Class: Collecting Biosamples From Site (CollectingBiosamplesFromSite)
URI: nmdc:CollectingBiosamplesFromSite
classDiagram
class CollectingBiosamplesFromSite
PlannedProcess <|-- CollectingBiosamplesFromSite
CollectingBiosamplesFromSite : alternative_identifiers
CollectingBiosamplesFromSite : description
CollectingBiosamplesFromSite : designated_class
CollectingBiosamplesFromSite : end_date
CollectingBiosamplesFromSite : has_failure_categorization
CollectingBiosamplesFromSite --|> FailureCategorization : has_failure_categorization
CollectingBiosamplesFromSite : has_input
CollectingBiosamplesFromSite --|> Site : has_input
CollectingBiosamplesFromSite : has_output
CollectingBiosamplesFromSite --|> Biosample : has_output
CollectingBiosamplesFromSite : id
CollectingBiosamplesFromSite : instrument_name
CollectingBiosamplesFromSite : name
CollectingBiosamplesFromSite : processing_institution
CollectingBiosamplesFromSite --|> processing_institution_enum : processing_institution
CollectingBiosamplesFromSite : protocol_link
CollectingBiosamplesFromSite --|> Protocol : protocol_link
CollectingBiosamplesFromSite : qc_comment
CollectingBiosamplesFromSite : qc_status
CollectingBiosamplesFromSite --|> StatusEnum : qc_status
CollectingBiosamplesFromSite : start_date
Inheritance
- NamedThing
- PlannedProcess
- CollectingBiosamplesFromSite
- PlannedProcess
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
designated_class | 0..1 Uriorcurie |
PlannedProcess | |
end_date | 0..1 String |
The date on which any process or activity was ended | PlannedProcess |
has_input | 1..* Site |
An input to a process | PlannedProcess |
has_output | 1..* Biosample |
An output biosample to a processing step | 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 |
instrument_name | 0..1 String |
The name of the instrument that was used for processing the sample | 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 | 0..* FailureCategorization |
PlannedProcess | |
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
used by | used in | type | used |
---|---|---|---|
Database | collecting_biosamples_from_site_set | range | CollectingBiosamplesFromSite |
Comments
- this illustrates implementing a Biosample relation with a process class
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:CollectingBiosamplesFromSite |
native | nmdc:CollectingBiosamplesFromSite |
close | OBI:0000744 |
LinkML Source
Direct
name: CollectingBiosamplesFromSite
title: Collecting Biosamples From Site
comments:
- this illustrates implementing a Biosample relation with a process class
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- OBI:0000744
is_a: PlannedProcess
slot_usage:
has_input:
name: has_input
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Site
required: true
has_output:
name: has_output
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Biosample
required: true
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
Induced
name: CollectingBiosamplesFromSite
title: Collecting Biosamples From Site
comments:
- this illustrates implementing a Biosample relation with a process class
from_schema: https://w3id.org/nmdc/nmdc
close_mappings:
- OBI:0000744
is_a: PlannedProcess
slot_usage:
has_input:
name: has_input
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Site
required: true
has_output:
name: has_output
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Biosample
required: true
id:
name: id
domain_of:
- Biosample
- Study
- NamedThing
- Activity
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'
interpolated: true
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
domain_of:
- PlannedProcess
range: string
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: CollectingBiosamplesFromSite
domain_of:
- BiosampleProcessing
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Site
required: 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
multivalued: true
alias: has_output
owner: CollectingBiosamplesFromSite
domain_of:
- OmicsProcessing
- PlannedProcess
- WorkflowExecutionActivity
range: Biosample
required: true
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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}:clsite-{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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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: CollectingBiosamplesFromSite
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_\-\/\.,]*$