The Reference Dataset Ontology
type: Ontology
version IRI: https://purls.helmholtz-metadaten.de/rdo/1.0.0
contributor: https://orcid.org/0000-0001-9560-4728
created: 2024-15-11
creator: https://orcid.org/0000-0001-9560-4728
description: The Reference Dataset Ontology describes general concepts, which are related to a reference dataset, including aspects of referencing, documentation and certification. The reference can be digital, bibliographical or material. The dataset can be related to any domain. This version encompasses datasets related to the domain of Material Science, and therefore also the concept of a reference material. The purpose of the Reference Dataset Ontology is to describe concepts, which are required to qualify a dataset as a reference dataset.
license: https://creativecommons.org/licenses/by/4.0/
version info: 1.0.0

Reference dataset
type: Class
equivalent class: ReferenceDataset
subclass of: DataSet
textual definition: Reference data of materials are - documented according to certain standards as well as - curated (i.e., generated, maintained, preserved, validated) according to certain standards - quantitative data sets (i.e., data + their corresponding metadata) and - have been measured or simulated to a particularly high standard - for a material that has either experienced a well-documented process or is reference material or its composition and structure has been completely characterized. Reference data of materials can also be derived data from reference data. These data are distributed with a license (e.g., GPL) The here addressed standards for documentation, curation and measurement need to be defined for specific materials characteristics (e.g., creep tests) in terms of domain standards. These domain standards are the result of a steered community process. Standards should integrate as much as possible existing standards (e.g., the individual MatWerk domain standards should be as much as possible consistent).

Dataset
type: Class
equivalent class: Dataset
subclass of: CreativeWork
textual definition: A creative work that refers to a structured collection of data, organized typically for a specific goal such as analysis, research, or reference.
comment: A collection of data that consists of one or more files.

Reference
type: Class
equivalent class: Reference
subclass of: Resource
textual definition: Citation to another standard, part of a standard, or other material.

Reference material
type: Class
subclass of: Material
equivalent class: CHMO_0002913
textual definition: Material, sufficiently homogeneous and stable with respect to one or more specified properties, which has been established to be fit for its intended use in a measurement process.
comment: Properties can be quantitative or qualitative, e.g. identity of substances or species. Uses may include the calibration of a measurement system, assessment of a measurement procedure, assigning values to other materials, and quality control.
is defined by: DIN EN ISO 17034:2017

Bibliographic reference
type: Class
subclass of: Reference
equivalent class: BibliographicReference
textual definition: An expression of a bibliographic record in a specific format, that references a particular textual or data publication (or a work in preparation for publication). Each bibliographic reference is a list of items containing entities that describe aspects of the referenced work - for example authors, title, journal, publication year - selected from the bibliographic record. Note that because different journal styles may require omission of elements of the bibliographic record in references included in a paper's reference list (e.g. the title, the identifier, the names of the eighth and subsequent authors), and because errors can be introduced when an author creates a bibliographic reference, the bibliographic reference to a published work may not be a complete or fully accurate expression of the information contained within the authoritative bibliographic record for that work.

Certified reference material
type: Class
subclass of: Reference material
textual definition: 1) Reference material accompanied by documentation issued by an authoritative body and providing one or more specified property values with associated uncertainties and traceabilities, using valid procedures. 2) Reference material characterized by a metrologically valid procedure for one or more specified properties, accompanied by a reference material certificate that provides the value of the specified property, its associated uncertainty, and a statement of metrological traceability.
comment: The concept of value includes a nominal property or a qualitative attribute such as identity or sequence. Uncertainties for such attributes may be expressed as probabilities or levels of confidence.
is defined by: 1) ISO/IEC Guide 99: 2007, 2) ISO Guide 30:2015
equivalent class: CHMO_0002879

Standard
type: Class
textual definition: A documented instance of rules, guidelines, or characteristics for activities and/or their results, established by consensus and approved by a recognized body, aimed at the achievement of the optimum degree of order in a given context. Note 1: All instances identified by the same standard’s designation are often referred to as a standards’ family. Source: NISO SSOS WG adapting definitions of pre-existing standards
subclass of: specification
subclass of: IAO_0000030
equivalent class: Standard
equivalent class: Norm
is defined by: NISO SSOS WG adapting definitions of pre-existing standards

Norm
type: Class
textual definition: Document established by consensus and approved by a recognized body, that provides, for common and repeated use, rules, guidelines or characteristics for activities or their results, aimed at the achievement of the optimum degree of order in a given context
is defined by: SO/IEC Guide 2:2004

Measurement standard
type: Class
subclass of: Standard
textual definition: Realization of the definition of a given quantity, with stated quantity value and associated measurement uncertainty, used as a reference.
is defined by: ISO/IEC Guide 99: 2007

Certificate
type: Class
subclass of: Specification
equivalent class: Certificate
textual definition: An Information Bearing Artifact that bears an Information Content Entity which attests to certain demonstrated characteristics of an Object, Person, or Organization.

Documentation
type: Class
subclass of: specification
textual definition: Documentation is any communicable material that is used to describe, explain or instruct regarding some attributes of an object, system or procedure, such as its parts, assembly, installation, maintenance and use
equivalent class: Documentation

Licence
type: Class
textual definition: A legal document giving official permission to do something with the resource.
comment: An information content entity that refers to a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
equivalent class: License
subclass of: Resource
example: Creative Commons license

Metadata
type: Class
equivalent class: Metadata
textual definition: Attributes and additional data concerning the manufacturing of the tested material, test set-up, test system (measuring and test equipment), and the test piece, which allow for the evaluation of the quality/reliability of the measurements and a systematic search task of a database.
subclass of: DataScope
disjoint with: PrimaryData
disjoint with: SecondaryData

Primary data
type: Class
equivalent class: PrimaryData
textual definition: Data directly acquired by sensors or measuring instruments during or after an experiment or simulation.
subclass of: DataScope
disjoint with: Metaata
disjoint with: SecondaryData

Secondary data
type: Class
equivalent class: PrimaryData
textual definition: Data determined by equations or algorithms using primary data and/or metadata.
subclass of: DataScope
disjoint with: PrimaryData
disjoint with: Metadata

Material
type: Class
equivalent class: Material

Matirial description
type: Class
textual definition: This information is used to qualitatively and quantitatively describe a material by providing information on e.g. material properties, material structure, etc.
subclass of: specification
equivalent class: MaterialRelated

Data processing
type: Class
subclass of: BFO_0000015
textual definition: .

Curation process
type: Class
equivalent class: curation
subclass of: BFO_0000015
textual definition: A planned process of managing and evaluating resources and data from the point of their creation to ensure that they are fit for contemporary purpose and available for discovery and reuse.

specification
type: Class
subclass of: Class
  intersection of: IAO_0000104
  intersection of: CreativeWork
textual definition: A creative work that defines the requirements, characteristics, or standards for the design, implementation, or operation of a system, product, or process.
comment: A set of requirements, guidelines, standards contributed by an organization or a person.

CreativeWork
type: Class
comment: The most generic kind of creative work, including books, movies, photographs, software programs, etc.

curation
type: Class
subclass of: T4FS_0000012
subclass of: Restriction
  on property: T4FS_0000575
  some values from: Class
    intersection of: T4FS_0000519
    intersection of: Restriction
      on property: T4FS_0000560
      some values from: T4FS_0000447
textual definition: The activity of managing and promoting the use of data from their point of creation to ensure that they are fit for contemporary purpose and available for discovery and reuse.
term editor: Peter McQuilton

digital material identifier
type: DatatypeProperty
sub property of: identifier
domain: Resource
range: Material
textual definition: The Digital Material Identifier value object refers to a dmi:DigitalMaterialIdentifier. A dmi:DigitalMaterialIdentifier is a resource identifier (IRI) that represents the specification of a material (in the sense of a material class) described in a specification document. The specification document can be, e.g., a standard, a datasheet, or any other citable document. Typically, a specification document requires some qualities that a material (in the sense of a portion of matter) has to comply with. Typical requirements include chemical compositions or physical properties.

url
type: DatatypeProperty
domain: Thing
range: anyURI
comment: URL of a thing.

description
type: DatatypeProperty
textual definition: A data property linking an entity to its description.

has DOI
type: DatatypeProperty
sub property of: identifier
domain: Resource
textual definition: A data property relating a work to its Digital Object Identifier (DOI).

has project identifier
type: DatatypeProperty
sub property of: identifier
domain: Project
textual definition: A data property relating a research project with a unique identifier, defined in a given context.

has serial number
type: DatatypeProperty
sub property of: identifier
domain: Metadata
comment: A data property linking something, for example a piece of equipment, to its serial number.

has version
type: DatatypeProperty
domain: Resource
textual definition: A number or string that identifies different variants or releases of a resource.

instrument model
type: DatatypeProperty
domain: Instrument
textual definition: A data property relating an instrument with the model information.

title
type: DatatypeProperty
sub property of: hasPersonalInformation
domain: Person
comment: Title (Mr, Mrs, Ms, Dr. etc)

dateCreated
type: DatatypeProperty
domain: Resource
comment: The date on which the CreativeWork was created or the item was added to a DataFeed.

datePublished
type: DatatypeProperty
domain: Resource
comment: Date of first broadcast/publication.

startTime
type: DatatypeProperty
domain: TestOrder
comment: The startTime of something. For a reserved event or service (eg FoodEstablishmentReservation), the time that it is expected to start.

duration
type: DatatypeProperty
domain: OrganisedEvent
comment: duration

end date
type: DatatypeProperty
domain: OrganisedEvent
comment: end date

start date
type: DatatypeProperty
domain: OrganisedEvent
comment: start date

has description
type: ObjectProperty
equivalent property: description
domain: Resource
textual definition: Relation between a resource, e.g. Material and it's description resource, e.g. Material description.

issues certificate
type: ObjectProperty
domain: BFO_0000015
range: Certificate
textual definition: A general relation linking a certification process to the certificate it produces.

curates
type: ObjectProperty
domain: Curation process
range: Resource
textual definition: Links a curation process to the resource it curates.

about material
type: ObjectProperty
domain: CreativeWork
range: Material
textual definition: A relation between a dataset and the material it contains data on.

in scope of
type: ObjectProperty
range: Dataset
domain: Metadata

is about
type: ObjectProperty
sub property of: topObjectProperty
domain: Resource
range: Person
domain: IAO_0000030
example of usage: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
textual definition: A (currently) primitive relation that relates an information artifact to an entity.
textual definition: 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
definition source: IAO
definition source: James Malone
creator: Alan Ruttenberg
type: AnnotationProperty

standard of
type: ObjectProperty

has standard
type: ObjectProperty
inverse of: standardOf
domain: Resource
range: Standard
comment: The property relates a resource to the standard it relies on.

has author
type: ObjectProperty
domain: Resource
range: Person
textual definition: A relation between a resource and a person, who is the author.

has contributor
type: ObjectProperty
inverse of: isContributorOf

has creator
type: ObjectProperty
sub property of: has author
domain: Dataset
range: Class
  union of: Organization
  union of: Person
textual definition: A relation between a dataset and a person or organization, who has created the data.

has documentation
type: ObjectProperty
domain: Resource
range: Documentation
textual definition: A relation between a resource and its documentation.

has format
type: ObjectProperty
domain: Resource
range: FileFormat
textual definition: The file format of the resource

has material type
type: ObjectProperty
domain: Material
range: MaterialType
textual definition: A relation which relates a material to its type or classification.

has material condition
type: ObjectProperty
domain: Material
range: MaterialCondition
textual definition: A relation between a material and a specific condition describing the current state of the material.

has material property
type: ObjectProperty
domain: Material
range: MaterialProperty
textual definition: A relation between a material and the material property investigated in a certain study, e.g. a dataset or workflow.

has member
type: ObjectProperty
inverse of: memberOf
domain: Project
range: ProjectMember
textual definition: A relation between a research project and its members.

has related resource
type: ObjectProperty
type: SymmetricProperty
domain: Resource
range: Resource
textual definition: A relation between two different resources, which indicates both are associated.

has repository
type: ObjectProperty
domain: Resource
range: Repository
textual definition: A relation between a software and the website of the repository where it is stored.

uses method
type: ObjectProperty
domain: Resource
range: Method
textual definition: A relation between a resource and method it implements, uses or describes.

has license
type: ObjectProperty
inverse of: is license for
domain: Resource
range: SWO_0000002
textual definition: The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license.

is license for
type: ObjectProperty
textual definition: The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it.

is compatible license of
type: ObjectProperty
type: SymmetricProperty
domain: SWO_0000002
range: SWO_0000002
textual definition: 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program.
definition source: http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013.
creator: Allyson Lister

citation
type: ObjectProperty
domain: Resource
range: Resource
comment: A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.

part of
type: ObjectProperty
equivalent property: partOf
inverse of: has part
type: TransitiveProperty
editor preferred term~editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
textual definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
RO_0001900: RO_0001901

has part
type: ObjectProperty
equivalent property: part
type: TransitiveProperty
editor preferred term~editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
textual definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901

realized in
type: ObjectProperty
inverse of: BFO_0000055
domain: BFO_0000017
range: BFO_0000015
editor preferred term~editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: OBI_0000312
sub property of: RO_0000057
domain: OBI_0000011
editor preferred term~editor preferred label: has_specified_output
IAO_0000114: IAO_0000122
textual definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
IAO_0000412: obi.owl

editor preferred term~editor preferred label
type: AnnotationProperty
editor preferred term~editor preferred label: editor preferred label
editor preferred term~editor preferred label: editor preferred term
editor preferred term~editor preferred label: editor preferred term~editor preferred label
IAO_0000114: IAO_0000122
textual definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred label
label: editor preferred term

example of usage
type: AnnotationProperty
editor preferred term~editor preferred label: example of usage
IAO_0000114: IAO_0000122
textual definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
textual definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: IAO

textual definition
type: AnnotationProperty
editor preferred term~editor preferred label: definition
editor preferred term~editor preferred label: textual definition
IAO_0000114: IAO_0000122
textual definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
textual definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: definition

editor note
type: AnnotationProperty
editor preferred term~editor preferred label: editor note
IAO_0000114: IAO_0000122
textual definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term~editor preferred label: term editor
IAO_0000114: IAO_0000122
textual definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred term~editor preferred label: definition source
IAO_0000114: IAO_0000122
textual definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator note
type: AnnotationProperty
editor preferred term~editor preferred label: curator note
IAO_0000114: IAO_0000122
textual definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

abbreviation
type: AnnotationProperty
textual definition: A shortened form of a word or phrase. [Definition Source: NCI]
sub property of: altLabel

acronym
type: AnnotationProperty
textual definition: The non-unique initials or abbreviated name used for identification. [Definition Source: NCI]
sub property of: altLabel

Format
type: AnnotationProperty
bibliographic citation: [MIME] http://www.iana.org/assignments/media-types/
comment: Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME].
comment: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types.
label: has format
definition: The file format, physical medium, or dimensions of the resource.
sub property of: format
range: contributor

has_broad_synonym
type: AnnotationProperty
sub property of: has_synonym

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty
sub property of: has_synonym

has_narrow_synonym
type: AnnotationProperty
sub property of: has_synonym

has_related_synonym
type: AnnotationProperty
sub property of: has_synonym

has_synonym
type: AnnotationProperty
comment: Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL