id: https://concepts.trr379.de/s/research-information/unreleased
name: trr379-research-information-schema
version: UNRELEASED
status: eunal:concept-status/DRAFT
title: Data model for capturing information on TRR379 research (progress)
description: |
  This schema is using the FLAT approach (Flexbile Low-complexity
  Annotation Technique) and is geared toward metadata entry and
  submission for pooling information across consortium sites and
  partners.

  More information may be available on the schema's [about page](about).

  The schema definition is available as

  - [JSON-LD context](../unreleased.context.jsonld)
  - [LinkML YAML](../unreleased.yaml)
  - [LinkML YAML (static/resolved)](../unreleased.static.yaml)
  - [OWL TTL](../unreleased.owl.ttl)
  - [SHACL TTL](../unreleased.shacl.ttl)

comments:
  - ALL CONTENT HERE IS UNRELEASED AND MAY CHANGE ANY TIME

license: MIT

prefixes:
  CiTO: http://purl.org/spar/cito/
  ISSN: http://identifiers.org/issn/
  ODRL: http://www.w3.org/ns/odrl/2/
  bibo: http://purl.org/ontology/bibo/
  # TODO preliminary definition, pointing to a future resolver
  datalad: https://pid.datalad.org/datasets/
  dash: http://datashapes.org/dash#
  dcat: http://www.w3.org/ns/dcat#
  dcterms: http://purl.org/dc/terms/
  # TODO preliminary definition, pointing to a future resolver
  dldi: https://pid.datalad.org/distributions/
  dlschemas: https://concepts.datalad.org/s/
  dlthings: https://concepts.datalad.org/s/things/unreleased/
  dlvocab: https://concepts.datalad.org/vocab/
  doi: https://doi.org/
  eunal: http://publications.europa.eu/resource/authority/
  ex: http://example.org/
  fabio: http://purl.org/spar/fabio/
  foaf: http://xmlns.com/foaf/0.1/
  FRAPO: http://purl.org/cerif/frapo/
  geodata: http://sws.geonames.org/
  gepris: https://gepris.dfg.de/gepris/
  linkml: https://w3id.org/linkml/
  marcrel: http://id.loc.gov/vocabulary/relators/
  nfo: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#
  obo: http://purl.obolibrary.org/obo/
  orcid: https://orcid.org/
  owl: http://www.w3.org/2002/07/owl#
  prov: http://www.w3.org/ns/prov#
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  ror: https://ror.org/
  rrid: "https://scicrunch.org/resolver/RRID:"
  schema: http://schema.org/
  sct: http://snomed.info/id/
  sh: http://www.w3.org/ns/shacl#
  shaclvue: https://concepts.datalad.org/ns/shaclvue/
  sio: http://semanticscience.org/resource/
  skos: http://www.w3.org/2004/02/skos/core#
  spdx: http://spdx.org/rdf/terms#
  spdxlic: https://spdx.org/licenses/
  vcard: http://www.w3.org/2006/vcard/ns#
  xsd: http://www.w3.org/2001/XMLSchema#
  trr379: https://trr379.de/ns/
  trr379ri: https://concepts.trr379.de/s/research-information/unreleased/
  trr379root: https://trr379.de/
  trr379schemas: https://concepts.trr379.de/s/

default_prefix: trr379ri

emit_prefixes:
  - dldi
  - dlthings
  - rdf
  - rdfs
  - skos
  - xsd
  # a bunch more that are not needed for the structural aspects
  # of the schema, but for records using the schema
  - ISSN
  - bibo
  - datalad
  - dcterms
  - dldi
  - doi
  - geodata
  - obo
  - orcid
  - ror
  - rrid
  - schema
  - shaclvue
  - sio
  - trr379
  - trr379root

imports:
  - dlschemas:things-data/unreleased
  - dlschemas:things-files/unreleased
  - dlschemas:things-publications/unreleased
  - dlschemas:things-resources/unreleased
  - dlschemas:things-prov/unreleased
  - dlschemas:things-social/unreleased
  - dlschemas:things-study/unreleased
  - dlschemas:things-rules/unreleased

slots:
  application_deadline:
    title: Application deadline
    description: >-
      The date by which an application, for example a job application,
      a fellowship application or a grant application, has to be submitted
      if it is to be considered for acceptance or funding.
    range: W3CISO8601

  entity:
    description: >-
      An entity is a physical, digital, conceptual, or other kind of
      thing with some fixed aspects; entities may be real or imaginary.
    range: Thing
    notes:
      - This property exists, because in some cases the needs to be
        an `object` and an additional property that broadly use a
        range `Thing`. The concrete, initial use case was PROV's
        Communication.


classes:
  # Classes here are grouped by their nature:
  # - Things with a provenance interface
  # - Thing that are "classifiers" (i.e., tags) without a provenance interface
  # - Non-Things, such as association classes
  #
  # otherwise the order is alphanumeric

  #
  #Things with a provenance interface
  #
  TRR379Accolade:
    is_a: Thing
    mixins:
      - EntityMixin
    title: Accolade
    description: >-
      An award, prize, or other honor received in recognition of an achievement.
    slots:
      - title

  TRR379Activity:
    is_a: Thing
    mixins:
      - ActivityMixin
    title: Activity
    description: >-
      An activity is something that occurs over a period of time and acts upon
      or with entities; it may include consuming, processing, transforming,
      modifying, relocating, using, or generating entities.
    slots:
      - name
      - part_of
    slot_usage:
      part_of:
        range: TRR379Activity
        multivalued: true
    broad_mappings:
      - obo:BFO_0000015
    exact_mappings:
      - prov:Activity

  TRR379Competition:
    is_a: Thing
    mixins:
      - ActivityMixin
    title: Competition
    description: >-
      A process where multiple agents compete for a resource, such as funding,
      recognition, or participation.
    slots:
      - application_deadline
      - title
    slot_usage:
      kind:
        range: TRR379CompetitionType
      about:
        recommended: true
        title: Topic(s)
        description: >-
          Topics related to this competition.
        range: TRR379Topic
        multivalued: true
      associated_with:
        multivalued: true
        inlined_as_list: true
      informed_by:
        range: TRR379Communication
        multivalued: true
        inlined_as_list: true
      ended:
        title: End
        description: >-
          The conclusion of the competition, typically the point of decision-making, or
          announcement of the winners.
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true
    narrow_mappings:
      - FRAPO:FundingProgramme

  TRR379DataItem:
    is_a: DataItem
    mixins:
      - EntityMixin
    title: Data item
    description: >-
      An information content entity that is intended to be a truthful statement about
      something (modulo, e.g., measurement precision or other systematic errors) and
      is constructed/acquired by a method which reliably tends to produce
      (approximately) truthful statements.

      This is a conceptual entity. A single data item might be available in more than
      one representation, with differing formats, and serializations.
    slot_usage:
      part_of:
        range: TRR379Dataset
        multivalued: true
      kind:
        range: TRR379DataType

  TRR379Dataset:
    is_a: Dataset
    title: Dataset
    mixins:
      - EntityMixin
    description: >-
      A collection of data, published or curated by a single agent. This is a
      conceptual entity. A single dataset might be available in more than
      one representation, with differing schematic layouts, formats, and
      serializations.
    slots:
      - rules
    slot_usage:
      part_of:
        range: TRR379Dataset
        multivalued: true
      attributed_to:
        title: Contributors
        multivalued: true
        inlined_as_list: true
      generated_by:
        multivalued: true
        inlined_as_list: true
      derived_from:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Depiction:
    is_a: Thing
    mixins:
      - EntityMixin
    title: Depiction
    description: >-
      Reference conveyed through pictures.

      This is a conceptual entity. A single depiction can be available,
      for example, as a digital images in various (file) formats.
    slots:
      # e.g. passport picture, social media card, ...
      - conforms_to
      - distributions
      - rules
    slot_usage:
      kind:
        # portrait photo, oil painting, figure, clipart
        range: TRR379DepictionType
      distributions:
        range: TRR379File
        multivalued: true
      conforms_to:
        range: Convention
        multivalued: true

  TRR379File:
    is_a: File
    mixins:
      - EntityMixin
    title: File
    description: >-
      A specific representation of a data item, which may come in the form of an electronic file,
      or an archive or (also) a directory comprising many files.
    slots:
      - conforms_to
      - rules
    slot_usage:
      kind:
        range: TRR379DataType
      distribution_of:
        multivalued: true
      conforms_to:
        range: Convention
        multivalued: true
      generated_by:
        # one and the same file content can be produced in different ways
        # (for an extreme case, think "empty file")
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Document:
    is_a: Document
    mixins:
      - EntityMixin
    title: Document
    description: >-
      A conceptual entity representing things which a, broadly conceived, "documents. This includes non-textual things like images. A conceputal document is to be distinguished from its physical, or electronic distributions.
    slots:
      - rules
      - distributions
    slot_usage:
      kind:
        title: Document type
        description: >-
          The type of this document, e.g. journal article, book, webpage
        range: TRR379BibliographicType
      part_of:
        multivalued: true
      attributed_to:
        title: Contributors
        multivalued: true
        inlined_as_list: true
      generated_by:
        multivalued: true
        inlined_as_list: true
      derived_from:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Grant:
    is_a: Grant
    mixins:
      - EntityMixin
    title: Grant
    description: >-
      A grant, typically financial or otherwise quantifiable, resources.
    slots:
      - rules
    slot_usage:
      part_of:
        range: TRR379Grant
        multivalued: true
      attributed_to:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Instrument:
    is_a: Instrument
    mixins:
      - EntityMixin
    title: Instrument
    description: >-
      A thing that enables an agent to perform an action. This is typically a device (e.g., a machine to perform a particular type of measurement), but it can also be a questionnaire that is used to perform a particular kind of assessment. An instrument is typically not a "reagent".
    slots:
      - part_of
      - rules
    slot_usage:
      kind:
        title: Instrument type
        description: >-
          The type of this instrument, e.g. microscope, software, chainsaw
        range: TRR379InstrumentType
      part_of:
        range: TRR379Instrument
        multivalued: true
      attributed_to:
        multivalued: true
        inlined_as_list: true
      generated_by:
        multivalued: true
        inlined_as_list: true
      alternate_of:
        range: Thing
        multivalued: true
      specialization_of:
        range: Thing
        multivalued: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Organization:
    is_a: Organization
    mixins:
      - AgentMixin
    title: Organization
    description: >-
      A social or legal institution such as a company, a society, or a university.
    slot_usage:
      part_of:
        description: >-
          An organization that the subject is part of.
        range: TRR379Organization
        multivalued: true
      delegated_by:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Person:
    is_a: Person
    mixins:
      - AgentMixin
    title: Person
    description: >-
      Person agents are people, alive, dead, or fictional.
    slots:
      - nickname
      - depiction
    slot_usage:
      depiction:
        title: Photo
        range: TRR379Depiction
        multivalued: true
      delegated_by:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Project:
    is_a: Project
    title: Project
    mixins:
      - ActivityMixin
    description: >-
      A collective endeavour of some kind. Typically it is a planned process that is undertaken or attempted to meet some requirement, or to achieve a particular goal.
    slots:
      - part_of
    slot_usage:
      part_of:
        range: TRR379Project
        multivalued: true
      associated_with:
        multivalued: true
        inlined_as_list: true
      used:
        multivalued: true
        inlined_as_list: true
      informed_by:
        range: TRR379Communication
        multivalued: true
        inlined_as_list: true
      started:
        title: Start
      ended:
        title: End
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Publication:
    is_a: Publication
    mixins:
      - EntityMixin
    title: Publication
    description: >-
      A resource that is the output of a publishing process.
    slots:
      - rules
    slot_usage:
      kind:
        title: Publication type
        description: >-
          The type of this publication, e.g. journal article, book, webpage
        range: TRR379BibliographicType
      title:
        description: >-
          The full title of the publication.
        required: false
      description:
        title: Abstract
      published_at:
        range: TRR379PublicationVenue
      locator:
        title: Location within publication venue
        description: >-
          A descriptive identifier that the publication within the
          venue it was published at. For a journal article, this would
          be a volume and/or page range. Format according to the conventions
          of the publication venue.
      about:
        recommended: true
        title: Topic(s)
        description: >-
          Topics covered by this publication.
        range: TRR379Topic
        multivalued: true
      date_published:
        range: W3CISO8601
        description: >-
          The date when a publication became available at the publication venue.
      attributed_to:
        multivalued: true
        inlined_as_list: true
        title: Contributors
      generated_by:
        multivalued: true
        inlined_as_list: true
      influenced_by:
        range: TRR379Influence
        multivalued: true
        inlined_as_list: true

  TRR379Study:
    is_a: Study
    mixins:
      - EntityMixin
    title: Study
    description: >-
      A planned process that consists of parts: planning, study design
      execution, documentation and which produce conclusion(s). An investigational
      endeavour that involves research, enabled by a project. The study
      relates to the scholarly and practical aspects of conducting the research
      itself, including the hypotheses being investigated, the data being
      gathered and analysed, the interpretations being drawn from the data,
      and the results obtained. In contrast, a project that enables it
      encompasses the administrative aspects of undertaking the endeavour,
      including the funding obtained, the people involved, and the management
      of the project in terms of deadlines and deliverables.
    slots:
      # for stuff like "secret" subject identifiers imposed by DUAs
      - rules
    slot_usage:
      dimensions:
        range: TRR379Concept
      factors:
        range: TRR379Concept
      kind:
        range: TRR379SubjectType

  TRR379Subject:
    is_a: Subject
    mixins:
      - EntityMixin
    title: Subject
    description: >-
      A subject is an entity being investigated in a study.
      This is a contextual entity. One and the same individual can be different
      subjects in two different studies.
    slots:
      # for stuff like "secret" subject identifiers imposed by DUAs
      - rules
    slot_usage:
      study:
        range: TRR379Study
      kind:
        range: TRR379SubjectType

  # Thing that are "classifiers" (i.e., tags) without a provenance interface
  #
  TRR379AgentRole:
    is_a: Thing
    title: Agent role
    description: >-
      A role is the function of an agent with respect to a subject,
      in the context of an attribution.
    slots:
      - name
    broad_mappings:
      - prov:Role
      - dcat:Role

  TRR379BibliographicType:
    is_a: Thing
    title: Bibliographic type
    description: >-
      Type of a publication or document, e.g., journal article, book, or webpage.

  TRR379CompetitionType:
    is_a: Thing
    title: Competition type
    description: >-
      Type of a competitions, e.g., call for proposals, horse race, job opening.

  TRR379Concept:
    is_a: Thing
    title: Concept
    description: >-
      An idea or notion; a unit of thought.

      In the context of a study, this can be a tag associated with a
      categorical, independent variable in a study design, an
      investigative role (e.g., treatments), or an organizational
      nature (e.g., site labels), or a dependent or outcome variable.

      `Concept` is related to `Topic`. However a concept is more focused
      and more clearly delineated in comparison.
    comments:
      - The relationship of a focused concept with the broader concept
        can be described via `broader_mappings`.
    slots:
      - title

  TRR379DataType:
    is_a: Thing
    title: Data type or format
    description: >-
      Type of an data item.
    slots:
      - version_of
    slot_usage:
      version_of:
        title: Variant of
        range: TRR379DataType
    broad_mappings:
      - dcterms:format
    narrow_mappings:
      # Electronic File Format
      - obo:NCIT_C171252
      # Data Type
      - obo:NCIT_C42645
      # Electronic File Content Type
      - obo:NCIT_C172272

  TRR379DepictionType:
    is_a: Thing
    title: Depiction type
    description: >-
      Type of a depiction.

  TRR379InstrumentType:
    is_a: Thing
    title: Instrument type
    description: >-
      Type of an instrument.

  TRR379Objective:
    is_a: Thing
    title: Objective
    description: >-
      A proposition that indicates a planned or anticipated outcome.
    slots:
      - title
      - part_of
      - depends_on
    slot_usage:
      part_of:
        range: TRR379Objective
        multivalued: true
      depends_on:
        range: TRR379Objective

  TRR379PublicationVenue:
    is_a: Thing
    title: Publication venue
    description: >-
      "Place" of a publication, e.g., a journal, a website, an edited collection.
    slots:
      - title
      - kind
    slot_usage:
      title:
        description: >-
          The full title of the publication.
        required: false
      kind:
        title: Publication venue type
        description: >-
          The type of this publication venue, e.g. journal article, book, webpage
        range: TRR379BibliographicType

  TRR379Quality:
    is_a: Thing
    title: Quality
    description: >-
      A quality is an attribute that is intrinsically associated with its
      bearer (or its parts), but whose presence/absence and observed/measured
      value may vary.

  TRR379SubjectType:
    is_a: Thing
    title: Subject type
    description: >-
      Type of a subject (e.g., human study participant, soil sample,
      cell culture).

  TRR379Topic:
    is_a: Thing
    title: Topic
    description: >-
      Topic a subject is about, e.g., a particular research question or domain
    slots:
      - part_of
    slot_usage:
      part_of:
        range: TRR379Topic
        multivalued: true

  #
  # Non-Things, such as association classes
  #
  ORCID:
    is_a: Identifier
    description: >-
      Unique persistent identifier for a person, provided by the Open Researcher
      and Contributor ID (ORCID) organisation.
    slot_usage:
      notation:
        description: >-
          The identifier notation is specified without a URL-prefix,
          or a `orcid:` prefix.
        pattern: '^\d{4}-\d{4}-\d{4}-\d{3}[0-9X]{1}$'
    unique_keys:
      value:
        description: The ORCID notation is globally unique within the scope of ORCIDs
        unique_key_slots:
          - notation
    exact_mappings:
      - obo:IAO_0000708

  TRR379AgentInfluence:
    # this is not derived from AgentInfluence, because we only need it for UI
    # purposed. it shows up as an alternative wherever TRR379Influence is the
    # range (e.g. influenced_by). it provides an effective way to constrain
    # the space for possible object and roles instances. other than that
    # it does not change the semantics or structure compared to TRR379Influence,
    # hence any instance continues to be fully compatible with no loss of
    # information when "seen" through the interface of TRR379Influence
    is_a: TRR379Influence
    description: >-
      Influence is the capacity of an agent to have an effect on the character,
      development, or behavior of a subject.
    slot_usage:
      object:
        title: Agent
        any_of:
          - range: TRR379Person
          - range: TRR379Organization
      roles:
        title: Roles
        range: TRR379AgentRole

  TRR379Communication:
    is_a: Communication
    title: Communication
    description: >-
      The exchange of an entity by two activities, one activity using the entity
      generated by the other. This implies a dependency of the subject
      activity on the associated activity.
    slots:
      - entity
    slot_usage:
      entity:
        description: >-
          An entity used by the subject, and produced by the associated
          activity.

  TRR379Influence:
    is_a: Influence
    description: >-
      Influence is the capacity of an entity, activity, or agent to have
      an effect on the character, development, or behavior of another by
      means of usage, start, end, generation, invalidation, communication,
      derivation, attribution, association, or delegation.
    slots:
      - ended
      - started

  TRR379ObjectiveInfluence:
    # see TRR379AgentRole for rationale on deriving from TRR379Influence rather
    # than EntityInfluence
    is_a: TRR379Influence
    description: >-
      Influence of an objective on the subject.
    slot_usage:
      object:
        title: Objective
        range: TRR379Objective
      roles:
        title: Roles
        # TODO adopt some kind of classification of objective types
        # (longterm goal, deliverable, ambition, contractual obligation, ...)
        # range: TRR379ObjectiveRole
