetagenomeAssembly : ctg_logsum
MetagenomeAssembly : ctg_max
MetagenomeAssembly : ctg_n50
MetagenomeAssembly : ctg_n90
MetagenomeAssembly : ctg_powsum
MetagenomeAssembly : ended_at_time
MetagenomeAssembly : execution_resource
MetagenomeAssembly : gap_pct
MetagenomeAssembly : gc_avg
MetagenomeAssembly : gc_std
MetagenomeAssembly : git_url
MetagenomeAssembly : has_failure_categorization
MetagenomeAssembly --> "0..*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
MetagenomeAssembly : has_input
MetagenomeAssembly --> "1..*" NamedThing : has_input
click NamedThing href "../NamedThing"
MetagenomeAssembly : has_output
MetagenomeAssembly --> "0..*" NamedThing : has_output
click NamedThing href "../NamedThing"
MetagenomeAssembly : id
MetagenomeAssembly : insdc_assembly_identifiers
MetagenomeAssembly : name
MetagenomeAssembly : num_aligned_reads
MetagenomeAssembly : num_input_reads
MetagenomeAssembly : part_of
MetagenomeAssembly --> "0..*" NamedThing : part_of
click NamedThing href "../NamedThing"
MetagenomeAssembly : qc_comment
MetagenomeAssembly : qc_status
MetagenomeAssembly --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
MetagenomeAssembly : scaf_bp
MetagenomeAssembly : scaf_l50
MetagenomeAssembly : scaf_l90
MetagenomeAssembly : scaf_l_gt50k
MetagenomeAssembly : scaf_logsum
MetagenomeAssembly : scaf_max
MetagenomeAssembly : scaf_n50
MetagenomeAssembly : scaf_n90
MetagenomeAssembly : scaf_n_gt50k
MetagenomeAssembly : scaf_pct_gt50k
MetagenomeAssembly : scaf_powsum
MetagenomeAssembly : scaffolds
MetagenomeAssembly : started_at_time
MetagenomeAssembly : type
MetagenomeAssembly : used
MetagenomeAssembly : version
MetagenomeAssembly : was_informed_by
MetagenomeAssembly --> "0..1" Activity : was_informed_by
click Activity href "../Activity"
Inheritance
- Activity
- WorkflowExecutionActivity
- MetagenomeAssembly
- WorkflowExecutionActivity
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
type | 1..1 String |
An optional string that specifies the type object | direct |
asm_score | 0..1 Float |
A score for comparing metagenomic assembly quality from same sample | direct |
scaffolds | 0..1 Float |
Total sequence count of all scaffolds | direct |
scaf_logsum | 0..1 Float |
The sum of the (length*log(length)) of all scaffolds, times some constant | direct |
scaf_powsum | 0..1 Float |
Powersum of all scaffolds is the same as logsum except that it uses the sum o... | direct |
scaf_max | 0..1 Float |
Maximum scaffold length | direct |
scaf_bp | 0..1 Float |
Total size in bp of all scaffolds | direct |
scaf_n50 | 0..1 Float |
Given a set of scaffolds, each with its own length, the N50 count is defined ... | direct |
scaf_n90 | 0..1 Float |
Given a set of scaffolds, each with its own length, the N90 count is defined ... | direct |
scaf_l50 | 0..1 Float |
Given a set of scaffolds, the L50 is defined as the sequence length of the sh... | direct |
scaf_l90 | 0..1 Float |
The L90 statistic is less than or equal to the L50 statistic; it is the lengt... | direct |
scaf_n_gt50k | 0..1 Float |
Total sequence count of scaffolds greater than 50 KB | direct |
scaf_l_gt50k | 0..1 Float |
Total size in bp of all scaffolds greater than 50 KB | direct |
scaf_pct_gt50k | 0..1 Float |
Total sequence size percentage of scaffolds greater than 50 KB | direct |
contigs | 0..1 Float |
The sum of the (length*log(length)) of all contigs, times some constant | direct |
contig_bp | 0..1 Float |
Total size in bp of all contigs | direct |
ctg_n50 | 0..1 Float |
Given a set of contigs, each with its own length, the N50 count is defined as... | direct |
ctg_l50 | 0..1 Float |
Given a set of contigs, the L50 is defined as the sequence length of the shor... | direct |
ctg_n90 | 0..1 Float |
Given a set of contigs, each with its own length, the N90 count is defined as... | direct |
ctg_l90 | 0..1 Float |
The L90 statistic is less than or equal to the L50 statistic; it is the lengt... | direct |
ctg_logsum | 0..1 Float |
Maximum contig length | direct |
ctg_powsum | 0..1 Float |
Powersum of all contigs is the same as logsum except that it uses the sum of ... | direct |
ctg_max | 0..1 Float |
Maximum contig length | direct |
gap_pct | 0..1 Float |
The gap size percentage of all scaffolds | direct |
gc_std | 0..1 Float |
Standard deviation of GC content of all contigs | direct |
gc_avg | 0..1 Float |
Average of GC content of all contigs | direct |
num_input_reads | 0..1 Float |
The sequence count number of input reads for assembly | direct |
num_aligned_reads | 0..1 Float |
The sequence count number of input reads aligned to assembled contigs | direct |
insdc_assembly_identifiers | 0..1 String |
direct | |
execution_resource | 1..1 String |
WorkflowExecutionActivity | |
git_url | 1..1 String |
WorkflowExecutionActivity | |
has_input | 1..* NamedThing |
An input to a process | WorkflowExecutionActivity |
has_output | 0..* NamedThing |
An output biosample to a processing step | WorkflowExecutionActivity |
part_of | 0..* NamedThing |
Links a resource to another resource that either logically or physically incl... | WorkflowExecutionActivity |
version | 0..1 String |
WorkflowExecutionActivity | |
qc_status | 0..1 StatusEnum |
Stores information about the result of a process (ie the process of sequencin... | WorkflowExecutionActivity |
qc_comment | 0..1 String |
Slot to store additional comments about laboratory or workflow output | WorkflowExecutionActivity |
has_failure_categorization | 0..* FailureCategorization |
WorkflowExecutionActivity | |
id | 1..1 Uriorcurie |
A unique identifier for a thing | Activity |
name | 0..1 String |
A human readable label for an entity | Activity |
started_at_time | 1..1 String |
Activity | |
ended_at_time | 1..1 String |
Activity | |
was_informed_by | 0..1 Activity |
Activity | |
used | 0..1 String |
Activity |
Usages
used by | used in | type | used |
---|---|---|---|
Database | metagenome_assembly_set | range | MetagenomeAssembly |
Comments
- instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:MetagenomeAssembly |
native | nmdc:MetagenomeAssembly |
LinkML Source
Direct
name: MetagenomeAssembly
description: A workflow execution activity that converts sequencing reads into an
assembled metagenome.
comments:
- instances of this class may use a de novo assembly strategy in most or all cases
relevant to NMDC
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slots:
- type
- asm_score
- scaffolds
- scaf_logsum
- scaf_powsum
- scaf_max
- scaf_bp
- scaf_n50
- scaf_n90
- scaf_l50
- scaf_l90
- scaf_n_gt50k
- scaf_l_gt50k
- scaf_pct_gt50k
- contigs
- contig_bp
- ctg_n50
- ctg_l50
- ctg_n90
- ctg_l90
- ctg_logsum
- ctg_powsum
- ctg_max
- gap_pct
- gc_std
- gc_avg
- num_input_reads
- num_aligned_reads
- insdc_assembly_identifiers
slot_usage:
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
Induced
name: MetagenomeAssembly
description: A workflow execution activity that converts sequencing reads into an
assembled metagenome.
comments:
- instances of this class may use a de novo assembly strategy in most or all cases
relevant to NMDC
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slot_usage:
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
attributes:
type:
name: type
description: An optional string that specifies the type object. This is used
to allow for searches for different kinds of objects.
deprecated: Due to confusion about what values are used for this slot, it is best
not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.
MAM removed designates_type and rdf:type slot uri 2022-11-30
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: type
owner: MetagenomeAssembly
domain_of:
- DataObject
- Biosample
- Study
- OmicsProcessing
- CreditAssociation
- MagBin
- GenomeFeature
- WorkflowExecutionActivity
- MetagenomeAssembly
- MetagenomeAnnotationActivity
- MetatranscriptomeAnnotationActivity
- MetatranscriptomeActivity
- MagsAnalysisActivity
- ReadQcAnalysisActivity
- ReadBasedTaxonomyAnalysisActivity
range: string
required: true
asm_score:
name: asm_score
description: A score for comparing metagenomic assembly quality from same sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: asm_score
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaffolds:
name: scaffolds
description: Total sequence count of all scaffolds.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaffolds
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_logsum:
name: scaf_logsum
description: The sum of the (length*log(length)) of all scaffolds, times some
constant. Increase the contiguity, the score will increase
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_logsum
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_powsum:
name: scaf_powsum
description: Powersum of all scaffolds is the same as logsum except that it uses
the sum of (length*(length^P)) for some power P (default P=0.25).
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_powsum
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_max:
name: scaf_max
description: Maximum scaffold length.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_max
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_bp:
name: scaf_bp
description: Total size in bp of all scaffolds.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_bp
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_n50:
name: scaf_n50
description: Given a set of scaffolds, each with its own length, the N50 count
is defined as the smallest number of scaffolds whose length sum makes up half
of genome size.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_n50
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_n90:
name: scaf_n90
description: Given a set of scaffolds, each with its own length, the N90 count
is defined as the smallest number of scaffolds whose length sum makes up 90%
of genome size.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_n90
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_l50:
name: scaf_l50
description: Given a set of scaffolds, the L50 is defined as the sequence length
of the shortest scaffold at 50% of the total genome length.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_l50
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_l90:
name: scaf_l90
description: The L90 statistic is less than or equal to the L50 statistic; it
is the length for which the collection of all scaffolds of that length or longer
contains at least 90% of the sum of the lengths of all scaffolds.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_l90
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_n_gt50k:
name: scaf_n_gt50k
description: Total sequence count of scaffolds greater than 50 KB.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_n_gt50k
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_l_gt50k:
name: scaf_l_gt50k
description: Total size in bp of all scaffolds greater than 50 KB.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_l_gt50k
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
scaf_pct_gt50k:
name: scaf_pct_gt50k
description: Total sequence size percentage of scaffolds greater than 50 KB.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: scaf_pct_gt50k
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
contigs:
name: contigs
description: The sum of the (length*log(length)) of all contigs, times some constant. Increase
the contiguity, the score will increase
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: contigs
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
contig_bp:
name: contig_bp
description: Total size in bp of all contigs.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: contig_bp
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_n50:
name: ctg_n50
description: Given a set of contigs, each with its own length, the N50 count is
defined as the smallest number_of_contigs whose length sum makes up half of
genome size.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_n50
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_l50:
name: ctg_l50
description: Given a set of contigs, the L50 is defined as the sequence length
of the shortest contig at 50% of the total genome length.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_l50
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_n90:
name: ctg_n90
description: Given a set of contigs, each with its own length, the N90 count is
defined as the smallest number of contigs whose length sum makes up 90% of genome
size.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_n90
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_l90:
name: ctg_l90
description: The L90 statistic is less than or equal to the L50 statistic; it
is the length for which the collection of all contigs of that length or longer
contains at least 90% of the sum of the lengths of all contigs.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_l90
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_logsum:
name: ctg_logsum
description: Maximum contig length.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_logsum
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_powsum:
name: ctg_powsum
description: Powersum of all contigs is the same as logsum except that it uses
the sum of (length*(length^P)) for some power P (default P=0.25).
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_powsum
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
ctg_max:
name: ctg_max
description: Maximum contig length.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: ctg_max
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
gap_pct:
name: gap_pct
description: The gap size percentage of all scaffolds.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: gap_pct
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
gc_std:
name: gc_std
description: Standard deviation of GC content of all contigs.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: gc_std
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
gc_avg:
name: gc_avg
description: Average of GC content of all contigs.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: gc_avg
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
num_input_reads:
name: num_input_reads
description: The sequence count number of input reads for assembly.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: num_input_reads
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
num_aligned_reads:
name: num_aligned_reads
description: The sequence count number of input reads aligned to assembled contigs.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: metagenome_assembly_parameter
alias: num_aligned_reads
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: float
insdc_assembly_identifiers:
name: insdc_assembly_identifiers
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: assembly_identifiers
mixins:
- insdc_identifiers
alias: insdc_assembly_identifiers
owner: MetagenomeAssembly
domain_of:
- MetagenomeAssembly
- MetatranscriptomeAssembly
range: string
pattern: ^insdc.sra:[A-Z]+[0-9]+(\.[0-9]+)?$
execution_resource:
name: execution_resource
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: execution_resource
owner: MetagenomeAssembly
domain_of:
- WorkflowExecutionActivity
range: string
required: true
git_url:
name: git_url
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: git_url
owner: MetagenomeAssembly
domain_of:
- WorkflowExecutionActivity
range: string
required: true
has_input:
name: has_input
description: An input to a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: NamedThing
multivalued: true
alias: has_input
owner: MetagenomeAssembly
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
required: true
has_output:
name: has_output
description: An output biosample to a processing step
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- output
rank: 1000
domain: NamedThing
multivalued: true
alias: has_output
owner: MetagenomeAssembly
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
part_of:
name: part_of
description: Links a resource to another resource that either logically or physically
includes it.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- is part of
rank: 1000
domain: NamedThing
slot_uri: dcterms:isPartOf
multivalued: true
alias: part_of
owner: MetagenomeAssembly
domain_of:
- FieldResearchSite
- Biosample
- Study
- OmicsProcessing
- WorkflowExecutionActivity
range: NamedThing
version:
name: version
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: version
owner: MetagenomeAssembly
domain_of:
- WorkflowExecutionActivity
- ReadQcAnalysisActivity
range: string
qc_status:
name: qc_status
description: Stores information about the result of a process (ie the process
of sequencing a library may have for qc_status of 'fail' if not enough data
was generated)
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: qc_status
owner: MetagenomeAssembly
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: StatusEnum
qc_comment:
name: qc_comment
description: Slot to store additional comments about laboratory or workflow output.
For workflow output it may describe the particular workflow stage that failed.
(ie Failed at call-stage due to a malformed fastq file).
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: qc_comment
owner: MetagenomeAssembly
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: string
has_failure_categorization:
name: has_failure_categorization
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
multivalued: true
alias: has_failure_categorization
owner: MetagenomeAssembly
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: FailureCategorization
id:
name: id
description: A unique identifier for a thing. Must be either a CURIE shorthand
for a URI or a complete URI
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: MetagenomeAssembly
domain_of:
- Biosample
- Study
- NamedThing
- Activity
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
structured_pattern:
syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: MetagenomeAssembly
domain_of:
- Protocol
- NamedThing
- PersonValue
- Activity
range: string
started_at_time:
name: started_at_time
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: started_at_time
owner: MetagenomeAssembly
domain_of:
- Activity
range: string
required: true
pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
ended_at_time:
name: ended_at_time
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: ended_at_time
owner: MetagenomeAssembly
domain_of:
- Activity
range: string
required: true
pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
was_informed_by:
name: was_informed_by
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- prov:wasInformedBy
rank: 1000
domain: Activity
alias: was_informed_by
owner: MetagenomeAssembly
domain_of:
- Activity
range: Activity
used:
name: used
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- prov:used
rank: 1000
domain: Activity
alias: used
owner: MetagenomeAssembly
domain_of:
- Activity
range: string