Biocode Commons Ontology Hackathon members
The BCO supports the interoperability of biodiversity and biodiversity related data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. A key aspect of the BCO is distinguishing among material samples (i.e. specimens), observing processes, and data about either of those entities.
This is the editor's version of the ontology. Use with caution. For the live version of the ontology, use http://purl.obolibrary.org/obo/bco.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.
taxonomic inventory metadata preferred name
The label preferred for use with this ontology. To be added only with imported terms.
BCO preferred label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
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.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
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
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
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.
curator note
An administrative note of use for a curator but of no use for a user
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
is denotator type
relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
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)"
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
Chris Mungall
expand assertion to
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)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
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 .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
has ID digit count
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
has ID prefix
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.
may be identical to
Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
Chris Mungall, Jie Zheng
GO ontology
scheduled for obsoletion on or after
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
The relationship between an independent continuant and a role. Slightly more specific than the parent class bearer of.
This property was originally created in OBI, but in OBI it was deprecated and replaced by BFO:0000087. However, BFO:0000087 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 'has role' in both BCO and OBI. There are currently two versions of 'has role', the old one from BFO (which is used in OBI's definition of specimen) and the RO version. For consistency with OBI, we have used the BFO relation in BCO, but this should be resolved at a higher level.
obsolete has role
obsolete derives from by planned process
This property used an old version of the has input relation, so it has been deprecated.
obsotlete is derived into by planned process
A relation used to link a taxonomic association to a taxon. Should be used with the of organism relation.
to taxon
A relation used to link an identification association to an organismal entity. Should be used together with the to taxon relation.
of organism
A shortcut relation from an organsimal entity to a taxon.
member of taxon
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(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.
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.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), 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.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
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.
is_specified_input_of
has_specified_output
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.
PERSON: Alan Ruttenberg
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
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.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
A relation between an information content entity and a value specification that specifies its value.
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
causally downstream of
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
DEPRECATED inheres in
DEPRECATED bearer of
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
The currently valid (zoological) or accepted (botanical) name for the ScientificName.
A global unique identifier for the parent to the AcceptedTaxon.
A description of constraints on the use of the data as shared or access to further data that is not shared.
The numeric value of the catalogNumber, used to facilitate numerical sorting and searching by ranges.
Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
The earliest date-time in a period during which a event occurred. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
The time of day when the event ended, expressed as decimal hours from midnight, local time.
Example: "0.01", "normal distribution with variation of 2 m"
The description of the error associated with the EventAttributeValue.
The agent responsible for having determined the value of the measurement or characteristic of the sampling event.
The date on which the the measurement or characteristic of the sampling event was made.
An identifier for the event attribute. May be a global unique identifier or an identifier specific to the data set.
Comments or notes accompanying the measurement or characteristic of the sampling event.
The nature of the measurement or characteristic of the sampling event. Recommended best practice is to use a controlled vocabulary.
The units for the value of the measurement or characteristic of the sampling event. Recommended best practice is to use International System of Units (SI) units.
The value of the measurement or characteristic of the sampling event.
Examples: "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell", "locality information given only to nearest county".
Actions taken to make the data as shared less specific or complete than in its original form. Suggests that alternative data of highly quality may be available on request.
Example: "Animalia, Chordata, Vertebrata, Mammalia, Theria, Eutheria, Rodentia, Hystricognatha, Hystricognathi, Ctenomyidae, Ctenomyini, Ctenomys".
A list (concatenated and separated) of the names for the taxonomic ranks less specific than the ScientificName.
A global unique identifier for the parent to the taxon.
The latest date-time in a period during which a event occurred. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
A list (concatenated and separated) of previous ScientificNames to which the sample was identified.
The nature of the related resource. Recommended best practice is to use the same controlled vocabulary as for basisOfRecord.
The description of the error associated with the SampleAttributeValue.
The agent responsible for having determined the value of the measurement or characteristic of the sample.
The date on which the the measurement or characteristic of the sample was made.
Comments or notes accompanying the measurement or characteristic of the sample.
The units for the value of the measurement or characteristic of the sample. Recommended best practice is to use International System of Units (SI) units.
The value of the measurement or characteristic of the sample.
Comments or notes about the sample or record.
An identifier for the sampling attribute. May be a global unique identifier or an identifier specific to the data set.
The nature of the measurement or characteristic of the sample. Recommended best practice is to use a controlled vocabulary.
Example: "Relative humidity: 28 %; Temperature: 22 C; Sample size: 10 kg"
A list (concatenated and separated) of additional measurements or characteristics of the sampling event.
An identifier for the sampling event. May be a global unique identifier or an identifier specific to the data set.
Comments or notes about the sampling event.
An identifier for the sampling location. May be a global unique identifier or an identifier specific to the data set.
Comments or notes about the sampling location.
The time of day when the event began, expressed as decimal hours from midnight, local time.
A global unique identifier for the taxon (name in a classification).
The full scientific name, with authorship and date information if known, of the accepted (botanical) or valid (zoological) name in cases where the provided scientificName is considered by the reference indicated in the accordingTo property, or of the content provider, to be a synonym or misapplied name. When applied to an Organism or Occurrence, this term should be used in cases where a content provider regards the provided scientificName to be inconsistent with the taxonomic perspective of the content provider. For example, there are many discrepancies within specimen collections and observation datasets between the recorded name (e.g., the most recent identification from an expert who examined a specimen, or a field identification for an observed organism), and the name asserted by the content provider to be taxonomically accepted.
`Tamias minimus` (valid name for Eutamias minimus).
The full name, with authorship and date information if known, of the currently valid (zoological) or accepted (botanical) taxon.
This term should be used for synonyms or misapplied names to refer to the taxonID of a Taxon record that represents the accepted (botanical) or valid (zoological) name. For Darwin Core Archives the related record should be present locally in the same archive.
An identifier for the name usage (documented meaning of the name according to a source) of the currently valid (zoological) or accepted (botanical) taxon.
Example: "Tamias minimus" valid name for "Eutamias minimus"
The currently valid (zoological) or accepted (botanical) name for the scientificName.
A unique identifier for the acceptedScientificName.
An identifier for the name of the currently valid (zoological) or accepted (botanical) taxon. See acceptedTaxon.
A unique identifier for the acceptedTaxonName.
Abstract term to attribute information to a source.
Abstract term to capture error information about a measurement or fact.
`https://arctos.database.museum/media/10520962 | https://arctos.database.museum/media/10520964`
A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.
This term can be used to provide a list of associations to other Occurrences. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
`"parasite collected from":"https://arctos.database.museum/guid/MSB:Mamm:215895?seid=950760"`, `"encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3175067" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177393" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177394" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3177392" | "encounter previous to":"http://arctos.database.museum/guid/MSB:Mamm:292063?seid=3609139"`
A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence.
This term can be used to provide a list of associations to other Organisms. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
`"sibling of":"http://arctos.database.museum/guid/DMNS:Mamm:14171"`, `"parent of":"http://arctos.database.museum/guid/MSB:Mamm:196208" | "parent of":"http://arctos.database.museum/guid/MSB:Mamm:196523" | "sibling of":"http://arctos.database.museum/guid/MSB:Mamm:142638"`
A list (concatenated and separated) of identifiers of other Organisms and the associations of this Organism to each of them.
Recommended best practice is to separate the values in a list with space vertical bar space ( | ). Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. Note also that the intended usage of the term dcterms:references in Darwin Core when applied to an Occurrence is to point to the definitive source representation of that Occurrence if one is available. Note also that the intended usage of dcterms:bibliographicCitation in Darwin Core when applied to an Occurrence is to provide the preferred way to cite the Occurrence itself.
`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.`, `Steven R. Hoofer and Ronald A. Van Den Bussche. 2001. Phylogenetic Relationships of Plecotine Bats and Allies Based on Mitochondrial Ribosomal Sequences. Journal of Mammalogy 82(1):131-137. | Walker, Faith M., Jeffrey T. Foster, Kevin P. Drees, Carol L. Chambers. 2014. Spotted bat (Euderma maculatum) microsatellite discovery using illumina sequencing. Conservation Genetics Resources.`
A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
`http://www.ncbi.nlm.nih.gov/nuccore/U34853.1`, `http://www.ncbi.nlm.nih.gov/nuccore/GU328060 | http://www.ncbi.nlm.nih.gov/nuccore/AF326093`
A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
This term can be used to provide a list of associations to Taxa other than the one defined in the Occurrence. Note that the ResourceRelationship class is an alternative means of representing associations, and with more detail. This term is not apt for establishing relationships between Taxa, only between specific Occurrences of an Organism with other Taxa. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
`"host":"Quercus alba"`, `"host":"gbif.org/species/2879737"`,`"parasitoid of":"Cyclocephala signaticollis" | "predator of":"Apis mellifera"`
A list (concatenated and separated) of identifiers or names of taxa and the associations of this Occurrence to each of them.
The basionym (botany) or basonym (bacteriology) of the scientificName.
A unique identifier for the basionym (botany) or basonym (bacteriology) of the scientificName.
Recommended best practice is to use the standard label of one of the Darwin Core classes.
`PreservedSpecimen`, `FossilSpecimen`, `LivingSpecimen`, `MaterialSample`, `Event`, `HumanObservation`, `MachineObservation`, `Taxon`, `Occurrence`, `MaterialCitation`
The full name of the lithostratigraphic bed from which the cataloged item was collected.
The behavior shown by the subject at the time the Occurrence was recorded.
The combination of genus and first (species) epithet of the scientificName.
An identifier (preferably unique) for the record within the data set or collection.
The full scientific name of the class in which the taxon is classified.
The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
For physical specimens, the recommended best practice is to use an identifier from a collections registry such as the Global Registry of Biodiversity Repositories (http://grbio.org/).
`http://biocol.org/urn:lsid:biocol.org:col:1001`, `http://grbio.org/cool/p5fp-c036`
An identifier for the collection or dataset from which the record was derived.
Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
`Africa`, `Antarctica`, `Asia`, `Europe`, `North America`, `Oceania`, `South America`
The name of the continent in which the Location occurs.
`0.00001` (normal GPS limit for decimal degrees). `0.000278` (nearest second). `0.01667` (nearest minute). `1.0` (nearest degree).
A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.
`30` (reasonable lower limit on or after 2020-05-01 of a GPS reading under good conditions if the actual precision was not recorded at the time). `100` (reasonable lower limit before 2020-05-01 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).
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.
Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names. Recommended best practice is to leave this field blank if the Location spans multiple entities at this administrative level or if the Location might be in one or another of multiple possible entities at this level. Multiplicity and uncertainty of the geographic entity can be captured either in the term higherGeography or in the term locality, or both.
The name of the country or major administrative unit in which the Location occurs.
Recommended best practice is to use an ISO 3166-1-alpha-2 country code.
The standard code for the country in which the Location occurs.
The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.
According to the Rules of the Cultivated Plant Code, a cultivar name consists of a botanical name followed by a cultivar epithet. The value given as the cultivarEpithet should exclude any quotes. The term taxonRank should be used to indicate which type of cultivated plant name (e.g. cultivar, cultivar group, grex) is concerned. This epithet, including any enclosing apostrophes or suffix, should be provided in scientificName as well.
`King Edward` (for scientificName "Solanum tuberosum 'King Edward'" and taxonRank "cultivar"); `Mishmiense` (for scientificName "Rhododendron boothii Mishmiense Group" and taxonRank "cultivar group"); `Atlantis` (for scientificName "Paphiopedilum Atlantis grex" and taxonRank "grex").
Part of the name of a cultivar, cultivar group or grex that follows the scientific name.
`Coordinates generalized from original GPS coordinates to the nearest half degree grid cell`.
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.
An identifier for the set of data. May be a global unique identifier or an identifier specific to a collection or institution.
`Grinnell Resurvey Mammals`, `Lacey Ctenomys Recaptures`
The name identifying the data set from which the record was derived.
Recommended best practice is to use a date that conforms to ISO 8601-1:2019.
`1963-03-08T14:07-0600` (8 Mar 1963 at 2:07pm in the time zone six hours earlier than UTC). `2009-02-20T08:40Z` (20 February 2009 8:40am UTC). `2018-08-29T15:19` (3:19pm local time on 29 August 2018). `1809-02-12` (some time during 12 February 1809). `1906-06` (some time in June 1906). `1971` (some time in the year 1971). `2007-03-01T13:00:00Z/2008-05-11T15:30:00Z` (some time during the interval between 1 March 2007 1pm UTC and 11 May 2008 3:30pm UTC). `1900/1909` (some time during the interval between the beginning of the year 1900 and the end of the year 1909). `2007-11-13/15` (some time in the interval between 13 November 2007 and 15 November 2007).
The date on which the subject was determined as representing the Taxon.
The integer day of the month on which the Event occurred.
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.
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.
Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/doe/. For details, refer to https://doi.org/10.3897/biss.3.38084
`native`, `captive`, `cultivated`, `released`, `failing`, `casual`, `reproducing`, `established`, `colonising`, `invasive`, `widespreadInvasive`
The degree to which an Organism survives, reproduces, and expands its range at the given place and time.
Recommended best practice is to use a controlled vocabulary.
`in collection`, `missing`, `voucher elsewhere`, `duplicates elsewhere`
The current state of a specimen with respect to the collection identified in collectionCode or collectionID.
Recommended best practice is to use a key:value encoding schema for a data interchange format such as JSON.
`{"heightInMeters":1.5}`, `{"tragusLengthInMeters":0.014, "weightInGrams":120}`, `{"natureOfID":"expert identification", "identificationEvidence":"cytochrome B sequence"}`, `{"relativeHumidity":28, "airTemperatureInCelsius":22, "sampleSizeInKilograms":10}`, `{"aspectHeading":277, "slopeInDegrees":6}`, `{"iucnStatus":"vulnerable", "taxonDistribution":"Neuquén, Argentina"}`
A list of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content.
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.
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.
`Holocene`, `Pleistocene`, `Ibexian Series`
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.
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.
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.
`1` (1 January). `32` (1 February). `366` (31 December). `365` (30 December in a leap year, 31 December in a non-leap year).
The latest integer 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).
Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/em/. For details, refer to https://doi.org/10.3897/biss.3.38084
`native`, `nativeReintroduced`, `introduced`, `introducedAssistedColonisation`, `vagrant`, `uncertain`
Statement about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans.
A list (concatenated and separated) of additional measurements or characteristics of the Event.
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.
An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set.
The agent responsible for having determined the value of the measurement or characteristic of the event.
The date on which the the measurement or characteristic of the event was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Comments or notes accompanying the measurement or characteristic of the event.
The nature of the measurement or characteristic of the event. Recommended best practice is to use a controlled vocabulary.
The units for the value of the measurement or characteristic of the event. Recommended best practice is to use International System of Units (SI) units.
The value of the measurement or characteristic of the event.
`After the recent rains the river is nearly at flood stage.`
`14:07-0600` (2:07pm in the time zone six hours earlier than UTC). `08:40:21Z` (8:40:21am UTC). `13:00:00Z/15:30:00Z` (the interval between 1pm UTC and 3:30pm UTC).
The time or interval during which an Event occurred.
The full scientific name of the family in which the taxon is classified.
`Notes available in the Grinnell-Miller Library.`
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.
An identifier given to the event in the field. Often serves as a link between field notes and the Event.
Recommended best practice is to use the EPSG code of the 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`. It is also permitted to provide the SRS in Well-Known-Text, especially if no EPSG code provides the necessary values for the attributes of the SRS. Do not use this term to describe the SRS of the decimalLatitude and decimalLongitude, nor of any verbatim coordinates - use the geodeticDatum and verbatimSRS instead.
`epsg:4326`, `GEOGCS["GCS_WGS_1984", DATUM["D_WGS_1984", SPHEROID["WGS_1984",6378137,298.257223563]], PRIMEM["Greenwich",0], UNIT["Degree",0.0174532925199433]]` (WKT for the standard WGS84 Spatial Reference System EPSG:4326)
The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geometry given in footprintWKT is based.
Detailed explanations with graphical examples can be found in the Georeferencing Best Practices, Chapman and Wieczorek, 2020 (https://doi.org/10.15468/doc-gg7h-s853).
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 empty) 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 footprintSpatialFit is 1.
`POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20))` (the one-degree bounding box with opposite corners at longitude=10, latitude=20 and longitude=11, latitude=21)
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.
`Notch Peak Formation`, `House Limestone`, `Fillmore Formation`
The full name of the lithostratigraphic formation from which the cataloged item was collected.
For synonyms the accepted genus and the genus part of the name may be different. The term genericName should be used together with specificEpithet to form a binomial and with infraspecificEpithet to form a trinomial. The term genericName should only be used for combinations. Uninomials of generic rank do not have a genericName.
`Felis` (for scientificName "Felis concolor", with accompanying values of "Puma concolor" in acceptedNameUsage and "Puma" in genus).
The genus part of the scientificName without authorship.
The full scientific name of the genus in which the taxon is classified.
Recommended best practice is to use the EPSG code of the 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`.
`EPSG:4326`, `WGS84`, `NAD27`, `Campo Inchauspe`, `European 1950`, `Clarke 1866`, `unknown`
The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based.
An identifier for the set of information associated with a GeologicalContext (the location within a geological context, such as stratigraphy). May be a global unique identifier or an identifier specific to the data set.
`Georeferencing Quick Reference Guide (Zermoglio et al. 2020, https://doi.org/10.35035/e09p-h128)`
A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.
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.
Recommended best practice is to separate the values in a list with space vertical bar space (` | `).
`https://www.geonames.org/`, `USGS 1:24000 Florence Montana Quad 1967 | Terrametrics 2008 on Google Earth`, `GeoLocate`
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.
`unable to georeference`, `requires georeference`, `requires verification`, `verified by data custodian`, `verified by contributor`
A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description for the Location of the Occurrence.
`Brad Millen (ROM)`, `Kristina Yamamoto | Janet Fang`
A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.
The date on which the Location was georeferenced.
The full name of the lithostratigraphic group from which the cataloged item was collected.
A category or description of the habitat in which the Event occurred.
Recommended best practice is to separate the values in a list with space vertical bar space (` | `), with terms in order from the highest taxonomic rank to the lowest.
`Plantae | Tracheophyta | Magnoliopsida | Ranunculales | Ranunculaceae | Ranunculus`, `Animalia`, `Animalia | Chordata | Vertebrata | Mammalia | Theria | Eutheria | Rodentia | Hystricognatha | Hystricognathi | Ctenomyidae | Ctenomyini | Ctenomys`
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 separate the values in a list with space vertical bar space (` | `), with terms in order from least specific to most specific.
`North Atlantic Ocean`. `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.
A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.
Recommended best practice is to use a persistent identifier from a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
`http://vocab.getty.edu/tgn/1002002` (Antártida e Islas del Atlántico Sur, Territorio Nacional de la Tierra del Fuego, Argentina).
An identifier for the geographic region within which the Location occurred.
Example: "Animalia; Chordata; Vertebrata; Mammalia; Theria; Eutheria; Rodentia; Hystricognatha; Hystricognathi; Ctenomyidae; Ctenomyini; Ctenomys"
A list (concatenated and separated) of the names for the taxonomic ranks less specific than that given in the scientificName.
A unique identifier for the name of the next higher rank than the scientificName in a taxonomic classification. See higherTaxonName.
A unique identifier for the taxon concept less specific than that given in the taxonConceptID.
The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Example: "natureOfID=expert identification; identificationEvidence=cytochrome B sequence"
A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the Identification.
An identifier for the Identification (the body of information associated with the assignment of a scientific name). May be a global unique identifier or an identifier specific to the data set.
`aff. agrifolia var. oxyadenia` (for `Quercus aff. agrifolia var. oxyadenia` with accompanying values `Quercus` in genus, `agrifolia` in specificEpithet, `oxyadenia` in infraspecificEpithet, and `var.` in taxonRank. `cf. var. oxyadenia` for `Quercus agrifolia cf. var. oxyadenia` with accompanying values `Quercus` in genus, `agrifolia` in specificEpithet, `oxyadenia` in infraspecificEpithet, and `var.` in taxonRank.
A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.
`Aves del Noroeste Patagonico. Christie et al. 2004.`, `Stebbins, R. Field Guide to Western Reptiles and Amphibians. 3rd Edition. 2003. | Irschick, D.J. and Shaffer, H.B. (1997). The polytypic species revisited: Morphological differentiation among tiger salamanders (Ambystoma tigrinum) (Amphibia: Caudata). Herpetologica, 53(1), 30-49.`
A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.
`Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas.`
Comments or notes about the Identification.
Recommended best practice is to use a controlled vocabulary such as that used in HISPID and ABCD.
A categorical indicator of the extent to which the taxonomic identification has been verified to be correct.
`James L. Patton`, `Theodore Pappenfuss | Robert Macey`
A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.
Recommended best practice is to provide a single identifier that disambiguates the details of the identifying agent. If a list is used, the order of the identifiers on the list should not be assumed to convey any semantics. Recommended best practice is to separate the values in a list with space vertical bar space ( | ).
A list (concatenated and separated) of the globally unique identifier for the person, people, groups, or organizations responsible for assigning the Taxon to the subject.
The number of individuals present at the time of the Occurrence.
Examples: "U.amer. 44", "Smedley", "Orca J 23"
An identifier for an individual or named group of individual organisms represented in the Occurrence. Meant to accommodate resampling of the same individual or group for monitoring purposes. May be a global unique identifier or an identifier specific to a data set.
`location information not given for endangered species`, `collector identities withheld | ask about tissue samples`
Additional information that exists, but that has not been shared in the given record.
The term infragenericEpithet should be used in conjunction with genericName, specificEpithet, infraspecificEpithet, taxonRank and scientificNameAuthorship to represent the individual elements of the complete scientificName. It can be used to indicate the subgenus placement of a species, which in zoology is often given in parentheses. Can also be used to share infrageneric names such as botanical sections (e.g., `Vicia sect. Cracca`).
`Abacetillus` (for scientificName "Abacetus (Abacetillus) ambiguus", `Cracca` (for scientificName "Vicia sect. Cracca")
The infrageneric part of a binomial name at ranks above species but below genus.
In botany, where there can be more than one infraspecific rank, name strings may be provided, in literature and in identifications, that have more than two epithets. Only the last of these epithets is the infraspecificEpithet and only the first and the last epithets belong to the scientificName. For example: the infraspecificEpithet in the string "Indigofera charlieriana subsp. sessilis var. scaberrima" is `scaberrima` and the scientificName is `Indigophera charlieriana var. scaberrima`.
`concolor` (for scientificName "Puma concolor concolor"), `oxyadenia` (for scientificName "Quercus agrifolia var. oxyadenia"), `laxa` (for scientificName "Cheilanthes hirta f. laxa"), `scaberrima` (for scientificName "Indigofera charlieriana var. scaberrima").
The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.
The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
`http://biocol.org/urn:lsid:biocol.org:col:34777`, `http://grbio.org/cool/km06-gtbn`
An identifier for the institution having custody of the object(s) or information referred to in the record.
`Nosy Be`, `Bikini Atoll`, `Vancouver`, `Viti Levu`, `Zanzibar`
The name of the island on or near which the Location occurs.
`Alexander Archipelago`, `Archipiélago Diego Ramírez`, `Seychelles`
The name of the island group in which the Location occurs.
`Animalia`, `Archaea`, `Bacteria`, `Chromista`, `Fungi`, `Plantae`, `Protozoa`, `Viruses`
The full scientific name of the kingdom in which the taxon is classified.
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.
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.
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.
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.
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.
`zygote`, `larva`, `juvenile`, `adult`, `seedling`, `flowering`, `fruiting`
The age class or life stage of the Organism(s) at the time the Occurrence was recorded.
The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.
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.
`Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)`, `Queets Rainforest, Olympic National Park`
`Getty Thesaurus of Geographic Names`, `GADM`
Information about the source of this Location information. Could be a publication (gazetteer), institution, or team of individuals.
Example: "aspectheading=277; slopeindegrees=6"
A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the location.
An identifier for the set of location information (data associated with dcterms:Location). May be a global unique identifier or an identifier specific to the data set.
The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Recommended best practice is to use a persistent, globally unique identifier.
An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique.
The greater depth of a range of depth below the local surface, in meters.
`-1.5` (below the surface). `4.2` (above the surface). For a 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`.
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.
Maximum Distance Above Surface In Meters
The upper limit of the range of elevation (altitude, usually above sea level), in meters.
`0.01`, `normal distribution with variation of 2 m`
The description of the potential error associated with the measurementValue.
`Rob Guralnick`, `Peter Desmet | Stijn Van Hoey`
A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.
The date on which the MeasurementOrFact was made.
An identifier for the MeasurementOrFact (information pertaining to measurements, facts, characteristics, or assertions). May be a global unique identifier or an identifier specific to the data set.
`minimum convex polygon around burrow entrances` (for a home range area). `barometric altimeter` (for an elevation).
A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion.
Comments or notes accompanying the MeasurementOrFact.
`tail length`, `temperature`, `trap line length`, `survey area`, `trap type`
The nature of the measurement, fact, characteristic, or assertion.
Recommended best practice is to use the International System of Units (SI).
The units associated with the measurementValue.
The value of the measurement, fact, characteristic, or assertion.
The full name of the lithostratigraphic member from which the cataloged item was collected.
The lesser depth of a range of depth below the local surface, in meters.
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.
Minimum Distance Above Surface In Meters
The lower limit of the range of elevation (altitude, usually above sea level), in meters.
The integer month in which the Event occurred.
`Holzminden`, `Araçatuba`, `Ga-Segonyana`
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.
This term provides context to the `scientificName`. Together with the `scientificName`, separated by ‘sensu’ or ‘sec.’, it forms the taxon concept label, which may be seen as having the same relationship to `taxonConceptID` as, for example, `acceptedNameUsage` has to `acceptedNameUsageID`. When not provided, in Taxon Core data sets the `nameAccordingTo` can be taken to be the data set. In this case the data set mostly provides sufficient context to infer the delimitation of the taxon and its relationship with other taxa. In Occurrence Core data sets, when not provided, `nameAccordingTo` can be an underlying taxonomy of the data set, e.g. Plants of the World Online (http://powo.science.kew.org/) for vascular plant records in iNaturalist (in which case it should be provided), or, which is the case for most `PreservedSpecimen` data sets, the `Identification`, in which case there is no further context.
`Franz NM, Cardona-Duque J (2013) Description of two new species and phylogenetic reassessment of Perelleschus Wibmer & O’Brien, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013. Syst Biodivers. 11: 209–236.` (as the full citation of the Franz & Cardona-Duque (2013) in Perelleschus splendida sec. Franz & Cardona-Duque (2013))
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.
An identifier for the source in which the specific taxon concept circumscription is defined or implied. See nameAccordingTo.
Example: "http://hdl.handle.net/10199/7"
A resolvable globally unique identifier for the original publication of the scientificName.
`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`
A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.
An identifier for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.
The four-digit year in which the scientificName was published.
The nomenclatural code (or codes in the case of an ambiregnal name) under which the scientificName is constructed.
`nom. ambig.`, `nom. illeg.`, `nom. subnud.`
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.
Examples: "Tragus length: 14mm; Weight: 120g", "Height: 1-1.5 meters tall; flowers yellow; uncommon".
A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the Occurrence.
Example: "http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861"
A reference (publication, URI) to the most detailed information available about the Occurrence.
An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.
The description of the error associated with the occurrenceAttributeValue.
The agent responsible for having determined the value of the measurement or characteristic of the occurrence.
The date on which the the measurement or characteristic of the occurrence was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
An identifier for the occurrence attribute. May be a global unique identifier or an identifier specific to the data set.
Comments or notes accompanying the measurement or characteristic of the occurrence.
The nature of the measurement or characteristic of the occurrence. Recommended best practice is to use a controlled vocabulary.
The units for the value of the measurement or characteristic of the occurrence. Recommended best practice is to use International System of Units (SI) units.
The value of the measurement or characteristic of the occurrence.
For Occurrences, the default vocabulary is recommended to consist of "present" and "absent", but can be extended by implementers with good justification.
A statement about the presence or absence of a Taxon at a Location.
The full scientific name of the order in which the taxon is classified.
An identifier for the Organism instance (as opposed to a particular digital record of the Organism). May be a globally unique identifier or an identifier specific to the data set.
A textual name or label assigned to an Organism instance.
An organismQuantity must have a corresponding organismQuantityType.
`27` (organismQuantity) with `individuals` (organismQuantityType). `12.5` (organismQuantity) with `% biomass` (organismQuantityType). `r` (organismQuantity) with `Braun Blanquet Scale` (organismQuantityType). `many` (organismQuantity) with `individuals` (organismQuantityType).
A number or enumeration value for the quantity of organisms.
A dwc:organismQuantityType must have a corresponding dwc:organismQuantity.
`27` (organismQuantity) with `individuals` (organismQuantityType). `12.5` (organismQuantity) with `%biomass` (organismQuantityType). `r` (organismQuantity) with `BraunBlanquetScale` (organismQuantityType).
The type of quantification system used for the quantity of organisms.
Comments or notes about the Organism instance.
Recommended best practice is to use a controlled vocabulary. This term is not intended to be used to specify a type of taxon. To describe the kind of dwc:Organism using a URI object in RDF, use rdf:type (http://www.w3.org/1999/02/22-rdf-syntax-ns#type) instead.
`multicellular organism`, `virus`, `clone`, `pack`, `colony`
A description of the kind of Organism instance. Can be used to indicate whether the Organism instance represents a discrete organism or if it represents a particular type of aggregation.
The full scientific name, with authorship and date information if known, of the name usage in which the terminal element of the scientificName was originally established under the rules of the associated nomenclaturalCode. For example, for names governed by the ICNafp, this term would indicate the basionym of a record representing a subsequent combination. Unlike basionyms, however, this term can apply to scientific names at all ranks.
`Pinus abies`, `Gasterosteus saltatrix Linnaeus 1768`
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.
This term should be used to refer to the taxonID of a Taxon record that represents the usage of the terminal element of the scientificName as originally established under the rules of the associated nomenclaturalCode. For example, for names governed by the ICNafp, this term would establish the relationship between a record representing a subsequent combination and the record for its corresponding basionym. Unlike basionyms, however, this term can apply to scientific names at all ranks. For Darwin Core Archives the related record should be present locally in the same archive.
An identifier for the name usage (documented meaning of the name according to a source) in which the terminal element of the scientificName was originally established under the rules of the associated nomenclaturalCode.
`FMNH:Mammal:1234`, `NPS YELLO6778 | MBG 33424`
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.
The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.
Use a globally unique identifier for a dwc:Event or an identifier for a dwc:Event that is specific to the data set.
`A1` (parentEventID to identify the main Whittaker Plot in nested samples, each with its own eventID - `A1:1`, `A1:2`).
An identifier for the broader Event that groups this and potentially other Events.
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.
This term should be used for accepted names to refer to the taxonID of a Taxon record that represents the next higher taxon rank in the same taxonomic classification. For Darwin Core Archives the related record should be present locally in the same archive.
An identifier for the name usage (documented meaning of the name according to a source) of the direct, most proximate higher-rank parent taxon (in a classification) of the most specific element of the scientificName.
Recommended best practice is to use controlled value strings from the controlled vocabulary designated for use with this term, listed at http://rs.tdwg.org/dwc/doc/pw/. For details, refer to https://doi.org/10.3897/biss.3.38084
`releasedForUse`, `otherEscape`, `transportContaminant`, `transportStowaway`, `corridor`, `unaided`
The process by which an Organism came to be in a given place at a given time.
`Chordata` (phylum). `Bryophyta` (division).
The full scientific name of the phylum or division in which the taxon is classified.
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 empty) 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.
`fossil`, `cast`, `photograph`, `DNA extract`, `skin | skull | skeleton`, `whole animal (ETOH) | tissue (EDTA)`
A list (concatenated and separated) of preparations and preservation methods for a specimen.
`Chalepidae`, `Pinus abies`, `Anthus sp., field ID by G. Iglesias | Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology`
A list (concatenated and separated) of previous assignments of names to the Organism.
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.
`José E. Crespo`. `Oliver P. Pearson | Anita K. Pearson` (where the value in recordNumber `OPP 7101` corresponds to the collector number for the specimen in the field catalog of Oliver P. Pearson).
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.
Recommended best practice is to provide a single identifier that disambiguates the details of the identifying agent. If a list is used, it is recommended to separate the values in the list with space vertical bar space ( | ). The order of the identifiers on any list for this term can not be guaranteed to convey any semantics.
A list (concatenated and separated) of the globally unique identifier for the person, people, groups, or organizations responsible for recording the original Occurrence.
An identifier for a related resource (the object, rather than the subject of the relationship).
Examples: "StillImage", "MovingImage", "Sound", PhysicalObject", "PreservedSpecimen", FossilSpecimen", LivingSpecimen", "HumanObservation", "MachineObservation", "Location", "Taxonomy", "NomeclaturalChecklist", "Publication"
The type of the related resource. Recommended best practice is to use a controlled vocabulary.
The source (person, organization, publication, reference) establishing the relationship between the two resources.
The date-time on which the relationship between the two resources was established.
`sameAs`, `duplicate of`, `mother of`, `offspring of`, `sibling of`, `parasite of`, `host of`, `valid synonym of`, `located within`, `pollinator of members of taxon`, `pollinated specific plant`, `pollinated by members of taxon`
The relationship of the subject (identified by resourceID) to the object (identified by relatedResourceID).
Recommended best practice is to use the identifiers of the terms in a controlled vocabulary, such as the OBO Relation Ontology.
`http://purl.obolibrary.org/obo/RO_0002456` (for the relation "pollinated by"), `http://purl.obolibrary.org/obo/RO_0002455` (for the relation "pollinates"), `https://www.inaturalist.org/observation_fields/879` (for the relation "eaten by")
An identifier for the relationship type (predicate) that connects the subject identified by resourceID to its object identified by relatedResourceID.
`mother and offspring collected from the same nest`, `pollinator captured in the act`
Comments or notes about the relationship between the two resources.
`non-reproductive`, `pregnant`, `in bloom`, `fruit-bearing`
The reproductive condition of the biological individual(s) represented in the Occurrence.
An identifier for the resource that is the subject of the relationship.
An identifier for an instance of relationship between one resource (the subject) and another (relatedResource, the object).
A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., `5` for sampleSizeValue with `metre` for sampleSizeUnit.
`minute`, `hour`, `day`, `metre`, `square metre`, `cubic metre`
The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
A sampleSizeValue must have a corresponding sampleSizeUnit.
`5` for sampleSizeValue with `metre` for sampleSizeUnit.
A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
`40 trap-nights`, `10 observer-hours`, `10 km by foot`, `30 km by car`
The amount of effort expended during an Event.
Recommended best practice is describe an Event with no more than one sampling protocol. In the case of a summary Event with multiple protocols, in which a specific protocol can not be attributed to specific Occurrences, the recommended best practice is to separate the values in a list with space vertical bar space ( | ).
`UV light trap`, `mist net`, `bottom trawl`, `ad hoc observation | point count`, `Penguins from space: faecal stains reveal the location of emperor penguin colonies, https://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`
The names of, references to, or descriptions of the methods or protocols used during an Event.
This term should not contain identification qualifications, which should instead be supplied in the IdentificationQualifier term. When applied to an Organism or Occurrence, this term should be used to represent the scientific name that was applied to the associated Organism in accordance with the Taxon to which it was or is currently identified.
`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).
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.
`(Torr.) J.T. Howell`, `(Martinovský) Tzvelev`, `(Györfi, 1952)`
The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
An identifier for the nomenclatural (not taxonomic) details of a scientific name.
Examples: "subsp.", "var.", "forma", "species", "genus"
The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
The sex of the biological individual(s) represented in the Occurrence.
The name of the first or species epithet of the scientificName.
`1` (1 January). `366` (31 December), `365` (30 December in a leap year, 31 December in a non-leap year).
The earliest integer 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).
The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
`Periptyctinae`, `Orchidoideae`, `Sphindociinae`
The full scientific name of the subfamily in which the taxon is classified.
The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.
Information about the authorship of this taxon concept which uses the scientificName in their sense (secundum, sensu). Could be a publication (identification key), institution or team of individuals.
Example: "iucnstatus=vulnerable; distribution=Neuquen, Argentina"
A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the taxon.
An identifier for the taxonomic concept to which the record refers - not for the nomenclatural details of a taxon.
An identifier for the set of taxon information (data associated with the Taxon class). May be a global unique identifier or an identifier specific to the data set.
A unique identifier for the scientificName.
`subspecies`, `varietas`, `forma`, `species`, `genus`
The taxonomic rank of the most specific name in the scientificName.
`this name is a misspelling in common use`
Comments or notes about the taxon or name.
`invalid`, `misapplied`, `homotypic synonym`, `accepted`
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.
`holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388`, `holotype of Pinus abies | holotype of Picea abies`
A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.
`decimal degrees`, `degrees decimal minutes`, `degrees minutes seconds`, `UTM`
The coordinate format for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location.
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.
The original description of the depth below the local surface.
The original description of the elevation (altitude, usually above sea level) of the Location.
The verbatim original representation of the date and time information for an Event.
This term is meant to allow the capture of an unaltered original identification/determination, including identification qualifiers, hybrid formulas, uncertainties, etc. This term is meant to be used in addition to `scientificName` (and `identificationQualifier` etc.), not instead of it.
`Peromyscus sp.`, `Ministrymon sp. nov. 1`, `Anser anser X Branta canadensis`, `Pachyporidae?`
A string representing the taxonomic identification as it appeared in the original record.
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.
The original textual description of the place.
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.
`unknown`, `EPSG:4326`, `WGS84`, `NAD27`, `Campo Inchauspe`, `European 1950`, `Clarke 1866`
The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which coordinates given in verbatimLatitude and verbatimLongitude, or verbatimCoordinates are based.
Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex".
The taxonomic rank of the most specific name in the scientificName as it appears in the original record.
`Agamospecies`, `sub-lesus`, `prole`, `apomict`, `nothogrex`, `sp.`, `subsp.`, `var.`
`Andean Condor`, `Condor Andino`, `American Eagle`, `Gänsegeier`
The vertical datum used as the reference upon which the values in the elevation terms are based.
`Indian Ocean`, `Baltic Sea`, `Hudson River`, `Lago Nahuel Huapi`
The name of the water body in which the Location occurs.
The four-digit year in which the Event occurred, according to the Common Era Calendar.
sighting
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.
Observing and recording the presence or absence of butterflies during a transect walk.
Seeing three pelicans flying overhead on Christmas day and report them as part of the Christmas Bird Count.
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.
This class replaces class bco_0000003, which was made obsolete because of identifier format.
We are having conversation with OBI developers about how this term relates to OBI:assay (). Is it equivalent, broader, narrower? What does it mean to be the input to an observation.
An observing process is distinguished from a specimen collecting process in by having an information content entity as an output rather than a specimen. The information artifact may be 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, which is an ad hoc reporting of, typically, a single taxon occurrence, usually motivated by rarity, individual interest in the taxon, or atypicality of circumstances.
observing process
a curator submitting a herbarium speciman to a museum
a researcher submitting a water sample to a laboratory storage collection
A planned process whereby a person submits a material sample to an organization.
submitting process
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.
This term replaces the obsolete class bco_0000025, but with the correct identifier format.
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.
locality description
The herbarium collection at the New York Botanical Garden.
the painting collection at the Louvre Museum
An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
This term replaced bco_0000031, which was made obsolete because of incorrect identifier format.
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.
museum collection
the insect collection at the Smithsonian Institution
A museum collection that has as member part a material sample that was derived from an organism.
This term replaced bco_0000032, which was made obsolete because of incorrect identifier format.
organismal museum collection
Associating a museum specimen with a specific taxonomic concept based on its characters.
Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
Using DNA barcoding to identify a plant species.
Using a key to identify a plant in the field.
A planned process by which an organismal entity is associated with a taxon or taxa.
Need to add a relation for has specified output some taxonomic association.
This term replaces bco_0000042, which was made obsolete because of incorrect identifier format.
taxonomic identification process
A bird observed during a Christmas Bird Count
A lizard observed in the field that is not collected but whose location is recorded in a field notebook.
A tree is forest plot that is measured for diameter at breast height (DBH).
A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
This term replaces bco_0000044, which was made obsolete because of incorrect identifier format.
material target of observation
the role borne by a bird during a Christmas Bird Count
A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
This term replaced bco_0000046, which was made obsolete because of incorrect identifier format.
material target of observation role
inventory type
A planned process by which a taxonomic inventory is created.
not sure if this should be a type of assay or a type of planned process
taxonomic inventory process
A list of names ascribed to biological entities of specified organismal scope recorded over some defined spatial and temporal scope following a described sampling protocol and sampling effort, potentially including values indicating abundance or biomass of the biological entities
The biological entities are almost always species and the organismal scope typically a taxon but potentially also an ecologically or functionally defined grouping (e.g. ‘water birds’ or ‘trees’) or other operational unit (e.g. genes). The list would typically contain multiple entities, but may be as short as a single entity or, if a sampling effort focused on a certain taxon yielded no results, even contain none.
taxonomic inventory
restricted search
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."
A taxonomic inventory process that is restricted to plots, transects, or points, in which a person or group of people is comprehensively covering the entire area, usually with a well-described survey time or pace. The search is restricted to a defined and human-scale geospatial area (usually 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.
restricted search taxonomic inventory process
open search
Individual Christmas Bird Count by some team. Organized field trip to a State Park.
A taxonomic inventory process in which the search is restricted within a larger defined geographic area, but where effort isn't even or complete across the region, and thus not a comprehensive accounting of taxa of interest. Temporal duration is typically longer than restricted searches, lasting hours to several days.
open search taxonomic inventory process
opportunistic search
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.
A taxonomic inventory process that is a more casual reporting of occurrences of taxa of interest, still intended to be a comprehensive accounting of the taxa of interest, but with no pre-specified investment of effort nor planned trajectory for discovery, thus of often idiosyncratic length or spatial scope.
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.
opportunistic search taxonomic inventory process
trap or sample inventory
an inventory of insects in a area using pheremone traps
an inventory of the large mammals of a park based on camera traps
inventories based on trawl samples
A taxonomic inventory process that is typically restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as a whole organisms, scat, fur, other material samples or information artifacts such as photographs or sound recordings
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).
trap or sample taxonomic inventory process
incidental or adventitious inventory
data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
A taxonomic inventory process in which taxon occurrences are recorded as co-variates of another study, or by happenstance, and later compiled as a taxonomic inventory.
adventitious taxonomic inventory process
compilation inventory
A taxonomic inventory process in which a list of taxa of interest is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
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.
compilation taxonomic inventory process
The Louvre Museum
The Smithsonian Institution
An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance.
A museum may make its collections available for public viewing through exhibits that may be permanent or temporary. The class museum has meaning that is much broader than biological collecitons. It may be better to import this term from another, more general ontology and create a specific subclass for natural history museum.
museum
a fossil housed in a natural history museum
A specimen that is derived from a fossil.
obsolete fossil specimen
a bacterial culture in a culture collection
a tree in an arboretum
an animal in a zoo
germplasm
A specimen that is alive.
obsolete living specimen
A specimen that has been preserved.
obsolete preserved specimen
obsolete darwin core class
a biologist recording an observation of an animal in a field notebook
an entomologist recording the presense of butterflies while walking a transect
An observing process in which the observing entity consists of one or more humans.
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.
human observation process
a camera trap recording the presence of a jaguar
a sensor periodically recording the surface temperature of a leaf over several hours
An observing process in which the observing entity consists of one or more machines.
May want to work with OBI to define this term in a more general sense for investigations.
machine observation process
A data item that is the output of a taxonomic identification process and associates some organismal entity with a taxon or taxa.
identification assertion
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
quality
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
function
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
Common Anatomy Reference Onotology - CARO2
organism or virus
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
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.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
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.
polymer
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A lymphocyte of B lineage that is capable of B cell mediated immunity.
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
human dwelling
https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
transferase activity, transferring phosphorus-containing groups
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
information carrier
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.
A quality of an information bearer that imparts the information content
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'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".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.
2013-05-30 Alan Ruttenberg: 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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
directive information entity
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
image
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.
person:Chris Stoeckert
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
material information bearer
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.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
GROUP: IAO
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
obsolescence reason specification
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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Melanie Courtot
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
PERSON: Lawrence Hunter
document
denotator type
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.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
An ontology module that is intended for usage in analysis or discovery applications.
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
ontology module subsetted by expressivity
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by OWL profile
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'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.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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)
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
evaluant role
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.
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
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)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
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.
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
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.
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.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
material sample
specimen role
An assay that produces a picture of an entity.
organization
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.
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.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
protocol
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.
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.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
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
A planned process with the objective of collecting a specimen.
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.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
An objective specification maintains some or all of the qualities of a material over time.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
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.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
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.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
A cytometry assay that measures the abundance and/or characteristics of lymphocytes
Epstein Barr virus transformed B cell
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
A jar of water, the microbes that were filtered from that water, the DNA extracted from those microbes, a subsample of that DNA.
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
IEDB
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
May be of the same or different species.
collection of organisms
An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people.
WEB: http://en.wikipedia.org/wiki/Household
household
A household in which the majority of the income of its members is derived from agricultural activities.
This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term.
agricultural household
A material entity that is one or more organisms, viruses or viroids.
organismal entity
A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other.
pair of interacting organisms
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
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.
primary structure of sequence macromolecule
Anatomical group that has its parts adjacent to one another.
A museum specimen that serves as evidence for a taxonomic identification process bears an evidence role.
A role that is borne by some entity as a result of the entity providing evidence to support an assertion.
Will be replaced by an external ontology class.
obsolete evidence role
An evidence role that persists through time.
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.
obsolete persistent evidence role
This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
obsolete collecting process
This class was made obsolete because of the incorrect identifier format. It has been replaced by BCO_0000003.
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.
obsolete observing process
A process of existing in a particular spatio-temporal region.
This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
obsolete being there process
a book
a field notebook
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.
obsolete printed report
A printed report that records the outcome of some observing process.
obolete printed observational report
Filtering sea water to extract only organisms smaller than a certain size.
deciding which branch to collect for a herbarium specimen
A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
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.
obsolete selecting process
This term was made obsolete because it had the incorrect identifier format. It has been replaced by BCO_0000016.
obsolete submitting process
removing a fish from the ocean with a net
A process that involves removing a material entity from its original site to another site.
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).
obsolete physical extraction process
collecting plant parts for herbarium specimens
collecting sea water samples as part of Ocean Sampling Day
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.
collecting event
This term has been replaced by OBI:specimen collection.
obsolete material sampling process
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.
obsolete data sampling process
obsolete statistical sampling process
This term was deprecated because it has the wrong ID format. It is replaced by BCO_0000025.
obsolete locality description
the role borne by a branch when it becomes a herbarium specimen
A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
This term has been replaced by OBI:specimen role.
obsolete material sample role
A sampling process that has as output some material sample.
Do not need this class. By virtue of the existance of the material sample, we know that the sampling process was successful.
obsolete successful material sampling process
A material sampling process that has as output exactly zero material samples.
Do not need this class. By virtue of the absence of the material sample, we know that the sampling process was unsuccessful.
obsolete unsuccessful material sampling process
At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
obsolete museum collection entity
A museum collections entity that derives from an organismal entity, has a persistent evidence role and 'depends on' a process of collecting.
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.
obsolete organismal museum collection entity
This term was made obsolete because of incorrect identifier format. It has been replaced by BCO_0000031.
obsolete museum collection
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000031.
obsolete organismal museum collection
Replaced by OBI organization. Request institution as synonym in OBI.
obsolete institution
A material entity that derives from an organism or virus or viroid.
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 organismal entity
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.
obsolete organism or virus or viroid
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.
This term has been replaced by OBI:specimen.
obsolete material sample
An information content entity (?) that is the result of some data sampling process.
obsolete data sample
obsolete statistical sample
If sampling is a OBI planned process, that captures that it is protocal governed.
obsolete protocol governed sampling activity
A process by which a material sample is associated with a taxon or taxa.
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000042.
obsolete taxonomic identification process
This term was made obsolete because of incorrect identifier format. It should be replaced by an external ontology term.
Consider term from OBI or IAO.
Includes as output rubbings, casts, photographic prints, audio or video tapes. Needs a better name. Current name is the definition.
obsolete process that yields a material representation of a material entity
An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
This term was made obsolete because of incorrected identifier format. It is replaced by BCO_0000044.
obsolete material target of observation
Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
obsolete process that yields an information artifact that is a representation of a material entity
This term was made obsolete because of incorrect identifier format. It is replaced by BCO_0000046.
obsolete material target of observation role
A set of gastropod and bivalve shells found in shell midden from an archaeological site in Alaska.
A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some animal.
Zooarchaeological specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.
zooarcheological specimen
Preserved seeds found in a storage jar at an archeological site.
A preserved specimen that is the output of an archaeological sampling process and is the remains of a part of some plant.
Archaeologicalbotanical specimens are typically collections of biological material generated as part of an archaeological collecting process that is separate from the type of processes that would yield other kinds of samples or collections of samples. This process almost always entails collecting in-situ from archaeological sites where there is evidence of past human material culture.
archeobotanical specimen
This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000080
obsolete zooarcheological specimen
This class was deprecated because the ID format is wrong. It is replaced by http://purl.obolibrary.org/obo/BCO_0000081.
obsolete archeobotanical specimen
location of an event
The site where a process occurs. In the context of Dawrin Core, this is generally where a specimen is collected, an organism is observed or a measurement is taken.
specimen collection process X
material entity A
material entity B
material entity C
specimen collection process Y
incorrect identifier format, replaced
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
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.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
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."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
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.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
core
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
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
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.
universal
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.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"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.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
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
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
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.
obsolete_the supplier role of Affymetrix
obsolete_the manufacturer role of Agilent
obsolete_manufacturer role of Bruker Daltonics
obsolete_the manufacturer role of Thermo
obsolete_the manufacturer role of Li-Cor
obsolete_the manufacturer role of Ambion
obsolete_the manufacturer role of BIO-RAD
obsolete_the manufacturer role of Illumina
obsolete_the manufacturer role of Helicos
obsolete_manufacturer role of Bruker Corporation
obsolete_the manufacturer role of Waters
obsolete_manufacturer role of applied biosystems
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
obsolete incorrect identifier format, do not use
The set of classes specified by the Darwin Core Type Vocabulary, used to categorize the nature or genre of the resource.
has_specified_input
see is_input_of example_of_usage
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.
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
The category of information pertaining to a logical set of records.
event
A specimen collection process. A camera trap image capture. A marine trawl.
An action that occurs at some location during some time.
Container class for information about attributes related to a given sampling event.
The category of information pertaining to measurements associated with an event.
fossil specimen
A body fossil. A coprolite. A gastrolith. An ichnofossil. A piece of a petrified tree.
Geological information, such as stratigraphy, that qualifies a region or place.
geological context
An output of a human observation process.
human observation
Evidence of an Occurrence taken from field notes or literature. A record of an Occurrence without physical evidence nor evidence captured with a machine.
identification
A taxonomic determination (e.g., the assignment to a taxon).
A subspecies determination of an organism.
living specimen
A living plant in a botanical garden. A living animal in a zoo.
A photograph. A video. An audio recording. A remote sensing image. A Occurrence record based on telemetry.
machine observation
An output of a machine observation process.
A reference to or citation of one, a part of, or multiple specimens in scholarly publications.
A citation of a physical specimen from a scientific collection in a taxonomic treatment in a scientific publication. A citation of a group of physical specimens, such as paratypes in a taxonomic treatment in a scientific publication. An occurrence mentioned in a field note book.
This class constitutes a new value for the controlled vocabulary in the recommendations for basisOfRecord. When importing Darwin Core Archives of literature-based datasets to GBIF, the basisOfRecord should be changed from “Occurrence”, "PreservedSpecimen" or "Literature" to “MaterialCitation”.
A physical result of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.
A whole organism preserved in a collection. A part of an organism isolated for some purpose. A soil sample. A marine microbial sample.
The weight of an organism in grams. The number of placental scars. Surface water temperature in Celsius.
This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
A measurement of or fact about an rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource).
Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to dwc:Occurrence, dwc:Organism, dwc:MaterialSample, dwc:Event, dwc:Location, dwc:GeologicalContext, dwc:Identification, or dwc:Taxon.
A wolf pack on the shore of Kluane Lake in 1988. A virus in a plant leaf in the New York Botanical Garden at 15:29 on 2014-10-23. A fungus in Central Park in the summer of 1929.
An existence of an Organism (sensu http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a particular time.
This Darwin Core class should not be used when annotating data with BCO. It is not mapped to BCO classes because its meaning is too ambiguous.
The category of information pertaining to measurements accociated with an occurrence.
Instances of the dwc:Organism class are intended to facilitate linking one or more dwc:Identification instances to one or more dwc:Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class.
A particular organism or defined group of organisms considered to be taxonomically homogeneous.
A specific bird. A specific wolf pack. A specific instance of a bacterial culture.
A plant on an herbarium sheet. A cataloged lot of fish in a jar.
preserved specimen
A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.
An instance of an Organism is the mother of another instance of an Organism. A uniquely identified Occurrence represents the same Occurrence as another uniquely identified Occurrence. A MaterialSample is a subsample of another MaterialSample.
Container class for information about the results of a sampling event (specimen, observation, etc.)
Container class for information about attributes related to a given sample.
Container class for information about the conditions and methods of acquisition of samples.
Container class for information about the location where a sampling event occurred.
The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820.
A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.
taxon
dwc_terms status
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).