Darwin Core as RDF as OWL
type: Ontology
label: The Biological Collections Ontology
has_obo_format_version: 1.2
date: 2009-07-31
version info: 2014-03-29
comment: This file is based on checkout of our SVN repository revision $Revision: 3931 $
comment: This version of the BCO has been pre-reasoned so that all inferred axioms are asserted. It is based on revision e98b4c682302. For a corresponding release where these axioms have not been asserted, use http://purl.obolibrary.org/obo/bco/2014-05-27/bco-non-classified.owl. The Biological Collections Ontology was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies. The Biological Collections Ontology (BCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
default language: en
modified: 2013-10-22
Contributor: Biocode Commons Ontology Hackathon members
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
subject: An ontology for the annotation of biomedical and functional genomics experiments.
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Stoeckert
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Eric Deutsch
creator: Gilberto Fragoso
Contributor: John Wieczorek
creator: Cristian Cocos
creator: Helen C. Causton
creator: Helen Parkinson
creator: James A. Overton
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
title: OBO Relations Ontology
Format: OWL-DL
title: Ontology for Biomedical Investigation
creator: Philip Lord
creator: Philippe Rocca-Serra
creator: Pierre Grenon
Contributor: Robert Guralnick
creator: Chris Mungall
creator: Chris Taylor
creator: Frank Gibson
creator: Holger Stenzhorn
creator: James Malone
creator: Matthew Pocock
creator: Richard Bruskiewich
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
comment: This document is an OWL representation of the Darwin Core (DwC) terminology, imported from DwC as RDF. In this document, DwC classes have been interpreted as classes in the Biological Collections Ontology and DwC properties have been interpreted as data properties. To comment on the OWL interpretation, please create an issue at https://code.google.com/p/bco/issues/list. DwC as RDF contains a list of Darwin Core terms that have the dwcattributes:status equal to "recommended". For the full normative RDF document of all Darwin Core terms, see dwctermshistory.rdf. To comment on this schema in the context of Darwin Core, please create a new issue in http://code.google.com/p/darwincore/issues/.
comment: This file contains terms from the Darwin Core (DwC) type vocabulary, imported from the RDF representation of that vocabulary and interpretted as classes in the Biological Collections Ontology. Some of the type vocabulary terms are replicated in DwC as RDF.
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
publisher: Biodiversity Information Standards (TDWG)
Contributor: John Deck
Contributor: Barry Smith
creator: Christian Bolling
creator: Jessica Turner
Contributor: Ramona Walls

taxonomic inventory metadata preferred name
type: AnnotationProperty
sub property of: alternative term

BCO preferred label
type: AnnotationProperty

dwc_bco mapping
type: AnnotationProperty

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

example of usage
type: AnnotationProperty
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
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: example
editor preferred term: example of usage
has curation status: ready for release

in branch
type: AnnotationProperty
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
definition editor: GROUP:OBI
definition source: OBI_0000277
editor preferred term: in branch

has curation status
type: AnnotationProperty
definition source: OBI_0000281
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
editor preferred term: has curation status

definition
type: AnnotationProperty
label: textual definition
definition editor: PERSON:Daniel Schober
editor preferred term: definition
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
has curation status: ready for release

editor note
type: AnnotationProperty
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.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: ready for release

definition editor
type: AnnotationProperty
label: term editor
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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
definition editor: PERSON:Daniel Schober
editor preferred term: definition editor
editor preferred term: term editor
has curation status: ready for release

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: alternative term
has curation status: pending final vetting

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: definition source
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
has curation status: ready for release

has obsolescence reason
type: AnnotationProperty
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
editor preferred term: has obsolescence reason

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
editor preferred term: curator note
has curation status: ready for release

is denotator type
type: AnnotationProperty
definition editor: Alan Ruttenberg
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
definition: relates an class defined in an ontology, to the type of it's denotator
editor preferred term: is denotator type

imported from
type: AnnotationProperty
definition: For external terms/classes, the ontology from which the term was imported
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
editor preferred term: imported from
has curation status: pending final vetting

expand expression to
type: AnnotationProperty
definition editor: Chris Mungall
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand expression to

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
definition editor: Chris Mungall
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand assertion to

first order logic expression
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
definition editor: PERSON:Alan Ruttenberg
editor preferred term: first order logic expression
sub property of: logical macro assertion on an object property

antisymmetric property
type: AnnotationProperty
definition editor: Alan Ruttenberg
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: use boolean value xsd:true to indicate that the property is an antisymmetric property

OBO foundry unique label
type: AnnotationProperty
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition: An alternative name for a class or property which is unique across the OBO Foundry.
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
editor preferred term: OBO foundry unique label
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
has curation status: pending final vetting

term replaced by
type: AnnotationProperty
definition source: Person:Alan Ruttenberg
definition editor: Person:Alan Ruttenberg
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
editor preferred term: term replaced by
has curation status: pending final vetting

ISA alternative term
type: AnnotationProperty
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
definition source: ISA tools project (http://isa-tools.org)
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
editor preferred term: ISA alternative term
sub property of: alternative term
has curation status: ready for release

NIAID GSCID-BRC alternative term
type: AnnotationProperty
definition source: NIAID GSCID-BRC metadata working group
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
editor preferred term: NIAID GSCID-BRC alternative term
sub property of: alternative term
has curation status: ready for release

IEDB alternative term
type: AnnotationProperty
definition: An alternative term used by the IEDB.
definition source: IEDB
editor preferred term: IEDB alternative term
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
sub property of: alternative term
has curation status: ready for release

temporal interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

never in taxon
type: AnnotationProperty
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
expand assertion to: ?X DisjointWith RO_0002162 some ?Y
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition editor: Chris Mungall
definition source: PMID:17921072
definition source: PMID:20973947
sub property of: taxonomic class assertion

mutually spatially disjoint with
type: AnnotationProperty
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
alternative term: non-overlapping with
alternative term: shares no parts with
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
sub property of: logical macro assertion on a class

taxonomic class assertion
type: AnnotationProperty
definition: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
sub property of: logical macro assertion on a class

ambiguous for taxon
type: AnnotationProperty
definition: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
sub property of: taxonomic class assertion

dubious for taxon
type: AnnotationProperty
definition editor: https://orcid.org/0000-0002-6601-2165
definition: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
comment: This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
sub property of: taxonomic class assertion

present in taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
definition editor: https://orcid.org/0000-0002-6601-2165
sub property of: taxonomic class assertion

logical macro assertion
type: AnnotationProperty
definition: An assertion that holds between two classes that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

annotation property cardinality
type: AnnotationProperty
definition: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
sub property of: logical macro assertion on an annotation property
range: nonNegativeInteger

logical macro assertion on a class
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a class
sub property of: logical macro assertion

logical macro assertion on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

dispositional interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
sub property of: logical macro assertion on an object property

has no connections with
type: AnnotationProperty
example of usage: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
alternative term: shares no connection with
sub property of: logical macro assertion on a class

inherited annotation property
type: AnnotationProperty

curator guidance link
type: AnnotationProperty
definition: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
sub property of: inherited annotation property

Contributor
type: AnnotationProperty

Creator
type: AnnotationProperty

Date
type: AnnotationProperty

Description
type: AnnotationProperty
comment: An account of the content of the resource.

Format
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty

Subject and Keywords
type: AnnotationProperty
comment: The topic of the content of the resource.

Title
type: AnnotationProperty
comment: A name given to the resource.

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

shorthand
type: AnnotationProperty

has role
type: ObjectProperty
definition: The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
comment: This property was originally created in OBI, but in OBI it was deprecated and replaced by BFO:0000087. However, the BFO relation was replaced by has role at some time, which is not yet part of a stable release. Once the BFO role has been tested and released, it may replace this relation.
domain: independent continuant
sub property of: bearer of

derives from by planned process
type: ObjectProperty
type: TransitiveProperty
range: material entity
domain: material entity
has curation status: to be replaced with external ontology term
sub property of: topObjectProperty
property chain axiom: is_specified_output_of
property chain axiom: has input

is derived into by planned process
type: ObjectProperty
type: TransitiveProperty
inverse of: derives from by planned process
has curation status: to be replaced with external ontology term
sub property of: topObjectProperty
property chain axiom: is_specified_input_of
property chain axiom: has output

part of
type: ObjectProperty
type: TransitiveProperty
editor note: Ambiguous between continuant-parthood and occurrent-parthood
editor preferred term: is part of
alternative term: part_of
inverse of: has part
temporal interpretation: axiom holds for all times
sub property of: overlaps

has part
type: ObjectProperty
type: TransitiveProperty
editor note: Ambiguous between continuant-parthood and occurrent-parthood
editor preferred term: has part
alternative term: has_part
temporal interpretation: axiom holds for all times
sub property of: overlaps
imported from: obi.owl

inheres in
type: ObjectProperty
type: FunctionalProperty
editor preferred term: inheres in
alternative term: inheres_in
range: independent continuant
domain: dependent continuant
inverse of: is bearer of
sub property of: s depends on
imported from: obi.owl

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of
editor preferred term: is bearer of
domain: independent continuant
range: dependent continuant
imported from: obi.owl

is realized by
type: ObjectProperty
label: realized in
alternative term: is realized by
editor preferred term: is realized by
alternative term: realized by
editor preferred term: realized in
alternative term: realized_by
alternative term: realized_in
range: process
imported from: obi.owl

realizes
type: ObjectProperty
editor preferred term: realizes
domain: process
range: realizable entity
inverse of: is realized by
imported from: obi.owl

participates in
type: ObjectProperty
editor preferred term: participates in
alternative term: participates_in
imported from: obi.owl

has participant
type: ObjectProperty
editor preferred term: has participant
alternative term: has_participant
range: continuant
inverse of: participates in
imported from: obi.owl
property chain axiom: realizes
property chain axiom: inheres in

is concretized as
type: ObjectProperty
editor preferred term: is concretized as
range: specifically dependent continuant
domain: generically dependent continuant
imported from: obi.owl

concretizes
type: ObjectProperty
editor preferred term: concretizes
domain: specifically dependent continuant
range: generically dependent continuant
inverse of: is concretized as
imported from: obi.owl

obsolete preceded by
type: ObjectProperty
type: TransitiveProperty
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062

preceded by
type: ObjectProperty
type: TransitiveProperty
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
editor preferred term: preceded by
alternative term: preceded_by
range: occurrent
domain: occurrent
inverse of: precedes
sub property of: ends_after
property chain axiom: starts_during
property chain axiom: happens_during

precedes
type: ObjectProperty
type: TransitiveProperty
editor preferred term: precedes
domain: occurrent
range: occurrent
sub property of: temporally related to

occurs in
type: ObjectProperty
alternative term: Intended meaning: domain: occurrent range: independent continuant time: atemporal
editor preferred term: occurs in
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
domain: occurrent
range: independent continuant
inverse of: contains process
property chain axiom: part of

contains process
type: ObjectProperty
editor preferred term: site of

s depends on
type: ObjectProperty
editor preferred term: s depends on
alternative term: s_depends_on
range: independent continuant
domain: specifically dependent continuant
imported from: obi.owl

has role
type: ObjectProperty
editor preferred term: has role
alternative term: has_role
imported from: obi.owl

is about
type: ObjectProperty
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
editor preferred term: is about
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting
imported from: iao.owl
imported from: obi.owl

has_specified_input
type: ObjectProperty
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
domain: planned process
sub property of: has input
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: input of

has_specified_output
type: ObjectProperty
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
editor preferred term: has_specified_output
has curation status: ready for release
domain: planned process
inverse of: is_specified_output_of
sub property of: has output
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
definition editor: PERSON:Bjoern Peters
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
editor preferred term: is_specified_output_of
has curation status: ready for release
range: planned process
sub property of: output of
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
editor preferred term: achieves_planned_objective
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
range: objective specification
has curation status: FossilSpecimen
domain: planned process
imported from: obi.owl

has value specification
type: ObjectProperty
definition: A relation between an information content entity and a value specification that specifies its value.
definition source: OBI
definition editor: PERSON: James A. Overton
editor preferred term: has value specification
sub property of: has part
domain: information content entity
has curation status: FossilSpecimen
range: value specification
imported from: obi.owl

inheres in
type: ObjectProperty
editor note: Intended meaning: domain: specifically dependent continuant range: independent continuant time: at all times A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists.
editor preferred term: inheres in
alternative term: inheres_in
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
editor preferred term: bearer of
alternative term: bearer_of
alternative term: is bearer of
range: specifically dependent continuant
inverse of: inheres in
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
editor preferred term: participates in
alternative term: participates_in
domain: continuant
range: occurrent

has participant
type: ObjectProperty
editor preferred term: has participant
alternative term: has_participant
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
range: continuant
domain: occurrent
inverse of: participates in
property chain axiom: has part

role of
type: ObjectProperty
alternative term: is role of
alternative term: role_of
sub property of: inheres in

has quality
type: ObjectProperty
range: quality
sub property of: bearer of

has role
type: ObjectProperty
alternative term: has_role
domain: independent continuant
range: role
sub property of: bearer of
inverse of: role of

derives from
type: ObjectProperty
has curation status: pending final vetting
sub property of: topObjectProperty

derives into
type: ObjectProperty
has curation status: pending final vetting
sub property of: topObjectProperty

location of
type: ObjectProperty
type: TransitiveProperty
editor preferred term: is location of
alternative term: location_of
temporal interpretation: axiom holds for all times

contained in
type: ObjectProperty
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
editor note: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
editor note: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
editor preferred term: contained in
alternative term: contained_in
range: independent continuant
domain: material entity
inverse of: contains
temporal interpretation: axiom holds for all times
property chain axiom: located in
property chain axiom: part of

contains
type: ObjectProperty
editor preferred term: contains
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
type: TransitiveProperty
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in
editor preferred term: located in
alternative term: located_in
inverse of: location of
temporal interpretation: axiom holds for all times

boundary of
type: ObjectProperty
definition: The relationships between a boundary (a 2D immaterial entity) and the material entity that it delimits.
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to

has boundary
type: ObjectProperty
definition: The relationship between a material entity and the boundary (2D immaterial entity) that delimits it.
domain: material entity
range: immaterial entity
temporal interpretation: axiom holds for all times
inverse of: boundary of
sub property of: mereotopologically related to

tracheates
type: ObjectProperty
definition editor: DOS
definition: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
sub property of: contained in

has synaptic terminal of
type: ObjectProperty
inverse of: has synaptic terminal in
sub property of: overlaps

bounding layer of
type: ObjectProperty
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
range: material entity
sub property of: part of
domain: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: laminar

coincident with
type: ObjectProperty
type: TransitiveProperty
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length. This relation is transitive. It i is agnostic about any parthood relationship between X and Y.
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
sub property of: mereotopologically related to
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: bearer of
    some values from: linear
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: bearer of
    some values from: linear

before_or_simultaneous_with
type: ObjectProperty
alternative term: <=
comment: Primitive instance level timing relation between events
sub property of: temporally related to

simultaneous_with
type: ObjectProperty
type: TransitiveProperty
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
sub property of: before_or_simultaneous_with

before
type: ObjectProperty
type: TransitiveProperty
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
sub property of: before_or_simultaneous_with

during_which_ends
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: ends_during
sub property of: temporally related to

encompasses
type: ObjectProperty
type: TransitiveProperty
alternative term: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
sub property of: during_which_starts
inverse of: happens_during

ends_after
type: ObjectProperty
type: TransitiveProperty
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
sub property of: temporally related to
property chain axiom: ends_during
property chain axiom: preceded by

immediately_preceded_by
type: ObjectProperty
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
alternative term: starts_at_end_of
sub property of: preceded by
inverse of: immediately_precedes

during_which_starts
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: starts_during
sub property of: temporally related to

starts_before
type: ObjectProperty
type: TransitiveProperty
sub property of: temporally related to
property chain axiom: starts_during
property chain axiom: obsolete preceded by

immediately_precedes
type: ObjectProperty
alternative term: meets
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
alternative term: ends_at_start_of
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with

starts_during
type: ObjectProperty
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
alternative term: io
domain: occurrent
range: occurrent
sub property of: temporally related to

happens_during
type: ObjectProperty
type: TransitiveProperty
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
alternative term: during
alternative term: d
sub property of: ends_during

ends_during
type: ObjectProperty
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
alternative term: overlaps
alternative term: o
sub property of: temporally related to

has soma location
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
definition: Relation between a neuron and an anatomical structure that its soma is part of.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: overlaps
property chain axiom: part of

fasciculates with
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
alternative term: fasciculates with
definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

axon synapses in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: has presynaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: part of

has plasma membrane part
type: ObjectProperty
definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
definition editor: Chris Mungall
example of usage: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition source: PMID:19243617
sub property of: has part
has curation status: pending final vetting
temporal interpretation: axiom holds for all times

has postsynaptic terminal in
type: ObjectProperty
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative term: synapsed in
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
inverse of: axon synapses in
sub property of: has synaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: part of

has presynaptic terminal in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative term: synapses in
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: has synaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: part of

dendrite synapsed in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: has postsynaptic terminal in
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: part of

has synaptic terminal in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
definition editor: David Osumi-Sutherland
alternative term: has synapse in
definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613
property chain axiom: part of

overlaps
type: ObjectProperty
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part

has fasciculating neuron projection
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
definition editor: David Osumi-Sutherland
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
alternative term: has fasciculating component
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
inverse of: fasciculates with
sub property of: overlaps
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
definition editor: David Osumi-Sutherland
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
curator note: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
alternative term: connected to
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to

Axiom
annotated target: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
Source: RO:cjm
annotated property: curator note
annotated source: continuous with

proper overlaps
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
alternative term: partially overlaps
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: overlaps

spatially disjoint from
type: ObjectProperty
definition: A is spatially_disjoint_from B if and only if they have no parts in common
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
definition editor: Chris Mungall
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: mereotopologically related to

connected to
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom:
  inverse of: connects
property chain axiom: connects

connects
type: ObjectProperty
definition: Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
sub property of: mereotopologically related to

attached to part of
type: ObjectProperty
definition: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
sub property of: mereotopologically related to
property chain axiom: attached to
property chain axiom: part of

supplies
type: ObjectProperty
definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
sub property of: connected to

drains
type: ObjectProperty
definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
sub property of: connected to

has component
type: ObjectProperty
comment: For use in recording has_part with a cardinality constraint.
sub property of: has part
has curation status: pending final vetting
temporal interpretation: axiom holds for all times

actively participates in
type: ObjectProperty
definition: x actively participates in y if and only if x participates in y and x realizes some active role
alternative term: agent in
has curation status: pending final vetting
sub property of: participates in
inverse of: has active participant

has active participant
type: ObjectProperty
definition: x has participant y if and only if x realizes some active role that inheres in y
alternative term: has agent
has curation status: pending final vetting
sub property of: has participant

surrounded by
type: ObjectProperty
definition: x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: adjacent to

adjacent to
type: ObjectProperty
definition: x adjacent to y if and only if x and y share a boundary
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
sub property of: spatially disjoint from

surrounds
type: ObjectProperty
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
inverse of: surrounded by
sub property of: adjacent to

temporally related to
type: ObjectProperty
Source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
definition source: Allen
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
domain: occurrent
range: occurrent
has curation status: pending final vetting

starts
type: ObjectProperty
definition source: Allen
definition editor: Chris Mungall
definition: inverse of starts with
sub property of: part of
has curation status: pending final vetting
sub property of: temporally related to

starts with
type: ObjectProperty
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
alternative term: started by
sub property of: has part
has curation status: pending final vetting
sub property of: temporally related to
inverse of: starts

ends
type: ObjectProperty
definition: inverse of ends with
sub property of: part of
has curation status: pending final vetting
sub property of: temporally related to
inverse of: ends with

ends with
type: ObjectProperty
type: TransitiveProperty
alternative term: finished by
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
sub property of: has part
has curation status: pending final vetting
sub property of: temporally related to

has start location
type: ObjectProperty
alternative term: starts with process that occurs in
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
range: independent continuant
domain: process
has curation status: pending final vetting
sub property of: has part that occurs in
property chain axiom: starts with
property chain axiom: occurs in

has end location
type: ObjectProperty
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
alternative term: ends with process that occurs in
range: independent continuant
domain: process
has curation status: pending final vetting
sub property of: has part that occurs in
property chain axiom: ends with
property chain axiom: occurs in

has input
type: ObjectProperty
definition: p has input c if either: p has direct input c or p has indirect input c. See subrelations for definitions.
has curation status: pending final vetting
sub property of: has participant
property chain axiom: starts with

has output
type: ObjectProperty
definition: p has output c if either: p has direct output c or p has output input c. See subrelations for definitions.
has curation status: pending final vetting
sub property of: has participant
property chain axiom: ends with

mereotopologically related to
type: ObjectProperty
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
definition editor: Chris Mungall
definition: A mereological relationship or a topological relationship
temporal interpretation: axiom holds for all times

colocalizes_with
type: ObjectProperty
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
creator: Gene Ontology Consortium
example of usage: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
curator note: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
sub property of: mereotopologically related to

member of
type: ObjectProperty
alternative term: is member of
alternative term: member part of
definition source: SIO
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
sub property of: part of
temporal interpretation: axiom holds for all times
inverse of: has member

has member
type: ObjectProperty
type: IrreflexiveProperty
definition source: SIO
definition: has member is a mereological relation between a collection and an item.
sub property of: has part
temporal interpretation: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
inverse of: has input

output of
type: ObjectProperty
sub property of: participates in
inverse of: has output

has dendrite location
type: ObjectProperty
Source: http://neurolex.org/wiki/Property:DendriteLocation
sub property of: overlaps

attached to
type: ObjectProperty
type: SymmetricProperty
sub property of: attached to part of

has muscle origin
type: ObjectProperty
definition source: Wikipedia:Insertion_(anatomy)
definition: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
sub property of: attached to

has muscle insertion
type: ObjectProperty
definition source: Wikipedia:Insertion_(anatomy)
definition: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
sub property of: attached to

in branching relationship with
type: ObjectProperty
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
sub property of: part of
has curation status: requires discussion
sub property of: mereotopologically related to

tributary of
type: ObjectProperty
curator note: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
alternative term: drains into
example of usage: Deschutes River tributary_of Columbia River
alternative term: drains to
definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
definition source: http://en.wikipedia.org/wiki/Tributary
definition source: http://www.medindia.net/glossary/venous_tributary.htm
alternative term: tributary channel of
example of usage: inferior epigastric vein tributary_of external iliac vein
has curation status: requires discussion
sub property of: in branching relationship with

Axiom
annotated target: drains to
Source: drainsTo
annotated property: alternative term
annotated source: tributary of

Axiom
Source: FMA
annotated target: inferior epigastric vein tributary_of external iliac vein
annotated property: example of usage
annotated source: tributary of

Axiom
Source: GAZ
annotated target: Deschutes River tributary_of Columbia River
annotated property: example of usage
annotated source: tributary of

distributary of
type: ObjectProperty
alternative term: branch of
definition source: http://en.wikipedia.org/wiki/Distributary
definition: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
alternative term: distributary channel of
example of usage: Deschutes River distributary_of Little Lava Lake
has curation status: requires discussion
sub property of: in branching relationship with

Axiom
annotated target: Deschutes River distributary_of Little Lava Lake
Source: GAZ
annotated property: example of usage
annotated source: distributary of

anabranch of
type: ObjectProperty
definition: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
alternative term: anastomoses with
has curation status: requires discussion
sub property of: distributary of
property disjoint with: proper distributary of
property disjoint with: proper tributary of
sub property of:
  inverse of: tributary of

spatially coextensive with
type: ObjectProperty
definition: x spatially_coextensive_with y if and inly if x and y have the same location
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in

branching part of
type: ObjectProperty
definition: x is a branching part of y if and only if x is part of y and x is a branch_of the main stem of y
has curation status: requires discussion
sub property of: in branching relationship with
property chain axiom: distributary of
property chain axiom: main stem of

main stem of
type: ObjectProperty
definition: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
has curation status: requires discussion
sub property of: in branching relationship with

proper distributary of
type: ObjectProperty
definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
has curation status: requires discussion
sub property of: distributary of

proper tributary of
type: ObjectProperty
definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
has curation status: requires discussion
sub property of: tributary of

has direct input
type: ObjectProperty
definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has curation status: requires discussion
sub property of: has input
property chain axiom: starts with

has indirect input
type: ObjectProperty
has curation status: requires discussion
sub property of: has input

has direct output
type: ObjectProperty
definition: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
has curation status: requires discussion
sub property of: has output
property chain axiom: ends with

has indirect output
type: ObjectProperty
has curation status: requires discussion
sub property of: has output

contributes to morphology of
type: ObjectProperty
definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
sub property of: overlaps

partner in
type: ObjectProperty
curator note: Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
sub property of: participates in

subject participant in
type: ObjectProperty
sub property of: partner in

target participant in
type: ObjectProperty
sub property of: partner in

is evidence for
type: ObjectProperty
definition: A relationship between a piece of evidence and an assertion where the evidence lends support to the assertion

composed primarily of
type: ObjectProperty
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
example of usage: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
sub property of: has part
temporal interpretation: axiom holds for all times

has part that occurs in
type: ObjectProperty
property chain axiom: has part
property chain axiom: occurs in

receives input from
type: ObjectProperty
editor note: See notes for inverse relation
sub property of: connected to
inverse of: sends output to

sends output to
type: ObjectProperty
editor note: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
sub property of: connected to

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:0000041
definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: SO:similar_to
has_related_synonym: correspondence
has_related_synonym: resemblance
has_exact_synonym: sameness
has_exact_synonym: similar to
creator: bgee.unil.ch
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: BGEE:curator
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
database_cross_reference: HOM_0000000
annotated property: definition
annotated source: in similarity relationship with

Axiom
annotated target: correspondence
database_cross_reference: http://dx.doi.org/10.1007/BF02814479
annotated source: in similarity relationship with
annotated property: has_related_synonym

in homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Similarity that results from common evolutionary origin.
comment: This broad definition encompasses all the working definitions proposed so far in the literature.
has_exact_synonym: homologous to
creator: bgee.unil.ch
sub property of: in similarity relationship with
property disjoint with: in homoplasy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Similarity that results from common evolutionary origin.
database_cross_reference: bies.950180611
database_cross_reference: jmor.1051730307
database_cross_reference: http://dx.doi.org/10.1007/BF02814480
database_cross_reference: HOM_0000001
annotated property: definition
annotated source: in homology relationship with

in homoplasy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Similarity that results from independent evolution.
has_related_synonym: analogy
has_exact_synonym: homoplasous to
creator: bgee.unil.ch
sub property of: in similarity relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Similarity that results from independent evolution.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000002
annotated property: definition
annotated source: in homoplasy relationship with

in homocracy relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:0000075
comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
has_exact_synonym: homocracous to
creator: bgee.unil.ch
sub property of: in similarity relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: s00427-003-0301-4
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000003
annotated property: definition
annotated source: in homocracy relationship with

in convergence relationship with
type: ObjectProperty
type: SymmetricProperty
comment: Convergence usually implies a notion of adaptation.
definition: Homoplasy that involves different underlying mechanisms or structures.
has_related_synonym: analogy
creator: bgee.unil.ch
sub property of: in homoplasy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homoplasy that involves different underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000004
annotated property: definition
annotated source: in convergence relationship with

in parallelism relationship with
type: ObjectProperty
type: SymmetricProperty
comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
definition: Homoplasy that involves homologous underlying mechanisms or structures.
has_exact_synonym: parallel evolution
creator: bgee.unil.ch
sub property of: in homoplasy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000005
annotated property: definition
annotated source: in parallelism relationship with

in structural homology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:0000071
definition: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: MI:2163
has_related_synonym: idealistic homology
has_exact_synonym: structural homologous to
creator: bgee.unil.ch
sub property of: in homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
database_cross_reference: ISBN:0123195837
database_cross_reference: j.jhevol.2006.11.014
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000006
annotated property: definition
annotated source: in structural homology relationship with

in historical homology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:0000080
definition: Homology that is defined by common descent.
database_cross_reference: RO_proposed_relation:homologous_to
database_cross_reference: SO:0000330
database_cross_reference: SO:0000853
database_cross_reference: SO:0000857
database_cross_reference: SO:homologous_to
database_cross_reference: TAO:homologous_to
has_exact_synonym: cladistic homology
has_exact_synonym: historical homologous to
has_broad_synonym: homology
has_exact_synonym: phylogenetic homology
has_exact_synonym: taxic homology
has_related_synonym: true homology
creator: bgee.unil.ch
sub property of: in homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homology that is defined by common descent.
database_cross_reference: ISBN:0123195837
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: HOM_0000007
annotated property: definition
annotated source: in historical homology relationship with

in biological homology relationship with
type: ObjectProperty
type: SymmetricProperty
comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
database_cross_reference: ECO:0000067
definition: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
has_exact_synonym: biological homologous to
has_related_synonym: transformational homology
creator: bgee.unil.ch
sub property of: in homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
database_cross_reference: S0169-5347(97)01125-7
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000008
annotated property: definition
annotated source: in biological homology relationship with

in reversal relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
has_exact_synonym: atavism
has_related_synonym: reversion
has_exact_synonym: rudiment
creator: bgee.unil.ch
sub property of: in homoplasy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: HOM_0000009
annotated property: definition
annotated source: in reversal relationship with

in syntenic homology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: MeSH:Synteny
database_cross_reference: SO:0000860
database_cross_reference: SO:0005858
definition: Structural homology that is detected by similarity in content and organization between chromosomes.
has_exact_synonym: syntenic homologous to
has_related_synonym: synteny
creator: bgee.unil.ch
sub property of: in structural homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: MeSH:Synteny
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
database_cross_reference: HOM_0000010
annotated property: definition
annotated source: in syntenic homology relationship with

in paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: SO:0000854
database_cross_reference: SO:0000859
database_cross_reference: SO:paralogous_to
has_exact_synonym: paralogous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
property disjoint with: in orthology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves genes that diverged after a duplication event.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000011
annotated property: definition
annotated source: in paralogy relationship with
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in syntenic paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that involves sets of syntenic blocks.
has_related_synonym: duplicon
has_related_synonym: paralogon
has_exact_synonym: syntenic paralogous to
creator: bgee.unil.ch
sub property of: in syntenic homology relationship with
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
annotated target: Paralogy that involves sets of syntenic blocks.
database_cross_reference: 1471-213X-7-100
database_cross_reference: HOM_0000012
annotated property: definition
annotated source: in syntenic paralogy relationship with

in syntenic orthology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Syntenic homology that involves chromosomes of different species.
has_exact_synonym: syntenic orthologous to
creator: bgee.unil.ch
sub property of: in syntenic homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Syntenic homology that involves chromosomes of different species.
database_cross_reference: gr.6380007
database_cross_reference: HOM_0000013
annotated property: definition
annotated source: in syntenic orthology relationship with

in partial homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
has_exact_synonym: fractional homology
has_related_synonym: mixed homology
has_related_synonym: modular homology
has_related_synonym: partial correspondence
has_exact_synonym: partial homologous to
has_related_synonym: percent homology
has_exact_synonym: segmental homology
creator: bgee.unil.ch
sub property of: in structural homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:0123195837
database_cross_reference: ISBN:978-0471984931
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
database_cross_reference: HOM_0000014
annotated property: definition
annotated source: in partial homology relationship with

in protein structural homology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: MeSH:Structural_Homology,_Protein
definition: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
has_exact_synonym: protein structural homologous to
creator: bgee.unil.ch
sub property of: in structural homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
database_cross_reference: 0022-2836(76)90195-9
database_cross_reference: HOM_0000015
annotated property: definition
annotated source: in protein structural homology relationship with

in non functional homology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: SO:non_functional_homolog_of
definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
has_exact_synonym: non functional homologous to
has_broad_synonym: pseudogene
creator: bgee.unil.ch
sub property of: in structural homology relationship with
property disjoint with: in equivalogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: SO:non_functional_homolog_of
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
database_cross_reference: HOM_0000016
annotated property: definition
annotated source: in non functional homology relationship with

in orthology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:00000060
definition: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: SO:0000855
database_cross_reference: SO:0000858
database_cross_reference: SO:orthologous_to
comment: The term is sometimes also used for anatomical structures.
has_exact_synonym: orthologous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves genes that diverged after a speciation event.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000017
annotated property: definition
annotated source: in orthology relationship with
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/5449325

in xenology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
has_exact_synonym: xenologous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000018
annotated property: definition
annotated source: in xenology relationship with

in 1 to 1 homology relationship with
type: ObjectProperty
type: SymmetricProperty
has_exact_synonym: 1 to 1 homologous to
has_exact_synonym: 1:1 homology
definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
has_exact_synonym: one-to-one homology
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: BGEE:curator
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
database_cross_reference: HOM_0000019
annotated property: definition
annotated source: in 1 to 1 homology relationship with

in 1 to 1 orthology relationship with
type: ObjectProperty
type: SymmetricProperty
has_exact_synonym: 1 to 1 orthologous to
has_exact_synonym: 1:1 orthology
definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
has_exact_synonym: one-to-one orthology
creator: bgee.unil.ch
sub property of: in orthology relationship with
sub property of: in 1 to 1 homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: HOM_0000020
annotated property: definition
annotated source: in 1 to 1 orthology relationship with
database_cross_reference: homology method.html

in ohnology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that results from a whole genome duplication event.
has_related_synonym: homoeology
has_exact_synonym: ohnologous to
creator: bgee.unil.ch
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that results from a whole genome duplication event.
database_cross_reference: http://dx.doi.org/10.1038/75560
database_cross_reference: HOM_0000022
annotated property: definition
annotated source: in ohnology relationship with

in in-paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
has_exact_synonym: in-paralogous to
has_exact_synonym: inparalogy
has_exact_synonym: symparalogy
creator: bgee.unil.ch
sub property of: in paralogy relationship with
property disjoint with: in out-paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000023
annotated property: definition
annotated source: in in-paralogy relationship with

in out-paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that results from a duplication preceding a given speciation event.
has_exact_synonym: alloparalogy
has_exact_synonym: out-paralogous to
has_exact_synonym: outparalogy
creator: bgee.unil.ch
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that results from a duplication preceding a given speciation event.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000024
annotated property: definition
annotated source: in out-paralogy relationship with

in pro-orthology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
has_exact_synonym: pro-orthologous to
creator: bgee.unil.ch
sub property of: in 1 to many orthology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000025
annotated property: definition
annotated source: in pro-orthology relationship with

in semi-orthology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
comment: The converse of pro-orthologous.
has_exact_synonym: semi-orthologous to
creator: bgee.unil.ch
sub property of: in 1 to many orthology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
database_cross_reference: scdb.1999.0338
database_cross_reference: nrg2099
database_cross_reference: HOM_0000026
annotated property: definition
annotated source: in semi-orthology relationship with

in serial homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Iterative homology that involves structures arranged along the main body axis.
has_related_synonym: homonomy
has_exact_synonym: serial homologous to
creator: bgee.unil.ch
sub property of: in iterative homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Iterative homology that involves structures arranged along the main body axis.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000027
annotated property: definition
annotated source: in serial homology relationship with

in heterochronous homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
has_exact_synonym: heterochronous homologous to
has_exact_synonym: heterochrony
creator: bgee.unil.ch
sub property of: in biological homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: HOM_0000028
annotated property: definition
annotated source: in heterochronous homology relationship with

in paedomorphorsis relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
has_exact_synonym: juvenification
has_exact_synonym: pedomorphosis
creator: bgee.unil.ch
sub property of: in heterochronous homology relationship with
property disjoint with: in peramorphosis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
database_cross_reference: ISBN:978-0674639416
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000029
annotated property: definition
annotated source: in paedomorphorsis relationship with

in peramorphosis relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
creator: bgee.unil.ch
sub property of: in heterochronous homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000030
annotated property: definition
annotated source: in peramorphosis relationship with

in progenesis relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
creator: bgee.unil.ch
sub property of: in paedomorphorsis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:978-0674639416
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
database_cross_reference: Progenesis
database_cross_reference: HOM_0000031
annotated property: definition
annotated source: in progenesis relationship with

in neoteny relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paedomorphosis that is produced by a retardation of somatic development.
has_exact_synonym: juvenilization
has_exact_synonym: neotenous to
creator: bgee.unil.ch
sub property of: in paedomorphorsis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:978-0674639416
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
database_cross_reference: Neoteny
database_cross_reference: HOM_0000032
annotated property: definition
annotated source: in neoteny relationship with

in mimicry relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
has_exact_synonym: mimicrous to
creator: bgee.unil.ch
sub property of: in convergence relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
database_cross_reference: HOM_0000033
annotated property: definition
annotated source: in mimicry relationship with
database_cross_reference: Mimicry

in 1 to many orthology relationship with
type: ObjectProperty
type: SymmetricProperty
has_exact_synonym: 1 to many orthologous to
has_exact_synonym: 1:many orthology
definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
has_related_synonym: co-orthology
has_related_synonym: many to 1 orthology
has_exact_synonym: one-to-many orthology
creator: bgee.unil.ch
sub property of: in orthology relationship with
sub property of: in 1 to many homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
database_cross_reference: 415741a
database_cross_reference: HOM_0000034
annotated property: definition
annotated source: in 1 to many orthology relationship with
database_cross_reference: homology method.html

in many to many homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves two members of a larger set of homologs.
has_exact_synonym: many to many homologous to
has_exact_synonym: many-to-many homology
has_exact_synonym: many:many homology
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves two members of a larger set of homologs.
database_cross_reference: msp002
database_cross_reference: HOM_0000036
annotated property: definition
annotated source: in many to many homology relationship with

in 1 to many homology relationship with
type: ObjectProperty
type: SymmetricProperty
has_exact_synonym: 1 to many homologous to
has_related_synonym: 1:many homology
definition: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
has_exact_synonym: one-to-many homology
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: BGEE:curator
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
database_cross_reference: HOM_0000037
annotated property: definition
annotated source: in 1 to many homology relationship with

in apomorphy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
has_exact_synonym: apomorphous to
has_related_synonym: synapomorphy
creator: bgee.unil.ch
sub property of: in historical homology relationship with
property disjoint with: in plesiomorphy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
database_cross_reference: ISBN:978-0252068140
database_cross_reference: HOM_0000042
annotated property: definition
annotated source: in apomorphy relationship with

in plesiomorphy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that is based on distant shared ancestry.
comment: This term is usually contrasted to apomorphy.
has_exact_synonym: plesiomorphous to
has_related_synonym: symplesiomorphy
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that is based on distant shared ancestry.
database_cross_reference: ISBN:978-0252068140
database_cross_reference: HOM_0000043
annotated property: definition
annotated source: in plesiomorphy relationship with

in deep homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
comment: Used for structures in distantly related taxa.
has_exact_synonym: deep genetic homology
has_exact_synonym: deep homologous to
has_related_synonym: generative homology
has_related_synonym: homoiology
creator: bgee.unil.ch
sub property of: in homocracy relationship with
sub property of: in parallelism relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: nature07891
database_cross_reference: HOM_0000044
annotated property: definition
annotated source: in deep homology relationship with

in hemiplasy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
has_exact_synonym: hemiplasous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
database_cross_reference: pnas.0807433105
database_cross_reference: HOM_0000045
annotated property: definition
annotated source: in hemiplasy relationship with

in gametology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
has_exact_synonym: gametologous to
creator: bgee.unil.ch
sub property of: in chromosomal homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
database_cross_reference: HOM_0000046
annotated property: definition
annotated source: in gametology relationship with
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/11110898

in chromosomal homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: MeSH:Chromosome_Pairing
has_exact_synonym: chromosomal homologous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
database_cross_reference: ISBN:0195307615
database_cross_reference: HOM_0000047
annotated property: definition
annotated source: in chromosomal homology relationship with

in many to many orthology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
has_related_synonym: co-orthology
has_exact_synonym: many to many orthologous to
has_exact_synonym: many-to-many orthology
has_exact_synonym: many:many orthology
has_related_synonym: trans-homology
has_exact_synonym: trans-orthology
creator: bgee.unil.ch
sub property of: in orthology relationship with
sub property of: in many to many homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
database_cross_reference: 415741a
database_cross_reference: HOM_0000048
annotated property: definition
annotated source: in many to many orthology relationship with
database_cross_reference: homology method.html

in within-species paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that involves genes from the same species.
has_exact_synonym: within-species paralogous to
creator: bgee.unil.ch
sub property of: in paralogy relationship with
property disjoint with: in between-species paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that involves genes from the same species.
database_cross_reference: HOM_0000049
annotated property: definition
annotated source: in within-species paralogy relationship with
database_cross_reference: homology method.html

in between-species paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that involves genes from different species.
comment: The genes have diverged before a speciation event.
has_exact_synonym: between-species paralogous to
creator: bgee.unil.ch
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that involves genes from different species.
database_cross_reference: HOM_0000050
annotated property: definition
annotated source: in between-species paralogy relationship with
database_cross_reference: homology method.html

in postdisplacement relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
has_exact_synonym: post-displacement
creator: bgee.unil.ch
sub property of: in paedomorphorsis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
database_cross_reference: Pedomorphosis
database_cross_reference: HOM_0000051
annotated property: definition
annotated source: in postdisplacement relationship with

in hypermorphosis relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Peramorphosis that is produced by a delay in the offset of development.
creator: bgee.unil.ch
sub property of: in peramorphosis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:978-0674639416
annotated target: Peramorphosis that is produced by a delay in the offset of development.
database_cross_reference: Peramorphosis
database_cross_reference: HOM_0000052
annotated property: definition
annotated source: in hypermorphosis relationship with

in synology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
has_exact_synonym: synologous to
creator: bgee.unil.ch
sub property of: in xenology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
database_cross_reference: http://dx.doi.org/10.1007/BF00173425
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000053
annotated property: definition
annotated source: in synology relationship with

in isoorthology relationship with
type: ObjectProperty
type: SymmetricProperty
database_cross_reference: ECO:0000080
definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
has_exact_synonym: isoorthologous to
creator: bgee.unil.ch
sub property of: in orthology relationship with
sub property of: in equivalogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000054
annotated property: definition
annotated source: in isoorthology relationship with

in tandem paralogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
has_related_synonym: iterative paralogy
has_related_synonym: serial paralogy
has_exact_synonym: tandem paralogous to
creator: bgee.unil.ch
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:978-0878932665
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
database_cross_reference: S0168-9525(00)02005-9
database_cross_reference: HOM_0000055
annotated property: definition
annotated source: in tandem paralogy relationship with

in latent homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
comment: Used for structures in closely related taxa.
has_exact_synonym: apomorphic tendency
has_exact_synonym: cryptic homology
has_related_synonym: homoiology
has_related_synonym: homoplastic tendency
has_exact_synonym: latent homologous to
has_related_synonym: re-awakening
has_exact_synonym: underlying synapomorphy
creator: bgee.unil.ch
sub property of: in parallelism relationship with
sub property of: in syngeny relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:0199141118
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.jhevol.2006.11.010
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000057
annotated property: definition
annotated source: in latent homology relationship with

in syngeny relationship with
type: ObjectProperty
type: SymmetricProperty
comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
has_exact_synonym: generative homology
has_exact_synonym: syngenous to
creator: bgee.unil.ch
sub property of: in homocracy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
database_cross_reference: http://dx.doi.org/10.1186/1742-9994-2-15
database_cross_reference: HOM_0000058
annotated property: definition
annotated source: in syngeny relationship with

in apparent orthology relationship with
type: ObjectProperty
type: SymmetricProperty
has_exact_synonym: 1:1 paralogy
definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
has_exact_synonym: apparent 1:1 orthology
has_exact_synonym: apparent orthologous to
has_exact_synonym: pseudoorthology
creator: bgee.unil.ch
sub property of: in 1 to 1 homology relationship with
sub property of: in between-species paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000060
annotated property: definition
annotated source: in apparent orthology relationship with
database_cross_reference: homology method.html

in pseudoparalogy relationship with
type: ObjectProperty
type: SymmetricProperty
comment: These genes may come out as paralogs in a single-genome analysis.
definition: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
has_exact_synonym: pseudoparalogous to
creator: bgee.unil.ch
sub property of: in xenology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
database_cross_reference: annurev.genet.39.073003.114725
database_cross_reference: HOM_0000061
annotated property: definition
annotated source: in pseudoparalogy relationship with

in equivalogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
comment: This may include examples of orthology, paralogy and xenology.
has_exact_synonym: equivalogous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
sub property of: in functional equivalence relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
database_cross_reference: gkl1043
database_cross_reference: HOM_0000062
annotated property: definition
annotated source: in equivalogy relationship with

in interology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
has_exact_synonym: interologous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: science.287.5450.116
database_cross_reference: HOM_0000063
annotated property: definition
annotated source: in interology relationship with

in functional equivalence relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Similarity that is characterized by interchangeability in function.
has_related_synonym: functional similarity
creator: bgee.unil.ch
sub property of: in similarity relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Similarity that is characterized by interchangeability in function.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: 415741a
database_cross_reference: HOM_0000065
annotated property: definition
annotated source: in functional equivalence relationship with

in iterative homology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Biological homology that involves parts of the same organism.
has_exact_synonym: iterative homologous to
creator: bgee.unil.ch
sub property of: in biological homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Biological homology that involves parts of the same organism.
database_cross_reference: annurev.es.20.110189.000411
database_cross_reference: HOM_0000066
annotated property: definition
annotated source: in iterative homology relationship with

in paraxenology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
has_exact_synonym: duplicate xenology
has_exact_synonym: multiple xenology
has_exact_synonym: paraxenologous to
creator: bgee.unil.ch
sub property of: in xenology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
database_cross_reference: HOM_0000068
annotated property: definition
annotated source: in paraxenology relationship with
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in plerology relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
comment: This phenomenon is usually due to gene conversion process.
has_exact_synonym: plerologous to
creator: bgee.unil.ch
sub property of: in paralogy relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
database_cross_reference: HOM_0000069
annotated property: definition
annotated source: in plerology relationship with
database_cross_reference: http://www.ncbi.nlm.nih.gov/pubmed/3065587

in homotopy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Structural homology that involves structures with the same or similar relative positions.
comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
has_exact_synonym: homotopous to
creator: bgee.unil.ch
sub property of: in structural homology relationship with
property disjoint with: in homeosis relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
database_cross_reference: ISBN:0123195837
annotated target: Structural homology that involves structures with the same or similar relative positions.
database_cross_reference: http://dx.doi.org/10.1007/BF02814484
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: HOM_0000071
annotated property: definition
annotated source: in homotopy relationship with

in homeosis relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Biological homology that involves an ectopic structure and the normally positioned structure.
has_related_synonym: heterotopy
creator: bgee.unil.ch
sub property of: in biological homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
database_cross_reference: http://dx.doi.org/10.1007/BF02814485
database_cross_reference: j.cell.2008.06.030
database_cross_reference: HOM_0000072
annotated property: definition
annotated source: in homeosis relationship with

in homoeology relationship with
type: ObjectProperty
type: SymmetricProperty
comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
definition: Synology that results from allopolyploidy.
has_exact_synonym: homoeologous to
creator: bgee.unil.ch
sub property of: in ohnology relationship with
sub property of: in synology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Synology that results from allopolyploidy.
database_cross_reference: pnas.0505156102
database_cross_reference: HOM_0000073
annotated property: definition
annotated source: in homoeology relationship with

in paramorphism relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
has_related_synonym: axis paramorphism
creator: bgee.unil.ch
sub property of: in homocracy relationship with
sub property of: in iterative homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
database_cross_reference: s10441-007-9023-8
database_cross_reference: j.1525-142x.2000.00054.x
database_cross_reference: HOM_0000074
annotated property: definition
annotated source: in paramorphism relationship with

in regulogy relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has_exact_synonym: regulogous to
creator: bgee.unil.ch
sub property of: in historical homology relationship with
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127

Axiom
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
database_cross_reference: gr.1774904
database_cross_reference: HOM_0000075
annotated property: definition
annotated source: in regulogy relationship with

bibliographicCitation
type: DatatypeProperty
comment: Organizational term to help define related terms. Do not use for data annotation with Darwin Core.

date
type: DatatypeProperty
comment: Organizational term to help define related terms. Do not use for data annotation with Darwin Core.

Accepted Name Usage
type: DatatypeProperty
status: recommended
description: Example: "Tamias minimus" valid name for "Eutamias minimus"
comment: The full name, with authorship and date information if known, of the currently valid (zoological) or accepted (botanical) taxon.
abcd equivalence: not in ABCD
issued: 2008-11-19
modified: 2009-09-21
organized in class: Taxon
replaces: acceptedScientificName-2009-07-06
has version: acceptedNameUsage-2009-09-21

According To
type: DatatypeProperty
abcd equivalence: not in ABCD
status: recommended
issued: 2009-01-21
modified: 2009-01-21
comment: Organizational term to help define related terms. Do not use for data annotation.
comment: Abstract term to attribute information to a source.
has version: accordingTo-2009-01-21

Associated Media
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
comment: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.
description: Example: "http://arctos.database.museum/SpecimenImages/UAMObs/Mamm/2/P7291179.JPG"
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/MultimediaObjects
replaces: ImageURL-2007-04-17
organized in class: Occurrence
has version: associatedMedia-2009-04-24

Associated Occurrences
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
issued: 2008-11-19
comment: A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence.
description: Example: "sibling of FMNH:Mammal:1234; sibling of FMNH:Mammal:1235"
status: recommended
organized in class: Occurrence
replaces: RelatedCatalogedItems-2007-04-17
has version: associatedOccurrences-2009-04-24

Associated References
type: DatatypeProperty
modified: 2009-04-24
comment: A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/UnitReferences
issued: 2008-11-19
description: Examples: "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767."
organized in class: Occurrence
has version: associatedReferences-2009-04-24

Associated Sequences
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Sequences/Sequence/ID-in-Database + constant
modified: 2009-04-24
issued: 2008-11-19
comment: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
description: Example: "GenBank: U34853.1"
status: recommended
replaces: GenBankNumber-2007-04-17
organized in class: Occurrence
has version: associatedSequences-2009-04-24

Associated Taxa
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Synecology/AssociatedTaxa
modified: 2009-04-24
issued: 2008-11-19
comment: A list (concatenated and separated) of identifiers or names of taxa and their associations with the Occurrence.
status: recommended
description: Example: "host: Quercus alba"
organized in class: Occurrence
has version: associatedTaxa-2009-04-24

Basis of Record
type: DatatypeProperty
modified: 2009-12-07
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/RecordBasis
description: Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"
comment: The specific nature of the data record - a subtype of the dcterms:type. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).
organized in class: all
replaces: basisOfRecord-2009-09-11
has version: basisOfRecord-2009-12-07
decision: Decision-2009-12-07 2

Bed
type: DatatypeProperty
issued: 2009-04-24
status: recommended
abcd equivalence: not in ABCD
modified: 2009-07-06
comment: The full name of the lithostratigraphic bed from which the cataloged item was collected.
replaces: http://rs.tdwg.org/dwc/terms/Bed-2005-07-03
organized in class: Geological Context
has version: http://rs.tdwg.org/dwc/terms/history/#bed-2009-04-24

Behavior
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2009-04-24
issued: 2009-03-06
comment: A description of the behavior shown by the subject at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.
status: recommended
description: Examples: "roosting", "foraging", "running"
organized in class: Occurrence
has version: behavior-2009-04-24

Catalog Number
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
comment: An identifier (preferably unique) for the record within the data set or collection.
abcd equivalence: DataSets/DataSet/Units/Unit/UnitID
description: Examples: "2008.1334", "145732a", "145732"
status: recommended
replaces: CatalogNumber-2007-04-17
organized in class: Occurrence
has version: catalogNumber-2009-04-24

Class
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-08-24
description: Examples: "Mammalia", "Hepaticopsida"
comment: The full scientific name of the class in which the taxon is classified.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = classis
organized in class: Taxon
replaces: class-2009-04-24
has version: class-2009-08-24

Collection Code
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
description: Examples: "Mammals", "Hildebrandt", "eBird"
comment: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
status: recommended
modified: 2013-10-04
issued: 2008-11-19
organized in class: all
replaces: collectionCode-2009-08-24
has version: collectionCode-2009-09-11

Collection ID
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
modified: 2013-10-04
issued: 2008-11-19
comment: An identifier for the collection or dataset from which the record was derived. For physical specimens, the recommended best practice is to use the identifier in a collections registry such as the Biodiversity Collections Index (http://www.biodiversitycollectionsindex.org/).
description: Example: "urn:lsid:biocol.org:col:34818"
status: recommended
organized in class: all
has version: collectionID-2009-09-11

Continent
type: DatatypeProperty
status: recommended
modified: 2013-10-04
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Continent
description: Examples: "Africa", "Antarctica", "Asia", "Europe", "North America", "Oceania", "South America"
comment: The name of the continent in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
organized in class: Location
replaces: Continent-2007-04-17
has version: continent-2009-04-24

Coordinate Precision
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
comment: A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/ISOAccuracy or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/AccuracyStatement
description: Examples: "0.00001" (normal GPS limit for decimal degrees), "0.000278" (nearest second), "0.01667" (nearest minute), "1.0" (nearest degree)
status: recommended
organized in class: Location
replaces: CoordinatePrecision-2003-06-13
has version: coordinatePrecision-2009-04-24

Coordinate Uncertainty In Meters
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "30" (reasonable lower limit of a GPS reading under good conditions if the actual precision was not recorded at the time), "71" (uncertainty for a UTM coordinate having 100 meter precision and a known spatial reference system).
comment: The horizontal distance (in meters) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinateErrorDistanceInMeters
organized in class: Location
replaces: CoordinateUncertaintyInMeters-2007-04-17
has version: coordinateUncertaintyInMeters-2009-04-24

Country
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Country/Name
issued: 2008-11-19
description: Examples: "Denmark", "Colombia", "España"
comment: The name of the country or major administrative unit in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
status: recommended
modified: 2009-04-24
organized in class: Location
replaces: Country-2007-04-17
has version: country-2009-04-24

Country Code
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Country/ISO3166Code
description: Examples: "AR" for Argentina, "SV" for El Salvador
comment: The standard code for the country in which the Location occurs. Recommended best practice is to use ISO 3166-1-alpha-2 country codes.
status: recommended
issued: 2008-11-19
organized in class: Location
has version: countryCode-2009-04-24

County
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= County
description: Examples: "Missoula", "Los Lagos", "Mataró"
status: recommended
issued: 2008-11-19
comment: The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.
organized in class: Location
replaces: County-2007-04-17
has version: county-2009-04-24

Data Generalizations
type: DatatypeProperty
issued: 2008-11-19
status: recommended
comment: Actions taken to make the shared data less specific or complete than in its original form. Suggests that alternative data of higher quality may be available on request.
description: Example: "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell"
abcd equivalence: not in ABCD
modified: 2009-04-24
replaces: Generalizations-2008-11-19
organized in class: all
has version: dataGeneralizations-2009-04-24

Dataset Name
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/SourceID
modified: 2009-09-11
issued: 2009-09-11
description: Examples: "Grinnell Resurvey Mammals", "Lacey Ctenomys Recaptures"
comment: The name identifying the data set from which the record was derived.
status: recommended
organized in class: all
has version: datasetName-2009-09-11

Date Identified
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-08-24
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Date/DateText
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
comment: The date on which the subject was identified as representing the Taxon. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
sub property of: date
organized in class: Identification
replaces: dateIdentified-2009-04-24
has version: dateIdentified-2009-08-24

Day
type: DatatypeProperty
issued: 2008-11-19
status: recommended
comment: The integer day of the month on which the Event occurred.
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
modified: 2009-04-24
description: Examples: "9", "28"
replaces: DayCollected-2003-06-17
organized in class: Event
has version: day-2009-04-24

Decimal Latitude
type: DatatypeProperty
modified: 2009-07-06
comment: The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/LatitudeDecimal
description: Example: "-41.0983423"
organized in class: Location
replaces: DecimalLatitude-2007-04-17
has version: decimalLatitude-2009-04-24

Decimal Longitude
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/LongitudeDecimal
issued: 2008-11-19
description: Example: "-121.1761111"
status: recommended
modified: 2009-07-06
comment: The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.
organized in class: Location
replaces: DecimalLongitude-2007-04-17
has version: decimalLongitude-2009-04-24

Disposition
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/Disposition
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "in collection", "missing", "voucher elsewhere", "duplicates elsewhere"
comment: The current state of a specimen with respect to the collection identified in collectionCode or collectionID. Recommended best practice is to use a controlled vocabulary.
replaces: Disposition-2007-04-17
organized in class: Occurrence
has version: disposition-2009-04-24

Dynamic Properties
type: DatatypeProperty
status: recommended
comment: A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content such as key-value pairs.
abcd equivalence: not in ABCD
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "tragusLengthInMeters=0.014; weightInGrams=120", "heightInMeters=1.5", "natureOfID=expert identification; identificationEvidence=cytochrome B sequence", "relativeHumidity=28; airTemperatureInC=22; sampleSizeInKilograms=10", "aspectHeading=277; slopeInDegrees=6", "iucnStatus=vulnerable; taxonDistribution=Neuquen, Argentina"
replaces: Attributes-2007-04-17
organized in class: all
has version: dynamicProperties-2009-04-24

Earliest Age Or Lowest Stage
type: DatatypeProperty
status: recommended
issued: 2009-04-24
abcd equivalence: not in ABCD
modified: 2009-07-06
description: Examples: "Atlantic", "Boreal", "Skullrockian"
comment: The full name of the earliest possible geochronologic age or lowest chronostratigraphic stage attributable to the stratigraphic horizon from which the cataloged item was collected.
replaces: EarliestAgeOrLowestStage-2005-07-03
organized in class: Geological Context
has version: earliestAgeOrLowestStage-2009-04-24

Earliest Eon Or Lowest Eonothem
type: DatatypeProperty
description: Examples: "Phanerozoic", "Proterozoic"
abcd equivalence: not in ABCD
modified: 2009-07-06
issued: 2009-04-24
status: recommended
comment: The full name of the earliest possible geochronologic eon or lowest chrono-stratigraphic eonothem or the informal name ("Precambrian") attributable to the stratigraphic horizon from which the cataloged item was collected.
replaces: EarliestEonOrLowestEonothem-2005-07-03
organized in class: Geological Context
has version: earliestEonOrLowestEonothem-2009-04-24

Earliest Epoch Or Lowest Series
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2009-07-06
issued: 2009-04-24
description: Examples: "Holocene", "Pleistocene", "Ibexian Series"
comment: The full name of the earliest possible geochronologic epoch or lowest chronostratigraphic series attributable to the stratigraphic horizon from which the cataloged item was collected.
status: recommended
replaces: EarliestEpochOrLowestSeries-2005-07-03
organized in class: Geological Context
has version: earliestEpochOrLowestSeries-2009-04-24

Earliest Era Or Lowest Erathem
type: DatatypeProperty
modified: 2009-07-06
issued: 2009-04-24
comment: The full name of the earliest possible geochronologic era or lowest chronostratigraphic erathem attributable to the stratigraphic horizon from which the cataloged item was collected.
status: recommended
description: Examples: "Cenozoic", "Mesozoic"
abcd equivalence: not in ABCD
replaces: EarliestEraOrLowestErathem-2005-07-03
organized in class: Geological Context
has version: earliestEraOrLowestErathem-2009-04-24

Earliest Period Or Lowest System
type: DatatypeProperty
comment: The full name of the earliest possible geochronologic period or lowest chronostratigraphic system attributable to the stratigraphic horizon from which the cataloged item was collected.
abcd equivalence: not in ABCD
issued: 2009-04-24
status: recommended
modified: 2009-07-06
description: Examples: "Neogene", "Tertiary", "Quaternary"
replaces: EarliestPeriodOrLowestSystem-2005-07-03
organized in class: Geological Context
has version: earliestPeriodOrLowestSystem-2009-04-24

End Day Of Year
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DayNumberEnd
modified: 2009-04-24
comment: The latest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).
status: recommended
issued: 2008-11-19
description: Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
replaces: DayOfYear-2007-04-17
organized in class: Event
has version: endDayOfYear-2009-04-24

Establishment Means
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/EstablishmentMeans
description: Examples: "native", "introduced", "naturalised", "invasive", "managed"
comment: The process by which the biological individual(s) represented in the Occurrence became established at the location. Recommended best practice is to use a controlled vocabulary.
organized in class: Occurrence
has version: establishmentMeans-2009-04-24

Event Date
type: DatatypeProperty
modified: 2009-07-01
issued: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
comment: 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. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
status: recommended
sub property of: date
replaces: EarliestDateCollected-2007-04-17
organized in class: Event
replaces: LatestDateCollected-2007-04-17
has version: eventDate-2009-04-24

Event Remarks
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Notes
comment: Comments or notes about the Event.
description: Example: "after the recent rains the river is nearly at flood stage"
status: recommended
issued: 2009-01-18
modified: 2009-04-24
organized in class: Event
has version: eventRemarks-2009-04-24

Event Time
type: DatatypeProperty
modified: 2009-04-24
issued: 2009-04-24
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin and DataSets/DataSet/Units/Unit/Gathering/ISODateTimeEnd
status: recommended
description: Examples: "14:07-0600" is 2:07pm in the time zone six hours earlier than UTC, "08:40:21Z" is 8:40:21am UTC, "13:00:00Z/15:30:00Z" is the interval between 1pm UTC and 3:30pm UTC.
comment: The time or interval during which an Event occurred. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
replaces: EndTimeOfDay-2005-07-10
organized in class: Event
replaces: StartTimeOfDay-2005-07-10
has version: eventTime-2009-04-24

Family
type: DatatypeProperty
modified: 2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = familia
status: recommended
issued: 2008-11-19
description: Examples: "Felidae", "Monocleaceae"
comment: The full scientific name of the family in which the taxon is classified.
organized in class: Taxon
replaces: family-2009-04-24
has version: family-2009-08-24

Field Notes
type: DatatypeProperty
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/FieldNotes
comment: One of a) an indicator of the existence of, b) a reference to (publication, URI), or c) the text of notes taken in the field about the Event.
status: recommended
modified: 2009-04-24
description: Example: "notes available in Grinnell-Miller Library"
organized in class: Event
replaces: FieldNotes-2007-04-17
has version: fieldNotes-2009-04-24

Field Number
type: DatatypeProperty
issued: 2008-11-19
status: recommended
comment: An identifier given to the event in the field. Often serves as a link between field notes and the Event.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Code
modified: 2009-04-24
description: Example: "RV Sol 87-03-08"
organized in class: Event
replaces: FieldNumber-2007-04-17
has version: fieldNumber-2009-04-24

Footprint SRS
type: DatatypeProperty
status: recommended
issued: 2009-07-06
modified: 2009-07-06
comment: A Well-Known Text (WKT) representation of the Spatial Reference System (SRS) for the footprintWKT of the Location. Do not use this term to describe the SRS of the decimalLatitude and decimalLongitude, even if it is the same as for the footprintWKT - use the geodeticDatum instead.
description: Example: The WKT for the standard WGS84 SRS (EPSG:4326) is "GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.0174532925199433]]" without the enclosing quotes.
abcd equivalence: not in ABCD
organized in class: Location
has version: footprintSRS-2009-07-06

Footprint Spatial Fit
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/FootprintSpatialFit (ABCD v2.06b)
description: Detailed explanations with graphical examples can be found in the "Guide to Best Practices for Georeferencing", Chapman and Wieczorek, eds. 2006 (http://www.gbif.org/prog/digit/Georeferencing).
comment: The ratio of the area of the footprint (footprintWKT) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given footprint does not completely contain the original representation. The footprintSpatialFit is undefined (and should be left blank) if the original representation is a point and the given is not that same point. If both the original and the given georeference are the same point, the footprintSpatialFit is 1.
status: recommended
issued: 2008-11-19
modified: 2009-04-24
organized in class: Location
replaces: FootprintSpatialFit-2007-04-17
has version: footprintSpatialFit-2009-04-24

Footprint WKT
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
comment: A Well-Known Text (WKT) representation of the shape (footprint, geometry) that defines the Location. A Location may have both a point-radius representation (see decimalLatitude) and a footprint representation, and they may differ from each other.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/FootprintWKT (ABCD v2.06b)
description: Example: the one-degree bounding box with opposite corners at (longitude=10, latitude=20) and (longitude=11, latitude=21) would be expressed in well-known text as POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20))
status: recommended
organized in class: Location
replaces: FootprintWKT-2007-04-17
has version: footprintWKT-2009-04-24

Formation
type: DatatypeProperty
description: Examples: "Notch Peak Fromation", "House Limestone", "Fillmore Formation"
comment: The full name of the lithostratigraphic formation from which the cataloged item was collected.
status: recommended
abcd equivalence: not in ABCD
modified: 2009-07-06
issued: 2009-04-24
replaces: Formation-2005-07-03
organized in class: Geological Context
has version: formation-2009-04-24

Genus
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-08-24
description: Examples: "Puma", "Monoclea"
comment: The full scientific name of the genus in which the taxon is classified.
status: recommended
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Viral/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/GenusOrMonomial}
organized in class: Taxon
replaces: genus-2009-04-24
has version: genus-2009-08-24

Geodetic Datum
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/SpatialDatum
issued: 2008-11-19
description: Examples: "EPSG:4326", "WGS84", "NAD27", "Campo Inchauspe", "European 1950", "Clarke 1866"
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".
status: recommended
modified: 2009-07-06
organized in class: Location
replaces: GeodeticDatum-2007-04-17
has version: geodeticDatum-2009-04-24

Georeference Protocol
type: DatatypeProperty
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinateMethod
modified: 2009-04-24
comment: A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.
description: Examples: "Guide to Best Practices for Georeferencing" (Chapman and Wieczorek, eds. 2006), Global Biodiversity Information Facility.", "MaNIS/HerpNet/ORNIS Georeferencing Guidelines", "Georeferencing Quick Reference Guide"
organized in class: Location
replaces: GeoreferenceProtocol-2007-04-17
has version: georeferenceProtocol-2009-04-24

Georeference Remarks
type: DatatypeProperty
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceRemarks
modified: 2009-04-24
description: Example: "assumed distance by road (Hwy. 101)"
comment: Notes or comments about the spatial description determination, explaining assumptions made in addition or opposition to the those formalized in the method referred to in georeferenceProtocol.
status: recommended
organized in class: Location
replaces: GeoreferenceRemarks-2007-04-17
has version: georeferenceRemarks-2009-04-24

Georeference Sources
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
comment: A list (concatenated and separated) of maps, gazetteers, or other resources used to georeference the Location, described specifically enough to allow anyone in the future to use the same resources.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceSources
description: Examples: "USGS 1:24000 Florence Montana Quad; Terrametrics 2008 on Google Earth"
status: recommended
organized in class: Location
replaces: GeoreferenceSources-2007-04-17
has version: georeferenceSources-2009-04-24

Georeference Verification Status
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
status: recommended
comment: A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description. Recommended best practice is to use a controlled vocabulary.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/GeoreferenceVerificationStatus
description: Examples: "requires verification", "verified by collector", "verified by curator".
organized in class: Location
replaces: GeoreferenceVerificationStatus-2007-04-17
has version: georeferenceVerificationStatus-2009-04-24

Georeferenced By
type: DatatypeProperty
issued: 2009-01-21
modified: 2009-04-24
comment: A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.
description: Examples: "Kristina Yamamoto (MVZ); Janet Fang (MVZ)", "Brad Millen (ROM)"
abcd equivalence: not in ABCD
status: recommended
organized in class: Location
sub property of: According To
has version: georeferencedBy-2009-04-24

Georeferenced Date
type: DatatypeProperty
modified: 2011-10-16
issued: 2011-10-16
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
comment: The date on which the Location was georeferenced. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
abcd equivalence: not in ABCD
status: recommended
organized in class: Location
sub property of: date
has version: georeferencedDate-2011-10-16
decision: Decision-2011-10-16 9

Group
type: DatatypeProperty
issued: 2009-04-24
abcd equivalence: not in ABCD
modified: 2009-07-06
comment: The full name of the lithostratigraphic group from which the cataloged item was collected.
status: recommended
organized in class: Geological Context
replaces: Group-2005-07-03
has version: group-2009-04-24

Habitat
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-05-17
description: Examples: "oak savanna", "pre-cordilleran steppe"
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Biotope/Text
comment: A category or description of the habitat in which the Event occurred.
organized in class: Event
has version: habitat-2009-04-24

Higher Classification
type: DatatypeProperty
issued: 2008-11-19
comment: A list (concatenated and separated) of taxa names terminating at the rank immediately superior to the taxon referenced in the taxon record. Recommended best practice is to order the list starting with the highest rank and separating the names for each rank with a semi-colon (";").
description: Example: "Animalia;Chordata;Vertebrata;Mammalia;Theria;Eutheria;Rodentia;Hystricognatha;Hystricognathi;Ctenomyidae;Ctenomyini;Ctenomys"
abcd equivalence: not in ABCD
status: recommended
modified: 2009-08-24
organized in class: Taxon
replaces: higherTaxonName-2009-04-24
has version: higherClassification-2009-08-24

Higher Geography
type: DatatypeProperty
abcd equivalence: {DataSets/DataSet/Units/Unit/Gathering/LocalityText or DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName}
issued: 2008-11-19
modified: 2009-04-24
comment: A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.
description: Example: "South America; Argentina; Patagonia; Parque Nacional Nahuel Huapi; Neuquén; Los Lagos" with accompanying values "South America" in Continent, "Argentina" in Country, "Neuquén" in StateProvince, and Los Lagos in County.
status: recommended
organized in class: Location
replaces: HigherGeography-2007-04-17
has version: higherGeography-2009-04-24

Highest Biostratigraphic Zone
type: DatatypeProperty
issued: 2009-04-24
modified: 2009-07-06
status: recommended
comment: The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
abcd equivalence: not in ABCD
organized in class: Geological Context
replaces: HighestBiostratigraphicZone-2005-07-03
has version: highestBiostratigraphicZone-2009-04-24

Identification Qualifier
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/IdentificationQualifier
status: recommended
modified: 2009-04-24
issued: 2008-11-19
comment: A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.
description: Examples: 1) For the determination "Quercus aff. agrifolia var. oxyadenia", identificationQualifier would be "aff. agrifolia var. oxyadenia" with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank. 2) For the determination "Quercus agrifolia cf. var. oxyadenia", identificationQualifier would be "cf. var. oxyadenia " with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank.
organized in class: Identification
replaces: IdentificationQualifier-2007-04-17
has version: identificationQualifier-2009-04-24

Identification References
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
comment: A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/References
description: Example: "Aves del Noroeste Patagonico. Christie et al. 2004."
status: recommended
organized in class: Identification
has version: identificationReferences-2009-04-24

Identification Remarks
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Notes
description: Example: "Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas."
status: recommended
issued: 2008-11-19
comment: Comments or notes about the Identification.
organized in class: Identification
has version: identificationRemarks-2009-04-24

Identification Verification Status
type: DatatypeProperty
issued: 2011-10-16
comment: A categorical indicator of the extent to which the taxonomic identification has been verified to be correct. Recommended best practice is to use a controlled vocabulary such as that used in HISPID/ABCD.
description: Examples: "0", "4"
status: recommended
modified: 2011-10-16
abcd equivalence: not in ABCD
organized in class: Identification
has version: identificationVerificationStatus-2011-10-16
decision: Decision-2011-10-16 10

Identified By
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/Identifiers/IdentifiersText
modified: 2009-08-24
issued: 2008-11-19
comment: A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.
description: Examples: "James L. Patton", "Theodore Pappenfuss; Robert Macey"
status: recommended
organized in class: Identification
sub property of: According To
replaces: identifiedBy-2009-04-24
has version: identifiedBy-2009-08-24

Individual Count
type: DatatypeProperty
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/LowerValue
modified: 2009-04-24
description: Examples: "1", "25"
comment: The number of individuals represented present at the time of the Occurrence.
replaces: IndividualCount-2007-04-17
organized in class: Occurrence
has version: individualCount-2009-04-24

Information Withheld
type: DatatypeProperty
modified: 2009-04-24
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/InformationWithheld
comment: Additional information that exists, but that has not been shared in the given record.
description: Examples: "location information not given for endangered species", "collector identities withheld", "ask about tissue samples"
replaces: InformationWithheld-2007-04-17
organized in class: all
has version: informationWithheld-2009-04-24

Infraspecific Epithet
type: DatatypeProperty
modified: 2009-08-24
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SubspeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/SecondEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SubspeciesEpithet}
status: recommended
issued: 2008-11-19
description: Examples: "concolor", "oxyadenia", "sayi"
comment: The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.
organized in class: Taxon
replaces: infraspecificEpithet-2009-04-24
has version: infraspecificEpithet-2009-08-24

Institution Code
type: DatatypeProperty
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/SourceInstitutionID
modified: 2013-10-04
description: Examples: "MVZ", "FMNH", "AKN-CLO", "University of California Museum of Paleontology (UCMP)"
comment: The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
status: recommended
organized in class: all
replaces: institutionCode-2009-08-24
has version: institutionCode-2009-09-11

Institution ID
type: DatatypeProperty
status: recommended
issued: 2009-09-11
modified: 2013-10-04
comment: An identifier for the institution having custody of the object(s) or information referred to in the record.
abcd equivalence: DataSets/DataSet/Units/Unit/SourceInstitutionID
organized in class: all
has version: institutionID-2009-09-11

Island
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island
modified: 2009-04-24
status: recommended
issued: 2008-11-19
description: Examples: "Isla Victoria", "Vancouver", "Viti Levu", "Zanzibar"
comment: The name of the island on or near which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
organized in class: Location
replaces: Island-2007-04-17
has version: island-2009-04-24

Island Group
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island group
status: recommended
description: Examples: "Alexander Archipelago", "Seychelles"
comment: The name of the island group in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
organized in class: Location
replaces: IslandGroup-2007-04-17
has version: islandGroup-2009-04-24

Kingdom
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = regnum
modified: 2009-08-24
description: Examples: "Animalia", "Plantae"
status: recommended
issued: 2008-11-19
comment: The full scientific name of the kingdom in which the taxon is classified.
organized in class: Taxon
replaces: kingdom-2009-04-24
has version: kingdom-2009-08-24

Latest AgeOr Highest Stage
type: DatatypeProperty
issued: 2009-04-24
description: Examples: "Atlantic", "Boreal", "Skullrockian"
abcd equivalence: not in ABCD
modified: 2009-07-06
status: recommended
comment: The full name of the latest possible geochronologic age or highest chronostratigraphic stage attributable to the stratigraphic horizon from which the cataloged item was collected.
organized in class: Geological Context
replaces: LatestAgeOrHighestStage-2005-07-03
has version: latestAgeOrHighestStage-2009-04-24

Latest Eon Or Highest Eonothem
type: DatatypeProperty
modified: 2009-07-06
issued: 2009-04-24
description: Examples: "Phanerozoic", "Proterozoic"
comment: The full name of the latest possible geochronologic eon or highest chrono-stratigraphic eonothem or the informal name ("Precambrian") attributable to the stratigraphic horizon from which the cataloged item was collected.
abcd equivalence: not in ABCD
status: recommended
organized in class: Geological Context
replaces: LatestEonOrLowestEonothem-2005-07-03
has version: latestEonOrHighestEonothem-2009-04-24

Latest Epoch Or Highest Series
type: DatatypeProperty
issued: 2009-04-24
modified: 2009-07-06
comment: The full name of the latest possible geochronologic epoch or highest chronostratigraphic series attributable to the stratigraphic horizon from which the cataloged item was collected.
abcd equivalence: not in ABCD
description: Examples: "Holocene", "Pleistocene", "Ibexian Series"
status: recommended
organized in class: Geological Context
replaces: LatestEpochOrHighestSeries-2005-07-03
has version: latestEpochOrHighestSeries-2009-04-24

Latest Era Or Highest Erathem
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2009-07-06
description: Examples: "Cenozoic", "Mesozoic"
comment: The full name of the latest possible geochronologic era or highest chronostratigraphic erathem attributable to the stratigraphic horizon from which the cataloged item was collected.
status: recommended
issued: 2009-04-24
organized in class: Geological Context
replaces: LatestEraOrHighestErathem-2005-07-03
has version: latestEraOrHighestErathem-2009-04-24

Latest Period Or Highest System
type: DatatypeProperty
status: recommended
modified: 2009-07-06
description: Examples: "Neogene", "Tertiary", "Quaternary"
comment: The full name of the latest possible geochronologic period or highest chronostratigraphic system attributable to the stratigraphic horizon from which the cataloged item was collected.
abcd equivalence: not in ABCD
issued: 2009-04-24
organized in class: Geological Context
replaces: LatestPeriodOrHighestSystem-2005-07-03
has version: latestPeriodOrHighestSystem-2009-04-24

Life Stage
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage (Note DwC spec uses ”MycologicalLifeStage” or DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "egg", "eft", "juvenile", "adult", "2 adults 4 juveniles"
comment: The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.
replaces: LifeStage-2007-04-17
organized in class: Occurrence
has version: lifeStage-2009-04-24

Lithostratigraphic Terms
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Stratigraphy/LithostratigraphicTerms
issued: 2009-04-24
modified: 2009-07-06
comment: The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.
status: recommended
organized in class: Geological Context
replaces: LithostratigraphicTerms-2005-07-03
has version: lithostratigraphicTerms-2009-04-24

Locality
type: DatatypeProperty
issued: 2008-11-19
description: Example: "Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)"
comment: 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.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
modified: 2009-04-24
organized in class: Location
replaces: Locality-2007-04-17
has version: locality-2009-04-24

Location According To
type: DatatypeProperty
modified: 2009-08-24
description: Examples: "Getty Thesaurus of Geographic Names", "GADM"
comment: Information about the source of this Location information. Could be a publication (gazetteer), institution, or team of individuals.
abcd equivalence: not in ABCD
issued: 2009-08-24
status: recommended
organized in class: Location
sub property of: According To
has version: locationAccordingTo-2009-08-24

Location Remarks
type: DatatypeProperty
status: recommended
modified: 2009-04-24
comment: Comments or notes about the Location.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/AreaDetail
issued: 2009-01-18
description: Example: "under water since 2005"
organized in class: Location
replaces: SamplingLocationRemarks-2009-01-18
has version: locationRemarks-2009-04-24

Lowest Biostratigraphic Zone
type: DatatypeProperty
modified: 2009-07-06
abcd equivalence: not in ABCD
status: recommended
issued: 2009-04-24
comment: The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
organized in class: Geological Context
replaces: LowestBiostratigraphicZone-2005-07-03
has version: lowestBiostratigraphicZone-2009-04-24

Maximum Depth In Meters
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/UpperValue
modified: 2009-04-24
comment: The greater depth of a range of depth below the local surface, in meters.
status: recommended
issued: 2008-11-19
description: Example: "200"
organized in class: Location
replaces: MaximumDepthInMeters-2007-04-17
has version: maximumDepthInMeters-2009-04-24

Maximum Distance Above Surface In Meters
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
description: Example: 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation; VerbatimElevation: "300m" MinimumElevationInMeters: "300", MaximumElevationInMeters: "300", VerbatimDepth: "20m", MinimumDepthInMeters: "20", MaximumDepthInMeters: "20", minimumDistanceAboveSurfaceInMeters: "0", maximumDistanceAboveSurfaceInMeters: "-1.5"
comment: The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/UpperValue
organized in class: Location
has version: maximumDistanceAboveSurfaceInMeters-2009-04-24

Maximum Elevation In Meters
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/UpperValue
status: recommended
issued: 2008-11-19
description: Example: "200"
comment: The upper limit of the range of elevation (altitude, usually above sea level), in meters.
organized in class: Location
replaces: MaximumElevationInMeters-2007-04-17
has version: maximumElevationInMeters-2009-04-24

Measurement Accuracy
type: DatatypeProperty
status: recommended
issued: 2009-01-18
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Aspect/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy
modified: 2009-04-24
description: Examples: "0.01", "normal distribution with variation of 2 m"
comment: The description of the potential error associated with the measurementValue.
organized in class: Measurement Or Fact
replaces: eventMeasurementAccuracy-2009-04-24
replaces: occurrenceMeasurementAccuracy-2009-04-24
has version: measurementAccuracy-2009-04-24

Measurement Determined By
type: DatatypeProperty
modified: 2009-04-24
issued: 2009-01-23
comment: A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasuredBy
description: Examples: "Javier de la Torre", "Julie Woodruff; Eileen Lacey"
status: recommended
organized in class: Measurement Or Fact
sub property of: According To
replaces: eventMeasurementDeterminedBy-2009-04-24
replaces: occurrenceMeasurementDeterminedBy-2009-04-24
has version: measurementDeterminedBy-2009-04-24

Measurement Determined Date
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasurementDateTime
issued: 2009-01-23
modified: 2009-04-24
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
comment: The date on which the MeasurementOrFact was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
sub property of: date
organized in class: Measurement Or Fact
replaces: eventMeasurementDeterminedDate-2009-04-24
replaces: occurrenceMeasurementDeterminedDate-2009-04-24
has version: measurementDeterminedDate-2009-04-24

Measurement Method
type: DatatypeProperty
abcd equivalence: /DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Method
modified: 2009-04-24
comment: A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion.
description: Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation
status: recommended
issued: 2008-11-19
organized in class: Measurement Or Fact
has version: measurementMethod-2009-04-24

Measurement Remarks
type: DatatypeProperty
modified: 2009-04-24
abcd equivalence: not in ABCD
status: recommended
issued: 2008-11-19
comment: Comments or notes accompanying the MeasurementOrFact.
description: Example: "tip of tail missing"
organized in class: Measurement Or Fact
replaces: eventMeasurementRemarks-2009-04-24
replaces: occurrenceMeasurementRemarks-2009-04-24
has version: measurementRemarks-2009-04-24

Measurement Type
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter
description: Examples: "tail length", "temperature", "trap line length", "survey area", "trap type"
comment: The nature of the measurement, fact, characteristic, or assertion. Recommended best practice is to use a controlled vocabulary.
status: recommended
organized in class: Measurement Or Fact
replaces: eventMeasurementType-2009-04-24
replaces: occurrenceMeasurementType-2009-04-24
has version: measurementType-2009-04-24

Measurement Unit
type: DatatypeProperty
modified: 2009-04-24
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement
issued: 2008-11-19
description: Examples: "mm", "C", "km", "ha"
comment: The units associated with the measurementValue. Recommended best practice is to use the International System of Units (SI).
organized in class: Measurement Or Fact
replaces: eventMeasurementUnit-2009-04-24
replaces: occurrenceMeasurementUnit-2009-04-24
has version: measurementUnit-2009-04-24

Measurement Value
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/UpperValue
description: Examples: "45", "20", "1", "14.5", "UV-light"
status: recommended
comment: The value of the measurement, fact, characteristic, or assertion.
organized in class: Measurement Or Fact
replaces: eventMeasurementValue-2009-04-24
replaces: occurrenceMeasurementValue-2009-04-24
has version: measurementValue-2009-04-24

Member
type: DatatypeProperty
status: recommended
modified: 2009-07-06
description: Examples: "Lava Dam Member", "Hellnmaria Member"
abcd equivalence: not in ABCD
issued: 2009-04-24
comment: The full name of the lithostratigraphic member from which the cataloged item was collected.
organized in class: Geological Context
replaces: Member-2005-07-03
has version: member-2009-04-24

Minimum Depth In Meters
type: DatatypeProperty
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/LowerValue
comment: The lesser depth of a range of depth below the local surface, in meters.
status: recommended
modified: 2009-04-24
description: Example: "100"
organized in class: Location
replaces: MinimumDepthInMeters-2007-04-17
has version: minimumDepthInMeters-2009-04-24

Minimum Distance Above Surface In Meters
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/LowerValue
description: Example: 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation; VerbatimElevation: "300m" MinimumElevationInMeters: "300", MaximumElevationInMeters: "300", VerbatimDepth: "20m", MinimumDepthInMeters: "20", MaximumDepthInMeters: "20", minimumDistanceAboveSurfaceInMeters: "0", maximumDistanceAboveSurfaceInMeters: "-1.5"
comment: The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
status: recommended
organized in class: Location
has version: minimumDistanceAboveSurfaceInMeters-2009-04-24

Minimum Elevation In Meters
type: DatatypeProperty
modified: 2009-04-24
comment: The lower limit of the range of elevation (altitude, usually above sea level), in meters.
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/LowerValue
description: Example: "100"
organized in class: Location
replaces: MinimumElevationInMeters-2007-04-17
has version: minimumElevationInMeters-2009-04-24

Month
type: DatatypeProperty
issued: 2008-11-19
comment: The ordinal month in which the Event occurred.
status: recommended
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
modified: 2009-04-24
description: Examples: "1" (=January), "10" (=October)
organized in class: Event
replaces: MonthCollected-2003-06-17
has version: month-2009-04-24

Municipality
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
description: Examples: "Holzminden"
comment: The full, unabbreviated name of the next smaller administrative region than county (city, municipality, etc.) in which the Location occurs. Do not use this term for a nearby named place that does not contain the actual location.
status: recommended
organized in class: Location
has version: municipality-2009-08-24

Name According To
type: DatatypeProperty
description: Example: "McCranie, J. R., D. B. Wake, and L. D. Wilson. 1996. The taxonomic status of Bolitoglossa schmidti, with comments on the biology of the Mesoamerican salamander Bolitoglossa dofleini (Caudata: Plethodontidae). Carib. J. Sci. 32:395-398.", "Werner Greuter 2008", "Lilljeborg 1861, Upsala Univ. Arsskrift, Math. Naturvet., pp. 4, 5"
comment: The reference to the source in which the specific taxon concept circumscription is defined or implied - traditionally signified by the Latin "sensu" or "sec." (from secundum, meaning "according to"). For taxa that result from identifications, a reference to the keys, monographs, experts and other sources should be given.
abcd equivalence: not in ABCD
issued: 2008-11-19
modified: 2009-09-21
status: recommended
organized in class: Taxon
sub property of: According To
replaces: taxonAccordingTo-2009-04-24
has version: nameAccordingTo-2009-09-21

Name Published In
type: DatatypeProperty
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation
modified: 2009-09-21
comment: A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.
description: Examples: "Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388", "Forel, Auguste, Diagnosies provisoires de quelques espèces nouvelles de fourmis de Madagascar, récoltées par M. Grandidier., Annales de la Societe Entomologique de Belgique, Comptes-rendus des Seances 30, 1886"
sub property of: bibliographicCitation
organized in class: Taxon
replaces: namePublishedIn-2009-04-24
has version: namePublishedIn-2009-09-21

Name Published In Year
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2011-10-16
status: recommended
issued: 2011-10-16
description: Examples: "1915", "2008"
comment: The four-digit year in which the scientificName was published.
organized in class: Taxon
has version: namePublishedInYear-2011-10-16
decision: Decision-2011-10-16 8

Nomenclatural Code
type: DatatypeProperty
modified: 2009-09-21
issued: 2008-11-19
comment: The nomenclatural code (or codes in the case of an ambiregnal name) under which the scientificName is constructed. Recommended best practice is to use a controlled vocabulary.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/Code
description: Examples: "ICBN", "ICZN", "BC", "ICNCP", "BioCode", "ICZN; ICBN"
replaces: NomenclaturalCode-2009-04-24
organized in class: Taxon
has version: nomenclaturalCode-2009-09-21

Nomenclatural Status
type: DatatypeProperty
modified: 2009-04-24
status: recommended
issued: 2009-01-18
abcd equivalence: (DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation) pro parte
description: Examples: "nom. ambig.", "nom. illeg.", "nom. subnud."
comment: The status related to the original publication of the name and its conformance to the relevant rules of nomenclature. It is based essentially on an algorithm according to the business rules of the code. It requires no taxonomic opinion.
organized in class: Taxon
has version: nomenclaturalStatus-2009-04-24

Occurrence Remarks
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Notes
status: recommended
issued: 2008-11-19
modified: 2009-04-24
comment: Comments or notes about the Occurrence.
description: Example: "found dead on road"
organized in class: Occurrence
replaces: SampleRemarks-2009-01-18
has version: occurrenceRemarks-2009-04-24

Occurrence Status
type: DatatypeProperty
abcd equivalence: not in ABCD
status: recommended
modified: 2009-09-17
issued: 2009-09-17
comment: A statement about the presence or absence of a Taxon at a Location. Recommended best practice is to use a controlled vocabulary.
description: Examples: "present", "absent"
organized in class: Occurrence
has version: occurrenceStatus-2009-09-17

Order
type: DatatypeProperty
modified: 2009-08-24
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = ordo
issued: 2008-11-19
description: Examples: "Carnivora", "Monocleales"
comment: The full scientific name of the order in which the taxon is classified.
organized in class: Taxon
replaces: order-2009-04-24
has version: order-2009-08-24

Original Name Usage
type: DatatypeProperty
description: Examples: "Pinus abies", "Gasterosteus saltatrix Linnaeus 1768"
comment: The taxon name, with authorship and date information if known, as it originally appeared when first established under the rules of the associated nomenclaturalCode. The basionym (botany) or basonym (bacteriology) of the scientificName or the senior/earlier homonym for replaced names.
status: recommended
abcd equivalence: not in ABCD
modified: 2009-09-21
issued: 2008-11-19
organized in class: Taxon
replaces: basionym-2009-04-24
has version: originalNameUsage-2009-09-21

Other Catalog Numbers
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/History/PreviousUnitsText
modified: 2009-04-24
issued: 2008-11-19
comment: 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.
status: recommended
description: Examples: "FMNH:Mammal:1234", "NPS YELLO6778; MBG 33424"
organized in class: Occurrence
replaces: OtherCatalogNumbers-2007-04-17
has version: otherCatalogNumbers-2009-04-24

Owner Institution Code
type: DatatypeProperty
modified: 2013-10-04
abcd equivalence: not in ABCD
issued: 2009-08-24
status: recommended
description: Examples: "NPS", "APN", "InBio"
comment: The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.
organized in class: all
has version: ownerInstitutionCode-2009-08-24

Parent Name Usage
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName
issued: 2009-08-24
modified: 2009-09-21
description: Examples: "Rubiaceae", "Gruiformes", "Testudinae"
comment: The full name, with authorship and date information if known, of the direct, most proximate higher-rank parent taxon (in a classification) of the most specific element of the scientificName.
status: recommended
organized in class: Taxon
has version: parentNameUsage-2009-09-21

Phylum
type: DatatypeProperty
modified: 2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = phylum
issued: 2008-11-19
description: Examples: "Chordata" (phylum), "Bryophyta" (division)
status: recommended
comment: The full scientific name of the phylum or division in which the taxon is classified.
organized in class: Taxon
replaces: phylum-2009-04-24
has version: phylum-2009-08-24

Point Radius Spatial Fit
type: DatatypeProperty
description: Detailed explanations with graphical examples can be found in the "Guide to Best Practices for Georeferencing", Chapman and Wieczorek, eds. 2006 (http://www.gbif.org/prog/digit/Georeferencing).
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/PointRadiusSpatialFit
issued: 2008-11-19
modified: 2009-04-24
comment: The ratio of the area of the point-radius (decimalLatitude, decimalLongitude, coordinateUncertaintyInMeters) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given point-radius does not completely contain the original representation. The pointRadiusSpatialFit is undefined (and should be left blank) if the original representation is a point without uncertainty and the given georeference is not that same point (without uncertainty). If both the original and the given georeference are the same point, the pointRadiusSpatialFit is 1.
organized in class: Location
replaces: PointRadiusSpatialFit-2007-04-17
has version: pointRadiusSpatialFit-2009-04-24

Preparations
type: DatatypeProperty
modified: 2009-04-24
comment: A list (concatenated and separated) of preparations and preservation methods for a specimen.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/Preparations/PreparationsText
issued: 2008-11-19
description: Examples: "skin; skull; skeleton", "whole animal (ETOH); tissue (EDTA)", "fossil", "cast", "photograph", "DNA extract"
organized in class: Occurrence
replaces: Preparations-2007-04-17
has version: preparations-2009-04-24

Previous Identifications
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification with PreferredFlag = false
issued: 2008-11-19
modified: 2009-05-18
comment: A list (concatenated and separated) of previous assignments of names to the Occurrence.
description: Example: "Anthus sp., field ID by G. Iglesias; Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology"
status: recommended
organized in class: Occurrence
replaces: previousIdentifications-2009-04-24
has version: previousIdentifications-2009-05-18

Record Number
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/CollectorsFieldNumber
issued: 2008-11-19
modified: 2009-05-18
comment: 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.
description: Example: "OPP 7101"
replaces: CollectorNumber-2007-04-17
organized in class: Occurrence
has version: recordNumber-2009-04-24

Recorded By
type: DatatypeProperty
modified: 2009-05-18
status: recommended
issued: 2008-11-19
comment: 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.
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/GatheringAgents/GatheringAgentsText
description: Example: "Oliver P. Pearson; Anita K. Pearson" where the value in recordNumber "OPP 7101" corresponds to the number for the specimen in the field catalog (collector number) of Oliver P. Pearson.
replaces: Collector-2007-04-17
organized in class: Occurrence
sub property of: According To
has version: recordedBy-2009-04-24

Relationship According To
type: DatatypeProperty
issued: 2009-04-24
modified: 2009-04-24
description: Example: "Julie Woodruff"
comment: The source (person, organization, publication, reference) establishing the relationship between the two resources.
abcd equivalence: not in ABCD
status: recommended
organized in class: Resource Relationship
sub property of: According To
has version: relationshipAccordingTo-2009-04-24

Relationship Established Date
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2009-04-24
issued: 2009-04-24
comment: The date-time on which the relationship between the two resources was established. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
status: recommended
description: Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
sub property of: date
organized in class: Resource Relationship
has version: relationshipEstablishedDate-2009-04-24

Relationship Of Resource
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociationType
description: Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within"
comment: The relationship of the resource identified by relatedResourceID to the subject (optionally identified by the resourceID). Recommended best practice is to use a controlled vocabulary.
status: recommended
organized in class: Resource Relationship
has version: relationshipOfResource-2009-04-24

Relationship Remarks
type: DatatypeProperty
modified: 2009-04-24
comment: Comments or notes about the relationship between the two resources.
abcd equivalence: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/Comments
status: recommended
issued: 2008-11-19
description: Examples: "mother and offspring collected from the same nest", "pollinator captured in the act"
organized in class: Resource Relationship
has version: relationshipRemarks-2009-04-24

Reproductive Condition
type: DatatypeProperty
modified: 2009-04-24
issued: 2008-11-19
description: Examples" "non-reproductive", "pregnant", "in bloom", "fruit-bearing"
status: recommended
abcd equivalence: not in ABCD
comment: The reproductive condition of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.
organized in class: Occurrence
has version: reproductiveCondition-2009-04-24

Sampling Effort
type: DatatypeProperty
abcd equivalence: not in ABCD
modified: 2009-08-24
issued: 2009-08-24
description: Examples: "40 trap-nights", "10 observer-hours; 10 km by foot; 30 km by car"
comment: The amount of effort expended during an Event.
status: recommended
organized in class: Event
has version: samplingEffort-2009-08-24

Sampling Protocol
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Method
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "UV light trap", "mist net", "bottom trawl", "ad hoc observation", "point count", "Penguins from space: faecal stains reveal the location of emperor penguin colonies, http://dx.doi.org/10.1111/j.1466-8238.2009.00467.x", "Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp.", "http://www.bsc-eoc.org/download/Owl.pdf"
comment: The name of, reference to, or description of the method or protocol used during an Event.
replaces: CollectingMethod-2007-04-17
organized in class: Event
has version: samplingProtocol-2009-04-24

Scientific Name
type: DatatypeProperty
status: recommended
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/FullScientificNameString
modified: 2009-09-21
description: Examples: "Coleoptera" (order), "Vespertilionidae" (family), "Manis" (genus), "Ctenomys sociabilis" (genus + specificEpithet), "Ambystoma tigrinum diaboli" (genus + specificEpithet + infraspecificEpithet), "Roptrocerus typographi (Györfi, 1952)" (genus + specificEpithet + scientificNameAuthorship), "Quercus agrifolia var. oxyadenia (Torr.) J.T. Howell" (genus + specificEpithet + taxonRank + infraspecificEpithet + scientificNameAuthorship)
comment: The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term.
organized in class: Taxon
replaces: scientificName-2009-04-24
has version: scientificName-2009-09-21

Scientific Name Authorship
type: DatatypeProperty
modified: 2009-04-24
description: Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)"
status: recommended
comment: The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/ParentheticalAuthorTeamAndYear + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/AuthorTeamAndYear} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeamParenthesis + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeam} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamOriginalAndYear + [= or] DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamParenthesisAndYear}
issued: 2008-11-19
replaces: AuthorYearOfScientificName-2007-04-17
organized in class: Taxon
has version: scientificNameAuthorship-2009-04-24

Sex
type: DatatypeProperty
issued: 2008-11-19
description: Examples: "female", "hermaphrodite", "8 males, 4 females"
comment: The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.
status: recommended
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Sex
organized in class: Occurrence
replaces: Sex-2007-04-17
has version: sex-2009-04-24

Specific Epithet
type: DatatypeProperty
modified: 2009-04-24
status: recommended
comment: The name of the first or species epithet of the scientificName.
abcd equivalence: {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SpeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/FirstEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SpeciesEpithet}
issued: 2008-11-19
description: Examples: "concolor", "gottschei"
replaces: SpecificEpithet-2007-04-17
organized in class: Taxon
has version: specificEpithet-2009-04-24

Start Day Of Year
type: DatatypeProperty
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DayNumberBegin
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
comment: The earliest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).
replaces: DayOfYear-2007-04-17
organized in class: Event
has version: startDayOfYear-2009-04-24

State Province
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= State or = Province (etc.)
status: recommended
issued: 2008-11-19
modified: 2009-04-24
description: Examples: "Montana", "Minas Gerais", "Córdoba"
comment: The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
organized in class: Location
replaces: StateProvince-2007-04-17
has version: stateProvince-2009-04-24

Subgenus
type: DatatypeProperty
modified: 2009-08-24
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/Subgenus
issued: 2008-11-19
comment: The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.
status: recommended
description: Examples: "Strobus (Pinus)", "Puma (Puma)" "Loligo (Amerigo)", "Hieracium subgen. Pilosella"
organized in class: Taxon
replaces: subgenus-2009-04-24
has version: subgenus-2009-08-24

Taxon Rank
type: DatatypeProperty
modified: 2009-09-21
issued: 2008-11-19
comment: The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/Rank
description: Examples: "subspecies", "varietas", "forma", "species", "genus"
organized in class: Taxon
replaces: scientificNameRank-2009-07-06
has version: taxonRank-2009-09-21

Taxon Remarks
type: DatatypeProperty
modified: 2009-08-24
issued: 2008-11-19
comment: Comments or notes about the taxon or name.
description: Example: "this name is a misspelling in common use"
abcd equivalence: not in ABCD
status: recommended
organized in class: Taxon
replaces: taxonRemarks-2009-04-24
has version: taxonRemarks-2009-08-24

Taxonomic Status
type: DatatypeProperty
status: recommended
modified: 2009-04-24
issued: 2008-11-19
abcd equivalence: not in ABCD
description: Examples: "invalid", "misapplied", "homotypic synonym", "accepted"
comment: The status of the use of the scientificName as a label for a taxon. Requires taxonomic opinion to define the scope of a taxon. Rules of priority then are used to define the taxonomic status of the nomenclature contained in that scope, combined with the experts opinion. It must be linked to a specific taxonomic reference that defines the concept. Recommended best practice is to use a controlled vocabulary.
organized in class: Taxon
has version: taxonomicStatus-2009-04-24

Type Status
type: DatatypeProperty
issued: 2008-11-19
comment: A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.
status: recommended
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeText
description: Example: "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388"
organized in class: Identification
replaces: TypeStatus-2007-04-17
has version: typeStatus-2009-04-24

Verbatim Coordinate System
type: DatatypeProperty
abcd equivalence: (partly) DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesGrid/GridCellSystem
modified: 2009-07-06
description: Examples: "decimal degrees", "degrees decimal minutes", "degrees minutes seconds", "UTM"
comment: The spatial coordinate system for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location. Recommended best practice is to use a controlled vocabulary.
status: recommended
issued: 2008-11-19
organized in class: Location
replaces: VerbatimCoordinateSystem-2007-04-17
has version: verbatimCoordinateSystem-2009-04-24

Verbatim Coordinates
type: DatatypeProperty
abcd equivalence: {DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinatesText or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesUTM/UTMText}
modified: 2009-07-06
status: recommended
issued: 2008-11-19
description: Examples: "41 05 54S 121 05 34W", "17T 630000 4833400"
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.
organized in class: Location
replaces: VerbatimCoordinates-2007-04-17
has version: verbatimCoordinates-2009-04-24

Verbatim Depth
type: DatatypeProperty
issued: 2008-11-19
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactText
modified: 2009-04-24
description: Example: "100-200 m"
comment: The original description of the depth below the local surface.
organized in class: Location
replaces: VerbatimDepth-2007-04-17
has version: verbatimDepth-2009-04-24

Verbatim Elevation
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactText
modified: 2009-04-24
issued: 2008-11-19
description: Example: "100-200 m"
comment: The original description of the elevation (altitude, usually above sea level) of the Location.
status: recommended
organized in class: Location
replaces: VerbatimElevation-2007-04-17
has version: verbatimElevation-2009-04-24

Verbatim EventDate
type: DatatypeProperty
issued: 2008-11-19
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/DateTime/DateText
description: Examples: "spring 1910", "Marzo 2002", "1999-03-XX", "17IV1934"
comment: The verbatim original representation of the date and time information for an Event.
status: recommended
organized in class: Event
replaces: VerbatimCollectingDate-2007-04-17
has version: verbatimEventDate-2009-04-24

Verbatim Latitude
type: DatatypeProperty
issued: 2008-11-19
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/VerbatimLatitude
modified: 2009-07-06
description: Example: "41 05 54.03S"
comment: The verbatim original latitude 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.
organized in class: Location
replaces: VerbatimLatitude-2007-04-17
has version: verbatimLatitude-2009-04-24

Verbatim Locality
type: DatatypeProperty
issued: 2008-11-19
description: Example: "25 km NNE Bariloche por R. Nac. 237"
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName
modified: 2009-04-24
comment: The original textual description of the place.
organized in class: Location
has version: verbatimLocality-2009-04-24

Verbatim Longitude
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/VerbatimLongitude
description: Example: "121d 10' 34" W"
comment: The verbatim original longitude 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.
status: recommended
issued: 2008-11-19
modified: 2009-07-06
organized in class: Location
replaces: VerbatimLongitude-2007-04-17
has version: verbatimLongitude-2009-04-24

Verbatim SRS
type: DatatypeProperty
modified: 2009-07-06
abcd equivalence: not in ABCD
status: recommended
issued: 2009-07-06
description: Examples: "EPSG:4326", "WGS84", "NAD27", "Campo Inchauspe", "European 1950", "Clarke 1866"
comment: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which coordinates given in verbatimLatitude and verbatimLongitude, or verbatimCoordinates are based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".
organized in class: Location
has version: verbatimSRS-2009-07-06

Verbatim Taxon Rank
type: DatatypeProperty
comment: The taxonomic rank of the most specific name in the scientificName as it appears in the original record.
status: recommended
description: Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex", "sp.", "subsp.", "var."
abcd equivalence: not in ABCD
issued: 2009-07-06
modified: 2009-09-21
organized in class: Taxon
replaces: verbatimScientificNameRank-2009-07-06
has version: verbatimRank-2009-09-21

Vernacular Name
type: DatatypeProperty
status: recommended
modified: 2009-07-06
issued: 2009-07-06
comment: A common or vernacular name.
description: Examples: "Andean Condor", "Condor Andino", "American Eagle", "Gänsegeier"
abcd equivalence: not in ABCD
organized in class: Taxon
has version: vernacularName-2009-07-06

Water Body
type: DatatypeProperty
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Water body
status: recommended
modified: 2009-04-24
issued: 2008-11-19
description: Examples: "Indian Ocean", "Baltic Sea", "Hudson River"
comment: The name of the water body in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
organized in class: Location
replaces: WaterBody-2007-04-17
has version: waterBody-2009-04-24

Year
type: DatatypeProperty
abcd equivalence: accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
modified: 2009-04-24
issued: 2008-11-19
description: Example: "2008"
comment: The four-digit year in which the Event occurred, according to the Common Era Calendar.
status: recommended
organized in class: Event
replaces: YearCollected-2003-06-17
has version: year-2009-04-24

taxonomic inventory process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: taxonomic inventory
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: taxonomic inventory
Source: https://docs.google.com/spreadsheet/ccc
comment: not sure if this should be a type of assay or a type of planned process
definition: A planned process by which a taxonomic inventory is created.
creator: Taxonomic Inventory Metadata Workshop
taxonomic inventory metadata preferred name: inventory type
has curation status: uncurated

taxonomic inventory
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: taxonomic inventory process
subclass of: information content entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: taxonomic inventory process
example of usage: The butterflies of Great Britain
definition: An information content entity that is a list of taxa recorded in some geospatially defined area over some stated time period using some method involving some actor.
example of usage: The plants of Yosemite National Park
creator: Taxonomic Inventory Metadata Workshop
example of usage: "The Flora of North America"
Source: https://docs.google.com/spreadsheet/ccc
has curation status: pending final vetting

restricted search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
definition: A taxonomic inventory process that is restricted to defined plots, transects, or points, in which a person or group of people is comprehensively covering the entire defined area, usually with a defined survey time or pace. The search is restricted to a well-defined and human-scale geospatial area (traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
creator: Taxonomic Inventory Metadata Workshop
example of usage: Pollard transect-- "walk a 1km transect at a slow&steady pace, and report on all TOI within 5m in front, and 2.5m on either side of you."
Source: https://docs.google.com/spreadsheet/ccc
taxonomic inventory metadata preferred name: restricted search
has curation status: uncurated

open search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
definition: Search restricted within a larger defined geographic area, but where effort isn't even or complete across the defined region. That is, a planned search restricted to a larger, defined geographic area, but effort isn't evenly distributed throughout the area, nor expected to be a complete and comprehensive accounting of TOI's across the defined region. Temporal duration is typically longer than restricted search-- lasting hours to all day.
example of usage: Individual Christmas Bird Count by some team. Organized field trip to a State Park.
creator: Taxonomic Inventory Metadata Workshop
Source: https://docs.google.com/spreadsheet/ccc
taxonomic inventory metadata preferred name: open search
has curation status: uncurated

opportunistic search taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
example of usage: Many E-Bird lists are of this nature; useful supplementary information is that observers should state whether they documented every taxon of interest they saw.
definition: A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, often intended to be comprehensive accounting of the taxa of interest, but with no planned trajectory for discovery, nor pre-specified investment of effort.
creator: Taxonomic Inventory Metadata Workshop
comment: This is more typically used to report multiple sightings, where the motivation is to record presence and abundance, rather than for individual anecdotal occurrences that are noteworthy.
Source: https://docs.google.com/spreadsheet/ccc
taxonomic inventory metadata preferred name: opportunistic search
has curation status: uncurated

trap or sample taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
creator: Taxonomic Inventory Metadata Workshop
definition: A taxonomic inventory process that is typically highly restricted in geospatial extent that involves either the physical extracton of some evidence of the presence of the taxa of interest, such as scat, fur, other material samples or information artifacts such as photographs or sound recordings.
comment: Can be highly targeted and or baited (pheromone trap), or general (pitfall). Trap events can either be "triggered" but of long-term deployment, or rigorously temporally specified (left out overnight).
example of usage: an inventory of insects in a area using pheremone traps
example of usage: an inventory of the large mammals of a park based on camera traps
Source: https://docs.google.com/spreadsheet/ccc
example of usage: inventories based on trawl samples
taxonomic inventory metadata preferred name: trap/sample inventory
has curation status: uncurated

adventitious taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
creator: Taxonomic Inventory Metadata Workshop
definition: A taxonomic inventory in which taxon occurrences are recorde as a co-variates of another study and later compiled as a taxonomic inventory.
taxonomic inventory metadata preferred name: adventitious inventory
example of usage: data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
Source: https://docs.google.com/spreadsheet/ccc
has curation status: uncurated

compilation taxonomic inventory process
type: Class
subclass of: taxonomic inventory process
comment: A compiliation taxonomic inventory process is typically required to document the occurences of taxa of interest over large geospatial areas, or to derive the most comprehensive accounting of presence and absence of taxa of interest in a larger region.
creator: Taxonomic Inventory Metadata Workshop
example of usage: Atlases and Checklists
definition: A taxonomic inventory process in which a list of taxa of interes is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
taxonomic inventory metadata preferred name: compilation inventory
Source: https://docs.google.com/spreadsheet/ccc
has curation status: uncurated

museum
type: Class
subclass of: organization
subclass of: Restriction
  on property: has part
  some values from: museum collection
definition source: ISBN:9780759105096
definition: An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance and makes them available for public viewing through exhibits that may be permanent or temporary.
example of usage: The Louvre Museum
example of usage: The Smithsonian Institution
comment: The class museum has meaning that is much broader than biological collecitons. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum.
has curation status: uncurated

fossil specimen
type: Class
subclass of: specimen
definition: A specimen that is derived from a fossil.
comment: Need to develop or import a class for fossil in order to define this class.
example of usage: a fossil housed in a natural history museum
has curation status: metadata incomplete

living specimen
type: Class
subclass of: specimen
definition: A specimen that is alive.
comment: Need to import alive from PATO and add logical definition.
example of usage: a bacterial culture in a culture collection
example of usage: a tree in an arboretum
example of usage: an animal in a zoo
example of usage: germplasm
has curation status: metadata incomplete

preserved specimen
type: Class
subclass of: specimen
definition: A specimen that has been preserved.
comment: request a term for preservation in OBI and/or preserved in PATO
has curation status: metadata incomplete

darwin core class
type: Class
subclass of: entity

human observation process
type: Class
subclass of: observing process
definition: An observing process in which the entity doing the observing is a human being.
comment: May be able to use the has agent = has active participant relationship for defining this. May want to work with OBI to define this term in a more general sense for investigations.
example of usage: a biologist recording an observation of an animal in a field notebook
example of usage: an entomologist recording the presense of butterflies while walking a transect
has curation status: metadata incomplete

machine observation process
type: Class
subclass of: observing process
definition: An observing process in which the entity doing the observing is a machine.
comment: May want to work with OBI to define this term in a more general sense for investigations.
example of usage: a camera trap recording the presense of a jaguar
example of usage: a sensor continuously recording the surface temperature of a leaf over several hours
has curation status: metadata incomplete

entity
type: Class
subclass of: Thing
editor preferred term: entity
imported from: obi.owl

continuant
type: Class
subclass of: entity
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
example of usage: a heart
example of usage: a person
example of usage: a symphony orchestra
editor preferred term: continuant
alternative term: endurant
example of usage: the color of a tomato
example of usage: the disposition of blood to coagulate
example of usage: the lawn and atmosphere in front of our building
example of usage: the mass of a cloud
imported from: obi.owl

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
example of usage: a surgical operation as processual context for a nosocomical infection
editor preferred term: occurrent
alternative term: perdurant
example of usage: the life of an organism
example of usage: the most interesting part of Van Gogh's life
example of usage: the spatiotemporal context occupied by a process of cellular meiosis
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
imported from: obi.owl

independent continuant
type: Class
subclass of: continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a person
example of usage: a symphony orchestra
example of usage: an organism
editor preferred term: independent continuant
alternative term: substantial entity
example of usage: the bottom right portion of a human torso
example of usage: the lawn and atmosphere in front of our building
imported from: obi.owl

dependent continuant
type: Class
subclass of: continuant
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
editor preferred term: dependent continuant
imported from: obi.owl

process
type: Class
subclass of: occurrent
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

realizable entity
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
editor note: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
editor preferred term: realizable entity
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the function of the reproductive organs
example of usage: the role of being a doctor
imported from: obi.owl

quality
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
editor preferred term: quality
example of usage: the ambient temperature of air
example of usage: the circumference of a waist
example of usage: the color of a tomato
example of usage: the mass of a piece of gold
example of usage: the shape of a nose
example of usage: the weight of a chimpanzee
imported from: obi.owl

specifically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
alternative term: mode
alternative term: property
editor preferred term: specifically dependent continuant
example of usage: the color of a tomato
example of usage: the disposition of fish to decay
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
example of usage: the liquidity of blood
example of usage: the mass of a cloud
example of usage: the role of being a doctor
example of usage: the smell of mozzarella
alternative term: trope
imported from: obi.owl

role
type: Class
subclass of: realizable entity
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor preferred term: role
example of usage: the role of a biological grandfather as legal guardian in the context of a system of laws
example of usage: the role of a chemical compound in an experiment
example of usage: the role of a patient relative as defined by a hospital administrative form
example of usage: the role of a person as a surgeon
example of usage: the role of a student in a university
example of usage: the role of a woman as a legal mother in the context of system of laws
example of usage: the role of ingested matter in digestion
imported from: obi.owl

object aggregate
type: Class
subclass of: material entity

object
type: Class
subclass of: material entity

generically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
example of usage: a certain PDF file that exists in different and in several hard drives
editor preferred term: generically dependent continuant
imported from: obi.owl

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: Examples: collection of random bacteria, a chair, dorsal surface of the body
editor note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
editor preferred term: material entity
imported from: obi.owl

immaterial entity
type: Class
subclass of: independent continuant

organism or virus or viroid
type: Class
subclass of: object
IAO creation date: 9/18/11
definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
definition editor: Melissa Haendel
imported from: Common Anatomy Reference Onotology - CARO2
OBO foundry unique label: organism or virus

peptide
type: Class
subclass of: macromolecule
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
editor preferred term: peptide
imported from: chebi.owl
imported from: obi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
editor preferred term: deoxyribonucleic acid
imported from: chebi.owl
imported from: obi.owl

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor preferred term: molecular entity
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: obi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
editor preferred term: nucleic acid
imported from: chebi.owl
imported from: obi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
editor preferred term: ribonucleic acid
imported from: chebi.owl
imported from: obi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
editor preferred term: macromolecule
alternative term: polymer
imported from: chebi.owl
imported from: obi.owl

objective specification
type: Class
subclass of: directive information entity
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint.
editor preferred term: objective specification
has curation status: ready for release
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  all values from: Class
    complement of: Class
      union of: objective specification
      union of: plan specification
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
editor preferred term: action specification
has curation status: ready for release
imported from: obi.owl

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
editor preferred term: information carrier
has curation status: ready for release
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
definition: 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 that reliably tends to produce (approximately) truthful statements.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
definition: a data item is 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.
alternative term: data
editor preferred term: data item
has curation status: ready for release
has curation status: pending final vetting
imported from: iao.owl
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
subclass of: Restriction
  on property: is concretized as
  some values from: Class
    intersection of: information carrier
    intersection of: Restriction
      on property: inheres in
      some values from: material information bearer
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
definition: an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
editor preferred term: information content entity
has curation status: ready for release
has curation status: pending final vetting
imported from: iao.owl
imported from: obi.owl

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
editor note: Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
editor preferred term: directive information entity
has curation status: ready for release
has curation status: metadata incomplete
imported from: iao.owl
imported from: obi.owl

curation status specification
type: Class
equivalent class: Class
  one of: uncurated
  one of: to be replaced with external ontology term
  one of: pending final vetting
  one of: ready for release
  one of: metadata incomplete
  one of: requires discussion
  one of: FossilSpecimen
  one of: organizational term
  one of: example to be eventually removed
subclass of: data about an ontology part
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
definition editor: PERSON:Bill Bug
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor preferred term: curation status specification
has curation status: pending final vetting
imported from: obi.owl

image
type: Class
subclass of: figure
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition source: OBI_0000030
definition source: group:OBI
editor preferred term: image
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
has curation status: ready for release
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
definition editor: Person:Alan Ruttenberg
editor preferred term: data about an ontology part
definition: data about an ontology part is a data item about a part of an ontology, for example a term
imported from: obi.owl

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
definition editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
definition: a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
editor preferred term: plan specification
has curation status: ready for release
imported from: obi.owl

measurement data item
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
subclass of: Restriction
  on property: is_specified_output_of
  some values from: assay
editor note: 2/2/2009 is_specified_output of some assay?
definition: A data item that is a recording of the output of an assay.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred term: measurement data item
alternative term: measurement datum
definition editor: person:Chris Stoeckert
has curation status: ready for release
imported from: obi.owl

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
definition: A material entity in which a concretization of an information content entity inheres.
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain.
definition editor: GROUP: IAO
editor preferred term: material information bearer
has curation status: ready for release
imported from: obi.owl

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
editor preferred term: photograph
has curation status: ready for release
imported from: obi.owl

obsolescence reason specification
type: Class
equivalent class: Class
  one of: other
  one of: terms merged
  one of: term imported
  one of: placeholder removed
  one of: failed exploratory term
  one of: term split
subclass of: data about an ontology part
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor preferred term: obsolescence reason specification
has curation status: pending final vetting

figure
type: Class
subclass of: information content entity
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
definition editor: PERSON: Lawrence Hunter
editor preferred term: figure
has curation status: FossilSpecimen
imported from: obi.owl

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
definition editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: FossilSpecimen
imported from: obi.owl

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
definition editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
editor preferred term: planned process
has curation status: ready for release
imported from: obi.owl

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: assay
subclass of: Restriction
  on property: inheres in
  some values from: material entity
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
definition editor: GROUP: Role Branch
definition source: OBI
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor preferred term: evaluant role
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
has curation status: ready for release
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IEDB alternative term: any method
ISA alternative term: study assay
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
editor preferred term: assay
alternative term: measuring
alternative term: scientific observation
has curation status: ready for release
imported from: obi.owl

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
definition editor: GROUP: Role Branch
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition source: OBI
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
alternative term: material sample
editor preferred term: specimen role
has curation status: ready for release
imported from: obi.owl

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition: An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
editor preferred term: imaging assay
has curation status: pending final vetting
imported from: obi.owl

organization
type: Class
subclass of: material entity
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
editor preferred term: organization
has curation status: ready for release
imported from: obi.owl

protocol
type: Class
subclass of: directive information entity
ISA alternative term: study protocol
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
definition editor: PlanAndPlannedProcess Branch
editor preferred term: protocol
has curation status: ready for release
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
definition source: PPPB branch
definition editor: PPPB branch
example of usage: the objective to determine the weight of a mouse.
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
editor preferred term: assay objective
has curation status: ready for release
imported from: obi.owl

specimen collection
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Event
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
definition: A planned process with the objective of collecting a specimen.
definition editor: Bjoern Peters
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor preferred term: specimen collection
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: ready for release
imported from: obi.owl

specimen collection objective
type: Class
subclass of: objective specification
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
definition source: Bjoern Peters
definition editor: Bjoern Peters
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
editor preferred term: specimen collection objective
has curation status: ready for release
imported from: obi.owl

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: region
definition editor: BP et al
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
editor preferred term: primary structure of DNA macromolecule
has curation status: metadata incomplete
imported from: obi.owl

sequence data
type: Class
subclass of: data item
subclass of: Class
  intersection of: measurement data item
  intersection of: Restriction
    on property: is about
    some values from: region
definition source: GROUP: OBI
definition editor: Person:Chris Stoeckert
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
editor preferred term: sequence data
has curation status: FossilSpecimen
imported from: obi.owl

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
curator note: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
definition: A sequence data item that is about the primary structure of DNA
editor preferred term: DNA sequence data
definition editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: FossilSpecimen
imported from: obi.owl

latitude coordinate measurement datum
type: Class
subclass of: measurement data item
definition: A measurement datum that is the measure of the latitude coordinate of a site.
NIAID GSCID-BRC alternative term: Specimen Collection Location - Latitude
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: latitude
editor preferred term: latitude coordinate measurement datum
has curation status: FossilSpecimen
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
definition editor: PERSON:Bjoern Peters
editor preferred term: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
has curation status: ready for release
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
example of usage: A herbarium or museum specimen.
example of usage: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition: A material entity that has the specimen role.
definition source: GROUP: OBI Biomaterial Branch
editor preferred term: specimen
has curation status: ready for release
imported from: obi.owl

sequencing assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: sequence data
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Class
      union of: deoxyribonucleic acid
      union of: ribonucleic acid
      union of: protein
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
definition source: OBI branch derived
definition editor: PlanAndPlannedProcess Branch
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
editor note: has_output should be sequence of input; we don't have sequence well defined yet
editor preferred term: sequencing assay
definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
has curation status: pending final vetting
imported from: obi.owl

quality
type: Class
subclass of: specifically dependent continuant
OBO foundry unique label: quality (PATO)

morphology
type: Class
subclass of: quality
subclass of: physical object quality

shape
type: Class
subclass of: morphology

structure
type: Class
subclass of: morphology

linear
type: Class
subclass of: shape

physical object quality
type: Class
subclass of: quality

laminar
type: Class
subclass of: structure

protein
type: Class
subclass of: peptide
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
example of usage: antithrombin III is a protein
editor preferred term: protein
imported from: obi.owl
imported from: pr.owl

region
type: Class
subclass of: generically dependent continuant
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative term: primary structure of sequence macromolecule
editor preferred term: region
alternative term: sequence
imported from: obi.owl
imported from: so.owl

evidence role
type: Class
subclass of: role
comment: It might be better to request this term in OBI or IAO.
example of usage: A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
definition: A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
has curation status: uncurated

persistent evidence role
type: Class
subclass of: Obsolete Class
deprecated: true
definition: An evidence role that persists through time.
comment: Could add relation that persistant evidence role is specifically dependent on a museum material samples. Deprecated because we do not need this term. Can use OBI:evidence role. Not clear what it means for an evidence role to persist through time.

collecting process
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
has obsolescence reason: terms merged

observing process
type: Class
subclass of: Event
subclass of: Restriction
  on property: has output
  some values from: information content entity
subclass of: Restriction
  on property: has part
  some values from: selecting process
subclass of: Restriction
  on property: has input
  some values from: material target of observation
definition: A process in which a person or machine sees or detects a material entity and selects it as worthy of observation, and which has as output an information content entity about the selected material entity.
creator: Biocode Commons Ontology Hackathon
example of usage: Seeing three pelicans flying overhead on Christmas day.
example of usage: Observing butterflies during a transect walk.
example of usage: A trip camera capture of an image of a jaguar is an observation, because it is "selected" by the camera as worthy of obsevation simply by virtue of moving in front of the camera.
comment: The information artifact may written or recorded or just be stored in someone's head (specifically depenedent upon that person). In the context of a taxonomic inventory, an observing process may be called a sighting, and is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
taxonomic inventory metadata preferred name: sighting
has curation status: pending final vetting

being there process
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
definition: A process of existing in a particular spatio-temporal region.
has obsolescence reason: failed exploratory term

printed report
type: Class
subclass of: object
comment: IAO has the term document, which is defined as "A collection of information content entities intended to be understood together as a whole" and has as examples journal article, patent application, laboratory notebook, and book. IAO also has a term for report, but it is not defined. With this term, we want to describe the physical object that corresponds to some information content entity, together with the information content contained in the document or report. This class may be less important for modeling collection data, but could be important for efforts to get hand written (specifically dependent) reports into an electronic (generically dependent) report, and monitoring that process.
creator: Biocode Commons Ontology Hackathon
example of usage: a book
example of usage: a field notebook
has curation status: uncurated

printed observational report
type: Class
equivalent class: Class
  intersection of: printed report
  intersection of: Restriction
    on property: output of
    some values from: observing process
subclass of: printed report
subclass of: Restriction
  on property: output of
  some values from: observing process
example of usage: A field notebook.
definition: A printed report that records the outcome of some observing process.
creator: Biocode Commons Ontology Hackathon
has curation status: uncurated

selecting process
type: Class
subclass of: process
subclass of: Restriction
  on property: has input
  some values from: material entity
definition: A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
creator: Biocode Commons Ontology Hackathon
example of usage: Filtering sea water to extract only organisms smaller than a certain size.
comment: The criteria for selection may be specified in a protocol or may be ad hoc. Should be replaced by OBI:selection, but first OBI needs to fix the definition.
example of usage: deciding which branch to collect for a herbarium specimen
has curation status: to be replaced with external ontology term

submitting process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has input
  some values from: material entity
creator: Biocode Commons Ontology Hackathon
definition: A planned process whereby a person submits a material sample to an organization.
example of usage: a curator submitting a herbarium speciman to a museum
example of usage: a researcher submitting a water sample to a laboratory storage collection
has curation status: requires discussion

physical extraction process
type: Class
subclass of: process
subclass of: Restriction
  on property: has input
  some values from: material entity
comment: Considered acquisition in OBI, but that is about taking possession. Physical extraction may involve taking pocession, but it may also just involve extraction of something that is already posessed (e.g. of dna from cells).
example of usage: removing a fish from the ocean with a net
example of usage: picking leaves from a plant
definition: A process that involves removing a material entity from its original site to another site.
example of usage: removing dna from cells
creator: Biocode Commons Ontology Hackathon
has curation status: requires discussion

material sampling process
type: Class
subclass of: Obsolete Class
comment: This term has been replaced by OBI:specimen collection.
deprecated: true
creator: Biocode Commons Ontology Hackathon
definition: A planned process that includes selecting a material entity for study, physically extracting the material entity, and submitting the material entity to some institution for preservation or study.
alternative term: collecting event
example of usage: collecting plant parts for herbarium specimens
example of usage: collecting sea water samples as part of Ocean Sampling Day
has obsolescence reason: failed exploratory term

data sampling process
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
has obsolescence reason: failed exploratory term

statistical sampling process
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
has obsolescence reason: failed exploratory term

locality description
type: Class
subclass of: information content entity
creator: Biocode Commons Ontology Hackathon
definition: An information artifact that is about a spatio-temporal region at which a process (such as collecting process, observing process, or material sampling process) occured.
comment: Darwin Core needs to describe both the site and time where some activity occurred as an information content entity (e.g., in recording data from a lab notebook),therefore, we made locality description about a spatial temporal region, rather than a site.
has curation status: requires discussion

material sample role
type: Class
subclass of: Obsolete Class
comment: This term has been replaced by OBI:specimen role.
deprecated: true
creator: Biocode Commons Ontology Hackathon
definition: A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
example of usage: the role borne by a branch when it becomes a herbarium specimen
has obsolescence reason: failed exploratory term

successful material sampling process
type: Class
subclass of: Obsolete Class
deprecated: true
definition: A sampling process that has as output some material sample.
comment: Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.
has obsolescence reason: failed exploratory term

unsuccessful material sampling process
type: Class
subclass of: Obsolete Class
deprecated: true
definition: A material sampling process that has as output exactly zero material samples.
comment: Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.
has obsolescence reason: failed exploratory term

museum collection entity
type: Class
subclass of: Obsolete Class
deprecated: true
comment: At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
has obsolescence reason: failed exploratory term

organismal museum collection entity
type: Class
subclass of: museum collection entity
deprecated: true
definition: A museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.
comment: The label for this on the original diagram was 'collection object'. However, not all entities in collections will fit the defition of 'object', so 'collection entity is probably a better name. The relation 'depends on' cannot really be used here. Old BFO has 'inverse depends on', but this is not in the current BFO. See dwc_bfo2_new.owl for the original logical definition. At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
has obsolescence reason: failed exploratory term

museum collection
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: has part
  some values from: specimen
creator: Biocode Commons Ontology Hackathon
definition: An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
comment: Intent is to document biodiversity for research and education. The class museum collection has meaning that is much broader than biological collections. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum collection.
example of usage: The herbarium collection at the New York Botanical Garden.
example of usage: the painting collection at the Louvre Museum
has curation status: requires discussion

organismal museum collection
type: Class
subclass of: museum collection
definition: A museum collection that has as member part a material sample that was derived from an organism.
creator: Biocode Commons Ontology Hackathon
example of usage: the insect collection at the Smithsonian Institution
has curation status: requires discussion

institution
type: Class
subclass of: Obsolete Class
deprecated: true
comment: Replaced by OBI organization. Request institution as synonym in OBI.
has obsolescence reason: to be replaced with external ontology term

organismal entity
type: Class
subclass of: Obsolete Class
deprecated: true
definition: A material entity that derives from an organism or virus or viroid.
comment: This class is understood to mean: A material entity that is either an organism, a part of an organism, a collection of organisms, or a fossil. The relation 'organismal entity derives from organism' was in the original diagram. Subclasses of organismal entity include organism, and It is not clear if it is valid to that an organism derives from an organism (is the derives from relation reflexive?). At the GSC14 hackathon in 09/2012, we decided to deprecate this term.

obsolete organism or virus or viroid
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This terms was replaced by a term imported from CARO. The original diagram only had organsim, but DWC and GOs both need to include viruses and viroids.
has obsolescence reason: to be replaced with external ontology term

material sample
type: Class
subclass of: Obsolete Class
comment: This term has been replaced by OBI:specimen.
deprecated: true
example of usage: A herbarium or museum specimen.
creator: Biocode Commons Ontology Hackathon
example of usage: A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
definition: A material entity that has a material sample role. A material entity takes on the material sample role by being the output of a material samping process. That is, is selected for study, collected, and submitted to an institution for preservation or study.
has obsolescence reason: failed exploratory term

data sample
type: Class
subclass of: Obsolete Class
deprecated: true
definition: An information content entity (?) that is the result of some data sampling process.
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
has obsolescence reason: failed exploratory term

statistical sample
type: Class
subclass of: Obsolete Class
deprecated: true
comment: This term has been deprecated until it is determined whether or not it is needed in the BCO. Should probably be replaced by a term from OBI or IAO.
has obsolescence reason: failed exploratory term

protocol governed sampling activity
type: Class
subclass of: Obsolete Class
deprecated: true
comment: If sampling is a OBI planned process, that captures that it is protocal governed.
has obsolescence reason: failed exploratory term

taxonomic identification process
type: Class
subclass of: planned process
example of usage: Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
example of usage: Associating a museum specimen with a specific taxonomic concept based on its characters.
example of usage: Using a key to identify a plant in the field.
example of usage: Using DNA barcoding to identify a plant species.
creator: Biocode Commons Ontology Hackathon
definition: A process by which a material sample is associated with a taxon or taxa.
has curation status: pending final vetting

process that yields a material representation of a material entity
type: Class
subclass of: process
creator: Biocode Commons Ontology Hackathon
curator note: Consider term from OBI or IAO.
comment: Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
has curation status: to be replaced with external ontology term

material target of observation
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material target of observation role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: material target of observation role
definition: A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
creator: Biocode Commons Ontology Hackathon
example of usage: A bird observed during a Christmas Bird Count
example of usage: A bird observed during a transect walk.
example of usage: An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
example of usage: A tree is forest plot that is measured for diameter at breast height (DBH).
has curation status: requires discussion

process that yields an information artifact that is a representation of a material entity
type: Class
subclass of: process
creator: Biocode Commons Ontology Hackathon
comment: Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
curator note: Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
has curation status: to be replaced with external ontology term

material target of observation role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: is realized by
    some values from: observing process
subclass of: role
subclass of: Restriction
  on property: is realized by
  some values from: observing process
creator: Biocode Commons Ontology Hackathon
definition: A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
example of usage: the role borne by a bird during a Christmas Bird Count
has curation status: pending final vetting

VocabularyEncodingScheme
type: Class
subclass of: Obsolete Class
deprecated: true

Fossil Specimen
type: Class
subclass of: darwin core class
status: recommended
issued: 2008-11-19
modified: 2011-10-16
comment: A resource describing a fossilized specimen.
abcd equivalence: RecordBasisEnum/FossileSpecimen
dwc_bco mapping: fossil specimen
has curation status: pending final vetting
replaces: FossilSpecimen-2008-11-19
has version: FossilSpecimen-2011-10-16
member of: Darwin Core Type
decision: Decision-2011-10-16 6

HumanObservation
type: Class
subclass of: darwin core class
abcd equivalence: RecordBasisEnum/HumanObservation
issued: 2008-11-19
comment: A resource describing an observation made by one or more people.
status: recommended
modified: 2008-11-19
dwc_bco mapping: human observation process
has curation status: pending final vetting
replaces: HumanObservation-2008-11-19
has version: HumanObservation-2011-10-16
member of: Darwin Core Type

LivingSpecimen
type: Class
subclass of: darwin core class
status: recommended
abcd equivalence: RecordBasisEnum/LivingSpecimen
modified: 2011-10-16
issued: 2008-11-19
comment: A resource describing a living specimen.
dwc_bco mapping: living specimen
has curation status: pending final vetting
replaces: LivingSpecimen-2008-11-19
has version: LivingSpecimen-2011-10-16
member of: Darwin Core Type
decision: Decision-2011-10-16 6

Location
type: Class
subclass of: darwin core class
issued: 2009-01-23
comment: A resource describing an instance of the Location class.
status: recommended
abcd equivalence: not in ABCD
modified: 2009-04-24
has curation status: uncurated
dwc_bco mapping: locality description
has version: Location-2009-04-24
member of: Darwin Core Type

MachineObservation
type: Class
subclass of: darwin core class
status: recommended
modified: 2008-11-19
issued: 2008-11-19
comment: A resource describing an observation made by a machine.
abcd equivalence: RecordBasisEnum/MachineObservation
dwc_bco mapping: machine observation process
has curation status: pending final vetting
replaces: MachineObservation-2008-11-19
has version: MachineObservation-2011-10-16
member of: Darwin Core Type

MaterialSample
type: Class
subclass of: darwin core class
status: recommended
modified: 2013-09-26
issued: 2013-03-28
abcd equivalence: DataSets/DataSet/Units/Unit
comment: A resource describing the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.
has curation status: FossilSpecimen
dwc_bco mapping: specimen collection
has version: MaterialSample-2013-06-24
member of: Darwin Core Type
decision: Decision 2013-10-09 12

NomenclaturalChecklist
type: Class
subclass of: darwin core class
issued: 2009-01-23
status: recommended
modified: 2009-01-23
comment: A resource describing a nomenclatural checklist.
abcd equivalence: not in ABCD
has curation status: uncurated
has version: NomenclaturalChecklist-2009-01-23
member of: Darwin Core Type

PreservedSpecimen
type: Class
subclass of: darwin core class
comment: A resource describing a preserved specimen.
abcd equivalence: RecordBasisEnum/PreservedSpecimen
status: recommended
issued: 2008-11-19
modified: 2011-10-16
dwc_bco mapping: preserved specimen
has curation status: pending final vetting
replaces: PreservedSpecimen-2008-11-19
has version: PreservedSpecimen-2011-10-16
member of: Darwin Core Type
decision: Decision-2011-10-16 6

Event
type: Class
equivalent class: Class
  union of: specimen collection
  union of: observing process
subclass of: darwin core class
subclass of: process
issued: 2008-11-19
modified: 2009-04-29
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering
comment: The category of information pertaining to an event (an action that occurs at a place and during a period of time).
status: recommended
has curation status: pending final vetting
replaces: SamplingEvent-2008-11-19
has version: Event-2009-04-29

Geological Context
type: Class
subclass of: darwin core class
issued: 2009-07-06
abcd equivalence: DataSets/DataSet/Units/Unit/Gathering/Stratigraphy
modified: 2009-07-06
comment: The category of information pertaining to a location within a geological context, such as stratigraphy.
status: recommended
has curation status: uncurated
has version: GeologicalContext-2009-07-06

Identification
type: Class
subclass of: darwin core class
modified: 2008-11-19
issued: 2008-11-19
status: recommended
abcd equivalence: DataSets/DataSet/Units/Unit/Identifications/Identification
comment: The category of information pertaining to taxonomic determinations (the assignment of a scientific name).
has curation status: pending final vetting
dwc_bco mapping: taxonomic identification process
has version: Identification-2008-11-19

Measurement Or Fact
type: Class
subclass of: darwin core class
modified: 2009-04-24
issued: 2009-04-24
status: recommended
abcd equivalence: Datasets/Dataset/Units/Unit/MeasurementsOrFacts or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts
comment: The category of information pertaining to measurements, facts, characteristics, or assertions about a resource (instance of data record, such as Occurrence, Taxon, Location, Event).
has curation status: uncurated
replaces: EventMeasurement-2008-11-19
replaces: OccurrenceMeasurement-2008-11-19
has version: MeasurementOrFact-2009-04-24

Occurrence
type: Class
subclass of: darwin core class
issued: 2008-11-19
status: recommended
modified: 2009-04-24
abcd equivalence: DataSets/DataSet/Units/Unit
comment: The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.).
has curation status: uncurated
replaces: Sample-2008-11-19
has version: Occurrence-2009-04-29

Resource Relationship
type: Class
subclass of: darwin core class
deprecated: true
modified: 2013-09-30
issued: 2008-11-19
abcd equivalence: DataSets/DataSet/Units/Unit/Associations
status: recommended
has obsolescence reason: This class has no use within the context of an ontology.
description: Resources can be thought of as identifiable records and may include, but need not be limited to Occurrences, Locations, Events, Identifications, or Taxon records.
comment: The category of information pertaining to relationships between resources (instances of data records, such as Occurrences, Taxa, Locations, Events).
has version: ResourceRelationship-2009-01-21

Taxon
type: Class
subclass of: darwin core class
abcd equivalence: no simple equivalent in ABCD
issued: 2008-11-19
comment: The category of information pertaining to taxonomic names, taxon name usages, or taxon concepts.
status: recommended
modified: 2009-09-21
has curation status: uncurated
replaces: Taxon-2008-11-19
has version: Taxon-2009-09-21

Obsolete Class
type: Class
subclass of: Thing

specimen collection process X
type: NamedIndividual

material entity A
type: NamedIndividual
is_specified_input_of: specimen collection process X

material entity B
type: NamedIndividual
is_specified_output_of: specimen collection process X
is_specified_input_of: specimen collection process Y

material entity C
type: NamedIndividual
is_specified_output_of: specimen collection process Y

specimen collection process Y
type: NamedIndividual

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

FossilSpecimen
type: NamedIndividual
type: curation status specification
label: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
editor preferred term: metadata complete

organizational term
type: NamedIndividual
type: curation status specification
definition editor: PERSON:Alan Ruttenberg
editor preferred term: organizational term
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
editor preferred term: ready for release
has curation status: pending final vetting

metadata incomplete
type: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
editor preferred term: metadata incomplete

uncurated
type: NamedIndividual
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
editor preferred term: uncurated

pending final vetting
type: NamedIndividual
type: curation status specification
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor.
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
editor preferred term: pending final vetting

core
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

other
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.

defined class
type: NamedIndividual
type: denotator type
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI
editor preferred term: to be replaced with external ontology term

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI
editor preferred term: requires discussion
has curation status: pending final vetting

axiom holds for all times
type: NamedIndividual
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

relation has no temporal argument
type: NamedIndividual
definition: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)

Darwin Core Type
type: NamedIndividual
deprecated: true
modified: 2008-11-19
comment: The set of classes specified by the Darwin Core Type Vocabulary, used to categorize the nature or genre of the resource.
status: recommended
issued: 2008-11-19
abcd equivalence: not in ABCD
has version: DwCType-2008-11-19

Darwin Core Type Terms
comment: This document contains a list of terms in the Darwin Core Type Vocabulary. For the full normative RDF document of all Darwin Core terms, see dwctermshistory.rdf. To comment on this schema, please create a new issue in http://code.google.com/p/darwincore/issues/
modified: 2013-10-22
publisher: Biodiversity Information Standards (TDWG)