This file is based on checkout of our SVN repository revision $Revision: 3931 $
This version of the BCO has been pre-reasoned so that all inferred axioms are asserted. It is based on revision e98b4c682302. For a corresponding release where these axioms have not been asserted, use http://purl.obolibrary.org/obo/bco/2014-05-27/bco-non-classified.owl. The Biological Collections Ontology was originally created at the Biocode Commons Hackathon at GSC14. Older versions can be viewed at http://code.google.com/p/biocode-commons/source/browse/#svn%2Ftrunk%2Fontologies%2Fbiocollections. Some of the classes in this ontology may be replaced by existing or newly requested terms from OBI or other ontologies. The Biological Collections Ontology (BCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
Biocode Commons Ontology Hackathon members
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
Allyson Lister
An ontology for the annotation of biomedical and functional genomics experiments.
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Stoeckert
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Eric Deutsch
Gilberto Fragoso
Cristian Cocos
Helen C. Causton
Helen Parkinson
James A. Overton
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
OBO Relations Ontology
OWL-DL
Ontology for Biomedical Investigation
Philip Lord
Philippe Rocca-Serra
Pierre Grenon
Chris Mungall
Chris Taylor
Frank Gibson
Holger Stenzhorn
James Malone
Matthew Pocock
Richard Bruskiewich
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
This document is an OWL representation of the Darwin Core (DwC) terminology, imported from DwC as RDF. In this document, DwC classes have been interpreted as classes in the Biological Collections Ontology and DwC properties have been interpreted as data properties. To comment on the OWL interpretation, please create an issue at https://code.google.com/p/bco/issues/list. DwC as RDF contains a list of Darwin Core terms that have the dwcattributes:status equal to "recommended". For the full normative RDF document of all Darwin Core terms, see dwctermshistory.rdf. To comment on this schema in the context of Darwin Core, please create a new issue in http://code.google.com/p/darwincore/issues/.
This file contains terms from the Darwin Core (DwC) type vocabulary, imported from the RDF representation of that vocabulary and interpretted as classes in the Biological Collections Ontology. Some of the type vocabulary terms are replicated in DwC as RDF.
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
Biodiversity Information Standards (TDWG)
Christian Bolling
Jessica Turner
Elisabetta Manduchi
Richard Scheuermann
Darwin Core Recommended Terms
taxonomic inventory metadata preferred name
BCO preferred label
dwc_bco mapping
editor preferred label
editor preferred term
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
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
example
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.
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.
definition editor
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has 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
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
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
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)"
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
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)"
first order logic expression
An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
OBO foundry unique label
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 .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
PERSON:Bjoern Peters
PERSON:Chris Mungall
term replaced by
Person:Alan Ruttenberg
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)
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
tooth SubClassOf 'never in taxon' value 'Aves'
mutually spatially disjoint with
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
taxonomic class assertion
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
ambiguous for taxon
S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]
dubious for taxon
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
present in taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
logical macro assertion
An assertion that holds between two classes that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
annotation property cardinality
An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a class
logical macro assertion on a property
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on an object property
logical macro assertion on an annotation property
An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.
'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))
Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)
Contributor
Creator
Date
Description
An account of the content of the resource.
Format
The physical or digital manifestation of the resource.
Source
Subject and Keywords
The topic of the content of the resource.
Title
A name given to the resource.
has role
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.
derives from by planned process
is derived into by planned process
part of
Ambiguous between continuant-parthood and occurrent-parthood
is part of
part_of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized in
realized by
realized_by
realized_in
realizes
participates in
participates_in
has participant
has_participant
is concretized as
concretizes
obsolete preceded by
accidentally included in BFO 1.2 proposal - should have been BFO_0000062
preceded by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
occurs in
Intended meaning: domain: occurrent range: independent continuant time: atemporal
occurs_in
unfolds in
unfolds_in
contains process
site of
s depends on
s_depends_on
has_role
is about
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
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.
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.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
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.
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.
Intended meaning: domain: specifically dependent continuant range: independent continuant time: at all times A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists.
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.
role of
is role of
role_of
has quality
derives from
derives into
location of
is location of
location_of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
located in
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
boundary of
The relationships between a boundary (a 2D immaterial entity) and the material entity that it delimits.
has boundary
The relationship between a material entity and the boundary (2D immaterial entity) that delimits it.
tracheates
The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
has synaptic terminal of
bounding layer of
X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
A relation that holds between two linear structures that are approximately parallel to each other for their entire length. This relation is transitive. It i is agnostic about any parthood relationship between X and Y.
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
before_or_simultaneous_with
Primitive instance level timing relation between events
simultaneous_with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
before
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
during_which_ends
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
ends_after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
during_which_starts
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
starts_before
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
starts_during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
happens_during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
ends_during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
has soma location
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
Relation between a neuron and an anatomical structure that its soma is part of.
fasciculates with
(forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
axon synapses in
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
David Osumi-Sutherland
Relation between a neuron and some structure its axon forms (chemical) synapses in.
has plasma membrane part
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
has postsynaptic terminal in
http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapsed in
has presynaptic terminal in
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
synapses in
dendrite synapsed in
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
has synaptic terminal in
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
overlaps
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
has fasciculating neuron projection
(forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
has fasciculating component
continuous with
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
proper overlaps
(forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
connected to
connects
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
attached to part of
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
supplies
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
drains
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
has component
For use in recording has_part with a cardinality constraint.
actively participates in
x actively participates in y if and only if x participates in y and x realizes some active role
has active participant
x has participant y if and only if x realizes some active role that inheres in y
surrounded by
x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
adjacent to
x adjacent to y if and only if x and y share a boundary
surrounds
temporally related to
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
starts
starts with
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends
ends with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
has start location
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has end location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has input
p has input c if either: p has direct input c or p has indirect input c. See subrelations for definitions.
has output
p has output c if either: p has direct output c or p has output input c. See subrelations for definitions.
mereotopologically related to
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
A mereological relationship or a topological relationship
colocalizes_with
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
member of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
has member
has member is a mereological relation between a collection and an item.
input of
output of
has dendrite location
attached to
has muscle origin
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
has muscle insertion
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
in branching relationship with
tributary of
Deschutes River tributary_of Columbia River
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
inferior epigastric vein tributary_of external iliac vein
distributary of
x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
Deschutes River distributary_of Little Lava Lake
anabranch of
x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
spatially coextensive with
x spatially_coextensive_with y if and inly if x and y have the same location
branching part of
x is a branching part of y if and only if x is part of y and x is a branch_of the main stem of y
main stem of
x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
proper distributary of
x proper_distributary_of y iff x distributary_of y and x does not flow back into y
proper tributary of
x proper_tributary_of y iff x tributary_of y and x does not originate from y
has direct input
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has indirect input
has direct output
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
has indirect output
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
A relationship between a piece of evidence and an assertion where the evidence lends support to the assertion
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
Similarity that results from common evolutionary origin.
This broad definition encompasses all the working definitions proposed so far in the literature.
Similarity that results from independent evolution.
Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues.
Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
Convergence usually implies a notion of adaptation.
Homoplasy that involves different underlying mechanisms or structures.
Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage.
Homoplasy that involves homologous underlying mechanisms or structures.
in structural homology relationship with
Homology that is defined by similarity with regard to selected structural parameters.
in historical homology relationship with
Homology that is defined by common descent.
in biological homology relationship with
Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism.
Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
Structural homology that is detected by similarity in content and organization between chromosomes.
Historical homology that involves genes that diverged after a duplication event.
Paralogy that involves sets of syntenic blocks.
Syntenic homology that involves chromosomes of different species.
Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
in protein structural homology relationship with
Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
in non functional homology relationship with
Structural homology that involves a pseudogenic feature and its functional ancestor.
Historical homology that involves genes that diverged after a speciation event.
The term is sometimes also used for anatomical structures.
Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis).
Historical homology that involves two members sharing no other homologs in the lineages considered.
Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
Paralogy that results from a whole genome duplication event.
Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
Paralogy that results from a duplication preceding a given speciation event.
1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
Iterative homology that involves structures arranged along the main body axis.
in heterochronous homology relationship with
Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
Paedomorphosis that is produced by a retardation of somatic development.
Convergence that results from co-evolution usually involving an evolutionary arms race.
in 1 to many orthology relationship with
Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
in many to many homology relationship with
Historical homology that involves two members of a larger set of homologs.
Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
Historical homology that is based on distant shared ancestry.
This term is usually contrasted to apomorphy.
Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
Used for structures in distantly related taxa.
Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
in chromosomal homology relationship with
Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
in many to many orthology relationship with
Orthology that involves two genes that experienced duplications more recent than the species split that created them.
in within-species paralogy relationship with
Paralogy that involves genes from the same species.
in between-species paralogy relationship with
Paralogy that involves genes from different species.
The genes have diverged before a speciation event.
Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
Peramorphosis that is produced by a delay in the offset of development.
Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
Orthology that involves functional equivalent genes with retention of the ancestral function.
Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
Used for structures in closely related taxa.
Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes.
Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss.
These genes may come out as paralogs in a single-genome analysis.
Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
Historical homology that involves functional equivalent genes with retention of the ancestral function.
This may include examples of orthology, paralogy and xenology.
Historical homology that involves orthologous pairs of interacting molecules in different organisms.
in functional equivalence relationship with
Similarity that is characterized by interchangeability in function.
Biological homology that involves parts of the same organism.
Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
This phenomenon is usually due to gene conversion process.
Structural homology that involves structures with the same or similar relative positions.
Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use.
Biological homology that involves an ectopic structure and the normally positioned structure.
On a long term, it is hard to distinguish allopolyploidy from whole genome duplication.
Synology that results from allopolyploidy.
Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
Organizational term to help define related terms. Do not use for data annotation with Darwin Core.
Accepted Name Usage
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.
According To
Organizational term to help define related terms. Do not use for data annotation.
Abstract term to attribute information to a source.
Associated Media
A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence.
Example: "http://arctos.database.museum/SpecimenImages/UAMObs/Mamm/2/P7291179.JPG"
Associated Occurrences
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.
Example: "sibling of FMNH:Mammal:1234; sibling of FMNH:Mammal:1235"
Associated References
A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
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."
Associated Sequences
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.
Example: "GenBank: U34853.1"
Associated Taxa
A list (concatenated and separated) of identifiers or names of taxa and their associations with the Occurrence.
Example: "host: Quercus alba"
Basis of Record
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).
Bed
The full name of the lithostratigraphic bed from which the cataloged item was collected.
Behavior
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.
Examples: "roosting", "foraging", "running"
Catalog Number
An identifier (preferably unique) for the record within the data set or collection.
Class
Examples: "Mammalia", "Hepaticopsida"
The full scientific name of the class in which the taxon is classified.
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = classis
Collection Code
Examples: "Mammals", "Hildebrandt", "eBird"
The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
Collection ID
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/).
Example: "urn:lsid:biocol.org:col:34818"
Continent
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Continent
Examples: "Africa", "Antarctica", "Asia", "Europe", "North America", "Oceania", "South America"
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.
Coordinate Precision
A decimal representation of the precision of the coordinates given in the decimalLatitude and decimalLongitude.
DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/ISOAccuracy or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/AccuracyStatement
Examples: "0.00001" (normal GPS limit for decimal degrees), "0.000278" (nearest second), "0.01667" (nearest minute), "1.0" (nearest degree)
Coordinate Uncertainty In Meters
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.
Country
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 Code
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.
County
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= County
Examples: "Missoula", "Los Lagos", "Mataró"
The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs.
Data Generalizations
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.
Example: "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell"
Dataset Name
Examples: "Grinnell Resurvey Mammals", "Lacey Ctenomys Recaptures"
The name identifying the data set from which the record was derived.
Date Identified
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).
Day
The integer day of the month on which the Event occurred.
accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin
Examples: "9", "28"
Decimal Latitude
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.
Example: "-41.0983423"
Decimal Longitude
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.
Disposition
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.
Dynamic Properties
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.
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"
Earliest Age Or Lowest Stage
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 Eon Or Lowest Eonothem
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 Epoch Or Lowest Series
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 Era Or Lowest Erathem
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.
Examples: "Cenozoic", "Mesozoic"
Earliest Period Or Lowest System
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.
Examples: "Neogene", "Tertiary", "Quaternary"
End Day Of 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).
Examples: "1" (=1 Jan), "366" (=31 Dec), "365" (=30 Dec in a leap year, 31 Dec in a non-leap year)
Establishment Means
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.
Event Date
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 Remarks
Comments or notes about the Event.
Example: "after the recent rains the river is nearly at flood stage"
Event Time
accessible from DataSets/DataSet/Units/Unit/Gathering/ISODateTimeBegin and DataSets/DataSet/Units/Unit/Gathering/ISODateTimeEnd
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.
The time or interval during which an Event occurred. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Family
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = familia
Examples: "Felidae", "Monocleaceae"
The full scientific name of the family in which the taxon is classified.
Field Notes
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.
Example: "notes available in Grinnell-Miller Library"
Field Number
An identifier given to the event in the field. Often serves as a link between field notes and the Event.
Example: "RV Sol 87-03-08"
Footprint SRS
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.
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.
Footprint Spatial Fit
DataSets/DataSet/Units/Unit/Gathering/FootprintSpatialFit (ABCD v2.06b)
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).
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 WKT
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.
DataSets/DataSet/Units/Unit/Gathering/FootprintWKT (ABCD v2.06b)
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))
Formation
Examples: "Notch Peak Fromation", "House Limestone", "Fillmore Formation"
The full name of the lithostratigraphic formation from which the cataloged item was collected.
Genus
Examples: "Puma", "Monoclea"
The full scientific name of the genus in which the taxon is classified.
{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}
Geodetic Datum
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".
Georeference Protocol
A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.
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"
Georeference Remarks
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 Sources
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.
Examples: "USGS 1:24000 Florence Montana Quad; Terrametrics 2008 on Google Earth"
Georeference Verification Status
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.
Examples: "requires verification", "verified by collector", "verified by curator".
Georeferenced By
A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the Location.
Examples: "Kristina Yamamoto (MVZ); Janet Fang (MVZ)", "Brad Millen (ROM)"
Georeferenced Date
The date on which the Location was georeferenced. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Group
The full name of the lithostratigraphic group from which the cataloged item was collected.
Habitat
Examples: "oak savanna", "pre-cordilleran steppe"
A category or description of the habitat in which the Event occurred.
Higher Classification
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 (";").
Example: "Animalia;Chordata;Vertebrata;Mammalia;Theria;Eutheria;Rodentia;Hystricognatha;Hystricognathi;Ctenomyidae;Ctenomyini;Ctenomys"
Higher Geography
{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.
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.
Highest Biostratigraphic Zone
The full name of the highest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Identification Qualifier
A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification.
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.
Identification References
A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the Identification.
Example: "Aves del Noroeste Patagonico. Christie et al. 2004."
Identification Remarks
Example: "Distinguished between Anthus correndera and Anthus hellmayri based on the comparative lengths of the uñas."
Comments or notes about the Identification.
Identification Verification Status
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.
Examples: "0", "4"
Identified By
A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject.
Examples: "James L. Patton", "Theodore Pappenfuss; Robert Macey"
Individual Count
Examples: "1", "25"
The number of individuals represented present at the time of the Occurrence.
Information Withheld
Additional information that exists, but that has not been shared in the given record.
Examples: "location information not given for endangered species", "collector identities withheld", "ask about tissue samples"
Infraspecific Epithet
{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}
Examples: "concolor", "oxyadenia", "sayi"
The name of the lowest or terminal infraspecific epithet of the scientificName, excluding any rank designation.
Institution Code
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 ID
An identifier for the institution having custody of the object(s) or information referred to in the record.
Island
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island
Examples: "Isla Victoria", "Vancouver", "Viti Levu", "Zanzibar"
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 Group
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Island group
Examples: "Alexander Archipelago", "Seychelles"
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.
Kingdom
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = regnum
Examples: "Animalia", "Plantae"
The full scientific name of the kingdom in which the taxon is classified.
Latest AgeOr Highest Stage
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 Eon Or Highest Eonothem
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 Epoch Or Highest Series
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 Era Or Highest Erathem
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 Period Or Highest System
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.
Life Stage
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
Examples: "egg", "eft", "juvenile", "adult", "2 adults 4 juveniles"
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.
Lithostratigraphic Terms
The combination of all litho-stratigraphic names for the rock from which the cataloged item was collected.
Locality
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.
Location According To
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 Remarks
Comments or notes about the Location.
Example: "under water since 2005"
Lowest Biostratigraphic Zone
The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the cataloged item was collected.
Maximum Depth In Meters
The greater depth of a range of depth below the local surface, in meters.
Example: "200"
Maximum Distance Above Surface 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 Elevation In Meters
The upper limit of the range of elevation (altitude, usually above sea level), in meters.
Measurement Accuracy
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
Examples: "0.01", "normal distribution with variation of 2 m"
The description of the potential error associated with the measurementValue.
Measurement Determined By
A list (concatenated and separated) of names of people, groups, or organizations who determined the value of the MeasurementOrFact.
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
Examples: "Javier de la Torre", "Julie Woodruff; Eileen Lacey"
Measurement Determined Date
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 Method
/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.
Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation
Measurement Remarks
Comments or notes accompanying the MeasurementOrFact.
Example: "tip of tail missing"
Measurement Type
DataSets/DataSet/Units/Unit/MeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/Parameter
Examples: "tail length", "temperature", "trap line length", "survey area", "trap type"
The nature of the measurement, fact, characteristic, or assertion. Recommended best practice is to use a controlled vocabulary.
Measurement Unit
DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts/MeasurementOrFact/MeasurementOrFactAtomised/UnitOfMeasurement
Examples: "mm", "C", "km", "ha"
The units associated with the measurementValue. Recommended best practice is to use the International System of Units (SI).
Measurement Value
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
Examples: "45", "20", "1", "14.5", "UV-light"
The value of the measurement, fact, characteristic, or assertion.
Member
Examples: "Lava Dam Member", "Hellnmaria Member"
The full name of the lithostratigraphic member from which the cataloged item was collected.
Minimum Depth In Meters
The lesser depth of a range of depth below the local surface, in meters.
Example: "100"
Minimum Distance Above Surface In Meters
The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
Minimum Elevation In Meters
The lower limit of the range of elevation (altitude, usually above sea level), in meters.
Month
The ordinal month in which the Event occurred.
Examples: "1" (=January), "10" (=October)
Municipality
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.
Name According To
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 Published In
A reference for the publication in which the scientificName was originally established under the rules of the associated nomenclaturalCode.
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"
Name Published In Year
Examples: "1915", "2008"
The four-digit year in which the scientificName was published.
Nomenclatural Code
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.
Examples: "ICBN", "ICZN", "BC", "ICNCP", "BioCode", "ICZN; ICBN"
Nomenclatural Status
(DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/NomenclaturalReference/TitleCitation) pro parte
Examples: "nom. ambig.", "nom. illeg.", "nom. subnud."
The status related to the original publication of the name and its conformance to the relevant rules of nomenclature. It is based essentially on an algorithm according to the business rules of the code. It requires no taxonomic opinion.
Occurrence Remarks
Comments or notes about the Occurrence.
Example: "found dead on road"
Occurrence Status
A statement about the presence or absence of a Taxon at a Location. Recommended best practice is to use a controlled vocabulary.
Examples: "present", "absent"
Order
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = ordo
Examples: "Carnivora", "Monocleales"
The full scientific name of the order in which the taxon is classified.
Original Name Usage
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.
Other Catalog Numbers
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.
Examples: "FMNH:Mammal:1234", "NPS YELLO6778; MBG 33424"
Owner Institution Code
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.
Parent Name Usage
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.
Phylum
DataSets/DataSet/Units/Unit/Identifications/Identification/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with HigherTaxa/HigherTaxon/HigherTaxonRank = phylum
Examples: "Chordata" (phylum), "Bryophyta" (division)
The full scientific name of the phylum or division in which the taxon is classified.
Point Radius Spatial Fit
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.
Preparations
A list (concatenated and separated) of preparations and preservation methods for a specimen.
Examples: "skin; skull; skeleton", "whole animal (ETOH); tissue (EDTA)", "fossil", "cast", "photograph", "DNA extract"
Previous Identifications
DataSets/DataSet/Units/Unit/Identifications/Identification with PreferredFlag = false
A list (concatenated and separated) of previous assignments of names to the Occurrence.
Example: "Anthus sp., field ID by G. Iglesias; Anthus correndera, expert ID by C. Cicero 2009-02-12 based on morphology"
Record Number
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.
Example: "OPP 7101"
Recorded By
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.
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.
Relationship According To
Example: "Julie Woodruff"
The source (person, organization, publication, reference) establishing the relationship between the two resources.
Relationship Established Date
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 Of Resource
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 Remarks
Comments or notes about the relationship between the two resources.
Examples: "mother and offspring collected from the same nest", "pollinator captured in the act"
Reproductive Condition
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.
Sampling Effort
Examples: "40 trap-nights", "10 observer-hours; 10 km by foot; 30 km by car"
The amount of effort expended during an Event.
Sampling Protocol
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.
Scientific Name
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 Authorship
Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)"
The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.
{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}
Sex
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.
Specific Epithet
The name of the first or species epithet of the scientificName.
{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}
Examples: "concolor", "gottschei"
Start Day Of Year
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).
State Province
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= State or = Province (etc.)
Examples: "Montana", "Minas Gerais", "Córdoba"
The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the Location occurs.
Subgenus
The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.
Examples: "Strobus (Pinus)", "Puma (Puma)" "Loligo (Amerigo)", "Hieracium subgen. Pilosella"
Taxon Rank
The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary.
Examples: "subspecies", "varietas", "forma", "species", "genus"
Taxon Remarks
Comments or notes about the taxon or name.
Example: "this name is a misspelling in common use"
Taxonomic Status
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.
Type Status
A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject.
Example: "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388"
Verbatim Coordinate System
(partly) DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesGrid/GridCellSystem
Examples: "decimal degrees", "degrees decimal minutes", "degrees minutes seconds", "UTM"
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 Coordinates
{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 Depth
Example: "100-200 m"
The original description of the depth below the local surface.
Verbatim Elevation
The original description of the elevation (altitude, usually above sea level) of the Location.
Verbatim EventDate
Examples: "spring 1910", "Marzo 2002", "1999-03-XX", "17IV1934"
The verbatim original representation of the date and time information for an Event.
Verbatim Latitude
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 Locality
Example: "25 km NNE Bariloche por R. Nac. 237"
The original textual description of the place.
Verbatim Longitude
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 SRS
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 Taxon Rank
The taxonomic rank of the most specific name in the scientificName as it appears in the original record.
Examples: "Agamospecies", "sub-lesus", "prole", "apomict", "nothogrex", "sp.", "subsp.", "var."
Vernacular Name
A common or vernacular name.
Examples: "Andean Condor", "Condor Andino", "American Eagle", "Gänsegeier"
Water Body
DataSets/DataSet/Units/Unit/Gathering/NamedAreas/NamedArea/AreaName with NamedAreas/NamedArea/AreaClass= Water body
Examples: "Indian Ocean", "Baltic Sea", "Hudson River"
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.
Year
Example: "2008"
The four-digit year in which the Event occurred, according to the Common Era Calendar.
taxonomic inventory process
not sure if this should be a type of assay or a type of planned process
A planned process by which a taxonomic inventory is created.
inventory type
taxonomic inventory
An information content entity that is a list of taxa recorded in some geospatially defined area over some stated time period using some method involving some actor.
restricted search taxonomic inventory process
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.
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."
restricted search
open search taxonomic inventory process
Search restricted within a larger defined geographic area, but where effort isn't even or complete across the defined region. That is, a planned search restricted to a larger, defined geographic area, but effort isn't evenly distributed throughout the area, nor expected to be a complete and comprehensive accounting of TOI's across the defined region. Temporal duration is typically longer than restricted search-- lasting hours to all day.
Individual Christmas Bird Count by some team. Organized field trip to a State Park.
open search
opportunistic search taxonomic inventory process
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
trap or sample taxonomic inventory process
A taxonomic inventory process that is typically highly restricted in geospatial extent that involves either the physical extracton of some evidence of the presence of the taxa of interest, such as scat, fur, other material samples or information artifacts such as photographs or sound recordings.
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).
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
trap/sample inventory
adventitious taxonomic inventory process
A taxonomic inventory in which taxon occurrences are recorde as a co-variates of another study and later compiled as a taxonomic inventory.
adventitious inventory
data from ecological studies in which presence of some taxa is recorded to clarify population or community parameters
compilation taxonomic inventory process
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.
A taxonomic inventory process in which a list of taxa of interes is assembled from various combinations of existing taxonomic inventories, rather than generated de novo from observations or samples.
compilation inventory
museum
An institution that cares for (conserves) a collection of artifacts and other objects of scientific, artistic, cultural, or historical importance and makes them available for public viewing through exhibits that may be permanent or temporary.
The Louvre Museum
The Smithsonian Institution
The class museum has meaning that is much broader than biological collecitons. It would probably be better to import this term from another, more general ontology and create a specific subclass for natural history museum.
fossil specimen
A specimen that is derived from a fossil.
Need to develop or import a class for fossil in order to define this class.
a fossil housed in a natural history museum
living specimen
A specimen that is alive.
Need to import alive from PATO and add logical definition.
a bacterial culture in a culture collection
a tree in an arboretum
an animal in a zoo
germplasm
preserved specimen
A specimen that has been preserved.
request a term for preservation in OBI and/or preserved in PATO
darwin core class
human observation process
An observing process in which the entity doing the observing is a human being.
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.
a biologist recording an observation of an animal in a field notebook
an entomologist recording the presense of butterflies while walking a transect
machine observation process
An observing process in which the entity doing the observing is a machine.
May want to work with OBI to define this term in a more general sense for investigations.
a camera trap recording the presense of a jaguar
a sensor continuously recording the surface temperature of a leaf over several hours
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
endurant
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
occurrent
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.
a surgical operation as processual context for a nosocomical infection
perdurant
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
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a leg
an organism
substantial entity
the bottom right portion of a human torso
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
process
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
realizable entity
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.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
the disposition of metal to conduct electricity
the function of the reproductive organs
the role of being a doctor
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
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
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 smell of mozzarella
trope
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
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
object aggregate
object
generically dependent continuant
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.
a certain PDF file that exists in different and in several hard drives
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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.
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
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
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
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint.
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
information carrier
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'.
A quality of an information bearer that imparts the information content
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.
data item
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.
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.
Data items include counts of things, analyte concentrations, and statistical summaries.
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
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 artifact and stands in relation of aboutness to some entity
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
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
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.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
person:Chris Stoeckert
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
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
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.
measurement data item
2/2/2009 is_specified_output of some assay?
A data item that is a recording of the output of an assay.
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,}.
material information bearer
A material entity in which a concretization of an information content entity inheres.
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.
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
PERSON: Melanie Courtot
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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.
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
PERSON: Lawrence Hunter
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
A denotator type indicates how a term should be interpreted from an ontological perspective.
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
planned process
'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
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.
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
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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)
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
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
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.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
OBI branch derived
PlanAndPlannedProcess Branch
measuring
scientific observation
specimen role
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.
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
material sample
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
organization
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.
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.
protocol
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)
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.
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)
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
A planned process with the objective of collecting a specimen.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
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.
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 objective specification to obtain a material entity for potential use as an input during an investigation.
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
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.
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
The part of a FASTA file that contains the letters ACTGGGAA
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
latitude
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
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
has_output should be sequence of input; we don't have sequence well defined yet
the use of a chemical or biochemical means to infer the sequence of a biomaterial
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
evidence role
It might be better to request this term in OBI or IAO.
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.
persistent 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.
collecting process
This term is now redundant and is merged with material sampling process http://purl.obolibrary.org/obo/bco_0000022.
observing process
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.
Seeing three pelicans flying overhead on Christmas day.
Observing butterflies during a transect walk.
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.
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.
sighting
being there process
This term was originally developed at the Semantics of Biodiversity workshop in 5/2012. It is no longer needed for the BCO.
A process of existing in a particular spatio-temporal region.
printed report
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.
a book
a field notebook
printed observational report
A printed report that records the outcome of some observing process.
selecting process
A process by which a person or machine decides that a particular material entity as worthy of collection or observation.
Filtering sea water to extract only organisms smaller than a certain size.
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.
deciding which branch to collect for a herbarium specimen
submitting process
A planned process whereby a person submits a material sample to an organization.
a curator submitting a herbarium speciman to a museum
a researcher submitting a water sample to a laboratory storage collection
physical extraction process
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).
removing a fish from the ocean with a net
A process that involves removing a material entity from its original site to another site.
material sampling process
This term has been replaced by OBI:specimen collection.
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
collecting plant parts for herbarium specimens
collecting sea water samples as part of Ocean Sampling Day
data 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.
statistical sampling process
locality description
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.
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.
material sample role
This term has been replaced by OBI:specimen role.
A role that is borne by some material entity and is realized by the material entity being the output of a material sampling process.
the role borne by a branch when it becomes a herbarium specimen
successful material sampling process
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.
unsuccessful 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.
museum collection entity
At the GSC14 hackathon in 09/2012, we decided to deprecate this term.
organismal 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.
museum collection
An object aggregate that has as member part a material sample that is located in museum as a result of a process of curation.
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.
The herbarium collection at the New York Botanical Garden.
the painting collection at the Louvre Museum
organismal museum collection
A museum collection that has as member part a material sample that was derived from an organism.
the insect collection at the Smithsonian Institution
institution
Replaced by OBI organization. Request institution as synonym in OBI.
organismal entity
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 organism or virus or viroid
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.
This term has been replaced by OBI:specimen.
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.
data sample
An information content entity (?) that is the result of some data sampling process.
statistical sample
protocol governed sampling activity
If sampling is a OBI planned process, that captures that it is protocal governed.
taxonomic identification process
Using BLAST to identify the taxa present in an environmental (metagenomic) sample.
Associating a museum specimen with a specific taxonomic concept based on its characters.
Using a key to identify a plant in the field.
Using DNA barcoding to identify a plant species.
A process by which a material sample is associated with a taxon or taxa.
process that yields a material representation of a material entity
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.
material target of observation
A material entity that has a target of observation role, that is, a material entity that is the input of some observing process.
A bird observed during a Christmas Bird Count
An lizard observed in the field that is not collected but whose location is recorded in a field notebook.
A tree is forest plot that is measured for diameter at breast height (DBH).
process that yields an information artifact that is a representation of a material entity
Includes audio recordings and photographs (which are information artifacts). Needs a better name. Current name is the definition.
Some instances of term could possibly be replaced by OBI:image acquisition. Maybe request another OBI term for audio recording acquisition.
material target of observation role
A role that is borne by some material entity and is realized by the material entity being the input of an observing process.
the role borne by a bird during a Christmas Bird Count
Fossil Specimen
A resource describing a fossilized specimen.
HumanObservation
A resource describing an observation made by one or more people.
LivingSpecimen
A resource describing a living specimen.
Location
A resource describing an instance of the Location class.
MachineObservation
A resource describing an observation made by a machine.
MaterialSample
A resource describing the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed.
NomenclaturalChecklist
A resource describing a nomenclatural checklist.
PreservedSpecimen
A resource describing a preserved specimen.
Event
The category of information pertaining to an event (an action that occurs at a place and during a period of time).
Geological Context
The category of information pertaining to a location within a geological context, such as stratigraphy.
Identification
The category of information pertaining to taxonomic determinations (the assignment of a scientific name).
Measurement Or Fact
Datasets/Dataset/Units/Unit/MeasurementsOrFacts or DataSets/DataSet/Units/Unit/Gathering/SiteMeasurementsOrFacts
The category of information pertaining to measurements, facts, characteristics, or assertions about a resource (instance of data record, such as Occurrence, Taxon, Location, Event).
Occurrence
The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.).
Resource Relationship
This class has no use within the context of an ontology.
Resources can be thought of as identifiable records and may include, but need not be limited to Occurrences, Locations, Events, Identifications, or Taxon records.
The category of information pertaining to relationships between resources (instances of data records, such as Occurrences, Taxa, Locations, Events).
Taxon
The category of information pertaining to taxonomic names, taxon name usages, or taxon concepts.
specimen collection process X
material entity A
material entity B
material entity C
specimen collection process Y
example to be eventually removed
failed exploratory term
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
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 definition editor.
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
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
other
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
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.
"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 defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a 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.
axiom holds for all times
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
relation has no temporal argument
## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)
Darwin Core Type
The set of classes specified by the Darwin Core Type Vocabulary, used to categorize the nature or genre of the resource.
This document contains a list of terms in the Darwin Core Type Vocabulary. For the full normative RDF document of all Darwin Core terms, see dwctermshistory.rdf. To comment on this schema, please create a new issue in http://code.google.com/p/darwincore/issues/
Darwin Core Type Terms