Class: Field Research Site (FieldResearchSite)
A site, outside of a laboratory, from which biosamples may be collected.
classDiagram
class FieldResearchSite
click FieldResearchSite href "../FieldResearchSite"
Site <|-- FieldResearchSite
click Site href "../Site"
FieldResearchSite : alternative_identifiers
FieldResearchSite : cur_vegetation
FieldResearchSite --> "0..1" TextValue : cur_vegetation
click TextValue href "../TextValue"
FieldResearchSite : description
FieldResearchSite : elev
FieldResearchSite : geo_loc_name
FieldResearchSite --> "0..1" TextValue : geo_loc_name
click TextValue href "../TextValue"
FieldResearchSite : habitat
FieldResearchSite : id
FieldResearchSite : lat_lon
FieldResearchSite --> "0..1" GeolocationValue : lat_lon
click GeolocationValue href "../GeolocationValue"
FieldResearchSite : local_class
FieldResearchSite --> "0..1" TextValue : local_class
click TextValue href "../TextValue"
FieldResearchSite : name
FieldResearchSite : part_of
FieldResearchSite --> "*" FieldResearchSite : part_of
click FieldResearchSite href "../FieldResearchSite"
FieldResearchSite : soil_type
FieldResearchSite --> "0..1" TextValue : soil_type
click TextValue href "../TextValue"
FieldResearchSite : type
Inheritance
- NamedThing
- MaterialEntity
- Site
- FieldResearchSite
- Site
- MaterialEntity
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
cur_vegetation | 0..1 TextValue |
Vegetation classification from one or more standard classification systems, o... | direct |
elev | 0..1 Float |
Elevation of the sampling site is its height above a fixed reference point, m... | direct |
geo_loc_name | 0..1 TextValue |
The geographical origin of the sample as defined by the country or sea name f... | direct |
habitat | 0..1 String |
direct | |
lat_lon | 0..1 GeolocationValue |
The geographical origin of the sample as defined by latitude and longitude | direct |
local_class | 0..1 TextValue |
Soil classification based on local soil classification system | direct |
part_of | * FieldResearchSite |
Links a resource to another resource that either logically or physically incl... | direct |
soil_type | 0..1 TextValue |
Description of the soil type or classification | direct |
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 |
Usages
used by | used in | type | used |
---|---|---|---|
Database | field_research_site_set | range | FieldResearchSite |
FieldResearchSite | part_of | range | FieldResearchSite |
Biosample | collected_from | range | FieldResearchSite |
Aliases
- research plot
Comments
- Provides grouping of biosamples at level that's more specific than belonging to the same study
- be very clear that this could be part of a larger site
- In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.
- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:FieldResearchSite |
native | nmdc:FieldResearchSite |
LinkML Source
Direct
name: FieldResearchSite
description: A site, outside of a laboratory, from which biosamples may be collected.
title: Field Research Site
comments:
- Provides grouping of biosamples at level that's more specific than belonging to
the same study
- be very clear that this could be part of a larger site
- In Bioscales, one might say that rhizosphere soil and bulk soil from around the
same plant were obtained at the same site. In this case, the site would correspond
to one tree.
- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- research plot
is_a: Site
slots:
- cur_vegetation
- elev
- geo_loc_name
- habitat
- lat_lon
- local_class
- part_of
- soil_type
slot_usage:
id:
name: id
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
part_of:
name: part_of
range: FieldResearchSite
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
class_uri: nmdc:FieldResearchSite
Induced
name: FieldResearchSite
description: A site, outside of a laboratory, from which biosamples may be collected.
title: Field Research Site
comments:
- Provides grouping of biosamples at level that's more specific than belonging to
the same study
- be very clear that this could be part of a larger site
- In Bioscales, one might say that rhizosphere soil and bulk soil from around the
same plant were obtained at the same site. In this case, the site would correspond
to one tree.
- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- research plot
is_a: Site
slot_usage:
id:
name: id
required: true
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
part_of:
name: part_of
range: FieldResearchSite
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
attributes:
cur_vegetation:
name: cur_vegetation
annotations:
expected_value:
tag: expected_value
value: current vegetation type
occurrence:
tag: occurrence
value: '1'
description: Vegetation classification from one or more standard classification
systems, or agricultural crop
title: current vegetation
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- current vegetation
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000312
alias: cur_vegetation
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
elev:
name: elev
annotations:
expected_value:
tag: expected_value
value: measurement value
description: Elevation of the sampling site is its height above a fixed reference
point, most commonly the mean sea level. Elevation is mainly used when referring
to points on the earth's surface, while altitude is used for points above the
surface, such as an aircraft in flight or a spacecraft in orbit.
title: elevation
examples:
- value: 100 meter
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- elevation
rank: 1000
is_a: environment field
slot_uri: MIXS:0000093
alias: elev
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: float
multivalued: false
geo_loc_name:
name: geo_loc_name
annotations:
expected_value:
tag: expected_value
value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location
name'
description: The geographical origin of the sample as defined by the country or
sea name followed by specific region name. Country or sea names should be chosen
from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
(http://purl.bioontology.org/ontology/GAZ)
title: geographic location (country and/or sea,region)
examples:
- value: 'USA: Maryland, Bethesda'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (country and/or sea,region)
rank: 1000
is_a: environment field
string_serialization: '{term}: {term}, {text}'
slot_uri: MIXS:0000010
alias: geo_loc_name
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
habitat:
name: habitat
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: habitat
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: string
lat_lon:
name: lat_lon
annotations:
expected_value:
tag: expected_value
value: decimal degrees, limit to 8 decimal points
description: The geographical origin of the sample as defined by latitude and
longitude. The values should be reported in decimal degrees and in WGS84 system
title: geographic location (latitude and longitude)
examples:
- value: 50.586825 6.408977
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- geographic location (latitude and longitude)
rank: 1000
is_a: environment field
string_serialization: '{float} {float}'
slot_uri: MIXS:0000009
alias: lat_lon
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: GeolocationValue
multivalued: false
local_class:
name: local_class
annotations:
expected_value:
tag: expected_value
value: local classification name
occurrence:
tag: occurrence
value: '1'
description: Soil classification based on local soil classification system
title: soil_taxonomic/local classification
examples:
- value: ''
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil_taxonomic/local classification
rank: 1000
is_a: core field
string_serialization: '{text}'
slot_uri: MIXS:0000330
alias: local_class
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
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
slot_uri: dcterms:isPartOf
alias: part_of
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Study
range: FieldResearchSite
multivalued: true
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
soil_type:
name: soil_type
annotations:
expected_value:
tag: expected_value
value: ENVO_00001998
occurrence:
tag: occurrence
value: '1'
description: Description of the soil type or classification. This field accepts
terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms
can be separated by pipes.
title: soil type
examples:
- value: plinthosol [ENVO:00002250]
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- soil type
rank: 1000
is_a: core field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000332
alias: soil_type
owner: FieldResearchSite
domain_of:
- FieldResearchSite
- Biosample
range: TextValue
multivalued: false
id:
name: id
description: A unique identifier for a thing. Must be either a CURIE shorthand
for a URI or a complete URI
notes:
- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
will be accepted
- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
via per-class id slot usage assertions
- minting authority shoulders should probably be enumerated and checked in the
pattern
examples:
- value: nmdc:mgmag-00-x012.1_7_c1
description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
identifier: true
alias: id
owner: FieldResearchSite
domain_of:
- NamedThing
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
structured_pattern:
syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'
interpolated: true
name:
name: name
description: A human readable label for an entity
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: name
owner: FieldResearchSite
domain_of:
- PersonValue
- NamedThing
- Protocol
range: string
description:
name: description
description: a human-readable description of a thing
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
slot_uri: dcterms:description
alias: description
owner: FieldResearchSite
domain_of:
- ImageValue
- NamedThing
range: string
alternative_identifiers:
name: alternative_identifiers
description: A list of alternative identifiers for the entity.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: alternative_identifiers
owner: FieldResearchSite
domain_of:
- MetaboliteIdentification
- NamedThing
range: uriorcurie
multivalued: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
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: FieldResearchSite
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:FieldResearchSite