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1049 lines (980 loc) · 30.8 KB
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---
id: https://w3id.org/nfdi4cat/pid4cat-model
name: pid4cat-model
title: pid4cat-model
description: >-
A LinkML model for persistent identifiers for resources in catalysis
(pid4cat). pid4cat are handle based persistent identifiers (PIDs) for digital
or physical resources used in the catalysis research process. PID-related
metadata besides the obligatory landing page URL are stored directly in the
handle records.
The model describes metadata for the PID itself and how to access the
identified resource. It does not describe the resource itself with the
exception of the resource category, which is a high-level description of
what is identified by the pid4cat handle, e.g. a sample or a device.
version: "0.0.0" # Managed by dynamic-versioning. Don't change this line!
todos:
- none
license: MIT
see_also:
- https://nfdi4cat.github.io/pid4cat-model
prefixes:
pid4cat_model: https://w3id.org/nfdi4cat/pid4cat-model/
linkml: https://w3id.org/linkml/
dcterms: https://purl.org/dc/terms/
dcat: https://www.w3.org/ns/dcat#
DataCite: https://purl.org/spar/datacite/
prov: https://www.w3.org/ns/prov#
voc4cat: https://w3id.org/nfdi4cat/voc4cat_
mediatype: https://www.iana.org/assignments/media-types/
default_prefix: pid4cat_model
imports:
- linkml:types
- media_types
# Added to prevent triggering linkML bugs (setting this is quasi standard)
default_range: string
# === C L A S S E S ==========================================================
classes:
# classes for mapping to handle API
HandleAPIRecord:
description: >-
A class representing a handle record query response of the REST (json)
API of a handle server.
slots:
- responseCode
- handle
- values
slot_usage:
handle:
# The pattern should be made more restrictive after agreement on the
# handle-suffix anatomy. The prefix values should also be checked.
# Here is an example for the NFDI4Cat handle servers:
# pattern: '(^21\.T11978\/.*$)|(^21\.11165\/.*$)'
pattern: '^\d{2}\.T?\d{4,}\/.*$'
required: true
values:
required: true
# Activate to validate a pid4cat handle record which has 8 values or
# more.
# minimum_cardinality: 8
HandleRecord:
description: >-
A base class for handle-data classes that represent a handle record in
the same way as in the REST (json) API of a handle server.
slots:
- timestamp
- ttl
- type
slot_usage:
timestamp:
required: true
ttl:
ifabsent: "86400"
type:
description: >-
The type of handledata stored in the handle record.
designates_type: true
required: true
URL:
is_a: HandleRecord
description: >-
The data element in the handle API for the landing page URL.
slots:
- index
- data
slot_usage:
index:
minimum_value: 1
maximum_value: 1
required: true
data:
range: HdlDataUrl
required: true
HdlDataUrl:
description: >-
The data class for the redirect url.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
pattern: '^https?:\/\/.*$'
required: true
EMAIL:
is_a: HandleRecord
description: >-
The data element in the handle API for the contact email.
slots:
- index
- data
slot_usage:
index:
minimum_value: 10
maximum_value: 10
required: true
data:
range: HdlDataContact
required: true
HdlDataContact:
description: >-
The data class for the handle-record contact email.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
pattern: "^\\S+@[\\S+\\.]+\\S+"
required: true
STATUS:
is_a: HandleRecord
description: >-
The data element in the handle API for the PID status information.
slots:
- index
- data
slot_usage:
index:
minimum_value: 11
maximum_value: 11
required: true
data:
range: HdlDataStatus
required: true
HdlDataStatus:
description: >-
The data class for the PID status information.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
range: Pid4CatStatus
required: true
SCHEMA_VER:
is_a: HandleRecord
description: >-
The data element in the handle API for the schema version.
slots:
- index
- data
slot_usage:
index:
minimum_value: 12
maximum_value: 12
required: true
data:
range: HdlDataSchemaVer
required: true
HdlDataSchemaVer:
description: >-
The data class for the schema version.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
pattern: '^v\d+\.\d+\.\d+$'
required: true
METADATA_LICENSE:
is_a: HandleRecord
description: >-
The data element in the handle API for the PID metadata license.
slots:
- index
- data
slot_usage:
index:
minimum_value: 13
maximum_value: 13
required: true
data:
range: HdlDataLicense
required: true
HdlDataLicense:
description: >-
The data class for the PID metadata license.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
equals_string: 'CC0-1.0'
required: true
RESOURCE:
is_a: HandleRecord
description: >-
The data element in the handle API for the resource info.
slots:
- index
- data
slot_usage:
index:
minimum_value: 14
maximum_value: 14
required: true
data:
range: HdlDataResourceInfo
required: true
HdlDataResourceInfo:
description: >-
The data class for the resource info.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
range: ResourceInfo
required: true
RELATED:
is_a: HandleRecord
description: >-
The data element in the handle API for related identifiers.
slots:
- index
- data
slot_usage:
index:
minimum_value: 15
maximum_value: 15
required: true
data:
range: HdlDataRelated
required: true
HdlDataRelated:
description: >-
The data class for related identifiers.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
multivalued: true
range: Pid4CatRelation
CHANGES:
is_a: HandleRecord
description: >-
The data element in the handle API for the change log.
slots:
- index
- data
slot_usage:
index:
minimum_value: 16
maximum_value: 16
required: true
data:
range: HdlDataLog
required: true
HdlDataLog:
description: >-
The data class for the change log.
slots:
- format
- value
slot_usage:
format:
equals_string: 'string'
ifabsent: 'string'
value:
range: LogRecord
multivalued: true
required: true
HandleRecordContainer:
description: >-
A container for all HandleRecords.
tree_root: true
attributes:
contains_pids:
multivalued: true
inlined: true
inlined_as_list: true
range: HandleAPIRecord
description: >-
The HandleRecords contained in the container.
Pid4CatRelation:
description: >-
Data class for a relation to another resource identified by a
pid4cat handle or another PID type.
slots:
- relation_type
- related_identifier
- datetime_log
ResourceInfo:
description: >-
Data class to hold information about the resource and its representation.
slots:
- label
- description
- resource_category
- representation_variants
slot_usage:
resource_category:
required: true
representation_variants:
required: true
LogRecord:
description: >-
Data class for a change log of modification made on a pid4cat handle
record starting from its registration.
slots:
- datetime_log
- has_agent
- changed_field
- description
slot_usage:
datetime_log:
required: true
has_agent:
required: true
changed_field:
required: true
description: # Should it be set as required?
# required: true
Agent:
class_uri: prov:Agent
description: >-
Data class for a person who plays a role relative to PID creation or
curation.
slots:
- name
- email_address
- orcid
- affiliation_ror
- role
slot_usage:
name:
required: true
email_address:
pattern: '^\S+@[\S+\.]+\S+'
required: true
orcid:
# https://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier
pattern: '^\d{4}-\d{4}-\d{4}-\d{3}[0-9X]$'
affiliation_ror:
# https://ror.readme.io/docs/identifier
pattern: '^https:\/\/ror\.org\/0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$'
role:
required: true
RepresentationVariant:
description: >-
Data class for representations of the resource in other media types than
text/html which is the default for landing_page_url.
slots:
- variant_url
- media_type
- encoding_format
- size
slot_usage:
media_type:
# Setting "required: true" causes an exception with linkML 1.8.5
# ValueError: Example tests/data/valid\HandleAPIRecord-001.yaml failed
# validation: unhashable type: 'MediaTypesEnum'
# required: true
RelatedIdentifier:
description: >-
A base class for all types of related identifiers.
attributes:
type:
description: >-
The type of the identifier.
designates_type: true
required: true
PurlIdentifier:
is_a: RelatedIdentifier
description: >-
A PURL (permanent uniform resource locator).
slots:
- resolving_url
slot_usage:
resolving_url:
pattern: '^https:\/\/(purl|pida|w3id)\.org\/.*$'
required: true
DoiIdentifier:
is_a: RelatedIdentifier
description: >-
A digital object identifier (DOI).
slots:
- resolving_url
- identifier
slot_usage:
identifier:
pattern: '^10\.\d{4,}\/.*$'
resolving_url:
pattern: '^https:\/\/doi\.org\/10.*$'
required: true
HandleIdentifier:
is_a: RelatedIdentifier
description: >-
A handle identifier.
slots:
- resolving_url
- identifier
slot_usage:
# The patterns allow test handles like "21.T11978/4cat-demo/3dks-27xc"
# In contrast, production handles have only numbers in the prefix.
identifier:
pattern: '^\d{2}\.T?\d{4,}\/.*$'
resolving_url:
pattern: '^https:\/\/hdl\.handle\.net\/\d{2}\.T?\d{4,}\/.*$'
required: true
ArkIdentifier:
is_a: RelatedIdentifier
description: >-
An ARK (Archival Resource Key).
slots:
- identifier
- resolving_url
slot_usage:
identifier:
pattern: '^ark:\/\d{5}/.*$'
resolving_url:
pattern: '^https?:\/\/.*\/ark:\/\d{5}/.*$'
required: true
UrnIdentifier:
is_a: RelatedIdentifier
description: >-
A URN (Uniform Resource Name).
slots:
- identifier
slot_usage:
identifier:
pattern: '^urn:[a-zA-Z0-9][a-zA-Z0-9-]{0,31}:[^\s]*$'
required: true
GtinIdentifier:
is_a: RelatedIdentifier
description: >-
A Global Trade Item Number (GTIN) previously called European Article
Number (EAN) often encoded as EAN13 barcode. The identifier is used to
identify products. GTINs don't have a resolvable URL.
slots:
- identifier
slot_usage:
identifier:
pattern: '^\d{13}$'
required: true
ExampleIdentifier:
is_a: RelatedIdentifier
description: >-
An example.org test identifier.
slots:
- identifier
- resolving_url
slot_usage:
identifier:
pattern: '^ex:.*$'
resolving_url:
pattern: '^https?:\/\/(.+\.)?example.(org|com)\/.*$'
Pid4CatRecord:
description: >-
A class representing pid4cat identifiers with its metadata as objects.
This is a neutral object-oriented representation that does not mirror the
record structure of the handle system but is provided as representation
that is more convenient to use in programming languages.
slots:
- landing_page_url
- status
- schema_version
- metadata_license
- curation_contact
- resource_info
- related_identifiers
- change_log
slot_usage:
landing_page_url:
pattern: '^https?:\/\/.*$'
required: true
status:
required: true
schema_version:
required: true
metadata_license:
equals_string: CC0-1.0
required: true
curation_contact:
pattern: "^\\S+@[\\S+\\.]+\\S+"
required: true
resource_info:
required: true
related_identifiers:
multivalued: true
change_log:
required: true
multivalued: true
# === S L O T S ==============================================================
slots:
# Slots for HandleAPIRecord
responseCode:
range: integer
# naming the slot "response_code" and defining "responseCode" as an alias
# lead to failures in example data validation with example_runner.
# aliases: responseCode
description: The response code of the handle API.
handle:
range: string
description: The handle of the pid4cat record.
identifier: true
values:
range: HandleRecord
multivalued: true
description: The values of the pid4cat record.
# Slots for HandleRecord and its sub-classes
timestamp:
range: datetime
description: >-
The iso datetime for the last update of the handle data.
ttl:
range: integer
description: >-
A time to live in seconds for the handle record.
Typically: 86400 => 1 day
type:
range: string
description: The type of the handle record data.
index:
range: integer
description: The index of the handle record.
data:
description: The data in the handle record.
# Slots for HdlData* classes
format:
range: string
description: The format of the handle data.
value:
description: The value of the handle data.
range: string
# Slots for Pid4CatRelation
relation_type:
range: RelationType
description: Relation type between the resources.
related_identifier:
range: RelatedIdentifier
description: The related identifier.
datetime_log:
range: datetime
description: The date and time of a log record.
# Slots for ResourceInfo
label:
range: string
description: A human-readable name for a resource.
description:
range: string
description: A human-readable description for a resource.
resource_category:
range: ResourceCategory
description: The category of the resource.
representation_variants:
range: RepresentationVariant
multivalued: true
description: >-
The representations of the resource in other media types than text/html.
# Slots for LogRecord
changed_field:
range: ChangeLogField
description: The field that was changed.
has_agent:
range: Agent
description: The person who registered or modified the PID record.
# Slots for Agent
name:
range: string
description: The name of the agent that created or modified the PID record.
email_address:
range: string
description: >-
Email address of the agent that created or modified the PID record.
orcid:
range: string
description: The ORCID of the person
affiliation_ror:
range: uri
description: The ROR of the agent's affiliation.
role:
range: Pid4CatAgentRole
description: The role of the agent relative to the resource
# Slots for RepresentationVariants
media_type:
range: MediaTypesEnum
description: >-
The media type of the representation as defined by
[IANA](https://www.iana.org/assignments/media-types/media-types.xhtml)
encoding_format:
range: string
description: >-
The encoding of the representation.
https://encoding.spec.whatwg.org/#names-and-labels
size:
range: integer
minimum_value: 0
description: The size of the representation in bytes.
variant_url:
range: uri
description: The URL of the representation variant.
# Slots for RelatedIdentifier
resolving_url:
range: uri
description: The URL that resolves the identifier.
identifier:
range: string
description: The identifier in recommended notation.
# Slots for Pid4CatRecord
landing_page_url:
range: string
description: >-
The URL of the landing page of the resource identified by the PID.
status:
range: Pid4CatStatus
description: >-
The status of the pid4cat record. The status is set to "SUBMITTED"
when the handle is reserved but the resource is not yet linked.
The status is set to "REGISTERED" when the handle is linked to a
concrete resource.
schema_version:
range: string
description: >-
The version of the pid4cat-model used to create the pid4cat record.
metadata_license:
range: string
description: >-
The license of the metadata of the pid4cat record. The license is
set to "CC0-1.0" by default.
curation_contact:
range: string
description: >-
The email address of the person responsible for the curation of the
pid4cat record.
resource_info:
range: ResourceInfo
description: >-
The resource info of the pid4cat record. The resource info contains
information about the resource identified by the PID.
related_identifiers:
range: Pid4CatRelation
multivalued: true
description: >-
The related identifiers for the pid4cat record. The related
identifiers are used to link the pid4cat record to other resources.
change_log:
range: LogRecord
description: >-
The change log of the pid4cat record. The change log contains
information about the changes made to the pid4cat record.
# === E N U M S ==============================================================
enums:
# Enumerations use singular form for names
# "meaning" should refer to URIS from DCMI vocabulary or Voc4Cat if possible.
# https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7
# https://w3id.org/nfdi4cat/voc4cat
ResourceCategory:
description: >-
The ResourceCategory expresses for which type of resource the PID is used,
e.g. if the PID is for a sample or a device.
# Could reference to parent concept voc4cat:0005011
# but unclear how/if it is possible in current LinkML version (1.8.5).
permissible_values:
COLLECTION:
description: >-
A collection is a group of resources and/or other collections.
meaning: voc4cat:0005012
close_mappings:
- http://purl.org/dc/dcmitype/Collection
SAMPLE:
description: >-
A representative part of a material of interest on which observations
are made.
meaning: voc4cat:0005013
close_mappings:
- voc4cat:0005056
broad_mappings:
- https://www.w3.org/ns/sosa/Sample
MATERIAL:
description: A material used in the research process (except samples).
meaning: voc4cat:0005014
DEVICE:
description: >-
A physical device used in a research or manufacturing process.
meaning: voc4cat:0005015
DATA_OBJECT:
description: >-
A collection of data available for access or download.
A data object might be a data file, a data set, a data collection.
meaning: voc4cat:0005016
close_mappings:
- dcat:dataset
DATA_SERVICE:
description: >-
An organized system of operations that provide data processing
functions or access to datasets.
meaning: voc4cat:0005017
close_mappings:
- dcat:DataService
RelationType:
description: >-
The type of relation between two resources referenced by their PIDs.
# could reference to parent concept voc4cat:0005018
# but unclear how/if it is possible in current LinkML version (1.8.5).
permissible_values:
# We adapt most DataCite relations (Metadata Schema V 4.6) except for:
# - IsReviewedBy, Reviews,
# - IsDescribedBy, Describes,
# - IsTranslationOf, HasTranslation
IS_CITED_BY:
description: The resource is cited by another resource.
meaning: voc4cat:0005019
CITES:
description: The resource cites another resource.
meaning: voc4cat:0005020
IS_SUPPLEMENT_TO:
description: The resource is supplemented by another resource.
meaning: voc4cat:0005021
IS_SUPPLEMENTED_BY:
description: The resource supplements another resource.
meaning: voc4cat:0005022
IS_CONTINUED_BY:
description: The resource is continued by another resource.
meaning: voc4cat:0005023
CONTINUES:
description: The resource continues another resource.
meaning: voc4cat:0005024
HAS_METADATA:
description: The resource has metadata in another resource.
meaning: voc4cat:0005025
IS_METADATA_FOR:
description: The resource is metadata for another resource.
meaning: voc4cat:0005026
HAS_VERSION:
description: >-
The resource has a version.
This is useful to express the relation between a abstract resource
to its versioned instances, for example,
"Python has_version Python 3.12".
meaning: voc4cat:0005027
close_mappings:
- dcterms:hasVersion
IS_VERSION_OF:
description: >-
The resource is a version of another resource.
This is useful to refer to an abstract resource that has different
versions, for example, "Python 3.12 is a version of Python".
meaning: voc4cat:0005028
close_mappings:
- dcterms:isVersionOf
IS_NEW_VERSION_OF:
description: >-
The resource is a new version of another versioned resource.
This is useful to refer between versioned resources, for example,
"Python 3.12.1 is_new_version_of Python 3.12.0".
meaning: voc4cat:0005029
IS_PREVIOUS_VERSION_OF:
description: >-
The resource is a previous version of another versioned resource.
This is useful to refer between versioned resources, for example,
"Python 3.12.0 is_previous_version_of Python 3.12.1".
meaning: voc4cat:0005030
IS_PART_OF:
description: >-
The resource is part of another resource.
This relation applies to container-contained type relationships.
If the relation refers to publishing one resource as part of
another resource, use "IS_PUBLISHED_IN" instead. If the relation
refers to a versioned resource and non-versioned resource,
use "IS_VERSION_OF" instead.
meaning: voc4cat:0005031
close_mappings:
- dcterms:isPartOf
HAS_PART:
description: >-
The resource has part another resource.
This relation applies to container-contained type relationships.
If the relation refers to publishing one resource as part of
another resource, "IS_PUBLISHED_IN" instead. If the relation
refers to a versioned resource and non-versioned resource,
use "HAS_VERSION" instead.
meaning: voc4cat:0005032
close_mappings:
- dcterms:hasPart
IS_PUBLISHED_IN:
description: >-
The resource is published in another resource.
A resource A that is_published_in a resource B is independent
from other resources published in the same resource B.
meaning: voc4cat:0005033
IS_REFERENCED_BY:
description: The resource is referenced by another resource.
meaning: voc4cat:0005034
close_mappings:
- dcterms:isReferencedBy
REFERENCES:
description: The resource references another resource.
meaning: voc4cat:0005035
IS_DOCUMENTED_BY:
description: The resource is documented by another resource.
meaning: voc4cat:0005036
DOCUMENTS:
description: The resource documents another resource.
meaning: voc4cat:0005037
IS_COMPILED_BY:
description: >-
The resource is compiled by another resource.
Resources may be text or software. The compiler may be a computer
program or a person.
meaning: voc4cat:0005038
COMPILES:
description: >-
The resource compiles another resource.
Resources may be text or software. The compiler may be a computer
program or a person.
meaning: voc4cat:0005039
IS_VARIANT_FORM_OF:
description: >-
The resource is variant form of another resource.
This may be used e.g. for relating architecture-specific builds
of a software program to a source-code release. It may also
be used to express the relation between data in different
formats (e.g. PNG, JPEG) of the same image.
meaning: voc4cat:0005040
IS_ORIGINAL_FORM_OF:
description: >-
The resource is original form of another resource.
This may be used e.g. for relating architecture-specific builds
of a software program to a source-code release. It may also
be used to express the relation between data in different
formats (e.g. PNG, JPEG) of the same image.
meaning: voc4cat:0005041
IS_IDENTICAL_TO:
description: >-
The resource is identical to another resource.
May be used to indicate the relationship between an exact copy of a
resource that is published at another location.
meaning: voc4cat:0005042
IS_DERIVED_FROM:
description: >-
The resource is derived from another resource.
This may be used for relating a new dataset created by data
processing to its original source dataset.
For samples it may express the relation between the original sample
and another sample derived from it by physical or chemical treatment.
meaning: voc4cat:0005043
IS_SOURCE_OF:
description: >-
The resource is source of another resource.
This may be used for example to express the relation between a
source dataset and a new dataset derived from it by data processing.
For samples it may express the relation between a sample processed
by physical or chemical treatment and the original sample.
meaning: voc4cat:0005044
IS_COLLECTED_BY:
description: >-
The resource is collected by another resource.
May be used to indicate the relationship between a dataset and an
instrument that is used to collect, measure, obtain, or observe data.
meaning: voc4cat:0005045
COLLECTS:
description: >-
The resource collects another resource.
May be used to indicate the relationship between an instrument and
where it has been used to collect, measure, obtain, or observe data.
meaning: voc4cat:0005046
IS_REQUIRED_BY:
description: The resource is required by another resource.
meaning: voc4cat:0005047
close_mappings:
- dcterms:isRequiredBy
REQUIRES:
description: The resource requires another resource.
meaning: voc4cat:0005048
close_mappings:
- dcterms:requires
IS_OBSOLETED_BY:
description: >-
The resource is obsoleted by another resource.
meaning: voc4cat:0005049
close_mappings:
- dcterms:replacedBy
OBSOLETES:
description: The resource obsoletes another resource.
meaning: voc4cat:0005050
close_mappings:
- dcterms:replaces
CONFORMS_TO:
description: >-
An established standard to which the described resource conforms.
This relation should be used to indicate the model, schema, ontology,
or profile that the resource content conforms to.
meaning: voc4cat:0005059
close_mappings:
- dcterms:conformsTo
Pid4CatStatus:
description: >-
The usage status of the pid4cat record.
# We could reference to the parent concept (voc4cat:0005051) but it is
# unclear how/if this is possible with current LinkML version (1.8.5).
permissible_values:
SUBMITTED: