Class: Read quality control analysis activity (ReadQcAnalysisActivity)
A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
URI: nmdc:ReadQcAnalysisActivity
classDiagram
class ReadQcAnalysisActivity
click ReadQcAnalysisActivity href "../ReadQcAnalysisActivity"
WorkflowExecutionActivity <|-- ReadQcAnalysisActivity
click WorkflowExecutionActivity href "../WorkflowExecutionActivity"
ReadQcAnalysisActivity : ended_at_time
ReadQcAnalysisActivity : execution_resource
ReadQcAnalysisActivity : git_url
ReadQcAnalysisActivity : has_failure_categorization
ReadQcAnalysisActivity --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
ReadQcAnalysisActivity : has_input
ReadQcAnalysisActivity --> "*" NamedThing : has_input
click NamedThing href "../NamedThing"
ReadQcAnalysisActivity : has_output
ReadQcAnalysisActivity --> "*" NamedThing : has_output
click NamedThing href "../NamedThing"
ReadQcAnalysisActivity : id
ReadQcAnalysisActivity : input_base_count
ReadQcAnalysisActivity : input_read_bases
ReadQcAnalysisActivity : input_read_count
ReadQcAnalysisActivity : name
ReadQcAnalysisActivity : output_base_count
ReadQcAnalysisActivity : output_read_bases
ReadQcAnalysisActivity : output_read_count
ReadQcAnalysisActivity : part_of
ReadQcAnalysisActivity --> "*" NamedThing : part_of
click NamedThing href "../NamedThing"
ReadQcAnalysisActivity : qc_comment
ReadQcAnalysisActivity : qc_status
ReadQcAnalysisActivity --> "1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
ReadQcAnalysisActivity : started_at_time
ReadQcAnalysisActivity : type
ReadQcAnalysisActivity : used
ReadQcAnalysisActivity : version
ReadQcAnalysisActivity : was_informed_by
ReadQcAnalysisActivity --> "1" Activity : was_informed_by
click Activity href "../Activity"
Inheritance
- Activity
- WorkflowExecutionActivity
- ReadQcAnalysisActivity
- WorkflowExecutionActivity
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
type | 1..1 String |
An optional string that specifies the type object | direct |
input_read_count | 0..1 Float |
The sequence count number of input reads for QC analysis | direct |
input_base_count | 0..1 Float |
The nucleotide base count number of input reads for QC analysis | direct |
output_read_count | 0..1 Float |
After QC analysis sequence count number | direct |
output_base_count | 0..1 Float |
After QC analysis nucleotide base count number | direct |
input_read_bases | 0..1 Float |
TODO | direct |
output_read_bases | 0..1 Float |
TODO | direct |
version | 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 |
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 | read_qc_analysis_activity_set | range | ReadQcAnalysisActivity |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:ReadQcAnalysisActivity |
native | nmdc:ReadQcAnalysisActivity |
LinkML Source
Direct
name: ReadQcAnalysisActivity
description: A workflow execution activity that performs quality control on raw Illumina
reads including quality trimming, artifact removal, linker trimming, adapter trimming,
spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
title: Read quality control analysis activity
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slots:
- type
- input_read_count
- input_base_count
- output_read_count
- output_base_count
- input_read_bases
- output_read_bases
- version
slot_usage:
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
Induced
name: ReadQcAnalysisActivity
description: A workflow execution activity that performs quality control on raw Illumina
reads including quality trimming, artifact removal, linker trimming, adapter trimming,
spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
title: Read quality control analysis activity
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}:wfrqc-{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: ReadQcAnalysisActivity
domain_of:
- DataObject
- Biosample
- Study
- OmicsProcessing
- CreditAssociation
- MagBin
- GenomeFeature
- WorkflowExecutionActivity
- MetagenomeAssembly
- MetagenomeAnnotationActivity
- MetatranscriptomeAnnotationActivity
- MetatranscriptomeActivity
- MagsAnalysisActivity
- ReadQcAnalysisActivity
- ReadBasedTaxonomyAnalysisActivity
range: string
required: true
input_read_count:
name: input_read_count
description: The sequence count number of input reads for QC analysis.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: read_qc_analysis_statistic
alias: input_read_count
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
input_base_count:
name: input_base_count
description: The nucleotide base count number of input reads for QC analysis.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: read_qc_analysis_statistic
alias: input_base_count
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
output_read_count:
name: output_read_count
description: After QC analysis sequence count number.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: read_qc_analysis_statistic
alias: output_read_count
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
output_base_count:
name: output_base_count
description: After QC analysis nucleotide base count number.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
is_a: read_qc_analysis_statistic
alias: output_base_count
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
input_read_bases:
name: input_read_bases
description: 'TODO '
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: input_read_bases
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
output_read_bases:
name: output_read_bases
description: TODO
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: output_read_bases
owner: ReadQcAnalysisActivity
domain_of:
- ReadQcAnalysisActivity
range: float
version:
name: version
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: version
owner: ReadQcAnalysisActivity
domain_of:
- WorkflowExecutionActivity
- ReadQcAnalysisActivity
range: string
execution_resource:
name: execution_resource
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: execution_resource
owner: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
domain_of:
- FieldResearchSite
- Biosample
- Study
- OmicsProcessing
- WorkflowExecutionActivity
range: NamedThing
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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}:wfrqc-{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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
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: ReadQcAnalysisActivity
domain_of:
- Activity
range: string