id: https://concepts.datalad.org/s/demo-research-assets/unreleased name: demo-research-assets-schema version: UNRELEASED status: eunal:concept-status/DRAFT title: Data models for an organization's research assets description: | This schema is using the FLAT approach (Flexible Low-complexity Annotation Technique) and is geared toward metadata entry and submission for pooling information across consortium sites and partners. It is to be taken as a demonstrator rather than a schema building block. 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: ADMS: http://www.w3.org/ns/adms# 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# dcterms: http://purl.org/dc/terms/ dlcommonmx: https://concepts.datalad.org/s/common-mixin/unreleased/ # TODO preliminary definition, pointing to a future resolver dldi: https://pid.datalad.org/distributions/ # TODO preliminary definition, just to have something short dlcdi: https://concepts.datalad.org/ns/content-defined-identifiers/ dlfilesmx: https://concepts.datalad.org/s/files-mixin/unreleased/ dlflat: https://concepts.datalad.org/s/flat/unreleased/ dlflatfiles: https://concepts.datalad.org/s/flat-files/unreleased/ dlflatpublications: https://concepts.datalad.org/s/flat-publications/unreleased/ dlflatres: https://concepts.datalad.org/s/flat-resources/unreleased/ dlflatsocial: https://concepts.datalad.org/s/flat-social/unreleased/ dlflatstudy: https://concepts.datalad.org/s/flat-study/unreleased/ dlidentifiers: https://concepts.datalad.org/s/identifiers/unreleased/ dlprovmx: https://concepts.datalad.org/s/prov-mixin/unreleased/ dlpublicationsmx: https://concepts.datalad.org/s/publications-mixin/unreleased/ dlquantmx: https://concepts.datalad.org/s/quantities-mixin/unreleased/ dlrelationsmx: https://concepts.datalad.org/s/relations-mixin/unreleased/ dlresmx: https://concepts.datalad.org/s/resources-mixin/unreleased/ dlschemas: https://concepts.datalad.org/s/ dlsocialmx: https://concepts.datalad.org/s/social-mixin/unreleased/ dlspatialmx: https://concepts.datalad.org/s/spatial-mixin/unreleased/ dlstudymx: https://concepts.datalad.org/s/study-mixin/unreleased/ dltemporalmx: https://concepts.datalad.org/s/temporal-mixin/unreleased/ dlthings: https://concepts.datalad.org/s/things/v1/ dltypes: https://concepts.datalad.org/s/types/v1/ dlvocab: https://concepts.datalad.org/vocab/ doi: https://doi.org/ eunal: http://publications.europa.eu/resource/authority/ geodata: http://sws.geonames.org/ 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/ sh: http://www.w3.org/ns/shacl# sio: http://semanticscience.org/resource/ skos: http://www.w3.org/2004/02/skos/core# spdx: http://spdx.org/rdf/terms# vcard: http://www.w3.org/2006/vcard/ns# w3ctr: https://www.w3.org/TR/ xsd: http://www.w3.org/2001/XMLSchema# xyzra: https://concepts.datalad.org/s/demo-research-assets/unreleased/ xyzrans: https://concepts.datalad.org/s/demo-research-assets/ns/ default_prefix: xyzra emit_prefixes: - dlcommonmx - dlfilesmx - dlflat - dlflatfiles - dlflatres - dlflatpublications - dlflatsocial - dlflatstudy - dlidentifiers - dlprovmx - dlpublicationsmx - dlquantmx - dlrelationsmx - dlresmx - dlspatialmx - dlsocialmx - dlstudymx - dltemporalmx - dlthings - dltypes - rdf - rdfs - skos - w3ctr - 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 - xyzrans imports: - dlschemas:flat-files/unreleased - dlschemas:flat-publications/unreleased - dlschemas:flat-resources/unreleased - dlschemas:flat-social/unreleased - dlschemas:flat-study/unreleased - dlschemas:prov-mixin/unreleased types: flexdate: # gen-shacl doesn't work without this uri: xyzra:flexdate base: str typeof: string description: W3C variant/subset of IS08601 for specifying date(times). Supported are - YYYY (eg 1997) - YYYY-MM (eg 1997-07) - YYYY-MM-DD (eg 1997-07-16) pattern: '^([-+]\d+)|(\d{4})|(\d{4}-[01]\d)|(\d{4}-[01]\d-[0-3]\d)$' enums: YesNoUnknownClassifcation: description: >- Boolean classification with a third option indicating that the true value is not known. permissible_values: "yes": description: >- Consent given "no": description: >- No consent given "unknown": description: The true value is not known (yet) slots: orcid: title: ORCID description: >- ORCID identifier of a person (see https://orcid.org). range: string pattern: '^\d{4}-\d{4}-\d{4}-\d{3}[0-9X]{1}$' # TODO: this better becomes an access method (through landing page) landing_page: title: Landing page description: >- A Web page that can be navigated to in a Web browser to gain access to a resource. range: uri exact_mappings: - dcat:landingPage target: title: Target description: >- An objective that is the focus of an activity. range: XYZObjective related_mappings: - obo:BFO_0000055 #exact_mappings: # - http://purl.allotrope.org/ontologies/property#AFX_0002750) #close_mappings: # - sct:363702006 classes: XYZAccolade: is_a: FlatThing mixins: - EntityMixin title: Accolade description: >- An award, prize, or other honor received in recognition of an achievement. slots: - title - at_time slot_usage: title: required: true at_time: title: Received on range: flexdate close_mappings: - schema:dateReceived XYZDataItem: 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: XYZDataset multivalued: true same_as: title: Qualitative value description: >- The value of a qualitative assessment. quantitative_value: title: Quantitative value description: >- The value of a quantitative assessment. kind: range: XYZDataType generated_by: range: XYZGeneration derived_from: range: XYZDerivation # TODO bring back somehow # any_of: # - range: XYZDataItem # - range: XYZSubject attributed_to: range: XYZAttribution XYZDataType: is_a: FlatThing title: Data type or format description: >- Type of an data item. slots: - version_of slot_usage: version_of: title: Variant of range: XYZDataType broad_mappings: - dcterms:format narrow_mappings: # Electronic File Format - obo:NCIT_C171252 # Data Type - obo:NCIT_C42645 # Electronic File Content Type - obo:NCIT_C172272 XYZConvention: is_a: Convention title: Convention description: >- A set of agreed, stipulated, or generally accepted standards, norms, social norms, or criteria, often taking the form of a custom. XYZDataset: is_a: Dataset title: Dataset 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: - about - attributed_to - generated_by - landing_page - rules - same_as slot_usage: about: title: Topic(s) description: >- Topics covered associated with this dataset. range: XYZTopic multivalued: true attributed_to: multivalued: true inlined_as_list: true inlined: true range: Attribution generated_by: range: XYZGeneration # TODO description explaining that this is about the dataset # as a whole (curation, compilation), not about individual # items part_of: range: XYZDataset multivalued: true rules: range: XYZRule same_as: range: XYZDataset multivalued: true XYZDistribution: is_a: Distribution title: Distribution description: >- A specific representation of a data item, which may come in the form of an electronic file, or an archive or directory of many files. slots: - conforms_to - rules slot_usage: kind: range: XYZDataType distribution_of: # XXX this should be a superfluous reannotation of the `Distribution.distribution_of` # slot as being multivalued (which it is in `Distribution`). But with linkml 1.9.4 # this information is not inherited multivalued: true parts: range: XYZNamedDistributionPart inlined: true rules: range: XYZRule conforms_to: range: XYZConvention multivalued: true XYZNamedDistributionPart: is_a: NamedDistributionPart description: >- An association class for attaching a `locator` as additional information to a `hasPart` relationship. slot_usage: roles: range: XYZDistributionPartType XYZDistributionPartType: is_a: FlatThing title: Distribution part type/role description: >- Type or role of a part of a distribution. For example, a part could be an item in an archive, or a file that is an executable. XYZDocument: is_a: Document 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: - about - attributed_to - rules slot_usage: kind: title: Document type description: >- The type of this document, e.g. journal article, book, webpage range: XYZBibliographicType attributed_to: title: Contributors multivalued: true inlined_as_list: true inlined: true range: XYZPersonAttribution part_of: multivalued: true rules: range: XYZRule about: title: Topic(s) description: >- Topics covered in this document. range: XYZTopic multivalued: true XYZConcept: is_a: FlatThing 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 XYZGenesis: is_a: FlatThing title: Genesis description: >- A process in which an entity comes into being as a result of the process. slots: - conforms_to - kind - name - part_of - target - used slot_usage: kind: range: XYZGenesis conforms_to: range: XYZConvention multivalued: true used: multivalued: true any_of: # target a concrete form, not a concept - range: XYZDistribution # think "tool" - range: XYZInstrument part_of: any_of: - range: XYZStudy - range: XYZGenesis multivalued: true target: multivalued: true broad_mappings: - obo:BFO_0000015 - prov:Activity exact_mappings: - obo:NCIT_C48151 - obo:IDO_0000607 comments: - This class is intended to cover generative processes and activities, while `Study` covers investigational (scientific) activities, and `Project` covers organizational activities. XYZGrant: is_a: Grant mixins: - EntityMixin title: Grant description: >- A grant, typically financial or otherwise quantifiable, resources. slots: - rules slot_usage: part_of: range: XYZGrant multivalued: true rules: range: XYZRule XYZInstrument: is_a: Instrument 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: - attributed_to - rules slot_usage: kind: title: Instrument type description: >- The type of this instrument, e.g. microscope, software, chainsaw range: XYZInstrumentType attributed_to: multivalued: true inlined_as_list: true inlined: true range: XYZPersonAttribution rules: range: XYZRule XYZOrganization: is_a: Organization 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: XYZOrganization multivalued: true XYZPerson: is_a: Person title: Person description: >- Person agents are people, alive, dead, or fictional. slots: - part_of slot_usage: part_of: title: Member of range: XYZOrganization multivalued: true XYZProject: is_a: Project title: Project 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: - attributed_to - part_of - target slot_usage: attributed_to: multivalued: true inlined_as_list: true inlined: true range: XYZPersonAttribution part_of: range: XYZProject multivalued: true target: multivalued: true XYZPublication: is_a: Publication title: Publication description: >- A resource that is the output of a publishing process. slots: - attributed_to - derived_from - doi - generated_by - rules slot_usage: doi: recommended: true title: DOI title: description: >- The full title of the publication. required: false attributed_to: multivalued: true inlined_as_list: true inlined: true title: Contributors range: XYZPersonAttribution published_at: range: XYZPublicationVenue 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. kind: title: Publication type description: >- The type of this publication, e.g. journal article, book, webpage range: XYZBibliographicType about: recommended: true title: Topic(s) description: >- Topics covered by this publication. range: XYZTopic multivalued: true date_published: range: flexdate description: >- The date when a publication became available at the publication venue. generated_by: recommended: true title: Contributing project(s) description: >- Any project that contributed to the outcomes described in the publication. range: XYZProject multivalued: true derived_from: recommended: true title: Associated dataset(s) description: >- Any dataset that informed the outcomes described in the publication. range: XYZDataset multivalued: true rules: range: XYZRule XYZBibliographicType: is_a: FlatThing title: Bibliographic type description: >- Type of a publication or document, e.g., journal article, book, or webpage. XYZInstrumentType: is_a: FlatThing title: Instrument type description: >- Type of an instrument. XYZPublicationVenue: is_a: FlatThing 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: XYZBibliographicType XYZStudy: is_a: Study title: Study description: >- A planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). slots: - attributed_to - target slot_usage: factors: multivalued: true range: XYZConcept instruments: multivalued: true range: XYZInstrument dimensions: multivalued: true range: XYZConcept attributed_to: multivalued: true inlined_as_list: true inlined: true title: Contributors range: XYZPersonAttribution part_of: range: XYZStudy multivalued: true associated_with: # TODO this is a bug. Association is with an agent, not an activity range: XYZProject multivalued: true target: multivalued: true XYZSubject: is_a: Subject title: Subject description: >- A subject is an entity being investigated in a study. This is a contextual entity. One and the same entity can be different subjects in two different studies. slots: - same_as slot_usage: study: range: XYZStudy kind: range: XYZSubjectType derived_from: range: XYZSubject same_as: range: XYZSubject XYZSubjectType: is_a: FlatThing title: Subject type description: >- Type of a subject. XYZTopic: is_a: FlatThing title: Topic description: >- Topic a subject is about, e.g., a particular research question or domain slots: - part_of slot_usage: part_of: range: XYZTopic multivalued: true XYZRule: is_a: FlatThing title: Rule description: >- Permissions, prohibitions, obligatations or other rights/policies. This can be a standard license, a custom usage agreement, or a codified policy. slots: # title because MIH thinks of these as documents - title # licenses often have them - short_name XYZAgentRole: is_a: FlatThing 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 XYZPersonAttribution: description: >- An association class for attributing a subject to a person and qualifying the relationship with particular roles. slots: - roles - object - display_label slot_usage: object: title: Person range: XYZPerson roles: description: >- Roles a person had with respect to the subject range: XYZAgentRole multivalued: true close_mappings: - prov:Attribution XYZObjective: is_a: FlatThing title: Objective description: >- A proposition that indicates a planned or anticipated outcome. slots: - attributed_to - title - part_of - depends_on slot_usage: part_of: range: XYZProject multivalued: true depends_on: range: XYZObjective multivalued: true attributed_to: multivalued: true inlined_as_list: true inlined: true title: Contributors range: XYZPersonAttribution # # PROV association classes # XYZAttribution: is_a: Attribution description: >- Attribution is the ascribing of an entity to an agent. When an entity e is attributed to agent ag, entity e was generated by some unspecified activity that in turn was associated to agent ag. Thus, this relation is useful when the activity is not known, or irrelevant. XYZDerivation: is_a: Derivation description: >- A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. slot_usage: used: range: XYZUsage generated_by: range: XYZGeneration XYZGeneration: is_a: Generation description: >- Generation is the completion of production of a new entity by an activity. This entity did not exist before generation and becomes available for usage after this generation. slots: - used slot_usage: object: range: XYZGenesis roles: # TODO ActivityRoles #range: used: range: XYZUsage comments: - >- The `used` slot is added to be able to express something like a sample generation using a generic activity and combine them with a target entity (like a subject) with an appropriate role declaration. PROV-O's approach is to have a dedicated activity (which has `used`) instance for each generation. Adding `used` here appears to be less effortful. XYZUsage: is_a: Usage description: >- Usage is the beginning of utilizing an entity by an activity. Before usage, the activity had not begun to utilize this entity and could not have been affected by the entity. slot_usage: roles: # TODO EntityRoles #range: