The Open Biodiversity Knowledge Management System Ontology
type: Ontology
version info: 1.0.1
comment: You are free to create derivative work as long as you cite the original authors.
subject: Biodiversity Informatics
label: OpenBiodiv Ontology
creator: Viktor Senderov, Kiril Simov
contributor: Mariya Dimitrova
license: CC-BY license version 4.0
imports: fabio

contains
type: ObjectProperty
inverse of: is contained by
domain: structured element
comment: A structured element contains another generic element.

is contained by
type: ObjectProperty
inverse of: contains
comment: An element that is contained by another structured element.

structured element
type: Class
subclass of: pattern-based element
comment: The class of elements that can contain other elements.

pattern-based element
type: Class
subclass of: Thing
comment: A structural pattern is an atomic component of a document, that is able to capture a recurrent and well known structure of a document. Any entity belonging to this class is compliant with exactly one structural pattern.

Mention
type: Class
subclass of: DiscourseElement
comment: An area of a document that can be considered a mention of something.

Statement
type: Class
comment: A message that is stated or declared; a communication (oral or written), setting forth particulars or facts, etc; "according to his statement he was in London on that day". WordNet 1.7.1

Agent
type: Class
comment: An agent (eg. person, group, software or physical artifact).
term status: stable

mentions
type: ObjectProperty
comment: A direct link between an information resource, like a document or a section and an entity.
domain: Mention

OpenBiodiv contains
type: ObjectProperty
type: TransitiveProperty
sub property of: contains

OpenBiodiv is contained by
type: ObjectProperty
type: TransitiveProperty
sub property of: is contained by

Publisher
type: Class
comment: The publisher of a journal, a type of `foaf:Agent`.
subclass of: Agent

Taxonomic Article
type: Class
subclass of: JournalArticle

Taxonomic Treatment
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Article
comment: A rhetorical element of a taxonomic publication, where taxon circumscription takes place.
comment: Таксономично пояснение или само Пояснение е риторчна част от таксономичната статия, където се случва описанието на дадена таксономична концепция. @bg

Nomenclature Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment
comment: A section of a taxonomic treatment, containing the scientific name of the taxon described by the treatment, and citations to previous descriptions, designations of type-genus, and type-species, and other information.

Nomenclature Heading
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Nomenclature Section
comment: Inside the taxonomic nomenclature section, we have the treatment title (name of the taxon).

Nomenclature Citations List
type: Class
subclass of: DiscourseElement
comment: A section in a treatment that includes the citation of one or several previous treatments of the taxon.

Biology Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Ecology Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Description Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Morphology Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Diagnosis Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Distribution Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Taxonomy Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Etymology Section
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Author of referenced material
type: Class
subclass of: Person

Taxonomic Key
type: Class
subclass of: DiscourseElement

Materials Examined
type: Class
subclass of: DiscourseElement

Molecular Data
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Conservation Status
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Type Locality
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Uses
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Treatment

Taxonomic Checklist
type: Class
subclass of: DiscourseElement
subclass of: Restriction
  on property: OpenBiodiv is contained by
  some values from: Taxonomic Article
comment: A section in a taxonomic article.

Taxonomic Name Usage
type: Class
subclass of: Mention
comment: A taxonomic name usage is the mentioning of a taxonomic name(scientific name, taxonomic concept label, etc.), optionally with a taxonomic status.

taxonomic status
type: ObjectProperty
comment: the IRI version of the DwC term taxonomic status

Taxonomic Name
type: Class
alternative label: Biological Name
equivalent class: NOMEN_0000030

Scientific Name
type: Class
subclass of: Taxonomic Name
equivalent class: NOMEN_0000036

Latinized Scientific Name
type: Class
subclass of: Scientific Name
alternative label: Linnaean Name

Taxon Concept Label
type: Class
subclass of: Latinized Scientific Name
comment: A taxon concept label is a taxonomic name usage accompanied by an additional part, consisting of 'sec.' + an identifier or a literature reference of a work containing the expression of a taxon concept (treatment).

Operational Taxonomic Unit Identifier
type: Class
subclass of: Scientific Name
comment: The identifier of an Operational Taxonomic Unit, such as BOLD BIN or a Unite SH ID

Vernacular Name
type: Class
subclass of: Taxonomic Name
equivalent class: NOMEN_0000037

name according to
type: ObjectProperty
comment: the IRI version of dwc:nameAccordingTo

OpenBiodiv name according to
type: ObjectProperty
sub property of: name according to
alternative label: sensu
range: Expression
domain: Taxon Concept Label
comment: The reference to the source in which the specific taxonomic concept circumscription is defined or implied - traditionally signified by the Latin 'sensu' or 'sec.'' (from secundum, meaning 'according to'). For taxa that are relevantly circumscribed by identifications, a reference to the keys, monographs, experts and other sources should be given. Should only be used with IRI's

has related name
type: ObjectProperty
type: TransitiveProperty
type: ReflexiveProperty
domain: Taxonomic Name
range: Taxonomic Name
comment: 'has related name' is an object property that we use in order to indicate that two taxonomic names are related somehow. This relationship is purposely vague as to encompass all situations where two taxonomic names co-occur in a text. It is transitive and reflexive.

has replacement name
type: ObjectProperty
type: TransitiveProperty
domain: Latinized Scientific Name
range: Latinized Scientific Name
comment: This is a uni-directional property. Its meaning is that one Linnaean name links to a different Linnaean name via the usage of this property, then the object name is more accurate and should be preferred given the information that system currently holds. This property is only defined for Linnaean names.

Taxon
type: Class
description: Example: The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820.
has version: Taxon-2014-10-23
issued: 2008-11-19
modified: 2014-10-23
replaces: Taxon-2009-09-21
abcd equivalence: no simple equivalent in ABCD
decision: Decision-2014-10-26 15
status: recommended
comment: A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.

Operational Taxonomic Unit
type: Class
subclass of: Concept
subclass of: Work
comment: A superclass for all kinds of taxonomic hypothesis

TaxonomicConcept
type: Class
equivalent class: Taxon
subclass of: Operational Taxonomic Unit
subclass of: Restriction
  on property: has taxon concept label
  min cardinality: 1
comment: A taxonomic concept in the sense of Berendsohn

has scientific name
type: ObjectProperty
comment: the IRI version of dwc:scientificName

has OpenBiodiv taxonomic name
type: ObjectProperty
domain: TaxonomicConcept
range: Taxonomic Name

has OpeonBiodiv scientific name
type: ObjectProperty
sub property of: has OpenBiodiv taxonomic name
sub property of: has scientific name
domain: TaxonomicConcept
range: Scientific Name

has taxon concept label
type: ObjectProperty
sub property of: has OpeonBiodiv scientific name
domain: TaxonomicConcept
range: Taxon Concept Label

has OTU Id
type: ObjectProperty
sub property of: has OpeonBiodiv scientific name
domain: TaxonomicConcept
range: Operational Taxonomic Unit Identifier

Dictionary of RCC5 Relations
type: Class
subclass of: ConceptScheme
subclass of: Restriction
  on property: isSchemeOf
  all values from: RCC5 Relation

RCC5 Relation
type: Class
subclass of: Concept
subclass of: Restriction
  on property: inScheme
  some values from: Dictionary of RCC5 Relations
comment: The of RCC 5 relation, e.g. 'partially overlaps'

RCC5 Statement
type: Class
subclass of: Statement
comment: A statement of RCC-5 relationship

from region
type: ObjectProperty
sub property of: rcc5Property
comment: Connects to the RCC5 statement to the originating region

to region
type: ObjectProperty
sub property of: rcc5Property
comment: Connects to the RCC5 statement to the target region

relation type
type: ObjectProperty
sub property of: rcc5Property
range: RCC5 Relation
comment: Connects an RCC-5 statement to the type of RCC-5 relation between the regions.

RCC5 statement according to
type: ObjectProperty
sub property of: rcc5Property
range: Expression
comment: In which publication was the statement made

Dictionary of Taxonomic Statuses
type: Class
subclass of: ConceptScheme
subclass of: Restriction
  on property: isSchemeOf
  all values from: Taxonomic Status Term
has discipline: Taxonomy (biology)
comment: The status following a taxonomic name usage in a taxonomic manuscript, i.e. 'n. sp.', 'comb. new', 'sec. Franz (2017)', etc

Taxonomic Status Term
type: Class
subclass of: Concept
subclass of: Restriction
  on property: inScheme
  some values from: Dictionary of Taxonomic Statuses
comment: The status following a taxonomic name usage in a taxonomic manuscript

Occurrence
is part of: terms
replaces: Sample
comment: An existence of an Organism at a particular place at a particular time.
description: Examples: A wolf pack on the shore of Kluane Lake in 1988.
type: Class

Identification
is part of: terms
comment: A taxonomic determination (e.g., the assignment to a taxon).
description: Example: A subspecies determination of an organism.
type: Class

Event
is part of: terms
replaces: SamplingEvent
comment: An action that occurs at some location during some time.
description: Examples: A specimen collection process. A machine observation.
type: Class

personal identifier
type: Class
comment: An identifier that uniquely identities an individual person, belonging to a particular identifier scheme such as ORCID specified by an individual within the class datacite:PersonalIdentifierScheme.

resource identifier
type: Class
comment: An identifier that is used to uniquely identifies a resource.

resource identifier scheme
type: Class
comment: The identifier scheme used to identify a resource. Individual schemes are defines as members of this class. For DataCite, the only permitted identifier scheme for the primary resource identifier is the Digital Object Identifier.

personal identifier scheme
type: Class
comment: The identifier scheme used to identify a person. Individual schemes are defines as members of this class.

an identifier scheme
type: resource identifier scheme
comment: boldsystems resource identifier scheme.

an identifier scheme
type: resource identifier scheme
comment: zenodo resource identifier scheme.

an identifier scheme
type: resource identifier scheme
comment: zoobank resource identifier scheme.

an identifier scheme
type: resource identifier scheme
comment: genbank resource identifier scheme.

orcid
type: personal identifier scheme
type: NamedIndividual
comment: Open Researcher and Contributor Identifier.

GenBankAccession
type: Class
comment: A GenBankAccession.

BOLDRecord
type: Class
comment: A BOLDRecord

BOLDBin
type: Class
comment: A BOLDBin

LitCitation
type: Class
comment: Inside class

Checklist
type: Class
comment: A checklist, usually contained in the treatment section

NomenclatureCitation
type: Class
comment: A nomenclature citation contained in the nomenclature citation list section

Institution
type: Class
comment: An institution - usually holds type material

TaxonomicDiscovery
type: Class
comment: A taxonomic discovery defined by the mentioning of a holotype in the treatment section

HolotypeDescription
type: Class
comment: Description of a holotype in a treatment

Institution Code
is part of: terms
replaces: InstitutionCode
comment: The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
type: Property

Type Status
is part of: terms
replaces: TypeStatus
comment: A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.
description: The recommended best practice is to separate the values with a vertical bar.
type: Property

verbatimCoordinates
type: Property
comment: The verbatim original spatial coordinates of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.

recordNumber
type: Property
description: An identifier given to the Occurrence at the time it was recorded. Often serves as a link between field notes and an Occurrence record, such as a specimen collector's number.
comment: The subject is a dwc:Occurrence and the object is a (possibly IRI-identified) resource that is the field notes.

recordedBy
type: Property
description: A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.
comment: Recommended best practice is to separate the values in a list with space vertical bar space.

country
type: Property
description: The name of the country or major administrative unit in which the Location occurs.
comment: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

stateProvince
type: Property
description: The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
comment: Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.

locality
type: Property
description: The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.

eventDate
type: Property
description: The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context.

occurrenceID
type: Property
description: An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.
comment: Recommended best practice is to use a persistent, globally unique identifier.

eventID
type: Property
description: An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set.

identificationID
type: Property
description: An identifier for the Identification (the body of information associated with the assignment of a scientific name). May be a global unique identifier or an identifier specific to the data set.

locationID
type: Property
description: An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the data set.

catalogNumber
type: Property
description: An identifier (preferably unique) for the record within the data set or collection.

otherCatalogNumbers
type: Property
description: A list (concatenated and separated) of previous or alternate fully qualified catalog numbers or other human-used identifiers for the same Occurrence, whether in the current or any other data set or collection.

individualCount
type: Property
description: The number of individuals represented present at the time of the Occurrence.

sex
type: Property
description: The sex of the biological individual(s) represented in the Occurrence.

lifeStage
type: Property
description: The age class or life stage of the biological individual(s) at the time the Occurrence was recorded.

verbatimLatitude
type: Property

verbatimLongitude
type: Property

decimalLongitude
type: Property

decimalLatitude
type: Property

elevation
type: Property

depth
type: Property

identifiedBy
type: Property

waterBody
type: Property

collectionYear
type: Property

collectionMonth
type: Property

collectionDay
type: Property

samplingProtocol
type: Property

habitat
type: Property

institutionID
type: Property

has identifier
type: ObjectProperty
comment: An object property specifying a datacite:Identifier that provides a unique identifer for the entity (either a funder, a person or a resource).

mentionsIdentifier
type: Property

mentionsHabitat
type: Property
comment: Has the same meaning as dwc:habitat but is a separate property because dwc:habitat has rdfs:domain dwc:Event. openbiodiv:mentionsHabitat is for habitats not related to a dwc:Event .

institutionName
type: Property

uses identifier scheme
type: ObjectProperty
comment: An object property permitting specification of the identifier scheme used to provide the identifier for an entity – either a funder, a person or a resource – defined as an individual of the class datacite:IdentifierScheme.

hasGbifTaxon
type: Property

hasDownloadLink
type: Property

hasBibReferenceID
type: Property

verbatimAuthor
type: Property

verbatimYear
type: Property