has_qualified_identifers_schema.yaml

name: has-qualified-identifers-schema
see_also:
- https://turbomam.github.io/reactions-for-owl
- https://gist.githubusercontent.com/turbomam/56956b2d7761fc669d2e8ab15e5cb1f0/raw/64f40292b81d3e04f873e076ae66756059651654/has_qualified_identifers_schema.yaml
id: http://example.com/has_qualified_identifers_schema

prefixes:
  has_qualified_identifers: http://example.com/has_qualified_identifers_schema/
  linkml: https://w3id.org/linkml/
  example: https://example.org/
  PATO: http://purl.obolibrary.org/obo/PATO_
  xsd: http://www.w3.org/2001/XMLSchema#
  shex: http://www.w3.org/ns/shex#
  schema: http://schema.org/

imports:
  - linkml:types

default_prefix: has_qualified_identifers
default_range: string

enums:
  PersonStatus:
    permissible_values:
      ALIVE:
        description: the person is living
        meaning: PATO:0001421
      DEAD:
        description: the person is deceased
        meaning: PATO:0001422
      UNKNOWN:
        description: the vital status is not known
        todos:
        - map this to an ontology
slots:
  external_identifier_value:
    description: This is the value of the identifier used in some external system
    comments:
    - Using a uriorcurie range ensures that we can consistently and atomically assert
      the source of the mapping and the local identifier (without requiring even more
      classes).
    - Using a uriorcurie range does require that we define prefixes for all external
      systems that we might map to. Prefixes from an external system like are strongly
      preferred. Ideally the CURIes expand to a resolvable URL, but this is not required.
    - '{''using curie as the range leads to "WARNING:root:UNKNOWN'': ''Curie // <class
      \''linkml_runtime.utils.yamlutils.extended_str\''>" when building the project...
      maybe from gen-owl?''}'
    range: uriorcurie
  provenance:
    description: comments about whether the mapping is 1:1 (from NMDC to the external
      system), many:1, 1:many, or many:many. - would we ever assert a many:many mapping?
      - use an enumeration and add some other comment-like string field?
    range: string
  assertion_date:
    description: A string representation of an ISO-8601 data when the mapping was
      asserted.
    comments:
    - provide a pattern? see if date/time objects work in LinkML now?
    range: string
  has_qualified_identifiers:
    description: A link from any (NamedTing?) in the NMDC database to an external
      identifier This would replace alternative identifiers, related identifiers,
      etc.
    multivalued: true
    range: QualifiedIdentifier
  id:
    description: A unique identifier for a thing
    slot_uri: schema:identifier
    identifier: true
    range: uriorcurie
  name:
    description: A human-readable name for a thing
    slot_uri: schema:name
  description:
    description: A human-readable description for a thing
    slot_uri: schema:description
  primary_email:
    description: The main email address of a person
    slot_uri: schema:email
  birth_date:
    description: Date on which a person is born
    slot_uri: schema:birthDate
    range: date
  age_in_years:
    description: Number of years since birth
    range: integer
  vital_status:
    description: living or dead status
    range: PersonStatus
classes:
  NamedThing:
    description: A generic grouping for any identifiable entity
    slots:
    - id
    - has_qualified_identifiers
    - name
    - description
    class_uri: schema:Thing
  Person:
    description: Represents a Person
    is_a: NamedThing
    slots:
    - primary_email
    - birth_date
    - age_in_years
    - vital_status
    slot_usage:
      primary_email:
        name: primary_email
        pattern: ^\S+@[\S+\.]+\S+
  Database:
    attributes:
      person_set:
        name: person_set
        from_schema: http://example.com/has_qualified_identifers_schema
        multivalued: true
        range: Person
        inlined: true
        inlined_as_list: true
    tree_root: true
  QualifiedIdentifier:
    description: A non-NMDC identifier for something that is also present in the NMDC
      database. Provides support for saying when the identifier was asserted and assessments
      about the quality of the identifier.
    slots:
    - external_identifier_value
    - provenance
    - assertion_date
    class_uri: linkml:QualifiedIdentifier

person_with_qualified_identifers_data.yaml

id: example:ck1
has_qualified_identifiers:
- external_identifier_value: example:superman1
  provenance: related
  assertion_date: '2021-01-01'
- external_identifier_value: example:kalel1
  provenance: alternative
  assertion_date: '2021-01-01'
name: Clark Kent
primary_email: [email protected]
age_in_years: 33

• create a new directory
• enter new directory
• deactivate any virtual environments
• python -m venv venv
• source venv/bin/activate
• curl both files
• gen-linkml --format yaml --no-materialize-attributes has_qualified_identifers_schema.yaml
• linkml-validate --schema has_qualified_identifers_schema.yaml --target-class Person person_with_qualified_identifers_data.yaml
• linkml-convert --output person_with_qualified_identifers_data.yaml --schema has_qualified_identifers_schema.yaml --target-class Person person_with_qualified_identifers_data.json