Class: Planned Process (PlannedProcess)
Note
This is an abstract class and should not be instantiated directly.
URI: OBI:0000011
classDiagram
class PlannedProcess
click PlannedProcess href "../PlannedProcess"
NamedThing <|-- PlannedProcess
click NamedThing href "../NamedThing"
PlannedProcess <|-- Extraction
click Extraction href "../Extraction"
PlannedProcess <|-- CollectingBiosamplesFromSite
click CollectingBiosamplesFromSite href "../CollectingBiosamplesFromSite"
PlannedProcess <|-- BiosampleProcessing
click BiosampleProcessing href "../BiosampleProcessing"
PlannedProcess <|-- SubSamplingProcess
click SubSamplingProcess href "../SubSamplingProcess"
PlannedProcess <|-- MixingProcess
click MixingProcess href "../MixingProcess"
PlannedProcess <|-- FiltrationProcess
click FiltrationProcess href "../FiltrationProcess"
PlannedProcess <|-- ChromatographicSeparationProcess
click ChromatographicSeparationProcess href "../ChromatographicSeparationProcess"
PlannedProcess <|-- OmicsProcessing
click OmicsProcessing href "../OmicsProcessing"
PlannedProcess : alternative_identifiers
PlannedProcess : description
PlannedProcess : designated_class
PlannedProcess : end_date
PlannedProcess : has_failure_categorization
PlannedProcess --> "*" FailureCategorization : has_failure_categorization
click FailureCategorization href "../FailureCategorization"
PlannedProcess : has_input
PlannedProcess --> "*" NamedThing : has_input
click NamedThing href "../NamedThing"
PlannedProcess : has_output
PlannedProcess --> "*" NamedThing : has_output
click NamedThing href "../NamedThing"
PlannedProcess : id
PlannedProcess : instrument_name
PlannedProcess : name
PlannedProcess : processing_institution
PlannedProcess --> "1" ProcessingInstitutionEnum : processing_institution
click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum"
PlannedProcess : protocol_link
PlannedProcess --> "1" Protocol : protocol_link
click Protocol href "../Protocol"
PlannedProcess : qc_comment
PlannedProcess : qc_status
PlannedProcess --> "1" StatusEnum : qc_status
click StatusEnum href "../StatusEnum"
PlannedProcess : start_date
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| designated_class | 0..1 Uriorcurie |
direct | |
| end_date | 0..1 String |
The date on which any process or activity was ended | direct |
| has_input | 0..* NamedThing |
An input to a process | direct |
| has_output | 0..* NamedThing |
An output biosample to a processing step | direct |
| processing_institution | 0..1 ProcessingInstitutionEnum |
The organization that processed the sample | direct |
| protocol_link | 0..1 Protocol |
direct | |
| start_date | 0..1 String |
The date on which any process or activity was started | direct |
| instrument_name | 0..1 String |
The name of the instrument that was used for processing the sample | direct |
| qc_status | 0..1 StatusEnum |
Stores information about the result of a process (ie the process of sequencin... | direct |
| qc_comment | 0..1 String |
Slot to store additional comments about laboratory or workflow output | direct |
| has_failure_categorization | 0..* FailureCategorization |
direct | |
| id | 1..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 | 0..* Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
Usages
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | OBI:0000011 |
| native | nmdc:PlannedProcess |
LinkML Source
Direct
name: PlannedProcess
title: Planned Process
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
abstract: true
slots:
- designated_class
- end_date
- has_input
- has_output
- processing_institution
- protocol_link
- start_date
- instrument_name
- qc_status
- qc_comment
- has_failure_categorization
slot_usage:
designated_class:
name: designated_class
comments:
- required on all instances in a polymorphic Database slot like planned_process_set
domain_of:
- PlannedProcess
class_uri: OBI:0000011
Induced
name: PlannedProcess
title: Planned Process
from_schema: https://w3id.org/nmdc/nmdc
is_a: NamedThing
abstract: true
slot_usage:
designated_class:
name: designated_class
comments:
- required on all instances in a polymorphic Database slot like planned_process_set
domain_of:
- PlannedProcess
attributes:
designated_class:
name: designated_class
comments:
- required on all instances in a polymorphic Database slot like planned_process_set
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
designates_type: true
alias: designated_class
owner: PlannedProcess
domain_of:
- PlannedProcess
range: uriorcurie
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: PlannedProcess
domain_of:
- PlannedProcess
range: string
has_input:
name: has_input
description: An input to a process.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- input
rank: 1000
domain: NamedThing
multivalued: true
alias: has_input
owner: PlannedProcess
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
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: PlannedProcess
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: NamedThing
processing_institution:
name: processing_institution
description: The organization that processed the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: processing_institution
owner: PlannedProcess
domain_of:
- OmicsProcessing
- PlannedProcess
range: processing_institution_enum
protocol_link:
name: protocol_link
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: protocol_link
owner: PlannedProcess
domain_of:
- PlannedProcess
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: PlannedProcess
domain_of:
- PlannedProcess
range: string
instrument_name:
name: instrument_name
description: The name of the instrument that was used for processing the sample.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
domain: PlannedProcess
alias: instrument_name
owner: PlannedProcess
domain_of:
- OmicsProcessing
- 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: PlannedProcess
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: PlannedProcess
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: PlannedProcess
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
notes:
- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
will be accepted
- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
via per-class id slot usage assertions
- minting authority shoulders should probably be enumerated and checked in the
pattern
examples:
- value: nmdc:mgmag-00-x012.1_7_c1
description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: PlannedProcess
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_\-\/\.,]*$
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: PlannedProcess
domain_of:
- Protocol
- NamedThing
- PersonValue
- Activity
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: PlannedProcess
domain_of:
- Study
- NamedThing
- ImageValue
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
multivalued: true
alias: alternative_identifiers
owner: PlannedProcess
domain_of:
- Biosample
- Study
- NamedThing
- MetaboliteQuantification
range: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
class_uri: OBI:0000011