Biocode Commons Ontology Hackathon members
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.
taxonomic inventory metadata preferred name
BCO preferred label
dwc_bco mapping
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor 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 class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=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
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
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
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.
Chris Mungall
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"
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
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
ISA tools project (http://isa-tools.org)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
temporal interpretation
Contributor
Creator
Date
An account of the content of the resource.
Description
The physical or digital manifestation of the resource.
Format
The topic of the content of the resource.
Subject and Keywords
A name given to the resource.
Title
dwc_terms status
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, the BFO relation was replaced by has role at some time, which is not yet part of a stable release. Once the BFO role has been tested and released, it may replace this relation.
has role
derives from by planned process
This property used an old version of the has input relation, so it has been deprecated.
is derived into by planned process
This relation is used specifically to link a taxonomic association to a taxon and is used with the of organism relation.
to taxon
This relation specifically links an identification association to an organismal entity and is used together with the to taxon relation.
of organism
A shortcut relation to an organsimal entity to a taxon or taxa.
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 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
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
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
realized by
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
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
s depends on
s_depends_on
has_role
is about
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is_specified_input_of
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.
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
A relation between an information content entity and a value specification that specifies its value.
this fragility inheres in this vase
this red color inheres in this apple
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.
this apple is bearer of this red color
this vase is bearer of this fragility
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.
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
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.
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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
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
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
Organizational term to help define related terms. Do not use for data annotation with Darwin Core.
Example: "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.
Accepted Name Usage
Abstract term to attribute information to a source.
Organizational term to help define related terms. Do not use for data annotation.
According To
Example: "http://arctos.database.museum/SpecimenImages/UAMObs/Mamm/2/P7291179.JPG"
A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.
Associated Media
Example: "sibling of FMNH:Mammal:1234; sibling of FMNH:Mammal:1235"
DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID
A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence.
Associated Occurrences
The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "sibling of MXA-232", "mother of MXA-231 | mother of MXA-232".
A list (concatenated and separated) of identifiers of other Organisms and their associations to this Organism.
Associated Organisms
Examples: "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767."
A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
Associated References
Example: "GenBank: U34853.1"
DataSets/DataSet/Units/Unit/Sequences/Sequence/ID-in-Database + constant
A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
Associated Sequences
Example: "host: Quercus alba"
A list (concatenated and separated) of identifiers or names of taxa and their associations with the Occurrence.
Associated Taxa
Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"
The specific nature of the data record - a subtype of the dcterms:type. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).
Basis of Record
The full name of the lithostratigraphic bed from which the cataloged item was collected.
Bed
Examples: "roosting", "foraging", "running"
A description of the behavior shown by the subject at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.
Behavior
An identifier (preferably unique) for the record within the data set or collection.
Catalog Number
Examples: "Mammalia", "Hepaticopsida"
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = classis
The full scientific name of the class in which the taxon is classified.
Class
Examples: "Mammals", "Hildebrandt", "eBird"
The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
Collection Code
Example: "urn:lsid:biocol.org:col:34818"
An identifier for the collection or dataset from which the record was derived. For physical specimens, the recommended best practice is to use the identifier in a collections registry such as the Biodiversity Collections Index (http://www.biodiversitycollectionsindex.org/).
Collection ID
Examples: "Africa", "Antarctica", "Asia", "Europe", "North America", "Oceania", "South America"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Continent
The name of the continent in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
Continent
Examples: "0.00001" (normal GPS limit for decimal degrees), "0.000278" (nearest second), "0.01667" (nearest minute), "1.0" (nearest degree)
DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/ISOAccuracy or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/AccuracyStatement
A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.
Coordinate Precision
Examples: "30" (reasonable lower limit of a GPS reading under good conditions if the actual precision was not recorded at the time), "71" (uncertainty for a UTM coordinate having 100 meter precision and a known spatial reference system).
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.
Coordinate Uncertainty In Meters
Examples: "Denmark", "Colombia", "España"
The name of the country or major administrative unit in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
Country
Examples: "AR" for Argentina, "SV" for El Salvador
The standard code for the country in which the Location occurs. Recommended best practice is to use ISO 3166-1-alpha-2 country codes.
Country Code
Examples: "Missoula", "Los Lagos", "Mataró"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= County
The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.
County
Example: "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.
Data Generalizations
Examples: "Grinnell Resurvey Mammals", "Lacey Ctenomys Recaptures"
The name identifying the data set from which the record was derived.
Dataset Name
Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
The date on which the subject was identified as representing the Taxon. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Date Identified
Examples: "9", "28"
accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
The integer day of the month on which the Event occurred.
Day
Example: "-41.0983423"
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.
Decimal Latitude
Example: "-121.1761111"
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.
Decimal Longitude
Examples: "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 controlled vocabulary.
Disposition
Examples: "tragusLengthInMeters=0.014; weightInGrams=120", "heightInMeters=1.5", "natureOfID=expert identification; identificationEvidence=cytochrome B sequence", "relativeHumidity=28; airTemperatureInC=22; sampleSizeInKilograms=10", "aspectHeading=277; slopeInDegrees=6", "iucnStatus=vulnerable; taxonDistribution=Neuquen, Argentina"
A list (concatenated and separated) of additional measurements, facts, characteristics, or assertions about the record. Meant to provide a mechanism for structured content such as key-value pairs.
Dynamic Properties
Examples: "Atlantic", "Boreal", "Skullrockian"
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.
Earliest Age Or Lowest Stage
Examples: "Phanerozoic", "Proterozoic"
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.
Earliest Eon Or Lowest Eonothem
Examples: "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.
Earliest Epoch Or Lowest Series
Examples: "Cenozoic", "Mesozoic"
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.
Earliest Era Or Lowest Erathem
Examples: "Neogene", "Tertiary", "Quaternary"
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.
Earliest Period Or Lowest System
Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
The latest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).
End Day Of Year
Examples: "native", "introduced", "naturalised", "invasive", "managed"
The process by which the biological individual(s) represented in the Occurrence became established at the location. Recommended best practice is to use a controlled vocabulary.
Establishment Means
The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Event Date
Example: "after the recent rains the river is nearly at flood stage"
Comments or notes about the Event.
Event Remarks
Examples: "14:07-0600" is 2:07pm in the time zone six hours earlier than UTC, "08:40:21Z" is 8:40:21am UTC, "13:00:00Z/15:30:00Z" is the interval between 1pm UTC and 3:30pm UTC.
accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin and DataSets/DataSet/Units/Unit/Gathering/ISODateTimeEnd
The time or interval during which an Event occurred. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Event Time
Examples: "Felidae", "Monocleaceae"
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = familia
The full scientific name of the family in which the taxon is classified.
Family
Example: "notes available in 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.
Field Notes
Example: "RV Sol 87-03-08"
An identifier given to the event in the field. Often serves as a link between field notes and the Event.
Field Number
Example: The WKT for the standard WGS84 SRS (EPSG:4326) is "GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137,298.257223563]],PRIMEM["Greenwich",0],UNIT["Degree",0.0174532925199433]]" without the enclosing quotes.
A Well-Known Text (WKT) representation of the Spatial Reference System (SRS) for the footprintWKT of the Location. Do not use this term to describe the SRS of the decimalLatitude and decimalLongitude, even if it is the same as for the footprintWKT - use the geodeticDatum instead.
Footprint SRS
Detailed explanations with graphical examples can be found in the "Guide to Best Practices for Georeferencing", Chapman and Wieczorek, eds. 2006 (http://www.gbif.org/prog/digit/Georeferencing).
DataSets/DataSet/Units/Unit/Gathering/FootprintSpatialFit (ABCD v2.06b)
The ratio of the area of the footprint (footprintWKT) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given footprint does not completely contain the original representation. The footprintSpatialFit is undefined (and should be left blank) if the original representation is a point and the given is not that same point. If both the original and the given georeference are the same point, the footprintSpatialFit is 1.
Footprint Spatial Fit
Example: the one-degree bounding box with opposite corners at (longitude=10, latitude=20) and (longitude=11, latitude=21) would be expressed in well-known text as POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20))
DataSets/DataSet/Units/Unit/Gathering/FootprintWKT (ABCD v2.06b)
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.
Footprint WKT
Examples: "Notch Peak Fromation", "House Limestone", "Fillmore Formation"
The full name of the lithostratigraphic formation from which the cataloged item was collected.
Formation
Examples: "Puma", "Monoclea"
{DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Viral/GenusOrMonomial or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/GenusOrMonomial}
The full scientific name of the genus in which the taxon is classified.
Genus
Examples: "EPSG:4326", "WGS84", "NAD27", "Campo Inchauspe", "European 1950", "Clarke 1866"
The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimalLatitude and decimalLongitude as based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".
Geodetic Datum
Examples: "Guide to Best Practices for Georeferencing" (Chapman and Wieczorek, eds. 2006), Global Biodiversity Information Facility.", "MaNIS/HerpNet/ORNIS Georeferencing Guidelines", "Georeferencing Quick Reference Guide"
A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.
Georeference Protocol
Example: "assumed distance by road (Hwy. 101)"
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.
Georeference Remarks
Examples: "USGS 1:24000 Florence Montana Quad; Terrametrics 2008 on Google Earth"
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.
Georeference Sources
Examples: "requires verification", "verified by collector", "verified by curator".
A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description. Recommended best practice is to use a controlled vocabulary.
Georeference Verification Status
Examples: "Kristina Yamamoto (MVZ); Janet Fang (MVZ)", "Brad Millen (ROM)"
A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.
Georeferenced By
The date on which the Location was georeferenced. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Georeferenced Date
The full name of the lithostratigraphic group from which the cataloged item was collected.
Group
Examples: "oak savanna", "pre-cordilleran steppe"
A category or description of the habitat in which the Event occurred.
Habitat
Example: "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 order the list starting with the highest rank and separating the names for each rank with a semi-colon (";").
Higher Classification
Example: "South America; Argentina; Patagonia; Parque Nacional Nahuel Huapi; Neuquén; Los Lagos" with accompanying values "South America" in Continent, "Argentina" in Country, "Neuquén" in StateProvince, and Los Lagos in County.
{DataSets/DataSet/Units/Unit/Gathering/LocalityText or DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName}
A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.
Higher Geography
The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Highest Biostratigraphic Zone
Examples: 1) For the determination "Quercus aff. agrifolia var. oxyadenia", identificationQualifier would be "aff. agrifolia var. oxyadenia" with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank. 2) For the determination "Quercus agrifolia cf. var. oxyadenia", identificationQualifier would be "cf. var. oxyadenia " with accompanying values "Quercus" in genus, "agrifolia" in specificEpithet, "oxyadenia" in infraspecificEpithet, and "var." in rank.
A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.
Identification Qualifier
Example: "Aves del Noroeste Patagonico. Christie et al. 2004."
A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.
Identification References
Example: "Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas."
Comments or notes about the Identification.
Identification Remarks
Examples: "0", "4"
A categorical indicator of the extent to which the taxonomic identification has been verified to be correct. Recommended best practice is to use a controlled vocabulary such as that used in HISPID/ABCD.
Identification Verification Status
Examples: "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.
Identified By
Examples: "1", "25"
The number of individuals represented present at the time of the Occurrence.
Individual Count
Examples: "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.
Information Withheld
Examples: "concolor", "oxyadenia", "sayi"
{DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SubspeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/SecondEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SubspeciesEpithet}
The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.
Infraspecific Epithet
Examples: "MVZ", "FMNH", "AKN-CLO", "University of California Museum of Paleontology (UCMP)"
The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
Institution Code
An identifier for the institution having custody of the object(s) or information referred to in the record.
Institution ID
Examples: "Isla Victoria", "Vancouver", "Viti Levu", "Zanzibar"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island
The name of the island on or near which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
Island
Examples: "Alexander Archipelago", "Seychelles"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island group
The name of the island group in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
Island Group
Examples: "Animalia", "Plantae"
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = regnum
The full scientific name of the kingdom in which the taxon is classified.
Kingdom
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.
Latest AgeOr Highest Stage
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.
Latest Eon Or Highest Eonothem
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.
Latest Epoch Or Highest Series
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.
Latest Era Or Highest Erathem
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.
Latest Period Or Highest System
Examples: "egg", "eft", "juvenile", "adult", "2 adults 4 juveniles"
DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage (Note DwC spec uses ”MycologicalLifeStage” or DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage
The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary.
Life Stage
The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.
Lithostratigraphic Terms
Example: "Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)"
The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.
Locality
Examples: "Getty Thesaurus of Geographic Names", "GADM"
Information about the source of this Location information. Could be a publication (gazetteer), institution, or team of individuals.
Location According To
Example: "under water since 2005"
Comments or notes about the Location.
Location Remarks
The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Lowest Biostratigraphic Zone
Example: "200"
The greater depth of a range of depth below the local surface, in meters.
Maximum Depth In Meters
Example: 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation; VerbatimElevation: "300m" MinimumElevationInMeters: "300", MaximumElevationInMeters: "300", VerbatimDepth: "20m", MinimumDepthInMeters: "20", MaximumDepthInMeters: "20", minimumDistanceAboveSurfaceInMeters: "0", maximumDistanceAboveSurfaceInMeters: "-1.5"
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.
Maximum Elevation In Meters
Examples: "0.01", "normal distribution with variation of 2 m"
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Aspect/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Accuracy or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Accuracy
The description of the potential error associated with the measurementValue.
Measurement Accuracy
Examples: "Javier de la Torre", "Julie Woodruff; Eileen Lacey"
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasuredBy or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasuredBy
A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.
Measurement Determined By
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/MeasurementDateTime or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/MeasurementDateTime
The date on which the MeasurementOrFact was made. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Measurement Determined Date
Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation
/DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/Method or /DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/Method
A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion.
Measurement Method
Example: "tip of tail missing"
Comments or notes accompanying the MeasurementOrFact.
Measurement Remarks
Examples: "tail length", "temperature", "trap line length", "survey area", "trap type"
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter
The nature of the measurement, fact, characteristic, or assertion. Recommended best practice is to use a controlled vocabulary.
Measurement Type
Examples: "mm", "C", "km", "ha"
DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement
The units associated with the measurementValue. Recommended best practice is to use the International System of Units (SI).
Measurement Unit
Examples: "45", "20", "1", "14.5", "UV-light"
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/SiteMeasurementOrFact/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Altitude/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Depth/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Biotope/MeasurementsOrFacts/MeasurementOrFactAtomised/UpperValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/LowerValue or DataSets/DataSet/Units/Unit/Gathering/Height/MeasurementOrFactAtomised/UpperValue
The value of the measurement, fact, characteristic, or assertion.
Measurement Value
Examples: "Lava Dam Member", "Hellnmaria Member"
The full name of the lithostratigraphic member from which the cataloged item was collected.
Member
Example: "100"
The lesser depth of a range of depth below the local surface, in meters.
Minimum Depth 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.
Minimum Elevation In Meters
Examples: "1" (=January), "10" (=October)
The ordinal month in which the Event occurred.
Month
Examples: "Holzminden"
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.
Municipality
Example: "McCranie, J. R., D. B. Wake, and L. D. Wilson. 1996. The taxonomic status of Bolitoglossa schmidti, with comments on the biology of the Mesoamerican salamander Bolitoglossa dofleini (Caudata: Plethodontidae). Carib. J. Sci. 32:395-398.", "Werner Greuter 2008", "Lilljeborg 1861, Upsala Univ. Arsskrift, Math. Naturvet., pp. 4, 5"
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.
Name According To
Examples: "Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388", "Forel, Auguste, Diagnosies provisoires de quelques espèces nouvelles de fourmis de Madagascar, récoltées par M. Grandidier., Annales de la Societe Entomologique de Belgique, Comptes-rendus des Seances 30, 1886"
A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.
Name Published In
Examples: "1915", "2008"
The four-digit year in which the scientificName was published.
Name Published In Year
Examples: "ICBN", "ICZN", "BC", "ICNCP", "BioCode", "ICZN; ICBN"
The nomenclatural code (or codes in the case of an ambiregnal name) under which the scientificName is constructed. Recommended best practice is to use a controlled vocabulary.
Nomenclatural Code
Examples: "nom. ambig.", "nom. illeg.", "nom. subnud."
(DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation) pro parte
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.
Nomenclatural Status
Example: "found dead on road"
Comments or notes about the Occurrence.
Occurrence Remarks
Examples: "present", "absent"
A statement about the presence or absence of a Taxon at a Location. Recommended best practice is to use a controlled vocabulary.
Occurrence Status
Examples: "Carnivora", "Monocleales"
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = ordo
The full scientific name of the order in which the taxon is classified.
Order
Examples: "Huberta", "Boab Prison Tree", "J pod".
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. Recommended best practice is to use a controlled vocabulary.
Organism Name
An organismQuantity must have a corresponding organismQuantityType, e.g., "27" for organismQuantity with "individuals" for organismQuantityType; "12.5" for organismQuantity with "%biomass" for organismQuantityType; "r" for organismQuantity with "BraunBlanquetScale" for organismQuantityType.
A number or enumeration value for the quantity of organisms.
Organism Quantity
An organismQuantityType must have a corresponding organismQuantity, e.g., "27" for organismQuantity with "individuals" for organismQuantityType; "12.5" for organismQuantity with "%biomass" for organismQuantityType; "r" for organismQuantity with "BraunBlanquetScale" for organismQuantityType.
The type of quantification system used for the quantity of organisms.
Organism Quantity Type
Example: "One of a litter of six."
Comments or notes about the Organism instance.
Organism Remarks
This term is not intended to be used to specify a type of taxon. To describe the kind of Organism using a URI object in RDF, use rdf:type (http://www.w3.org/1999/02/22-rdf-syntax-ns#type) instead. Examples: "multicellular organism", "virus", "clone" "pack", "colony".
A textual name or label assigned to an Organism instance.
Organism Scope
Examples: "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.
Original Name Usage
Examples: "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.
Other Catalog Numbers
Examples: "NPS", "APN", "InBio"
The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.
Owner Institution Code
Examples: "Rubiaceae", "Gruiformes", "Testudinae"
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.
Parent Name Usage
Examples: "Chordata" (phylum), "Bryophyta" (division)
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = phylum
The full scientific name of the phylum or division in which the taxon is classified.
Phylum
The ratio of the area of the point-radius (decimalLatitude, decimalLongitude, coordinateUncertaintyInMeters) to the area of the true (original, or most specific) spatial representation of the Location. Legal values are 0, greater than or equal to 1, or undefined. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given point-radius does not completely contain the original representation. The pointRadiusSpatialFit is undefined (and should be left blank) if the original representation is a point without uncertainty and the given georeference is not that same point (without uncertainty). If both the original and the given georeference are the same point, the pointRadiusSpatialFit is 1.
Point Radius Spatial Fit
Examples: "skin; skull; skeleton", "whole animal (ETOH); tissue (EDTA)", "fossil", "cast", "photograph", "DNA extract"
A list (concatenated and separated) of preparations and preservation methods for a specimen.
Preparations
Example: "Anthus sp., field ID by G. Iglesias; Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology"
DataSets/DataSet/Units/Unit/Identifications/Identification with PreferredFlag = false
A list (concatenated and separated) of previous assignments of names to the Occurrence.
Previous Identifications
Example: "OPP 7101"
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.
Record Number
Example: "Oliver P. Pearson; Anita K. Pearson" where the value in recordNumber "OPP 7101" corresponds to the number for the specimen in the field catalog (collector number) of Oliver P. Pearson.
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.
Recorded By
Example: "Julie Woodruff"
The source (person, organization, publication, reference) establishing the relationship between the two resources.
Relationship According To
The date-time on which the relationship between the two resources was established. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Relationship Established Date
Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within"
The relationship of the resource identified by relatedResourceID to the subject (optionally identified by the resourceID). Recommended best practice is to use a controlled vocabulary.
Relationship Of Resource
Examples: "mother and offspring collected from the same nest", "pollinator captured in the act"
Comments or notes about the relationship between the two resources.
Relationship Remarks
Examples" "non-reproductive", "pregnant", "in bloom", "fruit-bearing"
The reproductive condition of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.
Reproductive Condition
A sampleSizeUnit must have a corresponding sampleSizeValue, e.g., "5" for sampleSizeValue with "metre" for sampleSizeUnit. Examples: "minute", "hour", "day", "metre", "square metre", "cubic metre". Recommended best practice is to use a controlled vocabulary such as the Ontology of Units of Measure http://www.wurvoc.org/vocabularies/om-1.8/ of SI units, derived units, or other non-SI units accepted for use within the SI (e.g., minute, hour, day, litre).
The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
Sample Size Unit
A sampleSizeValue must have a corresponding sampleSizeUnit. Example: "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.
Sample Size Value
Examples: "40 trap-nights", "10 observer-hours; 10 km by foot; 30 km by car"
The amount of effort expended during an Event.
Sampling Effort
Examples: "UV light trap", "mist net", "bottom trawl", "ad hoc observation", "point count", "Penguins from space: faecal stains reveal the location of emperor penguin colonies, http://dx.doi.org/10.1111/j.1466-8238.2009.00467.x", "Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp.", "http://www.bsc-eoc.org/download/Owl.pdf"
The name of, reference to, or description of the method or protocol used during an Event.
Sampling Protocol
Examples: "Coleoptera" (order), "Vespertilionidae" (family), "Manis" (genus), "Ctenomys sociabilis" (genus + specificEpithet), "Ambystoma tigrinum diaboli" (genus + specificEpithet + infraspecificEpithet), "Roptrocerus typographi (Györfi, 1952)" (genus + specificEpithet + scientificNameAuthorship), "Quercus agrifolia var. oxyadenia (Torr.) J.T. Howell" (genus + specificEpithet + taxonRank + infraspecificEpithet + scientificNameAuthorship)
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.
Scientific Name
Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)"
{DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/ParentheticalAuthorTeamAndYear + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/AuthorTeamAndYear} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeamParenthesis + DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/AuthorTeam} or {DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamOriginalAndYear + [= or] DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/AuthorTeamParenthesisAndYear}
The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
Scientific Name Authorship
Examples: "female", "hermaphrodite", "8 males, 4 females"
The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary.
Sex
Examples: "concolor", "gottschei"
{DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Bacterial/SpeciesEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Botanical/FirstEpithet or DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/ScientificName/NameAtomised/Zoological/SpeciesEpithet}
The name of the first or species epithet of the scientificName.
Specific Epithet
The earliest ordinal day of the year on which the Event occurred (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366).
Start Day Of Year
Examples: "Montana", "Minas Gerais", "Córdoba"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= State or = Province (etc.)
The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
State Province
Examples: "Strobus (Pinus)", "Puma (Puma)" "Loligo (Amerigo)", "Hieracium subgen. Pilosella"
The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.
Subgenus
Examples: "subspecies", "varietas", "forma", "species", "genus"
The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
Taxon Rank
Example: "this name is a misspelling in common use"
Comments or notes about the taxon or name.
Taxon Remarks
Examples: "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. Recommended best practice is to use a controlled vocabulary.
Taxonomic Status
Example: "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388"
A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.
Type Status
Examples: "decimal degrees", "degrees decimal minutes", "degrees minutes seconds", "UTM"
(partly) DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesGrid/GridCellSystem
The spatial coordinate system for the verbatimLatitude and verbatimLongitude or the verbatimCoordinates of the Location. Recommended best practice is to use a controlled vocabulary.
Verbatim Coordinate System
{DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinatesText or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesUTM/UTMText}
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.
Verbatim Coordinates
Example: "100-200 m"
The original description of the depth below the local surface.
Verbatim Depth
The original description of the elevation (altitude, usually above sea level) of the Location.
Verbatim Elevation
Examples: "spring 1910", "Marzo 2002", "1999-03-XX", "17IV1934"
The verbatim original representation of the date and time information for an Event.
Verbatim EventDate
Example: "41 05 54.03S"
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.
Verbatim Latitude
Example: "25 km NNE Bariloche por R. Nac. 237"
The original textual description of the place.
Verbatim Locality
Example: "121d 10' 34" W"
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.
Verbatim Longitude
The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which coordinates given in verbatimLatitude and verbatimLongitude, or verbatimCoordinates are based. Recommended best practice is use the EPSG code as a controlled vocabulary to provide an SRS, if known. Otherwise use a controlled vocabulary for the name or code of the geodetic datum, if known. Otherwise use a controlled vocabulary for the name or code of the ellipsoid, if known. If none of these is known, use the value "unknown".
Verbatim SRS
Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex", "sp.", "subsp.", "var."
The taxonomic rank of the most specific name in the scientificName as it appears in the original record.
Verbatim Taxon Rank
Examples: "Andean Condor", "Condor Andino", "American Eagle", "Gänsegeier"
A common or vernacular name.
Vernacular Name
Examples: "Indian Ocean", "Baltic Sea", "Hudson River"
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Water body
The name of the water body in which the Location occurs. Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
Water Body
Example: "2008"
The four-digit year in which the Event occurred, according to the Common Era Calendar.
Year
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 tree is forest plot that is measured for diameter at breast height (DBH).
An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
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 defined plots, transects, or points, in which a person or group of people is comprehensively covering the entire defined area, usually with a defined survey time or pace. The search is restricted to a well-defined and human-scale geospatial area (traversable within a time course of less than a day) within which there is an expectation of a comprehensive accounting of the taxonomic items of interest.
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 defined region. That is, a planned search restricted to a larger, defined geographic area, but effort isn't evenly distributed throughout the area, nor expected to be a complete and comprehensive accounting of taxa of interest across the defined region. Temporal duration is typically longer than restricted search, lasting hours to all day.
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, often intended to be comprehensive accounting of the taxa of interest, but with no planned trajectory for discovery, nor pre-specified investment of effort.
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/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 highly restricted in geospatial extent that involves either the physical extraction of some evidence of the presence of the taxa of interest, such as scat, fur, other material samples or information artifacts such as photographs or sound recordings.
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
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 a 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.
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.
living specimen
A specimen that has been preserved.
preserved specimen
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
entity
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])
continuant
a heart
a person
a symphony orchestra
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
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.
endurant
occurrent
a surgical operation as processual context for a nosocomical infection
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
An entity that has temporal parts and that happens, unfolds or develops through time.
perdurant
independent continuant
a chair
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])
substantial entity
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]
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
obsolete dependent continuant
temporal region
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
An occurrent that is part of time.
All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
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.
realizable entity
quality
specifically dependent continuant
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the role of being a doctor
the smell 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.
mode
property
trope
role
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
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.
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
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
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
object
generically dependent continuant
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.
a certain PDF file that exists in different and in several hard drives
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]
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.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
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
organism
A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms.
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
objective specification
a directive information entity that describes an intended process endpoint.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
OBI Plan and Planned Process/Roles Branch
action specification
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
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'.
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 that 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.
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
directive information entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
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
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 is a data item about a part of an ontology, for example a term
data about an ontology part
plan specification
To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
measurement data item
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A data item that is a recording of the output of an assay.
2/2/2009 is_specified_output of some assay?
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. Additional examples: a hard drive, a brain.
A material entity in which a concretization of an information content entity inheres.
GROUP: IAO
photograph
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
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
document
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
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.
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity 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.)
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)
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
specimen role
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.
material sample
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
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.
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)
assay objective
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)
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.
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
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 quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
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.
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.
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
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
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
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
multispecies community
Ecological community is defined broadly here. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms.
ecological community
A collection of organisms that has as parts every organism of given species and no organisms of any other species.
At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible.
This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user.
species as a collection of organisms
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
Needs axioms for family relationships.
Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry.
family
A material 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 collection of organisms of the same species that has as members only humans.
human community
human population
collection of humans
A collection of organisms connected by social or biological relations (biotic interactions).
Need to specify axioms for the biological or social relations, once the relations are specified in the Relation Ontology.
These relations can include shared values, occupying the same spatial relation. A community be be a single species collection of organsisms (as in a human community) or a or multi-species collection of organisms (as in an ecological community).
community
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species.
multi-species collection of organisms
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
pair of interacting organisms
pair of interacting organisms of the same species
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
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.
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.
persistent evidence role
This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
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.
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.
printed report
A printed report that records the outcome of some observing process.
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.
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).
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.
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.
data sampling process
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.
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.
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.
unsuccessful material sampling process
At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
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.
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.
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.
An information content entity (?) that is the result of some data sampling process.
data sample
statistical sample
If sampling is a OBI planned process, that captures that it is protocal governed.
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.
process that yields a material representation of a material entity
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.
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
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.
event
Examples: A specimen collection process. A machine observation.
An action that occurs at some location during some time.
Event
A preserved specimen that is a fossil.
Fossil Specimen
geological context
Example: A lithostratigraphic layer.
Geological information, such as stratigraphy, that qualifies a region or place.
Geological Context
human observation
An output of a human observation process.
Human Observation
identification
Example: A subspecies determination of an organism.
A taxonomic determination (e.g., the assignment to a taxon).
Identification
Living Specimen
machine observation
An output of a machine observation process.
Machine Observation
Examples: A whole organism preserved in a collection. A part of an organism isolated for some purpose. A soil sample. A marine microbial sample.
A physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.
Material Sample
This term was not deprecated from the dwc terms vocabulary, merely from the dwcterms ontology, because it is not needed here.
Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to Occurrences, Organisms, MaterialSamples, Events, Locations, GeologicalContexts, Identifications, or Taxa. Examples: The weight of an organism in grams. The number of placental scars.
Datasets/Dataset/Units/Unit/MeasurementsOrFacts or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts
A measurement of or fact about an rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource).
Measurement or Fact
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.
Examples: A wolf pack on the shore of Kluane Lake in 1988. A virus in a plant leaf in a 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.
Occurrence
Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more 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.
Organism
Preserved Specimen
Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to Occurrences, Organisms, MaterialSamples, Events, Locations, GeologicalContexts, Identifications, or Taxa. Example: An instance of an Organism is the mother of another instance of an Organism.
A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.
Resource Relationship
taxon
Example: 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
specimen collection process X
material entity A
material entity B
material entity C
specimen collection process Y
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
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
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
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
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 imported
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.
term split
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
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.
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.
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)
relation has no temporal argument
incorrect identifier format, replaced
has_specified_input
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.
see is_input_of example_of_usage