%%{init: {'securityLevel': 'loose', 'theme':'neutral', 'themeVariables': { 'fontSize':'14px', 'fontFamily':'Roboto Mono'}}}%%
classDiagram
direction BT
class PhysicalSampleRecord {
alternate_identifiers : IdentifierObject[]
complies_with : string[]
curation : SpecimenCuration
dc_rights : string
description : string
has_context_category : IdentifierObject[]
has_material_category : IdentifierObject[]
has_specimen_category : IdentifierObject[]
keywords : Keyword[]
label : string
produced_by : SamplingEvent
registrant : Agent
related_resource : SampleRelation[]
sample_identifier : string
sampling_purpose : string
}
click PhysicalSampleRecord href "PhysicalSampleRecord.html" "Documentation"
IdentifierObject --o PhysicalSampleRecord : alternate_identifiers
SpecimenCuration --o PhysicalSampleRecord : curation
IdentifierObject --o PhysicalSampleRecord : has_context_category
IdentifierObject --o PhysicalSampleRecord : has_material_category
IdentifierObject --o PhysicalSampleRecord : has_specimen_category
Keyword --o PhysicalSampleRecord : keywords
SamplingEvent --o PhysicalSampleRecord : produced_by
Agent --o PhysicalSampleRecord : registrant
SampleRelation --o PhysicalSampleRecord : related_resource
class Agent {
affiliation : string
contact_information : string
identifier : uriorcurie
name : string
role : string
}
click Agent href "Agent.html" "Documentation"
class Keyword {
keyword : string
keyword_uri : string
scheme_name : string
scheme_uri : string
}
click Keyword href "Keyword.html" "Documentation"
class IdentifierObject {
identifier : uriorcurie
label : string
scheme_name : string
}
click IdentifierObject href "IdentifierObject.html" "Documentation"
class SamplingSite {
description : string
identifier : uriorcurie
is_part_of : uriorcurie[]
label : string
location : GeospatialCoordLocation
place_name : string[]
}
click SamplingSite href "SamplingSite.html" "Documentation"
GeospatialCoordLocation --o SamplingSite : location
class SamplingEvent {
authorized_by : string[]
description : string
has_feature_of_interest : string
identifier : uriorcurie
label : string
responsibility : Agent[]
result_time : date
sampling_site : SamplingSite
}
click SamplingEvent href "SamplingEvent.html" "Documentation"
Agent --o SamplingEvent : responsibility
SamplingSite --o SamplingEvent : sampling_site
class GeospatialCoordLocation {
elevation : string
latitude : decimal
longitude : decimal
obfuscated : boolean
}
click GeospatialCoordLocation href "GeospatialCoordLocation.html" "Documentation"
class SpecimenCuration {
access_constraints : string[]
curation_location : string
description : string
identifier : uriorcurie
label : string
responsibility : Agent[]
}
click SpecimenCuration href "SpecimenCuration.html" "Documentation"
Agent --o SpecimenCuration : responsibility
class SampleRelation {
description : string
label : string
relationship : string
target : uriorcurie
}
click SampleRelation href "SampleRelation.html" "Documentation"
Schema for documenting physical samples
Schema documentation generated from linkml sources.
Startup schema for iSamples sample registry integration. updated from 0.2 by synchronizing the vocabulary enumerations, change ‘id’ to ‘@id’ and ‘schema’ to ‘$schema’. Schema name is iSamplesSchemaBasic0.2.1.json. Target JSON schema version is http://json-schema.org/draft-07/schema# SMR 2022-10-07. SMR 2023-03-17. Move authorized_by into SamplingEvent, change keywords to list of Keyword objects with string, uri, scheme and scheme URI. Reorder elements in slot list. Update scheme URI to 1.0.
URI: http://resource.isamples.org/schema/1.0 Name: physicalSample
Classes
| Class | Description |
|---|---|
| Agent | object to represent a person who plays a role relative to sample collection o… |
| GeospatialCoordLocation | A physical location in decimal degrees using EPSG:4326 |
| IdentifierObject | object to represent an identified concept; property values from vocabularies … |
| Keyword | a simple string (tag) useful for guiding discovery of the sample, or a scoped… |
| PhysicalSampleRecord | This is a data object that is a digital representation of a physical sample, … |
| SampleRelation | semantic link to other samples or related resources |
| SamplingEvent | Information about the event resulting in the creation of the physical sample |
| SamplingSite | documentation of the site where the sample was collected, wtih place name(s) … |
| SpecimenCuration | Information about the current storage of sample, access to sample, and events… |
Slots
| Slot | Description |
|---|---|
| access_constraints | Cultural, legal, or other policy issues that bear on access to view, borrow, … |
| affiliation | Name of an organization that employes or sponsors a person for the role they … |
| alternate_identifiers | one or more identifiers used to identify the sample in other contexts |
| authorized_by | a list of permits or other formal permission documents under which the sample… |
| complies_with | a list of policies, recommendations, best practices (etc |
| contact_information | e-mail address, telephone number, mailing address, or web site through which … |
| curation | |
| curation_location | Information about where and how the sample is currently stored |
| dc_rights | a statement about various property rights associated with the resource, inclu… |
| description | Free text description of the subject of a triple |
| elevation | Should be a number and Unit of measure, and the vertical reference system |
| has_context_category | Top level context, based on the kind of feature sampled |
| has_feature_of_interest | What does the sample represent |
| has_material_category | The kind of material that constitutes the sample |
| has_specimen_category | The kind of object the specimen is |
| identifier | a string that identifies some resource |
| is_part_of | A link from a SamplingSite to a larger sampling site that spatially contains … |
| keyword | string label for a concept that characterizes the sample in some respect |
| keyword_uri | an identifier for the keyword concept |
| keywords | free text terms or formal categories associate with sample to support discove… |
| label | a human intelligible string used to identify a thing, i |
| latitude | angular coordinate measured positive north from the equator |
| location | geopatial location of site; required default is WGS84 latitude, longitude in … |
| longitude | angular coordinate measured positive eastward from the prime meridian |
| name | string, name of a person |
| obfuscated | Flag to indicate that accuracy of provided coordinate location has been reduc… |
| place_name | one or more names by which the sampling site is known |
| produced_by | object that documents the sampling event–who, where, when the specimen was o… |
| registrant | identification of the agent that registered the sample, with contact informat… |
| related_resource | link to related resource with relationship property to indicate nature of con… |
| relationship | term to identify realationship between host sample and the sample relation ta… |
| responsibility | Agent object includes person name, person identifier, affiliation, or organiz… |
| result_time | Date on which the sample was collected |
| role | term that specifies how a person is related to a sample curation or collectio… |
| sample_identifier | URI that identifies the physical sample described by this record |
| sampling_purpose | term to specify why a sample was collection |
| sampling_site | object that identifies the place where the sample was collected |
| scheme_name | string label for the concept scheme or vocabulary within which the keyword co… |
| scheme_uri | Identifier for the concept scheme or vocabulary within which the keyword conc… |
| target | identifier for the target resource in the relationship |
Enumerations
No enumerations are defined.
Types
| Type | Description |
|---|---|
| xsd:boolean | A binary (true or false) value |
| xsd:string | a compact URI |
| xsd:date | a date (year, month and day) in an idealized calendar |
| linkml:DateOrDatetime | Either a date or a datetime |
| xsd:dateTime | The combination of a date and time |
| xsd:decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci… |
| xsd:double | A real number that conforms to the xsd:double specification |
| xsd:float | A real number that conforms to the xsd:float specification |
| xsd:integer | An integer |
| xsd:string | A string encoding a JSON Path |
| xsd:string | A string encoding a JSON Pointer |
| xsd:string | Prefix part of CURIE |
| shex:nonLiteral | A URI, CURIE or BNODE that represents a node in a model |
| shex:iri | A URI or CURIE that represents an object in the model |
| xsd:string | A string encoding a SPARQL Property Path |
| xsd:string | A character string |
| xsd:time | A time object represents a (local) time of day, independent of any particular… |
| xsd:anyURI | a complete URI |
| xsd:anyURI | a URI or a CURIE |
Subsets
No subsets are defined.