Class: NomAnalysis
URI: nmdc:NomAnalysis
classDiagram
class NomAnalysis
click NomAnalysis href "../NomAnalysis"
WorkflowExecution <|-- NomAnalysis
click WorkflowExecution href "../WorkflowExecution"
NomAnalysis : alternative_identifiers
NomAnalysis : description
NomAnalysis : end_date
NomAnalysis : ended_at_time
NomAnalysis : execution_resource
NomAnalysis --> "1" ExecutionResourceEnum : execution_resource
click ExecutionResourceEnum href "../ExecutionResourceEnum"
NomAnalysis : git_url
NomAnalysis : has_calibration
NomAnalysis : has_failure_categorization
NomAnalysis --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
NomAnalysis : has_input
NomAnalysis --> "1..*" NamedThing : has_input
click NamedThing href "../NamedThing"
NomAnalysis : has_output
NomAnalysis --> "*" NamedThing : has_output
click NamedThing href "../NamedThing"
NomAnalysis : id
NomAnalysis : name
NomAnalysis : processing_institution
NomAnalysis --> "0..1" ProcessingInstitutionEnum : processing_institution
click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum"
NomAnalysis : protocol_link
NomAnalysis --> "0..1" Protocol : protocol_link
click Protocol href "../Protocol"
NomAnalysis : qc_comment
NomAnalysis : qc_status
NomAnalysis --> "0..1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
NomAnalysis : start_date
NomAnalysis : started_at_time
NomAnalysis : type
NomAnalysis : version
NomAnalysis : was_informed_by
NomAnalysis --> "1" DataGeneration : was_informed_by
click DataGeneration href "../DataGeneration"
Inheritance
- NamedThing
- PlannedProcess
- WorkflowExecution
- NomAnalysis
- WorkflowExecution
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
has_calibration | 0..1 String or CalibrationInformation or String |
a calibration instance associated with a process | direct |
ended_at_time | 0..1 String |
WorkflowExecution | |
execution_resource | 1 ExecutionResourceEnum |
The computing resource or facility where the workflow was executed | WorkflowExecution |
git_url | 1 String |
The url that points to the exact github location of a workflow | WorkflowExecution |
started_at_time | 1 String |
WorkflowExecution | |
version | 0..1 String |
WorkflowExecution | |
was_informed_by | 1 DataGeneration |
WorkflowExecution | |
has_input | 1..* NamedThing |
An input to a process | PlannedProcess |
has_output | * NamedThing |
An output from a process | PlannedProcess |
processing_institution | 0..1 ProcessingInstitutionEnum |
The organization that processed the sample | PlannedProcess |
protocol_link | 0..1 Protocol |
PlannedProcess | |
start_date | 0..1 String |
The date on which any process or activity was started | PlannedProcess |
end_date | 0..1 String |
The date on which any process or activity was ended | PlannedProcess |
qc_status | 0..1 StatusEnum |
Stores information about the result of a process (ie the process of sequencin... | PlannedProcess |
qc_comment | 0..1 String |
Slot to store additional comments about laboratory or workflow output | PlannedProcess |
has_failure_categorization | * FailureCategorization |
PlannedProcess | |
id | 1 Uriorcurie |
A unique identifier for a thing | NamedThing |
name | 0..1 String |
A human readable label for an entity | NamedThing |
description | 0..1 String |
a human-readable description of a thing | NamedThing |
alternative_identifiers | * Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | NamedThing |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:NomAnalysis |
native | nmdc:NomAnalysis |
LinkML Source
Direct
name: NomAnalysis
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecution
slots:
- has_calibration
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
was_informed_by:
name: was_informed_by
domain_of:
- WorkflowExecution
structured_pattern:
syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
interpolated: true
class_uri: nmdc:NomAnalysis
Induced
name: NomAnalysis
in_subset:
- workflow subset
from_schema: https://w3id.org/nmdc/nmdc
is_a: WorkflowExecution
slot_usage:
id:
name: id
domain_of:
- NamedThing
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
was_informed_by:
name: was_informed_by
domain_of:
- WorkflowExecution
structured_pattern:
syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
interpolated: true
attributes:
has_calibration:
name: has_calibration
description: a calibration instance associated with a process
notes:
- 'has_calibration slot will be removed from all WorkflowExecution classes but
remain on the MassSpectrometry class after an ingest of the appropriate set
has occurred. Once this has occurred, this slot''s range can be updated to
CalibrationInformation and class/slot definitions can move to nmdc.yaml. See
PR #29 in Berkeley schema.'
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_calibration
owner: NomAnalysis
domain_of:
- MassSpectrometry
- MetabolomicsAnalysis
- NomAnalysis
range: string
any_of:
- range: CalibrationInformation
- range: string
ended_at_time:
name: ended_at_time
notes:
- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/
It may not be complete, but it is good enough for now.'
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- prov:endedAtTime
rank: 1000
alias: ended_at_time
owner: NomAnalysis
domain_of:
- WorkflowExecution
range: string
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)?)?)?)?$
execution_resource:
name: execution_resource
description: The computing resource or facility where the workflow was executed.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: execution_resource
owner: NomAnalysis
domain_of:
- WorkflowExecution
range: ExecutionResourceEnum
required: true
git_url:
name: git_url
description: The url that points to the exact github location of a workflow.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: git_url
owner: NomAnalysis
domain_of:
- WorkflowExecution
range: string
required: true
started_at_time:
name: started_at_time
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: started_at_time
owner: NomAnalysis
domain_of:
- WorkflowExecution
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)?)?)?)?$
version:
name: version
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: version
owner: NomAnalysis
domain_of:
- WorkflowExecution
range: string
was_informed_by:
name: was_informed_by
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: was_informed_by
owner: NomAnalysis
domain_of:
- WorkflowExecution
range: DataGeneration
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'
interpolated: true
has_input:
name: has_input
description: An input to a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_input
owner: NomAnalysis
domain_of:
- PlannedProcess
range: NamedThing
required: true
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'
interpolated: true
has_output:
name: has_output
description: An output from a process.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_output
owner: NomAnalysis
domain_of:
- PlannedProcess
range: NamedThing
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'
interpolated: true
processing_institution:
name: processing_institution
description: The organization that processed the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: processing_institution
owner: NomAnalysis
domain_of:
- PlannedProcess
range: ProcessingInstitutionEnum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protocol_link
owner: NomAnalysis
domain_of:
- PlannedProcess
- Study
range: Protocol
start_date:
name: start_date
description: The date on which any process or activity was started
todos:
- add date string validation pattern
comments:
- We are using string representations of dates until all components of our ecosystem
can handle ISO 8610 dates
- The date should be formatted as YYYY-MM-DD
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: start_date
owner: NomAnalysis
domain_of:
- PlannedProcess
range: string
end_date:
name: end_date
description: The date on which any process or activity was ended
todos:
- add date string validation pattern
comments:
- We are using string representations of dates until all components of our ecosystem
can handle ISO 8610 dates
- The date should be formatted as YYYY-MM-DD
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: end_date
owner: NomAnalysis
domain_of:
- PlannedProcess
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: NomAnalysis
domain_of:
- PlannedProcess
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: NomAnalysis
domain_of:
- PlannedProcess
range: string
has_failure_categorization:
name: has_failure_categorization
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_failure_categorization
owner: NomAnalysis
domain_of:
- PlannedProcess
range: FailureCategorization
multivalued: true
inlined: true
inlined_as_list: true
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: NomAnalysis
domain_of:
- NamedThing
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}:wfnom-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: NomAnalysis
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: NomAnalysis
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: NomAnalysis
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
type:
name: type
description: the class_uri of the class that has been instantiated
notes:
- replaces legacy nmdc:type slot
- makes it easier to read example data files
- required for polymorphic MongoDB collections
examples:
- value: nmdc:Biosample
- value: nmdc:Study
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/1048
- https://github.com/microbiomedata/nmdc-schema/issues/1233
- https://github.com/microbiomedata/nmdc-schema/issues/248
rank: 1000
slot_uri: rdf:type
designates_type: true
alias: type
owner: NomAnalysis
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:NomAnalysis