Class: Metagenome-Assembled Genome analysis activity (MagsAnalysisActivity)
A workflow execution activity that uses computational binning tools to group assembled contigs into genomes
URI: nmdc:MagsAnalysisActivity
classDiagram
class MagsAnalysisActivity
click MagsAnalysisActivity href "../MagsAnalysisActivity"
WorkflowExecutionActivity <|-- MagsAnalysisActivity
click WorkflowExecutionActivity href "../WorkflowExecutionActivity"
MagsAnalysisActivity : alternative_identifiers
MagsAnalysisActivity : binned_contig_num
MagsAnalysisActivity : ended_at_time
MagsAnalysisActivity : execution_resource
MagsAnalysisActivity : git_url
MagsAnalysisActivity : has_failure_categorization
MagsAnalysisActivity --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
MagsAnalysisActivity : has_input
MagsAnalysisActivity --> "1..*" NamedThing : has_input
click NamedThing href "../NamedThing"
MagsAnalysisActivity : has_output
MagsAnalysisActivity --> "*" NamedThing : has_output
click NamedThing href "../NamedThing"
MagsAnalysisActivity : id
MagsAnalysisActivity : input_contig_num
MagsAnalysisActivity : low_depth_contig_num
MagsAnalysisActivity : mags_list
MagsAnalysisActivity --> "*" MagBin : mags_list
click MagBin href "../MagBin"
MagsAnalysisActivity : name
MagsAnalysisActivity : part_of
MagsAnalysisActivity --> "*" NamedThing : part_of
click NamedThing href "../NamedThing"
MagsAnalysisActivity : qc_comment
MagsAnalysisActivity : qc_status
MagsAnalysisActivity --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
MagsAnalysisActivity : started_at_time
MagsAnalysisActivity : too_short_contig_num
MagsAnalysisActivity : type
MagsAnalysisActivity : unbinned_contig_num
MagsAnalysisActivity : used
MagsAnalysisActivity : version
MagsAnalysisActivity : was_informed_by
MagsAnalysisActivity --> "0..1" OmicsProcessing : was_informed_by
click OmicsProcessing href "../OmicsProcessing"
Inheritance
- Activity
- WorkflowExecutionActivity
- MagsAnalysisActivity
- WorkflowExecutionActivity
Slots
Usages
used by | used in | type | used |
---|---|---|---|
Database | mags_activity_set | range | MagsAnalysisActivity |
MagsAnalysisActivity | mags_list | domain | MagsAnalysisActivity |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:MagsAnalysisActivity |
native | nmdc:MagsAnalysisActivity |
LinkML Source
Direct
name: MagsAnalysisActivity
description: A workflow execution activity that uses computational binning tools to
group assembled contigs into genomes
title: Metagenome-Assembled Genome analysis activity
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slots:
- type
- input_contig_num
- binned_contig_num
- too_short_contig_num
- low_depth_contig_num
- unbinned_contig_num
- mags_list
slot_usage:
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
Induced
name: MagsAnalysisActivity
description: A workflow execution activity that uses computational binning tools to
group assembled contigs into genomes
title: Metagenome-Assembled Genome analysis activity
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecutionActivity
slot_usage:
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'
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: MagsAnalysisActivity
domain_of:
- DataObject
- Biosample
- Study
- OmicsProcessing
- CreditAssociation
- MagBin
- WorkflowExecutionActivity
- MetagenomeAssembly
- MetagenomeAnnotationActivity
- MetatranscriptomeAnnotationActivity
- MetatranscriptomeExpressionAnalysis
- MagsAnalysisActivity
- ReadQcAnalysisActivity
- ReadBasedTaxonomyAnalysisActivity
range: string
required: true
input_contig_num:
name: input_contig_num
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: input_contig_num
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: integer
binned_contig_num:
name: binned_contig_num
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: binned_contig_num
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: integer
too_short_contig_num:
name: too_short_contig_num
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: too_short_contig_num
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: integer
low_depth_contig_num:
name: low_depth_contig_num
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: low_depth_contig_num
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: integer
unbinned_contig_num:
name: unbinned_contig_num
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: unbinned_contig_num
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: integer
mags_list:
name: mags_list
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: MagsAnalysisActivity
alias: mags_list
owner: MagsAnalysisActivity
domain_of:
- MagsAnalysisActivity
range: MagBin
multivalued: true
execution_resource:
name: execution_resource
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: execution_resource
owner: MagsAnalysisActivity
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: MagsAnalysisActivity
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
alias: has_input
owner: MagsAnalysisActivity
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
required: true
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'
interpolated: true
has_output:
name: has_output
description: An output biosample to a processing step
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: NamedThing
alias: has_output
owner: MagsAnalysisActivity
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'
interpolated: true
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
alias: part_of
owner: MagsAnalysisActivity
domain_of:
- FieldResearchSite
- Biosample
- Study
- OmicsProcessing
- WorkflowExecutionActivity
range: NamedThing
multivalued: true
version:
name: version
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: version
owner: MagsAnalysisActivity
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: MagsAnalysisActivity
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: MagsAnalysisActivity
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: string
has_failure_categorization:
name: has_failure_categorization
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_failure_categorization
owner: MagsAnalysisActivity
domain_of:
- PlannedProcess
- WorkflowExecutionActivity
range: FailureCategorization
multivalued: true
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: MagsAnalysisActivity
domain_of:
- Biosample
- Study
- NamedThing
- MetaboliteQuantification
- WorkflowExecutionActivity
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
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: MagsAnalysisActivity
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}:wfmag-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: MagsAnalysisActivity
domain_of:
- Protocol
- NamedThing
- PersonValue
- Activity
range: string
started_at_time:
name: started_at_time
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: started_at_time
owner: MagsAnalysisActivity
domain_of:
- Activity
range: string
required: true
pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$
ended_at_time:
name: ended_at_time
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: Activity
alias: ended_at_time
owner: MagsAnalysisActivity
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
rank: 1000
alias: was_informed_by
owner: MagsAnalysisActivity
domain_of:
- Activity
range: OmicsProcessing
structured_pattern:
syntax: '{id_nmdc_prefix}:(omprc)-{id_shoulder}-{id_blade}$'
interpolated: true
used:
name: used
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- prov:used
rank: 1000
domain: Activity
alias: used
owner: MagsAnalysisActivity
domain_of:
- Activity
range: string