The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Used to annotation axioms that define identity criteria for instances of a class.
is_identity_criteria
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
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.
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
alternative term
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
Defines the label for the property as shown in NASA Life Sciences Portal
Defines the label for the property in ARC SLIMS database
Defines the field label propery in NASA Life Sciences Portal
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Coverage
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
An unambiguous reference to the resource within a given context.
Resource Identifier
Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
A language of the intellectual content of the resource.
Language
Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
An entity responsible for making the resource available
Publisher
Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a related resource.
Relation
Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
Information about rights held in and over the resource.
Rights Management
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
The topic of the content of the resource.
Subject and Keywords
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Title
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
The nature or genre of the content of the resource.
Resource Type
A summary of the content of the resource.
Abstract
Access Rights may include information regarding access or restrictions based on privacy, security or other regulations.
Information about who can access the resource or an indication of its security status.
Access Rights
This qualifier can include Title abbreviations as well as translations.
Any form of the title used as a substitute or alternative to the formal title of the resource.
Alternative
A class of entity may be determined by the creator or the publisher or by a third party.
A class of entity for whom the resource is intended or useful.
Audience
Date (often a range) that the resource will become or did become available.
Available
Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible, whether or not the citation is in a standard form.
A bibliographic reference for the resource.
Bibliographic Citation
A reference to an established standard to which the resource conforms.
Conforms To
Date of creation of the resource.
Created
Date of acceptance of the resource (e.g. of thesis by university department, of article by journal, etc.).
Date Accepted
Date of a statement of copyright.
Date Copyrighted
Date of submission of the resource (e.g. thesis, articles, etc.).
Date Submitted
A general statement describing the education or training context. Alternatively, a more specific statement of the location of the audience in terms of its progression through an education or training context.
Audience Education Level
The size or duration of the resource.
Extent
The described resource pre-existed the referenced resource, which is essentially the same intellectual content presented in another format.
Has Format
The described resource includes the referenced resource either physically or logically.
Has Part
The described resource has a version, edition, or adaptation, namely, the referenced resource.
Has Version
The described resource is the same intellectual content of the referenced resource, but presented in another format.
Is Format Of
The described resource is a physical or logical part of the referenced resource.
Is Part Of
The described resource is referenced, cited, or otherwise pointed to by the referenced resource.
Is Referenced By
The described resource is supplanted, displaced, or superseded by the referenced resource.
Is Replaced By
The described resource is required by the referenced resource, either physically or logically.
Is Required By
The described resource is a version, edition, or adaptation of the referenced resource. Changes in version imply substantive changes in content rather than differences in format.
Is Version Of
Date of formal issuance (e.g., publication) of the resource.
Issued
The audiences for a resource are of two basic classes: (1) an ultimate beneficiary of the resource, and (2) frequently, an entity that mediates access to the resource. The mediator element refinement represents the second of these two classes.
A class of entity that mediates access to the resource and for whom the resource is intended or useful.
Mediator
The material or physical carrier of the resource.
Medium
Date on which the resource was changed.
Modified
The described resource references, cites, or otherwise points to the referenced resource.
References
The described resource supplants, displaces, or supersedes the referenced resource.
Replaces
The described resource requires the referenced resource to support its function, delivery, or coherence of content.
Requires
Spatial characteristics of the intellectual content of the resoure.
Spatial
A list of subunits of the content of the resource.
Table Of Contents
Temporal characteristics of the intellectual content of the resource.
Temporal
Date (often a range) of validity of a resource.
Valid
This axiom needed so that Protege loads DCAT2 without errors.
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x
Definition modified from 'surrounded by'.
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
derives from part of
A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities.
This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen.
Afforestation results in the expansion of a forest.
A process, p, results in the expansion of a material entity, m, if the spatial extent of m is increased as a result of participating in p.
A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process.
A relationship that holds between a biological entity and some level of genetic variation present in its genome.
This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype.
The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.
A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.
'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.
A relation used to describe a context or conditions that define and/or identify an entity.
Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features.
A relation linking a qualified sequence feature to its component sequence feature.
In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.
has_sequence_feature
A relation linking a sequence feature to the location it occupies on some reference sequence.
has_location
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of.
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
owns
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is owned by
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
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.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
has_specified_output
The inverse property of is_specified_output_of
is_specified_output_of
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.
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
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
A relation between an information content entity and a value specification that specifies its value.
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
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
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
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.
bounding layer of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
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.
during which ends
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
in taxon
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.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
David Osumi-Sutherland
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
directly develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
develops in
ends
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.
ends with
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 end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component
has member is a mereological relation between a collection and an item.
has member
input of
output of
formed as result of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
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.
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
provideInformationOn
providesAccessTo
consistOf
experimentalContextFor
generates
uses
componentOf
funds
organizedBy
createdBy
deployedOn
leadTo
resultsIn
usedIn
conductedAt
capableOfIdentifying
capableOfDetecting
contain
present
sameAs
isResultOf
aggregate
hasRole
characterizedBy
conductedOn
operatesOn
quantifiedBy
partOf
This object property has been mapped
address
This object property has been deprecated
agent
email
geo
Used to support property parameters for the additional name data property
has additional name
To specify the components of the delivery address for the object
has address
To specify the busy time associated with the object. (Was called FBURL in RFC6350)
has calendar busy
To specify the calendar associated with the object. (Was called CALURI in RFC6350)
has calendar link
To specify the calendar user address to which a scheduling request be sent for the object. (Was called CALADRURI in RFC6350)
has calendar request
Used to support property parameters for the category data property
has category
Used to support property parameters for the country name data property
has country name
To specify the electronic mail address for communication with the object
has email
Used to support property parameters for the formatted name data property
has formatted name
Used to support property parameters for the family name data property
has family name
To specify the sex or gender identity of the object. URIs are recommended to enable interoperable sex and gender codes to be used.
has gender
To specify information related to the global positioning of the object. May also be used as a property parameter.
has geo
Used to support property parameters for the given name data property
has given name
Used to support property parameters for the honorific prefix data property
has honorific prefix
Used to support property parameters for the honorific suffix data property
has honorific suffix
To specify the instant messaging and presence protocol communications with the object. (Was called IMPP in RFC6350)
has messaging
To specify a public key or authentication certificate associated with the object
has key
Used to support property parameters for the language data property
has language
Used to support property parameters for the locality data property
has locality
To specify a graphic image of a logo associated with the object
has logo
To include a member in the group this object represents. (This property can only be used by Group individuals)
To specify the components of the name of the object
has name
Used to support property parameters for the nickname data property
has nickname
Used to support property parameters for the note data property
has note
Used to support property parameters for the organization name data property
has organization name
Used to support property parameters for the organization unit name data property
has organization unit name
To specify an image or photograph information that annotates some aspect of the object
has photo
Used to support property parameters for the postal code data property
has postal code
Used to support property parameters for the region data property
has region
To specify a relationship between another entity and the entity represented by this object
has related
Used to support property parameters for the role data property
To specify a digital sound content information that annotates some aspect of the object
has sound
To identify the source of directory information of the object
has source
Used to support property parameters for the street address data property
has street address
To specify the telephone number for telephony communication with the object
has telephone
Used to support property parameters for the title data property
has title
To specify a value that represents a globally unique identifier corresponding to the object
has uid
To specify a uniform resource locator associated with the object
has url
Used to indicate the resource value of an object property that requires property parameters
has value
key
logo
name
This object property has been mapped. Use the organization-name data property.
organization
photo
sound
telephone
url
A site or end-point that gives access to the distribution of the dataset.
Et websted eller endpoint der giver adgang til en repræsentation af datasættet.
Umístění či přístupový bod zpřístupňující distribuci datové sady.
Un sitio o end-point que da acceso a la distribución de un conjunto de datos.
Un sito o end-point che dà accesso alla distribuzione del set di dati.
data access service
dataadgangstjeneste
servicio de acceso de datos
servizio di accesso ai dati
služba pro přístup k datům
New property added in DCAT 2.0.
Nová vlastnost přidaná ve verzi DCAT 2.0.
Nueva propiedad agregada en DCAT 2.0.
Nuova proprietà aggiunta in DCAT 2.0.
Ny egenskab tilføjet i DCAT 2.0.
A URL of a resource that gives access to a distribution of the dataset. E.g. landing page, feed, SPARQL endpoint. Use for all cases except a simple download link, in which case downloadURL is preferred.
Ceci peut être tout type d'URL qui donne accès à une distribution du jeu de données. Par exemple, un lien à une page HTML contenant un lien au jeu de données, un Flux RSS, un point d'accès SPARQL. Utilisez le lorsque votre catalogue ne contient pas d'information sur quoi il est ou quand ce n'est pas téléchargeable.
En URL for en ressource som giver adgang til en repræsentation af datsættet. Fx destinationsside, feed, SPARQL-endpoint. Anvendes i alle sammenhænge undtagen til angivelse af et simpelt download link hvor anvendelse af egenskaben downloadURL foretrækkes.
Puede ser cualquier tipo de URL que de acceso a una distribución del conjunto de datos, e.g., página de destino, descarga, URL feed, punto de acceso SPARQL. Esta propriedad se debe usar cuando su catálogo de datos no tiene información sobre donde está o cuando no se puede descargar.
URL zdroje, přes které je přístupná distribuce datové sady. Příkladem může být vstupní stránka, RSS kanál či SPARQL endpoint. Použijte ve všech případech kromě URL souboru ke stažení, pro které je lepší použít dcat:downloadURL.
Un URL di una risorsa che consente di accedere a una distribuzione del set di dati. Per esempio, pagina di destinazione, feed, endpoint SPARQL. Da utilizzare per tutti i casi, tranne quando si tratta di un semplice link per il download nel qual caso è preferito downloadURL.
Μπορεί να είναι οποιουδήποτε είδους URL που δίνει πρόσβαση στη διανομή ενός συνόλου δεδομένων. Π.χ. ιστοσελίδα αρχικής πρόσβασης, μεταφόρτωση, feed URL, σημείο διάθεσης SPARQL. Να χρησιμοποιείται όταν ο κατάλογος δεν περιέχει πληροφορίες εαν πρόκειται ή όχι για μεταφορτώσιμο αρχείο.
أي رابط يتيح الوصول إلى البيانات. إذا كان الرابط هو ربط مباشر لملف يمكن تحميله استخدم الخاصية downloadURL
データセットの配信にアクセス権を与えるランディング・ページ、フィード、SPARQLエンドポイント、その他の種類の資源。
URL d'accès
URL de acceso
URL πρόσβασης
access address
adgangsadresse
indirizzo di accesso
přístupová adresa
رابط وصول
アクセスURL
adgangsURL
Status: English Definition text modified by DCAT revision team, updated Italian and Czech translation provided, translations for other languages pending.
rdfs:label, rdfs:comment and skos:scopeNote have been modified. Non-english versions except for Italian must be updated.
El rango es una URL. Si la distribución es accesible solamente través de una página de destino (es decir, si no se conoce una URL de descarga directa), entonces el enlance a la página de destino debe ser duplicado como accessURL en la distribución.
Hvis en eller flere distributioner kun er tilgængelige via en destinationsside (dvs. en URL til direkte download er ikke kendt), så bør destinationssidelinket gentages som adgangsadresse for distributionen.
If the distribution(s) are accessible only through a landing page (i.e. direct download URLs are not known), then the landing page link should be duplicated as accessURL on a distribution.
La valeur est une URL. Si la distribution est accessible seulement au travers d'une page d'atterrissage (c-à-dire on n'ignore une URL de téléchargement direct), alors le lien à la page d'atterrissage doit être dupliqué comee accessURL sur la distribution.
Pokud jsou distribuce přístupné pouze přes vstupní stránku (tj. URL pro přímé stažení nejsou známa), pak by URL přístupové stránky mělo být duplikováno ve vlastnosti distribuce accessURL.
Se le distribuzioni sono accessibili solo attraverso una pagina web (ad esempio, gli URL per il download diretto non sono noti), allora il link della pagina web deve essere duplicato come accessURL sulla distribuzione.
Η τιμή είναι ένα URL. Αν η/οι διανομή/ές είναι προσβάσιμη/ες μόνο μέσω μίας ιστοσελίδας αρχικής πρόσβασης (δηλαδή αν δεν υπάρχουν γνωστές διευθύνσεις άμεσης μεταφόρτωσης), τότε ο σύνδεσμος της ιστοσελίδας αρχικής πρόσβασης πρέπει να αναπαραχθεί ως accessURL σε μία διανομή.
確実にダウンロードでない場合や、ダウンロードかどうかが不明である場合は、downloadURLではなく、accessURLを用いてください。ランディング・ページを通じてしか配信にアクセスできない場合（つまり、直接的なダウンロードURLが不明）は、配信におけるaccessURLとしてランディング・ページのリンクをコピーすべきです（SHOULD）。
A catalog whose contents are of interest in the context of this catalog.
Et katalog hvis indhold er relevant i forhold til det aktuelle katalog.
Katalog, jehož obsah je v kontextu tohoto katalogu zajímavý.
Un catalogo i cui contenuti sono di interesse nel contesto di questo catalogo.
Un catálogo cuyo contenido es de interés en el contexto del catálogo que está siendo descripto.
catalog
catalogo
catálogo
katalog
har delkatalog
El formato de la distribución en el que los datos están en forma comprimida, e.g. para reducir el tamaño del archivo a bajar.
Formát komprese souboru, ve kterém jsou data poskytována v komprimované podobě, např. ke snížení velikosti souboru ke stažení.
Il formato di compressione della distribuzione nel quale i dati sono in forma compressa, ad es. per ridurre le dimensioni del file da scaricare.
Kompressionsformatet for distributionen som indeholder data i et komprimeret format, fx for at reducere størrelsen af downloadfilen.
The compression format of the distribution in which the data is contained in a compressed form, e.g. to reduce the size of the downloadable file.
compression format
formato de compresión
formato di compressione
formát komprese
kompressionsformat
Denne egenskab kan anvendes når filerne i en distribution er blevet komprimeret, fx i en ZIP-fil. Formatet BØR udtrykkes ved en medietype som defineret i 'IANA media types registry', hvis der optræder en relevant medietype dér: https://www.iana.org/assignments/media-types/.
Esta propiedad se debe usar cuando los archivos de la distribución están comprimidos, por ejemplo en un archivo ZIP. El formato DEBERÍA expresarse usando un 'media type', tales como los definidos en el registro IANA de 'media types' https://www.iana.org/assignments/media-types/, si está disponibles.
Questa proprietà deve essere utilizzata quando i file nella distribuzione sono compressi, ad es. in un file ZIP. Il formato DOVREBBE essere espresso usando un tipo di media come definito dal registro dei tipi di media IANA https://www.iana.org/assignments/media-types/, se disponibile.
Tato vlastnost se použije, když jsou soubory v distribuci komprimovány, např. v ZIP souboru. Formát BY MĚL být vyjádřen pomocí typu média definovaného v registru IANA https://www.iana.org/assignments/media-types/, pokud existuje.
This property is to be used when the files in the distribution are compressed, e.g. in a ZIP file. The format SHOULD be expressed using a media type as defined by IANA media types registry https://www.iana.org/assignments/media-types/, if available.
Información relevante de contacto para el recurso catalogado. Se recomienda el uso de vCard.
Informazioni di contatto rilevanti per la risorsa catalogata. Si raccomanda l'uso di vCard.
Relevant contact information for the catalogued resource. Use of vCard is recommended.
Relevante kontaktoplysninger for den katalogiserede ressource. Anvendelse af vCard anbefales.
Relevantní kontaktní informace pro katalogizovaný zdroj. Doporučuje se použít slovník VCard.
Relie un jeu de données à une information de contact utile en utilisant VCard.
Συνδέει ένα σύνολο δεδομένων με ένα σχετικό σημείο επικοινωνίας, μέσω VCard.
تربط قائمة البيانات بعنوان اتصال موصف باستخدام VCard
データセットを、VCardを用いて提供されている適切な連絡先情報にリンクします。
Punto de contacto
contact point
kontaktní bod
kontaktpunkt
point de contact
punto di contatto
σημείο επικοινωνίας
عنوان اتصال
窓口
Status: English Definition text modified by DCAT revision team, Italian, Spanish and Czech translations provided, other translations pending.
A collection of data that is listed in the catalog.
En samling af data som er opført i kataloget.
Kolekce dat, která je katalogizována v katalogu.
Relie un catalogue à un jeu de données faisant partie de ce catalogue.
Un conjunto de datos que se lista en el catálogo.
Una raccolta di dati che è elencata nel catalogo.
Συνδέει έναν κατάλογο με ένα σύνολο δεδομένων το οποίο ανήκει στον εν λόγω κατάλογο.
تربط الفهرس بقائمة بيانات ضمنه
カタログの一部であるデータセット。
conjunto de datos
dataset
datasæt
datová sada
jeu de données
σύνολο δεδομένων
قائمة بيانات
データセット
datasamling
har datasæt
Status: English Definition text modified by DCAT revision team, Italian, Spanish and Czech translation provided, other translations pending.
An available distribution of the dataset.
Connecte un jeu de données à des distributions disponibles.
Dostupná distribuce datové sady.
En tilgængelig repræsentation af datasættet.
Una distribución disponible del conjunto de datos.
Una distribuzione disponibile per il set di dati.
Συνδέει ένα σύνολο δεδομένων με μία από τις διαθέσιμες διανομές του.
تربط قائمة البيانات بطريقة أو بشكل يسمح الوصول الى البيانات
データセットを、その利用可能な配信に接続します。
distribuce
distribución
distribution
distribuzione
διανομή
توزيع
データセット配信
har distribution
Status: English Definition text modified by DCAT revision team, translations pending (except for Italian, Spanish and Czech).
Ceci est un lien direct à un fichier téléchargeable en un format donnée. Exple fichier CSV ou RDF. Le format est décrit par les propriétés de distribution dct:format et/ou dcat:mediaType.
La URL de un archivo descargable en el formato dato. Por ejemplo, archivo CSV o archivo RDF. El formato se describe con las propiedades de la distribución dct:format y/o dcat:mediaType.
Questo è un link diretto al file scaricabile in un dato formato. E.g. un file CSV o un file RDF. Il formato è descritto dal dct:format e/o dal dcat:mediaType della distribuzione.
The URL of the downloadable file in a given format. E.g. CSV file or RDF file. The format is indicated by the distribution's dct:format and/or dcat:mediaType.
URL souboru ke stažení v daném formátu, například CSV nebo RDF soubor. Formát je popsán vlastností distribuce dct:format a/nebo dcat:mediaType.
URL til fil der kan downloades i et bestemt format. Fx en CSV-fil eller en RDF-fil. Formatet for distributionen angives ved hjælp af egenskaberne dct:format og/eller dcat:mediaType.
Είναι ένας σύνδεσμος άμεσης μεταφόρτωσης ενός αρχείου σε μια δεδομένη μορφή. Π.χ. ένα αρχείο CSV ή RDF. Η μορφη αρχείου περιγράφεται από τις ιδιότητες dct:format ή/και dcat:mediaType της διανομής.
رابط مباشر لملف يمكن تحميله. نوع الملف يتم توصيفه باستخدام الخاصية dct:format dcat:mediaType
URL de descarga
URL de téléchargement
URL di scarico
URL souboru ke stažení
URL μεταφόρτωσης
download URL
downloadURL
رابط تحميل
ダウンロードURL
Status: English Definition text modified by DCAT revision team, Italian, Spanish and Czech translation updated, other translations pending.
rdfs:label, rdfs:comment and/or skos:scopeNote have been modified. Non-english versions must be updated.
El valor es una URL.
La valeur est une URL.
dcat:downloadURL BY MĚLA být použita pro adresu, ze které je distribuce přímo přístupná, typicky skrze požadavek HTTP Get.
dcat:downloadURL BØR anvendes til angivelse af den adresse hvor distributionen er tilgængelig direkte, typisk gennem et HTTP Get request.
dcat:downloadURL DOVREBBE essere utilizzato per l'indirizzo a cui questa distribuzione è disponibile direttamente, in genere attraverso una richiesta Get HTTP.
dcat:downloadURL SHOULD be used for the address at which this distribution is available directly, typically through a HTTP Get request.
Η τιμή είναι ένα URL.
A description of the service end-point, including its operations, parameters etc.
En beskrivelse af det pågældende tjenesteendpoint, inklusiv dets operationer, parametre etc.
Popis přístupového bodu služby včetně operací, parametrů apod.
Una descripción del end-point del servicio, incluyendo sus operaciones, parámetros, etc.
Una descrizione dell'endpoint del servizio, incluse le sue operazioni, parametri, ecc.
descripción del end-point del servicio
description of service end-point
descrizione dell'endpoint del servizio
endpointbeskrivelse
popis přístupového bodu služby
New property in DCAT 2.0.
Nuova proprietà in DCAT 2.0.
Ny egenskab i DCAT 2.0.
An endpoint description may be expressed in a machine-readable form, such as an OpenAPI (Swagger) description, an OGC GetCapabilities response, a SPARQL Service Description, an OpenSearch or WSDL document, a Hydra API description, else in text or some other informal mode if a formal representation is not possible.
En beskrivelse af et endpoint kan udtrykkes i et maskinlæsbart format, såsom OpenAPI (Swagger)-beskrivelser, et OGC GetCapabilities svar, en SPARQL tjenestebeskrivelse, en OpenSearch- eller et WSDL-dokument, en Hydra-API-beskrivelse, eller i tekstformat eller i et andet uformelt format, hvis en formel repræsentation ikke er mulig.
Endpointbeskrivelsen giver specifikke oplysninger om den konkrete endpointinstans, mens dct:conformsTo anvendes til at indikere den overordnede standard eller specifikation som endpointet er i overensstemmelse med.
La descripción del endpoint brinda detalles específicos de la instancia del endpoint, mientras que dct:conformsTo se usa para indicar el estándar general o especificación que implementa el endpoint.
La descrizione dell'endpoint fornisce dettagli specifici dell'istanza dell'endpoint reale, mentre dct:conformsTo viene utilizzato per indicare lo standard o le specifiche implementate dall'endpoint.
Popis přístupového bodu dává specifické detaily jeho konkrétní instance, zatímco dct:conformsTo indikuje obecný standard či specifikaci kterou přístupový bod implementuje.
Popis přístupového bodu může být vyjádřen ve strojově čitelné formě, například jako popis OpenAPI (Swagger), odpověď služby OGC getCapabilities, pomocí slovníku SPARQL Service Description, jako OpenSearch či WSDL document, jako popis API dle slovníku Hydra, a nebo textově nebo jiným neformálním způsobem, pokud není možno použít formální reprezentaci.
The endpoint description gives specific details of the actual endpoint instance, while dct:conformsTo is used to indicate the general standard or specification that the endpoint implements.
Una descripción del endpoint del servicio puede expresarse en un formato que la máquina puede interpretar, tal como una descripción basada en OpenAPI (Swagger), una respuesta OGC GetCapabilities, una descripción de un servicio SPARQL, un documento OpenSearch o WSDL, una descripción con la Hydra API, o en texto u otro modo informal si la representación formal no es posible.
Una descrizione dell'endpoint può essere espressa in un formato leggibile dalla macchina, come una descrizione OpenAPI (Swagger), una risposta GetCapabilities OGC, una descrizione del servizio SPARQL, un documento OpenSearch o WSDL, una descrizione API Hydra, o con del testo o qualche altra modalità informale se una rappresentazione formale non è possibile.
Kořenové umístění nebo hlavní přístupový bod služby (IRI přístupné přes Web).
La locazione principale o l'endpoint primario del servizio (un IRI risolvibile via web).
La posición raíz o end-point principal del servicio (una IRI web).
Rodplaceringen eller det primære endpoint for en tjeneste (en web-resolverbar IRI).
The root location or primary endpoint of the service (a web-resolvable IRI).
end-point del servicio
end-point del servizio
přístupový bod služby
service end-point
tjenesteendpoint
Den funktion en entitet eller aktør har i forhold til en anden ressource.
Funkce entity či agenta ve vztahu k jiné entitě či zdroji.
La función de una entidad o agente con respecto a otra entidad o recurso.
La funzione di un'entità o un agente rispetto ad un'altra entità o risorsa.
The function of an entity or agent with respect to another entity or resource.
haRuolo
hadRole
havde rolle
sehraná role
tiene rol
Agregada en DCAT para complementar prov:hadRole (cuyo uso está limitado a roles en el contexto de una actividad, con dominio prov:Association.
Introdotta in DCAT per completare prov:hadRole (il cui uso è limitato ai ruoli nel contesto di un'attività, con il dominio di prov:Association.
Introduced into DCAT to complement prov:hadRole (whose use is limited to roles in the context of an activity, with the domain of prov:Association.
Introduceret i DCAT for at supplere prov:hadRole (hvis anvendelse er begrænset til roller i forbindelse med en aktivitet med domænet prov:Association).
Přidáno do DCAT pro doplnění vlastnosti prov:hadRole (jejíž užití je omezeno na role v kontextu aktivity, s definičním oborem prov:Association).
Kan vendes ved kvalificerede krediteringer til at angive en aktørs rolle i forhold en entitet. Det anbefales at værdierne styres som et kontrolleret udfaldsrum med aktørroller, såsom http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
May be used in a qualified-attribution to specify the role of an Agent with respect to an Entity. It is recommended that the value be taken from a controlled vocabulary of agent roles, such as http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
May be used in a qualified-relation to specify the role of an Entity with respect to another Entity. It is recommended that the value be taken from a controlled vocabulary of entity roles such as: ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode; IANA Registry of Link Relations https://www.iana.org/assignments/link-relation; DataCite metadata schema; MARC relators https://id.loc.gov/vocabulary/relators.
Může být použito v kvalifikovaném přiřazení pro specifikaci role Agenta ve vztahu k Entitě. Je doporučeno hodnotu vybrat z řízeného slovníku rolí agentů, jako například http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Může být použito v kvalifikovaném vztahu pro specifikaci role Entity ve vztahu k jiné Entitě. Je doporučeno použít hodnotu z řízeného slovníku rolí entit, jako například ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode, IANA Registry of Link Relations https://www.iana.org/assignments/link-relation, DataCite metadata schema, MARC relators https://id.loc.gov/vocabulary/relators.
Puede usarse en una atribución cualificada para especificar el rol de un Agente con respecto a una Entidad. Se recomienda que el valor sea de un vocabulario controlado de roles de agentes, como por ejemplo http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Puede usarse en una atribución cualificada para especificar el rol de una Entidad con respecto a otra Entidad. Se recomienda que su valor se tome de un vocabulario controlado de roles de entidades como por ejemplo: ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode; IANA Registry of Link Relations https://www.iana.org/assignments/link-relation; esquema de metadatos de DataCite; MARC relators https://id.loc.gov/vocabulary/relators.
Può essere utilizzata in una relazione qualificata per specificare il ruolo di un'entità rispetto a un'altra entità. Si raccomanda che il valore sia preso da un vocabolario controllato di ruoli di entità come ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode, IANA Registry of Link Relations https://www.iana.org/assignments/link-relation, DataCite metadata schema, o MARC relators https://id.loc.gov/vocabulary/relators.
Può essere utilizzato in un'attribuzione qualificata per specificare il ruolo di un agente rispetto a un'entità. Si raccomanda che il valore sia preso da un vocabolario controllato di ruoli di agente, come ad esempio http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
A Web page that can be navigated to in a Web browser to gain access to the catalog, a dataset, its distributions and/or additional information.
En webside som der kan navigeres til i en webbrowser for at få adgang til kataloget, et datasæt, dets distributioner og/eller yderligere information.
Una pagina web che può essere navigata per ottenere l'accesso al catalogo, ad un dataset, alle distribuzioni del dataset e/o ad informazioni addizionali.
Una página web que puede ser visitada en un explorador Web para tener acceso el catálogo, un conjunto de datos, sus distribuciones y/o información adicional.
Une page Web accessible par un navigateur Web donnant accès au catalogue, un jeu de données, ses distributions et/ou des informations additionnelles.
Webová stránka, na kterou lze pro získání přístupu ke katalogu, datové sadě, jejím distribucím a/nebo dalším informacím přistoupit webovým prohlížečem.
Μία ιστοσελίδα πλοηγίσιμη μέσω ενός φυλλομετρητή (Web browser) που δίνει πρόσβαση στο σύνολο δεδομένων, τις διανομές αυτού ή/και επιπρόσθετες πληροφορίες.
صفحة وب يمكن من خلالها الوصول الى قائمة البيانات أو إلى معلومات إضافية متعلقة بها
データセット、その配信および（または）追加情報にアクセスするためにウエブ・ブラウザでナビゲートできるウェブページ。
destinationsside
landing page
page d'atterrissage
pagina di destinazione
página de destino
vstupní stránka
ιστοσελίδα αρχικής πρόσβασης
صفحة وصول
ランディング・ページ
En webside som en webbrowser kan navigeres til for at få adgang til kataloget, et datasæt, dets distritbutioner og/eller yderligere information.
Hvis en eller flere distributioner kun er tilgængelige via en destinationsside (dvs. en URL til direkte download er ikke kendt), så bør destinationssidelinket gentages som adgangsadresse for en distribution.
Pokud je distribuce dostupná pouze přes vstupní stránku, t.j. přímý URL odkaz ke stažení není znám, URL přístupové stránky by mělo být duplikováno ve vlastnosti distribuce accessURL.
Se la distribuzione è accessibile solo attraverso una pagina di destinazione (cioè, un URL di download diretto non è noto), il link alla pagina di destinazione deve essere duplicato come accessURL sulla distribuzione.
Si la distribución es accesible solamente través de una página de aterrizaje (i.e., no se conoce una URL de descarga directa), entonces el enlance a la página de aterrizaje debe ser duplicado como accessURL sobre la distribución.
Si la distribution est seulement accessible à travers une page d'atterrissage (exple. pas de connaissance d'URLS de téléchargement direct ), alors le lien de la page d'atterrissage doit être dupliqué comme accessURL sur la distribution.
Αν η/οι διανομή/ές είναι προσβάσιμη/ες μόνο μέσω μίας ιστοσελίδας αρχικής πρόσβασης (δηλαδή αν δεν υπάρχουν γνωστές διευθύνσεις άμεσης μεταφόρτωσης), τότε ο σύνδεσμος της ιστοσελίδας αρχικής πρόσβασης πρέπει να αναπαραχθεί ως accessURL σε μία διανομή.
ランディング・ページを通じてしか配信にアクセスできない場合（つまり、直接的なダウンロードURLが不明）には、配信におけるaccessURLとしてランディング・ページのリンクをコピーすべきです（SHOULD）。
Cette propriété doit être utilisée quand c'est définit le type de média de la distribution en IANA, sinon dct:format DOIT être utilisé avec différentes valeurs.
Esta propiedad debe ser usada cuando está definido el tipo de media de la distribución en IANA, de otra manera dct:format puede ser utilizado con diferentes valores
Il tipo di media della distribuzione come definito da IANA
Medietypen for distributionen som den er defineret af IANA.
The media type of the distribution as defined by IANA
Typ média distribuce definovaný v IANA.
Η ιδιότητα αυτή ΘΑ ΠΡΕΠΕΙ να χρησιμοποιείται όταν ο τύπος μέσου μίας διανομής είναι ορισμένος στο IANA, αλλιώς η ιδιότητα dct:format ΔΥΝΑΤΑΙ να χρησιμοποιηθεί με διαφορετικές τιμές.
يجب استخدام هذه الخاصية إذا كان نوع الملف معرف ضمن IANA
このプロパティーは、配信のメディア・タイプがIANAで定義されているときに使用すべきで（SHOULD）、そうでない場合には、dct:formatを様々な値と共に使用できます（MAY）。
media type
medietype
tipo de media
tipo di media
typ média
type de média
τύπος μέσου
نوع الميديا
メディア・タイプ
Il range di dcat:mediaType è stato ristretto come parte della revisione di DCAT.
Obor hodnot dcat:mediaType byl zúžen v této revizi DCAT.
The range of dcat:mediaType has been tightened as part of the revision of DCAT.
Status: English Definition text modified by DCAT revision team, Italian and Czech translation provided, other translations pending. Note some inconsistency on def vs. usage.
Denne egenskab BØR anvendes hvis distributionens medietype optræder i 'IANA media types registry' https://www.iana.org/assignments/media-types/, ellers KAN egenskaben dct:format anvendes med et andet udfaldsrum.
Esta propiedad DEBERÍA usarse cuando el 'media type' de la distribución está definido en el registro IANA de 'media types' https://www.iana.org/assignments/media-types/, de lo contrario, dct:format PUEDE usarse con distintos valores.
Questa proprietà DEVE essere usata quando il tipo di media della distribuzione è definito nel registro dei tipi di media IANA https://www.iana.org/assignments/media-types/, altrimenti dct:format PUO 'essere usato con differenti valori.
Tato vlastnost BY MĚLA být použita, je-li typ média distribuce definován v registru IANA https://www.iana.org/assignments/media-types/. V ostatních případech MŮŽE být použita vlastnost dct:format s jinými hodnotami.
This property SHOULD be used when the media type of the distribution is defined in the IANA media types registry https://www.iana.org/assignments/media-types/, otherwise dct:format MAY be used with different values.
Balíčkový formát souboru, ve kterém je jeden či více souborů seskupeno dohromady, např. aby bylo možné stáhnout sadu souvisejících souborů naráz.
El formato del archivo en que se agrupan uno o más archivos de datos, e.g. para permitir que un conjunto de archivos relacionados se bajen juntos.
Format til pakning af data med henblik på distribution af en eller flere relaterede datafiler der samles til en enhed med henblik på samlet distribution.
Il formato di impacchettamento della distribuzione in cui uno o più file di dati sono raggruppati insieme, ad es. per abilitare un insieme di file correlati da scaricare insieme.
The package format of the distribution in which one or more data files are grouped together, e.g. to enable a set of related files to be downloaded together.
formato de empaquetado
formato di impacchettamento
formát balíčku
packaging format
pakkeformat
Denne egenskab kan anvendes hvis filerne i en distribution er pakket, fx i en TAR-fil, en Frictionless Data Package eller en Bagit-fil. Formatet BØR udtrykkes ved en medietype som defineret i 'IANA media types registry', hvis der optræder en relevant medietype dér: https://www.iana.org/assignments/media-types/.
Esta propiedad se debe usar cuando los archivos de la distribución están empaquetados, por ejemplo en un archivo TAR, Frictionless Data Package o Bagit. El formato DEBERÍA expresarse usando un 'media type', tales como los definidos en el registro IANA de 'media types' https://www.iana.org/assignments/media-types/, si está disponibles.
Questa proprietà deve essere utilizzata quando i file nella distribuzione sono impacchettati, ad esempio in un file TAR, Frictionless Data Package o Bagit. Il formato DOVREBBE essere espresso utilizzando un tipo di supporto come definito dal registro dei tipi di media IANA https://www.iana.org/assignments/media-types/, se disponibili.
Tato vlastnost se použije, když jsou soubory v distribuci zabaleny, např. v souboru TAR, v balíčku Frictionless Data Package nebo v souboru Bagit. Formát BY MĚL být vyjádřen pomocí typu média definovaného v registru IANA https://www.iana.org/assignments/media-types/, pokud existuje.
This property to be used when the files in the distribution are packaged, e.g. in a TAR file, a Frictionless Data Package or a Bagit file. The format SHOULD be expressed using a media type as defined by IANA media types registry https://www.iana.org/assignments/media-types/, if available.
Enlace a una descripción de la relación con otro recurso.
Link a una descrizione di una relazione con un'altra risorsa.
Link to a description of a relationship with another resource.
Odkaz na popis vztahu s jiným zdrojem.
Reference til en beskrivelse af en relation til en anden ressource.
Kvalificeret relation
kvalifikovaný vztah
qualified relation
relación calificada
relazione qualificata
Propiedad nueva añadida en DCAT 2.0.
Introdotta in DCAT per integrare le altre relazioni qualificate di PROV.
Introduced into DCAT to complement the other PROV qualified relations.
Introduceret i DCAT med henblik på at supplere de øvrige kvalificerede relationer fra PROV.
Přidáno do DCAT k doplnění jiných kvalifikovaných vztahů ze slovníku PROV.
Se incluyó en DCAT para complementar las relaciones calificadas disponibles en PROV.
Anvendes til at referere til en anden ressource hvor relationens betydning er kendt men ikke matcher en af de standardiserede egenskaber fra Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) eller PROV-O-egenskaber (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Použito pro odkazování na jiný zdroj, kde druh vztahu je znám, ale neodpovídá standardním vlastnostem ze slovníku Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) či slovníku PROV-O (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Se usa para asociar con otro recurso para el cuál la naturaleza de la relación es conocida pero no es ninguna de las propiedades que provee el estándar Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) or PROV-O properties (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Used to link to another resource where the nature of the relationship is known but does not match one of the standard Dublin Core properties (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) or PROV-O properties (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Viene utilizzato per associarsi a un'altra risorsa nei casi per i quali la natura della relazione è nota ma non è alcuna delle proprietà fornite dallo standard Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat , dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:require, dct:isRequiredBy) o dalle proprietà fornite da PROV-O (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom , prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
A record describing the registration of a single dataset or data service that is part of the catalog.
Describe la registración de un conjunto de datos o un servicio de datos en el catálogo.
En post der beskriver registreringen af et enkelt datasæt eller en datatjeneste som er opført i kataloget.
Propojuje katalog a jeho záznamy.
Relie un catalogue à ses registres.
Un record che descrive la registrazione di un singolo set di dati o di un servizio dati che fa parte del catalogo.
Záznam popisující registraci jedné datové sady či datové služby jakožto součásti katalogu.
Συνδέει έναν κατάλογο με τις καταγραφές του.
تربط الفهرس بسجل ضمنه
カタログの一部であるカタログ・レコード。
post
record
registre
registro
záznam
καταγραφή
سجل
カタログ・レコード
har post
Status: English, Italian, Spanish and Czech Definitions modified by DCAT revision team, other translations pending.
A collection of data that this DataService can distribute.
En samling af data som denne datatjeneste kan distribuere.
Kolekce dat, kterou je tato Datová služba schopna poskytnout.
Una colección de datos que este Servicio de Datos puede distribuir.
Una raccolta di dati che questo DataService può distribuire.
datatjeneste for datasæt
poskytuje datovou sadu
provee conjunto de datos
serve set di dati
serves dataset
distribuerer
ekspederer
udstiller
A site or endpoint that is listed in the catalog.
Et websted eller et endpoint som er opført i kataloget.
Umístění či přístupový bod registrovaný v katalogu.
Un sitio o 'endpoint' que está listado en el catálogo.
Un sito o endpoint elencato nel catalogo.
datatjeneste
service
servicio
servizio
služba
har datatjeneste
Nueva propiedad añadida en DCAT 2.0.
A main category of the resource. A resource can have multiple themes.
Et centralt emne for ressourcen. En ressource kan have flere centrale emner.
Hlavní téma zdroje. Zdroj může mít více témat.
La categoria principale della risorsa. Una risorsa può avere più temi.
La categoría principal del recurso. Un recurso puede tener varios temas.
La catégorie principale de la ressource. Une ressource peut avoir plusieurs thèmes.
Η κύρια κατηγορία του συνόλου δεδομένων. Ένα σύνολο δεδομένων δύναται να έχει πολλαπλά θέματα.
التصنيف الرئيسي لقائمة البيانات. قائمة البيانات يمكن أن تملك أكثر من تصنيف رئيسي واحد.
データセットの主要カテゴリー。データセットは複数のテーマを持つことができます。
emne
tema
theme
thème
téma
Θέμα
التصنيف
テーマ/カテゴリー
Status: English Definition text modified by DCAT revision team, all except for Italian and Czech translations are pending.
El conjunto de skos:Concepts utilizados para categorizar los recursos están organizados en un skos:ConceptScheme que describe todas las categorías y sus relaciones en el catálogo.
Il set di concetti skos usati per categorizzare le risorse sono organizzati in skos:ConceptScheme che descrive tutte le categorie e le loro relazioni nel catalogo.
Sada instancí třídy skos:Concept použitá pro kategorizaci zdrojů je organizována do schématu konceptů skos:ConceptScheme, které popisuje všechny kategorie v katalogu a jejich vztahy.
Samlingen af begreber (skos:Concept) der anvendes til at emneinddele ressourcer organiseres i et begrebssystem (skos:ConceptScheme) som beskriver alle emnerne og deres relationer i kataloget.
The set of skos:Concepts used to categorize the resources are organized in a skos:ConceptScheme describing all the categories and their relations in the catalog.
Un ensemble de skos:Concepts utilisés pour catégoriser les ressources sont organisés en un skos:ConceptScheme décrivant toutes les catégories et ses relations dans le catalogue.
Το σετ των skos:Concepts που χρησιμοποιείται για να κατηγοριοποιήσει τα σύνολα δεδομένων είναι οργανωμένο εντός ενός skos:ConceptScheme που περιγράφει όλες τις κατηγορίες και τις σχέσεις αυτών στον κατάλογο.
データセットを分類するために用いられるskos:Conceptの集合は、カタログのすべてのカテゴリーとそれらの関係を記述しているskos:ConceptSchemeで組織化されます。
El sistema de organización del conocimiento utilizado para clasificar conjuntos de datos de catálogos.
Il sistema di organizzazione della conoscenza (KOS) usato per classificare i dataset del catalogo.
Le systhème d'ogranisation de connaissances utilisé pour classifier les jeux de données du catalogue.
Systém organizace znalostí (KOS) použitý pro klasifikaci datových sad v katalogu.
The knowledge organization system (KOS) used to classify catalog's datasets.
Vidensorganiseringssystem (KOS) som anvendes til at klassificere datasæt i kataloget.
Το σύστημα οργάνωσης γνώσης που χρησιμοποιείται για την κατηγοριοποίηση των συνόλων δεδομένων του καταλόγου.
لائحة التصنيفات المستخدمه لتصنيف قوائم البيانات ضمن الفهرس
カタログのデータセットを分類するために用いられる知識組織化体系（KOS；knowledge organization system）。
emnetaksonomi
tassonomia dei temi
taxonomie de thèmes
taxonomie témat
taxonomía de temas
theme taxonomy
Ταξινομία θεματικών κατηγοριών.
قائمة التصنيفات
テーマ
temataksonomi
Det anbefales at taksonomien organiseres i et skos:ConceptScheme, skos:Collection, owl:Ontology eller lignende, som giver mulighed for at ethvert medlem af taksonomien kan forsynes med en IRI og udgives som linked-data.
It is recommended that the taxonomy is organized in a skos:ConceptScheme, skos:Collection, owl:Ontology or similar, which allows each member to be denoted by an IRI and published as linked-data.
Je doporučeno, aby byla taxonomie vyjádřena jako skos:ConceptScheme, skos:Collection, owl:Ontology nebo podobné, aby mohla být každá položka identifikována pomocí IRI a publikována jako propojená data.
Se recomienda que la taxonomía se organice como un skos:ConceptScheme, skos:Collection, owl:Ontology o similar, los cuáles permiten que cada miembro se denote con una IRI y se publique como datos enlazados.
Si raccomanda che la tassonomia sia organizzata in uno skos:ConceptScheme, skos:Collection, owl:Ontology o simili, che permette ad ogni membro di essere indicato da un IRI e pubblicato come linked-data.
The time needed to accelerate the vehicle from a given start velocity to a given target velocity. Typical unit code(s): SEC for seconds Note: There are unfortunately no standard unit codes for seconds/0..100 km/h or seconds/0..60 mph. Simply use "SEC" for seconds and indicate the velocities in the name of the QuantitativeValue, or use valueReference with a QuantitativeValue of 0..60 mph or 0..100 km/h to specify the reference speeds.
accelerationTime
The ACRISS Car Classification Code is a code used by many car rental companies, for classifying vehicles. ACRISS stands for Association of Car Rental Industry Systems and Standards.
acrissCode
Length of time to engage in the activity.
activityDuration
How often one should engage in the activity.
activityFrequency
Any additional component of the exercise prescription that may need to be articulated to the patient. This may include the order of exercises, the number of repetitions of movement, quantitative distance, progressions over time, etc.
additionalVariable
A route by which this drug may be administered, e.g. 'oral'.
administrationRoute
Any precaution, guidance, contraindication, etc. related to consumption of alcohol while taking this drug.
alcoholWarning
The algorithm or rules to follow to compute the score.
algorithm
An available dosage strength for the drug.
availableStrength
Indicates the design and body style of the vehicle (e.g. station wagon, hatchback, etc.).
bodyType
Any precaution, guidance, contraindication, etc. related to this drug's use by breastfeeding mothers.
breastfeedingWarning
The available volume for cargo or luggage. For automobiles, this is usually the trunk volume. Typical unit code(s): LTR for liters, FTQ for cubic foot/feet Note: You can use minValue and maxValue to indicate ranges.
cargoVolume
A data catalog which contains this dataset.
The name of a character played in some acting or performing role, i.e. in a PerformanceRole.
characterName
Description of the absorption and elimination of drugs, including their concentration (pharmacokinetics, pK) and biological effects (pharmacodynamics, pD).
clincalPharmacology
clinicalPharmacology
An item within a data feed. Data feeds may have many elements.
dataFeedElement
A dataset contained in this catalog.
The range of temporal applicability of a dataset, e.g. for a 2011 census dataset, the year 2011 (in ISO 8601 time interval format).
datasetTimeInterval
The date of the first registration of the vehicle with the respective public authorities.
dateVehicleFirstRegistered
A downloadable form of this dataset, at a specific location, in a specific format. This property can be repeated if different variations are available. There is no expectation that different downloadable distributions must contain exactly equivalent information (see also DCAT on this point). Different distributions might include or exclude different subsets of the entire dataset, for example.
A dosage form in which this drug/supplement is available, e.g. 'tablet', 'suspension', 'injection'.
dosageForm
The drive wheel configuration, i.e. which roadwheels will receive torque from the vehicle's engine via the drivetrain.
driveWheelConfiguration
The class of drug this belongs to (e.g., statins).
drugClass
The CO2 emissions in g/km. When used in combination with a QuantitativeValue, put "g/km" into the unitText property of that value, since there is no UN/CEFACT Common Code for "g/km".
emissionsCO2
Any precaution, guidance, contraindication, etc. related to consumption of specific foods while taking this drug.
foodWarning
The capacity of the fuel tank or in the case of electric cars, the battery. If there are multiple components for storage, this should indicate the total of all storage of the same type. Typical unit code(s): LTR for liters, GLL of US gallons, GLI for UK / imperial gallons, AMH for ampere-hours (for electrical vehicles).
fuelCapacity
The amount of fuel consumed for traveling a particular distance or temporal duration with the given vehicle (e.g. liters per 100 km). Note 1: There are unfortunately no standard unit codes for liters per 100 km. Use unitText to indicate the unit of measurement, e.g. L/100 km. Note 2: There are two ways of indicating the fuel consumption, fuelConsumption (e.g. 8 liters per 100 km) and fuelEfficiency (e.g. 30 miles per gallon). They are reciprocal. Note 3: Often, the absolute value is useful only when related to driving speed ("at 80 km/h") or usage pattern ("city traffic"). You can use valueReference to link the value for the fuel consumption to another value.
fuelConsumption
The distance traveled per unit of fuel used; most commonly miles per gallon (mpg) or kilometers per liter (km/L). Note 1: There are unfortunately no standard unit codes for miles per gallon or kilometers per liter. Use unitText to indicate the unit of measurement, e.g. mpg or km/L. Note 2: There are two ways of indicating the fuel consumption, fuelConsumption (e.g. 8 liters per 100 km) and fuelEfficiency (e.g. 30 miles per gallon). They are reciprocal. Note 3: Often, the absolute value is useful only when related to driving speed ("at 80 km/h") or usage pattern ("city traffic"). You can use valueReference to link the value for the fuel economy to another value.
fuelEfficiency
A hospital with which the physician or office is affiliated.
hospitalAffiliation
A data catalog which contains this dataset (this property was previously 'catalog', preferred name is now 'includedInDataCatalog').
includedDataCatalog
includedInDataCatalog
The insurance plans that cover this drug.
includedInHealthInsurancePlan
Quantitative measure gauging the degree of force involved in the exercise, for example, heartbeats per minute. May include the velocity of the movement.
intensity
Another drug that is known to interact with this drug in a way that impacts the effect of this drug or causes a risk to the patient. Note: disease interactions are typically captured as contraindications.
interactingDrug
True if the drug is available in a generic form (regardless of name).
isAvailableGenerically
A textual description of known damages, both repaired and unrepaired.
knownVehicleDamages
Link to the drug's label details.
labelDetails
Indicates the relationship type of a Web link.
linkRelationship
Indicates that the vehicle meets the respective emission standard.
meetsEmissionStandard
The total distance travelled by the particular vehicle since its initial production, as read from its odometer. Typical unit code(s): KMT for kilometers, SMI for statute miles
mileageFromOdometer
The release date of a vehicle model (often used to differentiate versions of the same make and model).
modelDate
A position played, performed or filled by a person or organization, as part of an organization. For example, an athlete in a SportsTeam might play in the position named 'Quarterback'.
namedPosition
The number or type of airbags in the vehicle.
numberOfAirbags
The number of axles. Typical unit code(s): C62
numberOfAxles
The number of doors. Typical unit code(s): C62
numberOfDoors
The total number of forward gears available for the transmission system of the vehicle. Typical unit code(s): C62
numberOfForwardGears
The number of owners of the vehicle, including the current one. Typical unit code(s): C62
numberOfPreviousOwners
A number associated with a role in an organization, for example, the number on an athlete's jersey.
numberedPosition
The vasculature the lymphatic structure originates, or afferents, from.
originatesFrom
Any information related to overdose on a drug, including signs or symptoms, treatments, contact information for emergency response.
overdosage
The permitted weight of passengers and cargo, EXCLUDING the weight of the empty vehicle. Typical unit code(s): KGM for kilogram, LBR for pound Note 1: Many databases specify the permitted TOTAL weight instead, which is the sum of weight and payload Note 2: You can indicate additional information in the name of the QuantitativeValue node. Note 3: You may also link to a QualitativeValue node that provides additional information using valueReference. Note 4: Note that you can use minValue and maxValue to indicate ranges.
payload
Pregnancy category of this drug.
pregnancyCategory
Any precaution, guidance, contraindication, etc. related to this drug's use during pregnancy.
pregnancyWarning
Link to prescribing information for the drug.
prescribingInfo
Indicates the status of drug prescription, e.g. local catalogs classifications or whether the drug is available by prescription or over-the-counter, etc.
prescriptionStatus
Strength of the guideline's recommendation (e.g. 'class I').
recommendationStrength
Any other drug related to this one, for example commonly-prescribed alternatives.
relatedDrug
Number of times one should repeat the activity.
repetitions
How often one should break from the activity.
restPeriods
A role played, performed or filled by a person or organization. For example, the team of creators for a comic book might fill the roles named 'inker', 'penciller', and 'letterer'; or an athlete in a SportsTeam might play in the position named 'Quarterback'.
roleName
The permitted total weight of cargo and installations (e.g. a roof rack) on top of the vehicle. Typical unit code(s): KGM for kilogram, LBR for pound Note 1: You can indicate additional information in the name of the QuantitativeValue node. Note 2: You may also link to a QualitativeValue node that provides additional information using valueReference Note 3: Note that you can use minValue and maxValue to indicate ranges.
roofLoad
The vasculature the lymphatic structure runs, or efferents, to.
runsTo
The RxCUI drug identifier from RXNORM.
rxcui
The number of persons that can be seated (e.g. in a vehicle), both in terms of the physical space available, and in terms of limitations set by law. Typical unit code(s): C62 for persons
seatingCapacity
The speed range of the vehicle. If the vehicle is powered by an engine, the upper limit of the speed range (indicated by maxValue) should be the maximum speed achievable under regular conditions. Typical unit code(s): KMH for km/h, HM for mile per hour (0.447 04 m/s), KNT for knot *Note 1: Use minValue and maxValue to indicate the range. Typically, the minimal value is zero. * Note 2: There are many different ways of measuring the speed range. You can link to information about how the given value has been determined using the valueReference property.
speed
The position of the steering wheel or similar device (mostly for cars).
steeringPosition
Specifics about the observational study design (enumerated).
studyDesign
The type of tissue sample required for the test.
tissueSample
The permitted vertical load (TWR) of a trailer attached to the vehicle. Also referred to as Tongue Load Rating (TLR) or Vertical Load Rating (VLR). Typical unit code(s): KGM for kilogram, LBR for pound Note 1: You can indicate additional information in the name of the QuantitativeValue node. Note 2: You may also link to a QualitativeValue node that provides additional information using valueReference. Note 3: Note that you can use minValue and maxValue to indicate ranges.
tongueWeight
The permitted weight of a trailer attached to the vehicle. Typical unit code(s): KGM for kilogram, LBR for pound * Note 1: You can indicate additional information in the name of the QuantitativeValue node. * Note 2: You may also link to a QualitativeValue node that provides additional information using valueReference. * Note 3: Note that you can use minValue and maxValue to indicate ranges.
trailerWeight
The variableMeasured property can indicate (repeated as necessary) the variables that are measured in some dataset, either described as text or as pairs of identifier and description using PropertyValue.
variableMeasured
Originally named variablesMeasured, the variableMeasured property can indicate (repeated as necessary) the variables that are measured in some dataset, either described as text or as pairs of identifier and description using PropertyValue.
variablesMeasured
A short text indicating the configuration of the vehicle, e.g. '5dr hatchback ST 2.5 MT 225 hp' or 'limited edition'.
vehicleConfiguration
Information about the engine or engines of the vehicle.
vehicleEngine
The Vehicle Identification Number (VIN) is a unique serial number used by the automotive industry to identify individual motor vehicles.
vehicleIdentificationNumber
The color or color combination of the interior of the vehicle.
vehicleInteriorColor
The type or material of the interior of the vehicle (e.g. synthetic fabric, leather, wood, etc.). While most interior types are characterized by the material used, an interior type can also be based on vehicle usage or target audience.
vehicleInteriorType
vehicleModelDate
The number of passengers that can be seated in the vehicle, both in terms of the physical space available, and in terms of limitations set by law. Typical unit code(s): C62 for persons.
vehicleSeatingCapacity
Indicates whether the vehicle has been used for special purposes, like commercial rental, driving school, or as a taxi. The legislation in many countries requires this information to be revealed when offering a car for sale.
vehicleSpecialUsage
The type of component used for transmitting the power from a rotating power source to the wheels or other relevant component(s) ("gearbox" for cars).
vehicleTransmission
Any FDA or other warnings about the drug (text or URL).
warning
The permitted total weight of the loaded vehicle, including passengers and cargo and the weight of the empty vehicle. Typical unit code(s): KGM for kilogram, LBR for pound Note 1: You can indicate additional information in the name of the QuantitativeValue node. Note 2: You may also link to a QualitativeValue node that provides additional information using valueReference. Note 3: Note that you can use minValue and maxValue to indicate ranges.
weightTotal
The distance between the centers of the front and rear wheels. Typical unit code(s): CMT for centimeters, MTR for meters, INH for inches, FOT for foot/feet
wheelbase
Quantitative measure of the physiologic output of the exercise; also referred to as energy expenditure.
workload
Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').
Describes the number of members in some set.
In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.
has_member_count
has measurement value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
This alphanumeric string is generated at data acquisition, and is used to uniquely identify the dataset.
ALSDA subject ID: Unique numeric identifier of a group to which the subject belongs. Examples of subject groups (Flight/Ground Control/Basal)
The UID assigned by NBISC and used in the Ames Life Science Data Archive
Original document number assigned by the JSC or ARC project, mission level offices, or headquarters level offices. For publication citations only, this is a number generated by the SQL database.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
equivalent or subproperty of http://purl.obolibrary.org/obo/UBERON_0000467
Date when data are released (usually by the PI) to the archive, or released to go on the public Website.
Magnitude of the temporal extent between the start of mission operations and the end of mission operations
Specified from the definition of http://purl.obolibrary.org/obo/PATO_0001309
This value denotes whether a dataset is available for download on the public site. Datasets are either available for download on-line, or available off-line in hardcopy form.
The family name associated with the object
owl:equivalentProperty IRI: http://www.w3.org/2006/vcard/ns#family-name
Phylogenetic classification of the subject or biospecimen host. Examples include: Homo sapiens, Mus musculus
A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized.
Typically, a Title will be a name by which the resource is formally known. cf IAO:0000305 document title as a class
equiv to http://purl.org/dc/elements/1.1/title
Experimental group that a subject belongs to (fixed choice: F, B, GC, V, etc.)
Identifier for NASA's research announcements or other "calls for proposals" (i.e. AO, NRA, etc.) soliciting the experiment
This field refers to the NASA classification of the experiment, in terms of the type of research project it originated from and/or is currently under (i.e AG, LSAH, CEVP), the type of payload or experiment it is, and/or the type of program it is related to.
The unique identifier assigned to each study
The given name associated with the object
A textual entity that specifies characteristics of some entity. cf. apollosv:00000476
Indicates the material obtained from an organism in order to be a representative of the whole
synonymous with rdfs:label as applied to institution
rdfs label (see https://www.w3.org/TR/rdf-schema/#ch_label)
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. cf. ExO:0000102 sex
The official name given to a study - usually the same name used when responding to a solicitation
equiv to http://purl.org/dc/terms/description
The proposed and/or actual start date of the experiment.
The city or town associated with the address of the object. cf. vcard:locality
owl:equivalentProperty http://www.w3.org/2006/vcard/ns#locality
owl:equivalentProperty http://purl.obolibrary.org/obo/NCIT_C91820
A small image that is representative of a larger image file.
The name (or part of a name) of a file (of any type)
owl:equivalentProperty http://edamontology.org/data_1050
These are the Medical Subject Headings (MeSH) terms assigned by LSDA archivists to the experiment.
Programmatic, or data acquisition or data quality information regarding this dataset.
A device used to preserve and store specimen (fixed choice: 2ml cryotube, etc.).
Date of euthanasia for animals. Can be the same day as dissection. Date of sample harvest for other type of experiments. .
Physical location where the data was collected
The mechanical equipment component used.
Describes the information, in terms of the group responsible for collecting and/or providing the data.
The physical or digital form in which the data are available.
An entity responsible for making the resource.
equiv to http://purl.org/dc/terms/creator
NASA center or other location where the document is archived; for hardcopy documents, this field also indicates where the document can be ordered
equiv to http://purl.org/dc/terms/available
Access restrictions for ordering/receiving the archived document.
File name for document available for online.
Defines the progress toward completion of archiving an experiment record, or other status information
Designates the NASA center assigned to preserving and curating an experiment's data and metadata. Note that It is not necessarily the same as the managing center.
Indicates the agency that is funding (sponsoring) the experiment.
Designates the research announcement (aka NRA) under which the study was funded.
Provides general spatial information on the environment of the mission's activities. This includes vehicle namess, crewed or uncrewed, which are designed to orbit bout the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space, satellites, space-analog ground facilities
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
The vendor of the animals. (eg. Jackson Laboratory, Charles River Laboratories). Or supplier of the plant/ cells.
A description of the subjects that were studied within the experiment
Animal body weight at launch. Unit is a separate field. cf. This is a literal value, See pato:0000128 for quality class
Indicates the center that is coordinating the implementation of the study.
The additional name associated with the object
additional name
The date of marriage, or equivalent, of the object
anniversary
To specify the birth date of the object
birth date
The category information about the object, also known as tags
category
This data property has been deprecated
class
The country name associated with the address of the object
country name
extended address
family name
The formatted text corresponding to the name of the object
formatted name
given name
The honorific prefix of the name associated with the object
honorific prefix
The honorific suffix of the name associated with the object
honorific suffix
label
To specify the language that may be used for contacting the object. May also be used as a property parameter.
language
This data property has been deprecated. See hasGeo
latitude
The locality (e.g. city or town) associated with the address of the object
locality
longitude
mailer
The nick name associated with the object
nickname
A note associated with the object
note
To specify the organizational name associated with the object
organization name
To specify the organizational unit name associated with the object
organizational unit name
post office box
The postal code associated with the address of the object
postal code
To specify the identifier for the product that created the object
product id
The region (e.g. state or province) associated with the address of the object
region
To specify revision information about the object
revision
To specify the function or part played in a particular situation by the object
role
To specify the string to be used for national-language-specific sorting. Used as a property parameter only.
sort as
The street address associated with the address of the object
street address
To specify the position or job of the object
title
To indicate time zone information that is specific to the object. May also be used as a property parameter.
time zone
Used to indicate the literal value of a data property that requires property parameters
value
bounding box
cuadro delimitador
ohraničení oblasti
quadro di delimitazione
Propiedad nueva agregada en DCAT 2.0.
Den geografiske omskrevne firkant af en ressource.
El cuadro delimitador geográfico para un recurso.
Il riquadro di delimitazione geografica di una risorsa.
Ohraničení geografické oblasti zdroje.
The geographic bounding box of a resource.
El rango de esta propiedad es intencionalmente genérico con el propósito de permitir distintas codificaciones geométricas. Por ejemplo, la geometría puede ser codificada como WKT (geosparql:wktLiteral [GeoSPARQL]) o [GML] (geosparql:asGML [GeoSPARQL]).
Il range di questa proprietà è volutamente generica, con lo scopo di consentire diverse codifiche geometriche. Ad esempio, la geometria potrebbe essere codificata con WKT (geosparql:wktLiteral [GeoSPARQL]) o [GML] (geosparql:asGML [GeoSPARQL]).
Obor hodnot této vlastnosti je úmyslně obecný, aby umožnil různé kódování geometrií. Geometrie by kupříkladu mohla být kódována jako WKT (geosparql:wktLiteral [GeoSPARQL]) či [GML] (geosparql:asGML [GeoSPARQL]).
Rækkevidden for denne egenskab er bevidst generisk defineret med det formål at tillade forskellige kodninger af geometrier. Geometrien kan eksempelvis repræsenteres som WKT (geosparql:asWKT [GeoSPARQL]) eller [GML] (geosparql:asGML [GeoSPARQL]).
The range of this property is intentionally generic, with the purpose of allowing different geometry encodings. E.g., the geometry could be encoded with as WKT (geosparql:wktLiteral [GeoSPARQL]) or [GML] (geosparql:asGML [GeoSPARQL]).
El tamaño de una distribución en bytes.
La dimensione di una distribuzione in byte.
La taille de la distribution en octects
Størrelsen af en distributionen angivet i bytes.
The size of a distribution in bytes.
Velikost distribuce v bajtech.
Το μέγεθος μιας διανομής σε bytes.
الحجم بالبايتات
バイトによる配信のサイズ。
byte size
bytestørrelse
dimensione in byte
taille en octects
tamaño en bytes
velikost v bajtech
μέγεθος σε bytes
الحجم بالبايت
バイト・サイズ
La taille de la distribution en octects.
Størrelsen af en distribution angivet i bytes.
Bytestørrelsen kan approximeres hvis den præcise størrelse ikke er kendt. Værdien af dcat:byteSize bør angives som xsd:decimal.
El tamaño en bytes puede ser aproximado cuando se desconoce el tamaño exacto. El valor literal de dcat:byteSize debe tener tipo 'xsd:decimal'.
La dimensione in byte può essere approssimata quando non si conosce la dimensione precisa. Il valore di dcat:byteSize dovrebbe essere espresso come un xsd:decimal.
La taille en octects peut être approximative lorsque l'on ignore la taille réelle. La valeur littérale de dcat:byteSize doit être de type xsd:decimal.
The size in bytes can be approximated when the precise size is not known. The literal value of dcat:byteSize should by typed as xsd:decimal.
Velikost v bajtech může být přibližná, pokud její přesná hodnota není známa. Literál s hodnotou dcat:byteSize by měl mít datový typ xsd:decimal.
Το μέγεθος σε bytes μπορεί να προσεγγιστεί όταν η ακριβής τιμή δεν είναι γνωστή. Η τιμή της dcat:byteSize θα πρέπει να δίνεται με τύπο δεδομένων xsd:decimal.
الحجم يمكن أن يكون تقريبي إذا كان الحجم الدقيق غير معروف
正確なサイズが不明である場合、サイズは、バイトによる近似値を示すことができます。
centroid
centroide
geometrisk tyngdepunkt
Det geometrisk tyngdepunkt (centroid) for en ressource.
El centro geográfico (centroide) de un recurso.
Geografický střed (centroid) zdroje.
Il centro geografico (centroide) di una risorsa.
The geographic center (centroid) of a resource.
El rango de esta propiedad es intencionalmente genérico con el objetivo de permitir distintas codificaciones geométricas. Por ejemplo, la geometría puede codificarse como WKT (geosparql:wktLiteral [GeoSPARQL]) o [GML] (geosparql:asGML [GeoSPARQL]).
Rækkevidden for denne egenskab er bevidst generisk definere med det formål at tillade forskellige geokodninger. Geometrien kan eksempelvis repræsenteres som WKT (geosparql:asWKT [GeoSPARQL]) eller [GML] (geosparql:asGML [GeoSPARQL]).
data di fine
datum konce
end date
fecha final
slutdato
sluttidspunkt
El fin del período.
Konec doby trvání.
La fine del periodo.
Slutningen på perioden.
The end of the period.
El rango de esta propiedad es intencionalmente genérico con el propósito de permitir distintos niveles de precisión temporal para especificar el fin del período. Por ejemplo, puede expresarse como una fecha (xsd:date), una fecha y un tiempo (xsd:dateTime), o un año (xsd:gYear).
La range di questa proprietà è volutamente generico, con lo scopo di consentire diversi livelli di precisione temporale per specificare la fine di un periodo. Ad esempio, può essere espresso con una data (xsd:date), una data e un'ora (xsd:dateTime), o un anno (xsd:gYear).
Obor hodnot této vlastnosti je úmyslně obecný, aby umožnil různé úrovně časového rozlišení pro specifikaci konce doby trvání. Ten může být kupříkladu vyjádřen datumem (xsd:date), datumem a časem (xsd:dateTime) či rokem (xsd:gYear).
Rækkeviden for denne egenskab er bevidst generisk defineret med det formål at tillade forskellige niveauer af tidslig præcision ifm. angivelse af slutdatoen for en periode. Den kan eksempelvis udtrykkes som en dato (xsd:date), en dato og et tidspunkt (xsd:dateTime), eller et årstal (xsd:gYear).
The range of this property is intentionally generic, with the purpose of allowing different level of temporal precision for specifying the end of a period. E.g., it can be expressed with a date (xsd:date), a date and time (xsd:dateTime), or a year (xsd:gYear).
A keyword or tag describing a resource.
Et nøgleord eller tag til beskrivelse af en ressource.
Klíčové slovo nebo značka popisující zdroj.
Un mot-clé ou étiquette décrivant une ressource.
Una palabra clave o etiqueta que describe un recurso.
Una parola chiave o un'etichetta per descrivere la risorsa.
Μία λέξη-κλειδί ή μία ετικέτα που περιγράφει το σύνολο δεδομένων.
كلمة مفتاحيه توصف قائمة البيانات
データセットを記述しているキーワードまたはタグ。
keyword
klíčové slovo
mot-clés
nøgleord
palabra clave
parola chiave
λέξη-κλειδί
كلمة مفتاحية
キーワード/タグ
mindste geografiske afstand som kan erkendes i et datasæt, målt i meter.
minimum spatial separation resolvable in a dataset, measured in meters.
minimum spatial separation resolvable in a dataset, measured in metres.
minimální prostorový rozestup rozeznatelný v datové sadě, měřeno v metrech.
mínima separacíon espacial disponible en un conjunto de datos, medida en metros.
separazione spaziale minima risolvibile in un set di dati, misurata in metri.
geografisk opløsning (meter)
prostorové rozlišení (metry)
resolución espacial (metros)
risoluzione spaziale (metros)
spatial resolution (meters)
spatial resolution (metres)
Ny genskab tilføjet i DCAT 2.0.
mindste geografiske afstand som kan resolveres i et datasæt, målt i meter.
Kan optræde i forbindelse med beskrivelse af datasættet eller datasætditributionen, så der er ikke angivet et domæne for egenskaben.
Might appear in the description of a Dataset or a Distribution, so no domain is specified.
Může se vyskytnout v popisu Datové sady nebo Distribuce, takže nebyl specifikován definiční obor.
Alternative geografiske opløsninger kan leveres som forskellige datasætdistributioner.
Alternative spatial resolutions might be provided as different dataset distributions.
Distintas distribuciones de un conjunto de datos pueden tener resoluciones espaciales diferentes.
Hvis datasættet udgøres af et billede eller et grid, så bør dette svare til afstanden mellem elementerne. For andre typer af spatiale datasæt, vil denne egenskab typisk indikere den mindste afstand mellem elementerne i datasættet.
If the dataset is an image or grid this should correspond to the spacing of items. For other kinds of spatial dataset, this property will usually indicate the smallest distance between items in the dataset.
Pokud je datová sada obraz či mřížka, měla by tato vlastnost odpovídat rozestupu položek. Pro ostatní druhy prostorových datových sad bude tato vlastnost obvykle indikovat nejmenší vzdálenost mezi položkami této datové sady.
Risoluzioni spaziali alternative possono essere fornite come diverse distribuzioni di set di dati.
Různá prostorová rozlišení mohou být poskytována jako různé distribuce datové sady.
Se il set di dati è un'immagine o una griglia, questo dovrebbe corrispondere alla spaziatura degli elementi. Per altri tipi di set di dati spaziali, questa proprietà di solito indica la distanza minima tra gli elementi nel set di dati.
Si el conjunto de datos es una imágen o grilla, esta propiedad corresponde al espaciado de los elementos. Para otro tipo de conjunto de datos espaciales, esta propieda usualmente indica la menor distancia entre los elementos de dichos datos.
data di inizio
datum začátku
start date
startdato
starttidspunkt
El comienzo del período
L'inizio del periodo
Start på perioden.
The start of the period
Začátek doby trvání
El rango de esta propiedad es intencionalmente genérico con el propósito de permitir distintos niveles de precisión temporal para especificar el comienzo de un período. Por ejemplo, puede expresarse como una fecha (xsd:date), una fecha y un tiempo (xsd:dateTime), o un año (xsd:gYear).
Il range di questa proprietà è volutamente generico, con lo scopo di consentire diversi livelli di precisione temporale per specificare l'inizio di un periodo. Ad esempio, può essere espresso con una data (xsd:date), una data e un'ora (xsd:dateTime), o un anno (xsd:gYear).
Obor hodnot této vlastnosti je úmyslně obecný, aby umožnil různé úrovně časového rozlišení pro specifikaci začátku doby trvání. Ten může být kupříkladu vyjádřen datumem (xsd:date), datumem a časem (xsd:dateTime) či rokem (xsd:gYear).
Rækkeviden for denne egenskab er bevidst generisk defineret med det formål at tillade forskellige niveauer af tidslig præcision ifm. angivelse af startdatoen for en periode. Den kan eksempelvis udtrykkes som en dato (xsd:date), en dato og et tidspunkt (xsd:dateTime), eller et årstal (xsd:gYear).
The range of this property is intentionally generic, with the purpose of allowing different level of temporal precision for specifying the start of a period. E.g., it can be expressed with a date (xsd:date), a date and time (xsd:dateTime), or a year (xsd:gYear).
mindste tidsperiode der kan resolveres i datasættet.
minimum time period resolvable in a dataset.
minimální doba trvání rozlišitelná v datové sadě.
periodo di tempo minimo risolvibile in un set di dati.
período de tiempo mínimo en el conjunto de datos.
resolución temporal
risoluzione temporale
temporal resolution
tidslig opløsning
časové rozlišení
Alternative temporal resolutions might be provided as different dataset distributions.
Alternative tidslige opløsninger kan leveres som forskellige datasætdistributioner.
Distintas distribuciones del conjunto de datos pueden tener resoluciones temporales diferentes.
Hvis datasættet er en tidsserie, så bør denne egenskab svare til afstanden mellem elementerne i tidsserien. For andre typer af datasæt indikerer denne egenskab den mindste tidsforskel mellem elementer i datasættet.
If the dataset is a time-series this should correspond to the spacing of items in the series. For other kinds of dataset, this property will usually indicate the smallest time difference between items in the dataset.
Pokud je datová sada časovou řadou, měla by tato vlastnost odpovídat rozestupu položek v řadě. Pro ostatní druhy datových sad bude tato vlastnost obvykle indikovat nejmenší časovou vzdálenost mezi položkami této datové sady.
Risoluzioni temporali alternative potrebbero essere fornite come diverse distribuzioni di set di dati.
Různá časová rozlišení mohou být poskytována jako různé distribuce datové sady.
Se il set di dati è una serie temporale, questo dovrebbe corrispondere alla spaziatura degli elementi della serie. Per altri tipi di set di dati, questa proprietà di solito indica la più piccola differenza di tempo tra gli elementi nel set di dati.
Si el conjunto de datos es una serie temporal, debe corresponder al espaciado de los elementos de la serie. Para otro tipo de conjuntos de datos, esta propiedad indicará usualmente la menor diferencia de tiempo entre elementos en el dataset.
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
A planned process resulting in a software product involving the creation of source code.
software development
creating a data set
A planned process that has a data set as its specified output.
data set creation
dataset creation
dataset creating
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
spatial region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
characteristic
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
fiat object
fiat object part
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
material entity
Collection of random bacteria, a chair, dorsal surface of the body.
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
immaterial entity
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).
A peptide containing ten or more amino acid residues.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A naturally occurring polypeptide synthesized at the ribosome.
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.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
An iron group element atom that has atomic number 26.
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
A salt is an assembly of cations and anions.
A molecular entity having a net electric charge.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
A molecule all atoms of which have the same atomic number.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
Any organic ion with a net negative charge.
Any organic ion with a net positive charge.
An oxide is a chemical compound of oxygen with other chemical elements.
An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
An onium cation obtained by protonation of ammonia.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.
Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
A monoatomic entity is a molecular entity consisting of a single atom.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An anion consisting of more than one atom.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
A molecular entity containing one or more atoms of an alkali metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
A molecular entity containing one or more atoms of a transition element.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
A main group molecular entity containing one or more atoms of any noble gas.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A cation consisting of more than one atom.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A carboxylic acid containing one or more amino groups.
An amino-acid residue derived from an alpha-amino acid.
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.
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
A substance that diminishes the rate of a chemical reaction.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A hadron with zero or integer spin; a strongly interacting boson. The term is derived from the Greek muepsilonsigmaomicronsigma (medium, middle).
A nucleus or any of its constituents in any of their energy states.
The collective name for zero-spin mesons pi(+), pi(-) and pi(0).
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals').
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
Any molecular entity that contains carbon.
A role is particular behaviour which a material entity may exhibit.
A poison that interferes with the functions of the nervous system.
A role played by the molecular entity or part thereof within a chemical context.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
An amino-acid residue protonated on nitrogen.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
A group that carries an overall positive charge.
A group that carries an overall negative charge.
An amino-acid residue carrying an overall negative charge.
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Saccharomyces cerevisiae secondary metabolites
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
An independent material continuant that is self-connected and retains its identity over time.
A piece of apparatus that is used to measure a physical quantity.
Measurement of the dose of a substance taken up by an object.
A sensor that is used to measure the dose of a substance taken by up an object.
An astrononmical body part which delimited by physical discontinuities with its surroundings.
This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
Mine tailings are the materials left over after the process of separating the valuable fraction from the uneconomic fraction (gangue) of an ore.
A construction which enables the movement of humans, their animals or their vehicles.
A geographical feature associated with water.
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
A large expanse of saline water usually connected with an ocean.
A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L).
A lake whose water contains a considerable concentration of dissolved salts.
A body of water or other liquid of considerable size contained in a depression on a landmass.
An vegetated area which overlaps a wetland ecosystem.
An accumulation of water of varying size.
The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.
A construction that has been assembled by deliberate human effort.
"constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
A permanent walled and roofed construction.
An excavation in the Earth for the purpose of extracting earth materials.
As with other classes that are "features", the subclasses of this class are being moved to more informative locations. Their relation to agriculture will be modelled by something more akin to a quality or relation to an agricultural process.
A region rendered barren or partially barren by environmental extremes, especially by low rainfall.
A depression which has been formed as a result of erosion by water or ice and which is low-lying, bordered by higher ground, and especially elongate.
Valleys are typically located between hills our mountains.
An area in which grasses (Graminae) are a significant component of the vegetation.
Land having a cover of trees, shrubs, or both.
An area with a high density of trees. A small forest may be called a wood.
The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome.
A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.
A valley which no longer has water flowing or accumulating over its surface.
Typically found in either Karst (limestone) or chalk terrain.
An environmental material which is 1) composed primarily of soil or rock and included ice or organic material and 2) at or below the freezing point of water for two or more years.
Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.
The region occupied by any more or less continuous, directed movement of ocean water that flows in one of the Earth's oceans. Ocean Currents are rivers of hot or cold water within the ocean. The currents are generated from the forces acting upon the water like the earth's rotation, the wind, the temperature and salinity differences and the gravitation of the moon. The depth contours, the shoreline and other movements influence the direction and strength of the movements of water that forms a given current.
Subclasses of this class are to be populated by inference. Definition modified from http://en.wikipedia.org/wiki/Ocean_current.
A landform elevated above the surrounding area.
elevation
A part of an astronomical body which is primarily composed of solid material.
A wetland ecosystem in which land mass is permanently inundated by shallow bodies of water, generally with a substantial number of hummocks, or dry-land protrusions.
A valley that contains, or contained, a glacier and was formed by glacial activity. Typically U-shaped in cross-section.
An open-pit mine from which rock or minerals are extracted.
A field of ice, formed in regions of perennial frost.
Ice mass may need to be resolved from ice field, the former referring simply to an accumulation of ice.
Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees.
A landform sunken or depressed below the surrounding area.
Clarify that this pertains to the planetary crust and create superclass for general topological depressions. https://github.com/EnvironmentOntology/envo/issues/486
depression
A mass of solid material which is composed primarily of rock.
A particle which 1) is composed primarily of and derived from rock or mineral sources and 2) is or was part of a portion of sand.
grain of sand
granule of sand
sand granule
In general, sand grains are larger than those of silt, but finer than those of gravel.
particle of sand
A particle which 1) is primarily composed of quartz or feldspar and 2) is or was part of a portion of silt.
grain of silt
granule of silt
The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam.
A biome is an ecosystem which is undergoing climactic ecological succession.
In this definition, there is an assumption that no major perturbations are occurring or have occurred in a time frame affects the successional dynamics of the ecosystem. A "major" perturbation is one which disrupts the community's ability to restore its (near) equilibrium. Usually, pioneer or early secondary successional processes would be in effect in such scenarios.
A biome which is primarily or completely situated on a landmass.
An aquatic biome which is determined by a marine water body.
This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt.
A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
The portion of the ground surface which lies below water.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
A lentic water body which is composed primarily of marine water.
A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land.
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
An environmental material primarily composed of dihydrogen oxide in its liquid form.
Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid.
Sediment is typically deposited on the bed or bottom of a body of water or other liquid.
Particulate environmental material with diameters less than 500 micrometers.
Do not oversimplify the particulate environmental material subclasses with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
Dust occurs in and may be deposited from the atmosphere.
Water which contains a significant concentration of dissolved salts.
The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.
A rock formed by deposition of either clastic sediments, organic matter, or chemical precipitates (evaporites), followed by compaction of the particulate matter and cementation during diagenesis.
A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water.
Sediment which has increased levels of one or more chemical compounds.
A portion of contaminated soil is a portion of soil with elevated levels of some contaminant.
"contaminant" is more of a disposition - any material entity can be a contaminant in particular circumstances.
Water which has physicochemical properties that have been determined by the processes occuring in a sea or ocean.
When we have more classes representing the various processes which make seawater seawater, we can further axiomatise this class.
This definition refers to water that is actually in a sea or ocean. This water may have a wide range of salinity levels.
A hospital is a building in which health care services are provided by specialized staff and equipment.
Chemically-enriched sediment which has increased levels of organic compounds.
Chemically-enriched sediment which has increased levels of inorganic compounds.
A power plant is a building which contains one or more generators which convert mechanical energy into electrical energy through the relative motion between a magnetic field and a conductor. The energy source harnessed to turn the generator varies widely.
A geothermal power plant is a power plant which uses heat generated by the decay of radioactive isotopes in the Earth's mantle and crust as well as primordial heat left over from the formation of the Earth to drive its generators.
A portion of soil which is found in a forested area.
A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process).
This seems more like a role than a material. Anything can be waste. Thus, a "waste" role or disposition will be created and this class can then be populated by inference: any environmental material which has [role,disposition] waste will be considered a waste material.
Industrial wastes are liquid, solid and gaseous wastes originating from the manufacture of specific products.
This will become a defined class, with subclasses added through inference based on material having a 'waste role' and being associated with industrial entities.
A nuclear power plant is a power plant which uses heat generated by a radioactive decay in a nuclear reactor to convert water into steam in order to drive turbines in electrical generators through pressure.
A manufactuered product which is capable of removing heat and controlling the humidity of the air within a site.
A/C
A/C unit
air conditioner
Particulate environmental material which 1) is composed primarily of clay particles, with only minor proportions of other materials, 2) demonstrates plasticity when wet, and 3) is capable of hardening when dried or fired.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities.The distinction between silt and clay varies by discipline. Geologists and soil scientists usually consider the separation to occur at a particle size of 2 μm (clays being finer than silts), sedimentologists often use 4–5 μm, and colloid chemists use 1 μm. Geotechnical engineers distinguish between silts and clays based on the plasticity properties of the soil, as measured by the soils' Atterberg limits. ISO 14688 grades clay particles as being smaller than 2 μm and silt particles as being larger. Mixtures of sand, silt and less than 40% clay are called loam. Similar mixtures with greater than 40% clay are often considered clay soils.
A house used for sheltering non-human animals.
While humans are animals, this class does not refer to human houses.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
A portion of enriched soil is a portion of soil with elevated levels of some material entity.
This could be demoted to an inferred class if issues with double inheritance arise.
An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered.
It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1.
A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery.
A building or collection of co-located buildings constructed for the purpose of undertaking scientific research.
A warehouse is a building which is used for the storage of goods.
An air filter is a device that removes some substance from air.
This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed.
Soil which has little to no water content and in which minerals and other soluble chemical entities have either bonded or become adsorbed to sold particles due to insufficient water availability.
A portion of soil which is part of a cropland or a rangeland biome.
A portion of soil which is found in a grassland.
Soil which is part of an agricultural field.
Soil which is part of some elevated land.
The dwelling of an animal or group of similar animals.
This class represents habitations of non-human animals. This distinction may be removed in future releases.
A bird nest is the spot in which a bird lays and incubates its eggs and raises its young.
A material entity which other material entities in an environmental system are primarily or partially composed of.
Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water".
Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
Airborne solid particles (also called dust or particulate matter (PM)) or liquid droplets.
Should connect to PATO as "quality of an aerosol"
Anthropogenic material in or on which organisms may live.
MERGED DEFINITION: TARGET DEFINITION: An oceanographic feature that involves wind-driven motion of dense, cooler, and usually nutrient-rich water towards the ocean surface, replacing the warmer, usually nutrient-deplete surface water. -------------------- SOURCE DEFINITION: A marine upwelling is a net flow of marine water to the surface of the water column from deeper regions. This is often a result of surface water displacement off continental coasts by wind action. Localised upwellings may also occur along divergent fronts around eddies and along some of the major oceanographic features. Deeper waters often have higher nutrient content; consequently blooms of primary producers, such as planktonic algae, are generally observed around upwelling zones.
This term is specific to marine upwellings.
Particulate environmental material which is primarily composed of silt particles.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider this soil material that contains 80% or more silt and less than 12% clay. In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances.
This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand.
Expressions of the estuarine biome occur at wide lower courses of a rivers where they flow into a sea. Estuaries experience tidal flows and their water is a changing mixture of fresh and salt.
The marine salt marsh biome comprises marshes that are transitional intertidals between land and salty or brackish marine water (e.g.: sloughs, bays, estuaries). It is dominated by halophytic (salt tolerant) herbaceous plants. The daily tidal surges bring in nutrients, which tend to settle in roots of the plants within the salt marsh. The natural chemical activity of salty (or brackish) water and the tendency of algae to bloom in the shallow unshaded water also allow for great biodiversity.
The marginal sea biome comprises parts of an ocean partially enclosed by land such as islands, archipelagos, or peninsulas. Unlike mediterranean seas, marginal seas have ocean currents caused by ocean winds. Many marginal seas are enclosed by island arcs that were formed from the subduction of one oceanic plate beneath another.
A marine biome which is determined by an ocean.
Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt.
An environmental material which is composed primarily of particles.
Do not oversimplify this branch with design patterns or similar. The materials have properties that their components do not - write full definitions including these where possible.
particulate matter
particulate environmental material
A portion of planktonic material is a portion of environmental material primarily composed of plankton.
See Issue #251. Awaiting class creation in PCO to attempt logical definitions.
planktonic material
A water current which is maintained by a continuous, directed movement of marine water, generated by forces caused by breaking waves, wind, Coriolis force, temperature and salinity differences, and tides caused by the gravitational pull of astronomical bodies. Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength.
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
A forest ecosystem which is undergoing climactic ecological succession.
A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor.
A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs.
A grassland ecosystem in which dominant ecological communities have reached their climax successional state.
A woodland biome which has seasonal water availability and includes trees spaced sufficiently far apart to allow an unbroken layer of grass, sedge (Cyperaceae) or rush (Juncaceae) communities to live.
A desert ecosystem which is undergoing climactic ecological succession.
A subtropical desert biome is a desert biome which has communities adapted to temperatures above a monthly average of 18 degrees Celsius, high daily temperature ranges of approximately 20 degrees Celsius, high insolation (but lower than that of a tropical desert biome), inhibited cloud formation, and very low precipitation. Subtropical desert biomes located near coasts with cold upwellings may have cooler temperatures and reduced insolution due to fog.
Preliminary definition. The semantics and definitions of "mediterranean", "subtropical", "tropical", "temperate", "polar", and similar climate types may be transferred to an "environmental condition" class once the semantics of this class have been established.
A savanna biome which is subject to temperate climate patterns.
A subtropical grassland in which dominant ecological communities have reached their climax successional state.
A coniferous forest biome is a forest biome which contains densely packed populations or communities of coniferous trees, strongly limiting light penetration to the forest floor.
A broadleaf forest ecosystem which is undergoing climactic ecological succession.
A mixed forest in which dominant ecological communities have reached their climax successional state.
A tropical broadleaf forest in which dominant ecological communities have reached their climax successional state.
A broadleaf forest which is subject to temperate climate patterns.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.
A tropical condition is an environmental condition in which an environmental system receives high yearly solar irradiance per unit area and, on Earth, the Sun reaches a subsolar point at least once during the solar year. This results in a hot and moist year-round climate at low elevations, which have a monthly average temperature above 18 degrees Celsius.
A subtropical condition is an environmental condition in which an envrionmental system receives more solar irradiance than those with temperate conditions, but less than those with tropical conditions. At low elevations, this typically results in eight months of the year having average temperatures greater than or equal to 10 degrees Celsius with the coldest monthly temperature averaging between 2 and 13 degrees Celsius.
As with most other climatic zones and conditions, multiple classification schemes have somehat different definitions and criteria. To quote from https://en.wikipedia.org/wiki/ "Several methods have been used to define the subtropical climate. In the Trewartha climate classification, a subtropical region should have at least eight months with a mean temperature of 10 °C (50.0 °F) or above. German climatologists Carl Troll and Karlheinz Paffen defined Warm temperate zones as plain and hilly lands having an average temperature of the coldest month between 2 °C (35.6 °F) and 13 °C (55.4 °F) in the Northern Hemisphere and between 6 °C (42.8 °F) and 13 °C (55.4 °F) in the Southern Hemisphere, excluding oceanic and continental climates. According to the Troll-Paffen climate classification, there generally exists one large subtropical zone named the warm-temperate subtropical zone,[4] which is subdivided into seven smaller areas.[5] According to the E. Neef climate classification, the subtropical zone is divided into two parts: Rainy winters of the west sides and Eastern subtropical climate.[6] According to the Wilhelm Lauer & Peter Frankenberg climate classification, the subtropical zone is divided into three parts: high-continental, continental, and maritime.[7] According to the Siegmund/Frankenberg climate classification, subtropical is one of six climate zones in the world.[8]"
A temperate condition is an environmental condition in which an environmental system receives less solar irradiance than those with subpolar conditions, but greater than those with subtropical conditions.
This class' definition is less satisfactory than the other latitudinal conditoins.
A coniferous forest biome which is subject to temperate climate patterns.
A temperate mixed forest in which dominant ecological communities have reached their climax successional state.
A shrubland biome which is subject to temperate climate patterns.
A montane shrubland biome is a shrubland biome which occurs in regions elevated above sea level and which has community structure determined by elevation-dependent environmental conditions.
An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity.
A woodland biome which is subject to temperate climate patterns.
An environmental condition in which annual precipitation is less than half of annual potential evapotranspiration.
A polar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area, resulting in colder climatic conditions.
On Earth, polar conditions are such that every month has average temperature lower than 10 degrees Celsius. Note that this class refers to a climatic rather than a positional condition.
A scrubland which is located in a desert.
A cropland ecosystem which is undergoing climactic ecological succession.
A village biome is an anthropogenic terrestrial biome which contains settlements such as villages, towns, and/or small cities and which is primarily used for agricultural activity.
Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined.
A rangeland biome is an anthropogenic terrestrial biome which is primarily used for the rearing and grazing of livestock.
A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use.
A coniferous forest biome which includes communities adapted to subpolar conditions.
A subpolar condition is an environmental condition in which an environmental system receives low, yearly solar irradiance per unit area and is surrounded by large land masses. This results in very cold winters with temperatures potentially falling to around -40 degrees Celsius and summers which last no more than 3 months of the year with a 24-hour average temperature of at least 10 degrees Celsius.
Note that this class refers to a climatic rather than a positional condition.
A system which has the disposition to environ one or more material entities.
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
Water vapour is a vapour which is the gas phase of water.
Perhaps a better relation between water vapour and water can be found in or added to RO?
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
Atmospheric water vapour is water vapour that is part of an atmosphere.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO.
Water ice can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance. When speaking about ice on Earth, usually water ice is meant - the solid, crystalline form of water found in the atmosphere as snow crystals, hail, ice pellets, etc., and on the earth's surface in forms such as hoarfrost, rime, glaze, sea ice, glacier ice, ground ice, frazil, anchor ice, etc. This form of water is, strictly speaking, called ice Ih, the Roman numeral I distinguishing it from more than a dozen other phases and the letter h distinguishing it from the metastable cubic phase ice Ic. Ice Ih is the only one of the several known phases of water ice that is stable at commonly occurring temperatures and pressures. (Some of the other forms have very unusual properties, ice VII, for example, being stable only at pressures above 22 400 kg/cm^2, but then existing at temperatures up to about 100C.) It has an open structure with a specific gravity of 0.9166 which is slightly less than water; because the water molecules bond to their neighbors covalently only in four directions; it therefore floats on higher density water, where broken molecular bonds permit closer packing. All commonly occurring forms of ice are crystalline, although large single crystals are relatively rare except in glaciers. The ice crystal lattice possesses hexagonal symmetry that manifests itself in the gross forms of such single crystals as are sometimes found in snow. At an air pressure of one atmosphere, ice melts at 0 C by definition of the Celsius temperature scale. (Strictly speaking the equilibrium point among water, ice, and vapor occurs at +0.01C, the triple point.) On the other hand, ice does not invariably form in liquid water cooled below this temperature; it has a tendency to supercool, more so in the absence of ice nuclei. In permafrost regions, ice may occupy voids in soils and rocks and may develop in a variety of forms. Ice may be colourless to pale blue or greenish-blue. It may appear white due to included gas bubbles; in exposures, ground ice may also appear black. In nature ice is formed either by: (a) the freezing of water, (b) the condensation of atmospheric water vapour direct into ice crystals, (c) the compaction of snow with or without the motion of a glacier, or (d) the impregnation of porous snow masses with water which subsequently freeze.
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories.
A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material.
Note that this class does not contain metalimnion as a subclass. The metaliminon is classified as a thermocline.
Class should be populated by inference and asserted subclasses redistributed.
A layer that is part of a marine water body.
An endolithic environment is an environment that exists within solid rock.
An environmental system which has its properties and dynamics determined by saline water.
An environment which has a lower temperature than some local or global average.
The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes.
An acidic environment is an environment in which material entities are exposed to a low pH.
An environment whose dynamics are strongly influenced by water.
A rocky slope is a slope which has a surface primarily composed of rock.
A marine environment and enviroment which is determined by a marine water body.
An environmental system determined by seawater.
The atmospheric boundary layer is the lowest layer of an atmosphere which is strongly influenced by its contact with a planetary surface with strong vertical mixing and in which physical quantities such as flow velocity, temperature, and moisture display rapid fluctuations (turbulence).
A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space.
a useful class: this can be used to define sub-terrestrial and sub-marine entities
A layer in a water mass, itself composed primarily of water.
This class will eventually be populated by inference, and its asserted subclasses removed.
A dome swamp is a swamp which occurs in a depression where deeper waters at the centre of the swamp allow trees to grow taller relative to those in shallower regions of the depression. This creates a dome-like shape.
The logical def should be improved with the idea of a vegetation unit growing in a depression expressed.
An understory is a layer of plant life which grows below the canopy without penetrating it.
A shrub layer is a layer of vegetation in a woodland or forest consisting of low, woody vegetation of frutescent form.
A herb and fern layer is a layer of a forest or woodland which is composed of all vascular plant life that are one metre or less in height.
This definition is inclusive of non-herbaceous plants that may be transiently present in the "herb layer". See Gilliam FS (2007) The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems. BioScience. 57(10):845-858. (http://dx.doi.org/10.1641/B571007) for rationale and a review of definitional and terminological variation.
A biome which is subject to polar climatic conditions.
This class is primarily for inference and, in general, should not be used directly by annotators. If you're an annotator, please consider using a more informative term such as 'tundra biome'.
An altitudinal condition which inheres in a bearer by virtue of the bearer having a monthly mean temperature is less than 10 degrees Celsius and being located at altitudes above the tree line and below the snowline.
Requested term with preliminary def. See Issue 29 on the envo tracker.
An altitudinal condition which inheres in a bearer by virtue of the bearer being located at an altitude between mid-altitude forests and the tree line.
The exact level of the tree line varies with local climate, but typically the tree line is found where mean monthly soil temperatures never exceed 10.0 degrees C and the mean annual soil temperatures are around 6.7 degrees C. In the tropics, this region is typified by montane rain forest (above 3,000 ft) while at higher latitudes coniferous forests often dominate.
An altitudinal condition is an environmental condition in which ranges of factors such as temperature, humidity, soil composition, solar irradiation, and tree density vary with ranges in altitude.
Depending on the latitude (and, to a lesser extent, other factors), the actual location of the zones where these conditions are in effect will change.
An organic material primarily composed of a portion of plant root.
Requested in Issue 115 as part of the annotation of metagenomic submissions present in the European Nucleotide Archive.
This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass.
A layer which is determined by a form of vegetation.
A portion of acidic water is a portion of water with a pH less than 7.
An evergreen needleleaf forest which is subject to temperate climate patterns.
This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000).
A deciduous broadleaf forest which is subject to temperate climate patterns.
A deciduous needleleaf forest which is subject to temperate climate patterns.
A temperate mixed forest which has communities of trees composed primarily of species with broad leaves.
This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed needleleaf forest" class can be made.
A temperate mixed forest which has communities of trees composed primarily of species with needle-like leaves (e.g. conifers).
This class corresponds to the "Temperate Mixed broadleaf / needleleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "temperate mixed broadleaf forest" class can be made.
A sclerophyllous forest which is subject to temperate climate patterns.
A broadleaf evergreen forest which is subject to temperate climate patterns.
A freshwater swamp forest which is subject to temperate climate patterns.
This class is one of the forest types as identified by the updated Global Forest Map (GFM 2000). It is currently unclear how to relate forests and swamps.
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A whole plant which is relatively young.
A house is a building that provides a dwelling-place for a living entity.
The provisioning of a dwelling-place can perhaps be modelled as a role.
A human house is a house which provides a dwelling-place for humans.
A building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls.
A forest biome which contains densely packed populations or communities of broadleaf trees, strongly limiting light penetration to the forest floor.
A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending.
A forest ecosystem which contains densely packed populations or communities of broadleaf and coniferous trees, strongly limiting light penetration to the forest floor.
A class created to group GFM 2000 terms by the dominant vegetation type. Definitions pending. The subclasses of this class need to be checked: are they properly placed under other classes or is this corrected and the dominant form of mixed vegetation noted in the label?
A concrete masonry unit is a large, rectangular masonry unit primarily composed of concrete.
A masonry unit is a solid piece of material, usually with a regular shape, used as a component in the construction of buildings. Masonry units are usually composed of brick, stone, marble, granite, travertine, limestone, cast stone, concrete block, glass block, stucco, tile, or cob.
Concrete is a composite material composed of an aggregate bonded together with a fluid cement which hardens over time.
Missing the class for "aggregate" - tricky to define what it is, exactly. Again, seems more like some sort of material/disposition hybrid.
Masonry cement is a substance used in construction that has the disposition to set and harden and thus may be used to bind materials together.
"Cement" refers more to a disposition than a specific material.
Building walls are bulding parts which serve to support roofs, floors and ceilings; enclose a space as part of the building envelope; give buildings form; and to provide shelter and security.
This is a building part and not the same as a standalone wall, which is a building in its own right.
An exterior wall is a building wall which separates the interior of a building from the buildings surrounding environment.
A building envelope is a building part composed of those building parts which physically separate the interior of a building from its surrounding environment. The building envelope provides resistance to air, water, heat, light, and noise transfer. The three basic elements of a building envelope are a weather barrier, air barrier, and thermal barrier.
A ceiling is an overhead interior surface that covers the upper limit of a room. It is not generally considered a structural element, but a finished surface concealing the underside of the floor or roof structure above.
A roof is the covering on the uppermost part of a building which provides protection from animals and weather, notably rain, but also heat, wind and sunlight. A roof is also the framing or structure which supports the covering
This class is meant to represent roofs which are parts of buildings, rather than a roofs of cave and other natural formations.
A portion of brick material is a material derived from a brick which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete that has been fire-hardened or air-dried.
A brick is a masonry unit which is composed of kneaded clay-bearing soil, expanded clay aggregate, sand and lime, or concrete material, fire-hardened or air-dried.
Generally used to refer to the masonry unit rather than a material.
A brick exterior wall is an exterior wall that is built from bricks.
A concrete exterior wall is an exterior wall that is composed primarily of concrete.
An iron sheet is a mass of iron which has been forged into a roughly planar form of less than 6 millimetres in thickness.
A sheet-iron building roof is a building roof that is built from sheets of iron.
An asbestos building roof is a building roof that is built from asbestos.
asbestos exists in CHEBI and will be imported to complete this class' logical def.
A tile is a manufactured piece of hard-wearing material such as ceramic, stone, metal, or even glass, generally used for covering roofs, floors, walls, showers, or other objects such as tabletops. Alternatively, tile can sometimes refer to similar units made from lightweight materials such as perlite, wood, and mineral wool, typically used for wall and ceiling applications.
A tile building roof is a building roof that is built using tiles.
A fixture which is used primarily for the collection and, in some cases, disposal of human urine and feces.
"disposal" may not be the most precise way to describe fill-in latrines. Note that no assertion is made on whether these fixtures are in- or outdoors.
A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another.
The layer of the atmosphere which is sandwiched between the troposphere and mesosphere. Of the energy that reaches the Earth from the sun, only 3% is absorbed in the stratosphere, but that includes the vitally important process of absorption of ultraviolet radiation by the stratospheric ozone layer. The stratosphere is cloudless and dust free, and almost unaffected by the turbulent conditions of the underlying level of the atmosphere. (Source: WRIGHT)
Definition from GEMET - will be refined.
The mesosphere is part of the earth's atmosphere which is between the stratosphere and the thermosphere in which temperature decreases with altitude to the atmosphere's absolute minimum
The lowest of the concentric layers of the atmosphere, occurring between the Earth's surface and the tropopause. It is the zone where atmospheric turbulence is at its greatest and where the bulk of the Earth's weather is generated. It contains almost all the water vapour and aerosols and three-quarters of the total gaseous mass of the atmosphere. Throughout the troposphere temperature decreases with height at a mean rate of 6.5°C/km and the whole zone is capped by either an inversion of temperature or an isothermal layer at the tropopause. (Source: WHIT)
The thermosphere is a part of the earth's atmosphere that begins at about 50 miles (80 kilometers) above the earth's surface, extends to outer space, and is characterized by steadily increasing temperature with height
This could be made into an inferred class, rather than having asserted subclasses.
atmospheric layer
A boundary layer is a layer of fluid in the immediate vicinity of a bounding surface where the effects of viscosity are significant enough to distort the surrounding non-viscous flow.
boundary layer
A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails.
motor vehicle
A vehicle is a mobile machine which transports people or cargo.
vehicle
A motor is a machine designed to convert one or more forms of energy into mechanical energy.
motor
A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow.
lentic water body
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
"process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog)
hydrological condensation process
planetary landmass
Adpated from https://en.wikipedia.org/wiki/Planetary_surface
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
outer space
A planetary crust is the outermost solid shell of a rocky planet or natural satellite, which is chemically distinct from the underlying mantle.
This class is meant to be applicable accross planets. Earth's crust would be an instance.
planetary crust
A planetary structural layer is laminar part of a terrestrial planet or other rocky body large enough to have differentiation by density. Planetary layers have differing physicochemical properties and composition.
Label should be improved to match definition.
planetary structural layer
A planetary mantle is a planetary layer which is an interior part of a terrestrial planet or other rocky body large enough to have differentiation by density.
This class is meant to be applicable accross planets. Earth's mantle would be an instance.
planetary mantle
A lithosphere is the outermost shell of a terrestrial-type planet or natural satellite that is defined by its rigid mechanical properties.
Earth's lithosphere includes the crust and uppermost mantle.
lithosphere
A settlement with a high density of buildings and inhabitants.
See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx
The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.
dense settlement
A role that is realized in some process wherein the bearer is discarded or not utilized further.
waste role
A geological fracture is any separation in a geologic formation, such as a joint or a fault that divides a mass of rock into two or more pieces.
geological fracture
A geological fault is a planar fracture or discontinuity in a volume of rock, across which there has been significant displacement as a result of rock mass movement.
The relationship between faults and active plate boundaries must be further developed, as there is some overlap.
geological fault
An active fault is a fault that is likely to become the source of another earthquake sometime in the future. Geologists commonly consider faults to be active if there has been movement observed or evidence of seismic activity during the last 10,000 years.
active geological fault
Contaminated air is air which has sufficient concentrations of environmental pollutants such that it may adversely affect a given ecosystem.
contaminated air
An earthquake is a process during which energy is released in an astronomical body's crust, causing the displacement of crustal parts and the generation of seismic waves.
Elastic strain, gravity, chemical reactions, or even the motion of massive bodies can produce earthquakes.
earthquake
Adapted from URL:http://www.britannica.com/science/earthquake-geology
An earthquake caused by the sudden release of energy accumulated in an astronomical body's crust, as the elastic strain placed on constituent rock masses causes them to fracture.
tectonic earthquake
A lake which has concentrations of environmental contaminants high enough to harm the ecosystems associated with it.
polluted lake
water mass
A coast is the area where land meets the sea, ocean, or lake.
Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore'
coast
A tsunami is a process during which a series of waves is generated in a water body, typically an ocean or large lake, by the displacement of a large volume of water. Earthquakes, volcanic eruptions and other underwater explosions (including detonations of underwater nuclear devices), landslides, glacier calvings, meteorite impacts and other disturbances above or below water all have the potential to generate a tsunami.
tsunami
A material transport process during which a geological surface shifts downward relative to a datum such as sea-level.
geological subsidence
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
Desublimation is a process in which a portion of some gas undergoes a phase transition into a portion of some solid.
desublimation process
An environmental system which can sustain and allow the growth of an ecological population.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
A process in which natural ecosystems present over an expanse of land are removed and replaced with anthropogenic ecosystems.
An SDGIO request. Likely to be refined and revised. This looks like an aggregate class, subsuming a range of processes which can lead to degradation.
These anthropogenic ecosystems may include urban or other built-up settlements or anthropogenic ecosystems used for activities such as forestry or agriculture.
land consumption process
Adapted from EEA (1997) The concept of environmental space, Copenhagen, URL: http://www.eea.europa.eu/publications/92-9167-078-2/at_download/file
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
human dwelling
https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015
An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
The range of entities that are considered "barren land" are not exhaustive, making axiomatisation risky at this stage.
According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition.
area of barren land
A part of an astronomical body which is primarily composed of a continuous volume of gaseous or aerosolised material held in shape by one or more environmental processes.
This may not need to be in the atmosphere, also note that "meteor" will do much of the same work.
Similar, in spirit, to landform. This class may need to be split into aerosols and 'pure' volumes of gas.
aeroform
A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
This class may be split. "urban village" doesn't sit well and prevents relations to village biomes.
village
The system of public works in a country, state or region, including roads, utility lines and public buildings.
We label this as 'public infrastructure', as the OECD definition refers specifically to public constructed features. The parts of public infrastructure are not exhaustive and should be extended as needed.
public infrastructure
A building which is publically accessible.
Created for SDGIO, we treat "public" as "publically accessible" where the semantics of access are dealt with in SDGIO.
public building
A planned process during which a portion of environmental material is removed from a material entity.
Created for SDGIO and intended to be a more general form of resource extraction process.
material extraction process
A process whereby a large volume of gas moves due to a disequilibrium of physical forces.
This class refers to all forms of "wind": from the familiar movement of air in the Earth's atmosphere to the solar wind. Use a subclass to be more precise.
mass gaseous flow
A mass gaseous flow which occurrs in a planet's atmosphere due to internal pressure disequilibria.
atmospheric wind
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gaseous environmental material
A material entity which is composed of a volume of unbound positive and negative particles in roughly equal numbers, conducts electricity, and possesses internal magnetic fields.
An NTR for `quality of a plasma` has been posted on the PATO tracker: https://github.com/pato-ontology/pato/issues/88
plasma
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
A planet is an astronomical body orbiting a star or stellar remnant that is massive enough to be rounded by its own gravity, is not massive enough to cause thermonuclear fusion, and has cleared its neighbouring region of planetesimals.
Considerable debate on the definition of planet exists.
planet
An astronomical object which is composed primarily of luminous plasma held in a spherical form by gravitational forces.
Add qualities such as spherical. Request NTRs if not available in PATO.
star
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
A material part of an astronomical body.
Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension.
Note that material entities may have immaterial entities (e.g. sites) as parts.
This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed.
Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.
astronomical body part
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
This is a defined class: most of its subclasses will not be asserted, but filled by inference.
liquid environmental material
An astronomical body part which includes all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
An astronomical body part which is composed of the combined mass of water found on, under, and over the surface of a planet.
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
hydrosphere
An astronomical body part which is composed of soil, subject to soil formation processes, and found on the surface of a lithosphere.
pedosphere
Air which has increased levels of water vapour.
humid air
Air which has a partial pressure of water vapour equal or near equal to its equilibrium vapor pressure at a given temperature.
"Near equal" is meant to reflect that there will be fluctuations around the equilibrium point.
water vapour saturated air
A hydrological precipitation process in which atmospheric water vapour condenses to form droplets of liquid water massive enough to fall to a planetary surface due to the planet's gravity.
This is the process which typically happens on Earth. Other planets may have different liquids involved in the process.
water-based rainfall
A droplet is a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid.
No attempt is made to differentiate between drops and droplets. This may be added, if requested.
droplet
A droplet formed by condensation of vapour in an atmosphere and which is sufficiently massive to overcome atmospheric resistance and fall to a planetary surface due to gravity.
raindrop
A defined class which should be filled by inference.
water droplet
This is the class intended for use when describing raindrops on Earth. These typically have a diamter of 0.1 to 9 millimetres.
water raindrop
A solid material whose constituents, such as atoms, molecules or ions, are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions.
This class refers to a portion of crystal and not an individual crystal.
crystal
A crystal which is primarily composed of water ice.
Any one of a number of macroscopic, crystalline forms in which ice appears, including hexagonal columns, hexagonal platelets, dendritic crystals, ice needles, and combinations of these forms. The crystal lattice of ice is hexagonal in its symmetry under most atmospheric conditions.
water ice crystal
A marginal sea biome which is located in a region with a temperate climate.
A component of the WWF Temperate Shelf and seas ecoregions grouping
temperate marginal sea biome
A marine biome which contains communities adapted to living in an environment determined by an upwelling process.
marine upwelling biome
A marine upwelling biome which is located in a region subject to temperate climate patterns.
temperate marine upwelling biome
An area of a planet's surface which is primarily covered by a shrubs, young trees, or stunted trees.. The surfaces of this area are in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
As noted in Wikipedia: "Because the criteria are matters of degree rather than of kind, the definition of a subshrub is not sharply distinguishable from that of a shrub"
According to the NLCD 2011, areas of scrub or shrub are dominated by shrubs; less than 5 meters tall with shrub canopy typically greater than 20% of total vegetation. This class includes true shrubs, young trees in an early successional stage or trees stunted from environmental conditions. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of scrub
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
An area of a planet's surface which is primarily covered by cultivated or anthropically maintained vegetation planted for recreation, erosion control, or aesthetic purposes interspersed by constructed or manufactured objects and materials. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
This class is in need of refinement, particularly in linking to other entities in the ontology. This would be helped by more clear listings of entities included in this classification. However, the class is suitable for use in annotating remotely sensed land types.
According to the NLCD 2011, areas of developed open space are dominated by vegetation such as lawn grasses and include large-lot single-family housing units, parks, golf courses. Further, it is asserted that "impervious surfaces", most likely referring to concrete and related substances, cover less than 20% of the area. Such thresholds - which are themselves fuzzy - are not asserted in this definition.
area of developed open space
An area of a planet's surface which is primarily covered by sedges or forbs, possibly interpersed with grasses or grass-like plants. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
This class is in need of refinement, particularly in linking to other entities in the ontology. However, it is suitable for use in annotating remotely sensed land types.
According to the NLCD 2011, at least 80% of these areas are covered by sedge or forbs. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that land covered by sedge tundra and sedge tussock tundra are subsumed in this category. The original definition notes that this is intended as an "Alaska only" category.
area of sedge- and forb-dominated herbaceous vegetation
An area of a planet's surface which is primarily covered by gramanoid or herbaceous vegetation and which is not subject to intensive management by humans. This area is in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction.
According to the NLCD 2011, at least 80% of these areas are covered by grasslands or non-woody, herbaceous plants. Such thresholds - which are themselves fuzzy - are not strictly asserted in this definition. The NLCD description also notes that, while no "intensive" management such as tilling is performed in these areas, they may be used for grazing.
area of gramanoid or herbaceous vegetation
A hydrological process in which irregular aggregates of snow fall to the surface of an astronomical body.
This is currently bound to water-based snow on Earth, may need revisions for interplanetary applications
snowfall
A human house which serves as a long-term shelter for its inhabitants and within which they store personal property.
This is under "human house" due to the broad definition of "house".
This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays.
residential building
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
A process during which a natural environmental system is altered by human action.
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A planet that is composed primarily of silicate rocks or metals.
terrestrial planet
A manufactured product which is designed to catch and hold animals.
animal trap
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
This class can refer to the flow of any material in a liquid phase.
mass liquid flow
A material transport process during which a volume of liquid water is transported due to a disequilibria in physical forces.
water flow process
A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body.
technosphere
An exchangeable device which can be connected to a plumbing system to deliver and drain water.
plumbing fixture
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
manufacturing process
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
The nature of "structures" must be further specified.
human-directed construction process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump).
environmental system determined by a material
An environmental system which is determined by a living organism.
environmental system determined by an organism
An environmental system determined by a green plant.
plant-associated environment
An environmental system determined by an animal.
animal-associated environment
A meteor is any matter- or energy-based entity which is located in the atmosphere of an astronomical body.
meteor
A meteor which is primarily composed of water.
hydrometeor
A meteor which is primarily composed of rock.
lithometeor
A lake which has formed as the result of processes that are not or are only minimally driven by human activity.
This class is to be filled by inference.
natural lake
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions).
radiation
A radiation process during which energy is transmitted or emitted by means of fast-moving subatomic particles.
particle radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
Note that this class is concerned only with active radiative processes: static electric and magnetic fields are not inlcuded. All electromagnetic radiation carries radiant energy.
electromagnetic radiation
An environment which is determined by materials which bear significant concentrations of salts.
The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request.
saline environment
An environmental system which has its properties and dynamics determined by soil.
soil environment
An environmental system which has its properties and dynamics determined by sediment.
sediment environment
An environmental system which has its properties and dynamics determined by an aerosol.
aerosol environment
An environmental system which has its properties and dynamics determined by a saline aerosol.
saline aerosol environment
seaspray or other aerosolized saline material (>5 psu)
An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes.
non-saline aerosol environment
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with an animal part or small animal
An environmental system determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
An astronomical body which is composed of rocky or metallic materials and is considerably smaller than asteroids.
meteoroid
A material which is composed primarily of one or more pure metals and which shows their properties.
Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
A process during which microscopic solid or liquid objects are formed.
particulate matter formation process
An aerosol formation process which occurs in an atmosphere.
atmospheric aerosol formation
A process during which an aerosol, consisting of solid particulates suspended in a gas, is formed in an atmosphere.
formation of solid particles in an atmosphere
formation of a solid aerosol in an atmosphere
A process during which an aerosol, consisting of droplets of liquid suspended in gas, is formed in an atmosphere.
formation of liquid droplets in an atmosphere
formation of liquid particles in an atmosphere
formation of a liquid aerosol in an atmosphere
An aerosol which has non-gaseous parts that are primarily composed of liquid droplets.
aerosolised liquids
An aerosol which has non-gaseous parts that are primarily composed of solid particles.
aerosolised solids
A process during which microscopic solid particulates are formed from gaseous materials in an atmosphere.
atmospheric formation of a solid aerosol
formation of a solid aerosol in the atmosphere
formation of solid particles from gaseous material in an atmosphere
formation of a solid aerosol from gaseous material in an atmosphere
A process during which microscopic liquid droplets are formed from gaseous materials in an atmosphere.
atmospheric formation of a liquid aerosol
formation of a liquid aerosol in the atmosphere
formation of liquid droplets from gaseous material in an atmosphere
formation of liquid particles from gaseous material in an atmosphere
formation of a liquid aerosol from gaseous material in an atmosphere
A process during which pieces of a planetary crust and uppermost mantle move.
tectonic movement
A part of a lithosphere which is separated by other such parts by geographic faults or similar geomorphological discontinuities.
tectonic plate
A geomorphological feature which is formed where two or more tectonic plates move towards, away from, or along one another, resulting in deformation of the lithosphere.
tectonic plate boundary
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
Organic material which is primarily composed of plant structures, living or dead.
plant matter
A planet which is primarily composed of hydrogen and helium.
Gas giants are composed of about 90% hydrogen and helium. Jupiter and Saturn are examples of gas giants.
gas planet
An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.
ice
A planet which has a surface layer that nearly completely or completely covered by water, and which has a substantial portion of its mass composed of water.
An axiom to express that the planet has a 'substantial' proportion of its mass in the form of water wound enhance this class.
While this planetary form is still mostly theoretical, strong candidates exist such as the extrasolar planet GJ 1214 b and ocean planet candidate Kepler-22b.
ocean planet
A planet which has a surface layer that nearly completely or completely covered by ice, and which has a substantial portion of its mass composed of ice.
While this planetary form is still mostly theoretical, strong candidates exist such as OGLE-2005-BLG-390Lb, OGLE-2013-BLG-0341L b and MOA-2007-BLG-192Lb. Pluto was considered an ice planet until its reclassification in 2006 CE. Surface temperatures of ice planets would have to be below 260 K (−13°C) if composed primarily of water, below 180 K (−93°C) if primarily composed of CO2 and ammonia, and below 80 K (−193°C) if composed primarily of methane.
ice planet
Ice which is primarily composed of carbon dioxide.
carbon dioxide ice
A gas planet which has an atmosphere composed primarily of helium.
The placement of this class assumes that some traces of hydrogen are left in the atmosphere. If this is not the case, the axiom on gas planet must be updated.
A helium planet might form via hydrogen evaporation from a gaseous planet orbiting close to a star. Low-mass white dwarfs may transition into objects which are essentially helium planets by hydrogen depletion through mass transfer to a massive object such as a neutron star. Gliese 436 b is a candidate helium planet.
helium planet
A material which is composed primarily of chemical elements and compounds with relatively low boiling points, equilibrium condensation temperatures below 1300 Kelvin, and which are part of the crust or atmosphere of a moon or planet.
Add and axiomatise with moon and lunar crust
Examples include nitrogen, water, carbon dioxide, ammonia, hydrogen, methane and sulfur dioxide. In astrogeology, these compounds, in their solid state, often comprise large proportions of the crusts of moons and dwarf planets.
volatile astrogeological material
An astrogeological volatile which is composed primarily of chemical compounds with boiling points around those of hydrogen and helium.
This is a term native to the fields of planetary science and astrophysics. Hydrogen has a boiling point of 20.271 Kelvin and a melting point of 13.99 Kelvin. Helium has a boiling point of 4.222 Kelvin and a melting point of 0.95 Kelvin.
astrogeological gas
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
An ecosystem which has been causally isolated from a larger ecosystem within which it was previously embedded, such that the direct exchange of materials, resources, and energy between these systems is severely or entirely curtailed.
Often, ecosystem fragments are unable to sustain themselves without human intervention and management as they are not large enough to perform self-sustaining functions (e.g. nutrient recycling) or hold sufficient ecological resources such as genetic diversity of populations.
ecosystem fragment
A process during which one or more parts of an ecosystem become causally isolated such that the direct flow or exchange of materials, resources, and energy between a given fragment and the remainder of the original system is severely curtailed or entirely halted.
ecosystem fragmentation process
A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective.
Umweltmaßnahme
active ecosystem management process
An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system.
environment associated with an aquatic invertebrate
Not currently live, may need to be switched to alternative PURLs.
Soil which has increased levels of molecules or ions capable of donating a hydron (proton or hydrogen ion) to other chemical entities, or, alternatively, capable of forming covalent bonds with other chemicals via the acceptance of an electron pair, resulting in a bulk pH measurement of less than 7.
acidic soil
This class will be axiomatised with "alga" once an approach to handle this term's ambiguous semantics has been agreed with PCO.
An organic material which is primarily composed of living or dead algae, along with their exudates.
algal material
water surface
The surface layer of a mass of sediment.
sediment surface
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities.
anthropised terrestrial environmental zone
A process during which sediments compact under pressure, expel connate fluids, and gradually become solid sedimentary rock.
lithification
An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics.
grassland ecosystem
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
wetland ecosystem
A planned process during which an environmental system is modified to mitigate or nullify the impacts of flooding.
defence against flooding
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a star.
stellar radiation
A process during which liquid water accumulates in a site, most often in some form of container.
water accumulation process
A commercial building which contains parts used as workplaces primarily for administrative and managerial workers.
"An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets."
office building
A building which is primarily used to facilitate the buying or selling of goods or services.
"Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally."
commercial building
A building part within which administrative work is done by an organisations users in order to support and realise the objectives of that organization.
office
A natural environment which is located on a land mass.
terrestrial natural environment
A natural environment which is within a water body.
aquatic natural environment
forest canopy
A canopy which is part of a woodland ecosystem.
woodland canopy
A canopy which is composed of the aboveground portion, or crowns, of a community of crop plants.
crop canopy
A vegetation layer which is formed by a collection of individual plant crowns, themselves constituting part of the aboveground portion of a plant community.
canopy
An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover.
The correct usage of FLOPO terms in the axiomatisation needs to be confirmed.
forest ecosystem
An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement.
cropland ecosystem
An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities are spaced sufficiently far apart to allow sunlight to illuminate the understory.
Woodland understories are often populated with communities of shrubs and herbaceous plants including grasses. There are varying distinctions between woodland and forest, with a large degree of ambiguity.
woodland ecosystem
A process during which humans rear animals or plants on land for harvest and consumption.
Expand the sites of occurrence listed as axioms as new terms emerge.
agricultural process
A layer which is primarily composed of some liquid material.
liquid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
A solid layer which is primarily composed of some water-based ice.
water ice layer
A vegetated area which has not been cleared or is sparsely settled, usually scrub-covered or forested
"Bush" is a rather loosely defined regional term, primarily used in Australia.
bush area
An environmental zone which is part of an atmosphere.
atmospheric zone
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
A liquid astronomical body part which is primarily composed of a continuous volume of liquid water and is held in shape or sustained by an environmental process.
Should create links to envrionmental process with new relation like "sustained_by"
A liquid surface layer which is in contact with air.
liquid air-water interface layer
A surface layer which is composed primarily of some liquid.
liquid surface layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A body of water which is primarily composed of saline water.
This class has its subclasses populated by inference.
saline water body
A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged.
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
A water flow process during which movements of water masses caused by varying gravitational and rotational forces from astronomical bodies, combined with the rotation of the astronomical body containing the water mass, cause waters to undergo periodic depth oscillations (tides).
tidal flow process
An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited.
erosion
A landform which has been rendered barren or partially barren by environmental extremes, especially by low rainfall, and which loses more liquid water by evapotranspiration than is supplied by precipitation.
desert
A process during which particles suspended in a gaseous medium are formed.
aerosolised particle formation process
A material transport process during which solid or liquid particles are directly introduced into a volume of gas.
primary aerosol formation process
An organic environmental material which is primarily composed of gill tissue.
gill tissue material
An anthropogenic environment which is bounded by the building envelope of a laboratory and in which a system of manufactured products exert control on one or more of its environmental conditions.
laboratory environment
A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed.
research laboratory
laboratory facility
An anthropisation process during which terrestrial environments - natural or anthropised - or parts thereof are altered to facilitate human activities such as agriculture, settlement, or commerce.
Further examples include subdividing real estate into lots, typically for the purpose of building homes and converting unused factories into condominia.
land conversion process
A land conversion process during which terrestrial ecosystems are altered to facilitate agricultural activities such as crop cultivation or the rearing of livestock.
This process typically relies on the conversion and development of forests, savannas or grassland. Creation of farmland from wasteland, deserts or previous impervious surfaces is considerably less frequent because of the presence of degraded soil or the lack of fertile soil.
agricultural land conversion process
An anthropogenic environmental process which includes all human activities undertaken in a natural, semi-natural, or anthropised environment.
There are multiple systems of land use classification. This hierarchy aims to be generally applicable, but national systems can be added on request.
land use process
A land use process during which materials of economic value are extracted from a planet, usually from an orebody, lode, vein, seam, reef or placer deposit.
terrestrial mining
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
A planned environmental usage process during which a non-renewable resource such as petroleum, natural gas, or water is extracted from an ecosystem.
mining
A mining process which occurs in a marine ecosystem.
marine mining
A mining process during which coal is extracted from the rocky portion of an astronomical body.
This may be either terrestrial or marine.
coal mining
A planned environmental usage process during which an environment facilitates the movement of materials and material objects (persons or goods) from place to place, typically with the assistance of a vehicle.
usage of an environment for transportation
A planned environmental usage process during which an environment supports 1) enterprises concerned with the provision to the public of essentials, such as electricity or water or 2) the basic network or foundation of capital facilities or community investments which are necessary to support economic and community activities.
usage of an environment for infrastructure and utilities
A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans.
This class does not include environments which are primarily used for commerce or industry.
usage of an environment for residential activity
A planned environmental usage process during which an environment supports manufacturing facilities producing commodities that are sold with the expectation of recovering the total cost of production.
This class includes environments used to support the facilities engaged with a broad variety of manufacturing activities from food and tobacco, to textiles, metals, vehicles, and chemicals.
usage of an environment for industry
A planned environmental usage process during which an environment supports facilities associated with commerce or the earning of a livelihood through means other than manufacturing or the provision of a public service.
This class includes activities carried out in commercial offices, meeting centres, art studios, recording studios, film sets, warehouses, and distribution centres.
usage of an environment for business
A liquid astronomical body part which is continuous and is delimited by physical discontinuities or non-liquid boundaries.
body of liquid
A part of an astronomical body which is primarily composed of liquid material.
liquid astronomical body part
A part of an astronomical body which is primarily composed of gaseous material.
gaseous astronomical body part
A part of an astronomical body which is primarily composed of fluid.
fluid astronomical body part
A building which is primarily used for the long-term habitation of humans.
domestic building
A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space.
land surface
surface of an astronomical body
A vehicle which is able to travel through air in an atmosphere.
aircraft
An elevation which is flattened across its highest surface.
flattened elevation
A pollution process during which artificial light with wavelengths in the visible spectrum is released into the environment.
Lichtverschmutzung
This form of pollution is typically the result of urbanisation or similar land use change.
anthropogenic light pollution
An electromagnetic radiation process during which electromagnetic waves or their quanta are emitted from a manufactured product.
radiation from a manufactured product
Radiation from a manufactured product during which light between the wavelenghts of 380 nm and 760 nm is emitted.
optical radiation from a manufactured product
visible spectrum radiation from a manufactured product
A material transformation process during which a material's viscosity increase either through a reduction in temperature, through chemical reactions, or other physical effects.
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
Land which is below the freezing point of water.
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
frozen land
Soil which is below the freezing point of water.
frozen soil
A material congelation process during which a liquid turns into a solid when its temperature is lowered below its melting point.
freezing
A freezing process during which liquid water is transformed into water ice.
freezing of water into water ice
A water surface that is part of a water body.
surface layer of a water body
An aggregate of raindrops falling to a planetary surface during a precipitation process.
rain
Rain which is composed of water droplets falling to a planetary surface during a rainfall process.
water-based rain
An ecoregion which is located on a landmass.
terrestrial ecoregion
A surface layer which is part of an ocean or sea.
envoPlastics
At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases. Sea surface layer is also used to refer to the surfaces of oceans.
sea surface layer
A hydroform which is maintained by a continuous, directed movement of water, generated by disequilibria in a water mass.
Depth contours, shoreline configurations and interaction with other currents influence a current's direction and strength.
water current
cryospheric layer
Permafrost which contains inclusions of water-based ice.
ice-bearing permafrost
A material accumulation process during which the mass of snow on a surface increases.
This term is used both as a process and as an amount of mass added. Semantically speaking these are two distinct concepts (e.g., accumulation results in accumulation_amount of ice or snow gain), though accumulation_amount would more likely be an attribute. The scope of this term varies depending on the definition. Some definitions constrain themselves snow or ice added to glaciers; while others also include ice fields, snow cover, and/or floating ice. How to resolve this depends on the scope desired. Some definitions include additional discussion of the the physics involved which would be useful for connecting glacier ontologies to atmospheric, hydrologic, etc. ontologies. This information should be captured no matter how the inconsistencies above are resolved.
snow accumulation process
A material accumulation process during which ice forms in an environmental material or an existing accumulation of ice increases in mass.
ice accumulation process
A material accumulation process during which a accumulation of snow and ice forms or increases in mass.
snow and ice accumulation process
A object which is composed primarily of water-based snow and ice.
mass of ice and snow
A process during which microscopic solid particulates are formed from liquid materials in an atmosphere.
formation of solid particles from liquid material in an atmosphere
formation of a solid aerosol from liquid material in an atmosphere
That part of an atmosphere which is composed of gaseous material.
gaseous part of an atmosphere
A solid material which does not have a regularly organised internal structure.
amorphous solid
An aerosol that is suspended in an atmosphere.
atmospheric aerosol
A material transformation process during which solid or liquid particles form and are suspended in a mass of air, thus creating an aerosol.
aerosol formation process
A surface layer which is composed primarily of some liquid or gas.
fluid surface layer
A surface layer which separates two portions of fluid with respect to either 1) a discontinuity of some fluid property or 2) some derivative of one of these properties in a direction normal to the interface.
fluid interface layer
A layer which is composed primarily of some fluid.
fluid layer
A fluid interface which separates two fluid masses with differing properties.
fluid front
A fluid front which is composed primarily of gaseous material and separates at least two gaseous masses.
gaseous front
A gaseous front which separates two masses of air with different densities and is a principal cause of meteorological phenomena.
This class refers to Earth's weather fronts. Other forms, not composed of air, are present on other planets and can be created on request. Note: "Since the temperature distribution is the most important regulator of atmospheric density, a front almost invariably separates air masses of different temperature. Along with the basic density criterion and the common temperature criterion, many other features may distinguish a front, such as a pressure trough, a change in wind direction, a moisture discontinuity, and certain characteristic cloud and precipitation forms."
weather front
An object which is composed of a continuous mass of air.
air mass
A fluid surface layer which is composed primarily of some gaseous material.
gaseous surface layer
A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface.
interface layer
An object which is composed primarily of an environmental material
This class and its subclasses refer to objects that are discrete accumulations of environmental materials, generally primarily composed of one or a few main material types.
mass of environmental material
An mass of environmental material which is composed primarily of a solid environmental material
mass of solid material
An object which is composed primarily of a fluid.
fluid mass
mass of fluid
An object which is composed primarily of a gas.
gaseous mass
mass of gas
An object which is composed primarily of a liquid.
liquid mass
mass of liquid
An mass of environmental materials which has appreciable quantities of several individual materials, such that the removal of one would convert the mass into a different entity.
mass of compounded environmental materials
A weather front which separates air masses of tropical and polar origin.
envoAtmo
envoPolar
polar front
An environment which has a climate with continually high temperatures and with considerable precipitation, at least during part of the year.
tropical environment
An environment which has a climate with warm temperatures and with meagre precipitation.
subtropical environment
An environment which is located in a part of an astronomical body subject to polar climatic conditions.
polar environment
An environment which is located in a part of an astronomical body subject to subpolar climatic conditions.
subpolar environment
An environment which is located in a part of an astronomical body subject to temperate climatic conditions.
temperate environment
An advective transport process during which a fluid moves.
mass fluid flow
A wind storm during which strong gusts of wind occur, transporting atmospheric gas in a linear fashion.
straight-line wind
A process during which the ability of a material entity to maintain its internal organisation fails, resulting in deformation and a breakdown of that organisation.
This is a very general concept, and should likely be elevated to OBO Core rather than held in ENVO.
structural collapse process
An environmental zone which includes those regions of an astronomical body which are not exposed to its atmosphere or space.
subsurface zone of an astronomical body
An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert.
desert ecosystem
A solid astronomical body part which is part of the landmass of that body.
part of a landmass
A large continuous area of land, either surrounded by sea or contiguous with another landmass.
landmass
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
compound astronomical body part
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
land
aquatic ecosystem
marine ecosystem
An ecosystem which primarily occurs on land.
terrestrial ecosystem
A broadleaf forest which is subject to tropical climate conditions.
tropical broadleaf forest
A broadleaf forest which is subject to temperate climate conditions.
temperate broadleaf forest
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
ecosystem process
A mixed forest which is subject to temperate climatic conditions.
temperate mixed forest
A mixed forest which is subject to tropical climatic conditions.
tropical mixed forest
A tropical mixed forest in which dominant ecological communities have reached their climax successional state.
tropical mixed forest biome
A forest ecosystem which is subject to tropical climate conditions.
This class is primarily to be populated by inference.
tropical forest
A forest ecosystem which is subject to subtropical climate conditions.
subtropical forest
A forest ecosystem which is subject to temperate climate conditions.
temperate forest
A grassland ecosystem which is subject to tropical climatic conditions.
tropical grassland
A grassland which is subject to subtropical climatic conditions.
subtropical grassland
temperate grassland
A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
construction
An object which is formed as a result of one or more biological processes and is composed primarily of organic material.
organic object
An ecosystem process during which the species composition of an ecosystem gradually changes as species which are more adapted to the prevailing conditions in the ecosystem replace those which are less adapted.
ecological succession
An ecological succession process during which 1) organisms in ecological communities possess high adaptation to the conditions in the ecosystem, 2) participant communities largely fill available niches, 3) individual organisms are typically replaced by others of the same species, 4) a near equilibrium is maintained between gross primary production and total respiration and across biogeochemical cycles.
climactic ecological succession
An ecosystem which is formed as a result of human activity or impact.
anthropised ecosystem
An anthropised ecosystem which is determined by the presence of humans and their constructions.
human settlement
A biome which is subject to tropical climatic conditions.
tropical biome
A biome which is subject to temperate climatic conditions.
temperate biome
A biome which is subject to subtropical climatic conditions.
subtropical biome
A biome which is subject to subpolar climatic conditions.
subpolar biome
A biome which is subject to alpine altitudinal conditions.
alpine biome
A biome which is subject to montane altitudinal conditions.
montane biome
A biome which is subject to arid environmental conditions.
arid biome
A process during which one entity loses energy to another entity.
energy transfer process
A material accumulation process during which the volume of liquid entity increases.
liquid accumulation process
An atmospheric wind which 1) has an increased rate relative to other winds in the same region and 2) is followed by a lull.
According to U.S. weather observing practice, gusts are reported when the peak wind speed reaches at least 16 knots and the variation in wind speed between the peaks and lulls is at least 9 knots. The duration of a gust is usually less than 20 seconds.
wind gust
The concentration of carbon dioxide when measured in air that is part of an atmosphere.
concentration of carbon dioxide in an atmosphere
A landform which occurs on the surface of an astronomical body.
geographic feature
The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.
surface landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.
landform
A disposition of a material entity which is realised when it is saturated with liquid water.
water-holding capacity
A mass of solid material which is either 1) a minute fragment of a larger mass or 2) one of a collection of small masses composing an aggregate.
particle
A particle which 1) is composed primarily of hydrous aluminium phyllosilicate minerals, in turn composed of aluminium and silicon ions bonded into tiny, thin plates by interconnecting oxygen and hydroxide ions, and 2) is or was part of a portion of clay.
clay particle
particle of clay
A material transport process which arises spontaneously due to physical heterogeneities in a portion of a material and forces which act throughout its volume.
Most commonly, convective flows are generated by heterogeneities in density or the effects of gravity. When the cause of the convection is unspecified, convection due to the effects of thermal expansion and buoyancy can be assumed. Convection frequently occurs in fluids, but may also take place in soft solids or mixtures where particles can flow.
convective transport process
A physical quality of a process which is characteristic of processes that transport material within a volume due to the combined effects of material property heterogeneity and body forces across that volume.
convective
A physical quality of a process which is characteristic of process that transport material without, themselves, changing the qualities of those materials or the processes that are unfolding within them.
advective
A material transport process during which material moves from a region of higher concentration to a region of lower concentration.
diffusion
Diffusion is also applied to the movement of energy, thus the more specific label. This class will be repositioned (but with the core of its definition intact) if we include other forms of diffusion in ENVO.
material diffusion process
A combustible black or brownish-black sedimentary rock usually occurring in rock strata in layers or veins called coal beds or coal seams.
a type of rock that contains sufficient minerals with important elements including metals that can be economically extracted from the rock.
The primary uranium ore mineral is uraninite
Dust which is derived from mineral material.
Dust which is composed primarily of some metallic material.
Dust which is derived from clay material.
A surface mine that utilizes a technique of extracting rock or minerals from the earth by their removal from an open pit or borrow.
A human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions.
nuclear reactor
A nuclear reactor which is used as a source of power.
nuclear power reactor
An environmental material which is unable to resist shear forces and continuously deforms when subject to them.
fluid environmental material
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A type of land degradation in which terrestrial ecosystem becomes increasingly dry, typically losing its bodies of water as well as vegetation and wildlife.
desertification
A general and temporary condition of partial or complete inundation of normally dry land areas from the overflow of inland and/or tidal waters, and/or the unusual and rapid accumulation or runoff of surface waters from any source. A great flow along a watercourse or a flow causing inundation of lands not normally covered by water.
flooding
GEMET: http://www.eionet.europa.eu/gemet/concept/3301
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
A process which diminishes the functioning of an ecosystem located on land.
An SDGIO request. Likely to be refined and revised.
This could include, for example, reducing soil health, pollinator activity, or an ecosystem's ability to sequester carbon.
Establishment of a new forest by seeding or planting of nonforested land.
Prior to afforestation, the land cover of a region must not include forests.
An ecosystem process during which the flora and fauna belonging to a forest are removed or destroyed.
To be populated through inference. Do not use for annotation.
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
Relabel the obo foundry unique label to be generic process
anthropogenic modulatory intervention process
An environmental process which is driven by the action of humans.
An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited.
An environmental process which has water - in any of its states - as a participant.
This classes asserted subclasses will be moved away as it should be an inferred class.
A planned process during which human agents establish plant communities in ecosystems which have previously been, partially or wholly, stripped of existing plant communities.
An environmental system process that results in the introduction of contaminants into an environment.
Pollutants may be material or immaterial (e.g. heat energy)
A pollution process during which particulates or other contaminants are released into a portion of air.
A pollution process during which contaminants are released into soil.
A pollution process during which contaminants are released into water.
An process in which environmental parameters and variables are continually assayed.
A planned process during which the amount of pollutants released into an environmental system is regulated.
A monitoring process that assays the level of environmental pollutants to determine the presence of effect of environmental pollution.
A physical process during which atoms, molecules, or other consituents of a material entity are forced closer together.
compaction process
A process during which the mass of one or more materials, present within a given site, increases.
Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process.
material accumulation process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
A depression which is part of a planetary crust, is of geographic scale, and is partially or completely enclosed.
The general semantics of depression and geographic basin are still to be worked out see https://github.com/EnvironmentOntology/envo/issues/486
geographic basin
Particulate environmental material which is composed primarily of carbon particles formed through the incomplete combustion of hydrocarbons.
soot
Sediment which has been transported through the marine water column, settling on the seafloor.
Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.
marine sediment
A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface.
sedimentation in a water body
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A desublimation process during which water vapour is frozen into water ice.
desublimation of water vapour into ice
A solid astronomical body part which is primarily composed of a continuous mass of snow and/or ice.
Place holder class. Also the axiom should be changed to something along the lines of 'primairly composed of’ some ‘environmental material’ and ‘has quality’ frozen once PATO:frozen is imported.
cryoform
snow mass
A water-based rainfall process during which water droplets with increased acidity fall towards a planetary surface.
On Earth, the acidity of raindrops is typically increased through interactions of water molecules with sulfur dioxide or nitrogen oxide, released into the atmosphere by natural or anthropogenic processes.
acid rainfall
Water-based rain which has increased acidity.
acidic water-based rain
An astronomical body part which is composed primarily of environmental materials in their frozen form.
For the moment the definition links to liquid water but in the future we might need to link to other materials for other planets, e.g., Mars. Need to make this planet agnostic. Might want to not have the definition link to years as some astronomical body parts might not be in systems with years. Note that in a strict sense, rocks are also frozen but in a practical sense we use terms like "solidified". This maybe something to revist if we add more astrogelogical content.
The term generally refers to the portions of the Earth where water is in solid form, including snow cover, floating ice, glaciers, ice caps, ice sheets, seasonally frozen ground and perennially frozen ground (permafrost). The Cryosphere may be divided into the cryoatmosphere, the cryohydrosphere (snow cover, glaciers, and river, lake and sea Ice) and the cryolithosphere (perennially and seasonally cryotic ground, rock glacier). Some definitions consider the cryosphere to include any area of Earth which is sufficiently cold for pure water to freeze for at least a part of each year. It should be noted that "Some authorities exclude the earth's atmosphere from the Earth's Cryosphere; others restrict the term Cryosphere to the regions of the earth's crust where Permafrost exists." Definitions of Cryosphere come from several glossaries including: - PhysicalGeography.net http://physicalgeography.net/ - van Everdingen, Robert, ed., 2005 (1998 revised May 2005). Multi-language glossary of permafrost and related ground-ice terms. Boulder, CO: National Snow and Ice Data Center/World Data Center for Glaciology. [https://globalcryospherewatch.org/reference/glossary_docs/Glossary_of_Permafrost_and_Ground-Ice_IPA_2005.pdf] - American Meteorological Society, 2015. Glossary of Meteorology [online], Available at: http://glossary.ametsoc.org/wiki/Main_Page. [Accessed 27/01/2017]. - EU Climate-ADAPT (The European Climate Adaptation Platform), no date, Glossary, Available from: http://climate-adapt.eea.europa.eu/glossary - IPCC, 2014: Annex II: Glossary [Agard, J., Schipper, E. L. F., (ed.)]. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Birkmann, J., Campos, M., Dubeux, C., Nojiri, Y., Olsson, L., Osman-Elasha, B., Pelling, M., Prather, M. J., Rivera-Ferre M. G., Ruppel, O. C., Sallenger, A., Smith, K. R., St. Clair, A. L.,]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. [Link] - NSIDC, The National Snow and Ice Data Center glossary is available at https://nsidc.org/cryosphere/glossary, Last accessed [26/01/2016]. - Trombotto, D., P. Wainstein & L. Arenson, 2014, Guía Terminológica de la Geocriología Sudamericana” / “Terminological Guide of the South American Geocryology, 1a ed. 128 pp. [Link] - UNESCO-WMO, 2012, International Glossary of Hydrology, 3rd edition, WMO-No. 385. [Link]
cryosphere
A human construction in which healthcare is provided.
health facility
medical facility
healthcare facility
Any material containing unstable atoms that emit ionizing radiation as it decays.
radioactive material
A water ice crystal which is constituted by water molecules aligned in a hexagonal array.
snowflake
snow crystal
Snow crystals and snowflakes are often noted as synonyms, however, the term "snowflake" is generally used more loosely. Some sites mention that snow crystals refer to individual crystals of ice, while the term "snowflake" can refer both to an individual crystal of ice and to a bundle of snow crystals. Please see here [https://github.com/EnvironmentOntology/envo/issues/998#issuecomment-685649444]
Sediment which contains some chemical contaminant.
See https://github.com/EnvironmentOntology/envo/issues/1102 for a possible design pattern. Uses undesirability standard, compared to polluted river's ecological impact standard. What is the relation to ENVO:00002114 'chemically enriched sediment'? Does 'element' in the definition refer to something found in the periosic table (like selenium) or the member of some set, aka an entity?
chemically contaminated sediment
A human construction which is used to transport a material which is primarily composed of liquid or gas through a system of pipes.
Getting an example of use could be helpful. Are some environmental samples collected from the outside of a pipe or its fittings? Or taken from inside the pipe? Removing "transport" from the label may make the labels of sublasses more readable. However, "pipeline" alone could mean several unrelated things, like software pipelines. https://www.eia.gov/energyexplained/natural-gas/natural-gas-pipelines.php uses the term "pipeline network". ALSO could this be a transport feature? Xref https://github.com/EnvironmentOntology/envo/issues/1111.
Pipeline networks typically materials either from 1) a production area to a market area for consumption, 2) a production area to an area for waste disposal.
pipeline network
A human construction which is used as a storage area for mining tailings.
not placing under 'pond' class becasue contents may not be primarily be composed of water. consider revising 'pond' semantics
tailings pond
The concentration of carbon dioxide when measured in soil.
concentration of carbon dioxide in soil
The concentration of carbon dioxide when measured in air.
concentration of carbon dioxide in air
The concentration of carbon dioxide when measured in seawater.
concentration of carbon dioxide in seawater
Organic material in soil, which consists of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms.
soil organic matter
A surface layer which is composed primarily of soil.
soil surface layer
A soil which has a high bulk density and/or a low porosity. A compacted soil has a reduced rate of both water infiltration and drainage
compacted soil
A layer that is composed primarily of soil.
soil layer
Texture which inheres in soil.
soil texture
Water-holding capacity which inheres in some soil.
soil water-holding capacity
water-holding capacity of soil
The concentration of a clay when measured in soil.
The concentration of a slit when measured in soil.
The concentration of a sand when measured in soil.
The concentration of a liquid water when measured in soil.
soil moisture content
soil water content
The concentration of a salt when measured in soil.
The concentration of a soil organic matter when measured in soil.
concentration of soil organic matter in soil
The temperature of some environmental material.
The quality of a environmental system process.
soil pH
The generation of energy for use by humans
A disposition which is realized during the execution of work, the emission of heat, or the possession of mass.
Consider replacing with PATO class; note that PATO class is not a disposition. This should likely go into OBO Core and also have a physicist look at it.
Energy possessed by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors.
Energy which is realised through motion.
Energy which is the sum of 1) kinetic energy and 2) potential energy.
potential energy that binds nucleons to form the atomic nucleus (and nuclear reactions).
Potential energy which is stored in the fields of propagated by electromagnetic radiation.
Kinetic energy which is realised through the microscopic motion of particles.
A form of disordered mechanical energy.
Thermal energy which propagates through a solid (typically rocky) astronomical body.
Often, this term is used specifically for thermal energy spreading from heat sources (e.g. magma chambers, the planetary core) within the Earth. However, it is also used for extraterrestrial bodies.
A power station which burns a fossil fuel such as coal, natural gas, or petroleum to produce electricity.
An environment which is determined by an anatomical entity.
The concentration of dioxygen when measured in liquid water.
concentration of dioxygen in liquid water
The concentration of dioxygen when measured in sea water.
The concentration of oxygen when measured in soil.
The concentration of iron molecular entity when measured in soil.
soil iron molecular entity concentration
concentration of iron molecular entity in soil
The concentration of sodium molecular entity when measured in soil.
soil sodium molecular entity concentration
concentration of sodium molecular entity in soil
The concentration of organic molecular entity when measured in soil.
soil organic molecular entity concentration
concentration of organic molecular entity in soil
An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure_receptor during an exposure event.
An entity (e.g., a human, human population, or a human organ) that interacts with an exposure stressor during an exposure event.
An interaction between an exposure stressor and an exposure_receptor.
The earth, all of the organisms living on it, and all of the environmental factors, which act on the organisms. The volume of area where biological matter can exist, slightly above, on or below ground level.
MERGED DEFINITION:\nTARGET DEFINITION: An exposure_receptor that is the global ecological system integrating all living beings and their relationships, including their interaction with the elements of the lithosphere, hydrosphere and atmosphere.\n--------------------\nSOURCE DEFINITION: An exposure_receptor that is the part of the environment that is made or modified by humans for use in human activities and human habitats.
An exposure_receptor that is a group of Homo sapiens inhabiting a given area.
The condition of an organism in all aspects (e.g., functional or metabolic efficiency).
Being or characteristic of a single thing or person.
An attribute describing some aspect of an individual or human population.
How long something or someone has existed; elapsed time since birth.
Other conditions with the power to have an effect on health status.
The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female.
A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)
This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology.
1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. 2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). 3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.
genomic feature
1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus 2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. 3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}
'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270
sequence feature set
A set of genomic features (i.e. sequence features that are of genomic origin).
In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member.
A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.
genomic feature set
A sequence feature or a set of such features.
GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.
sequence feature or set
A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).
GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.
biological sequence
In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele.
A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.
qualified sequence feature or collection
Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes).
A qualified sequence feature that carries sequence derived from the genome of a cell or organism.
qualified genomic feature
This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise.
Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position).
A set of qualified sequence features that carry genomic sequence.
Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member.
A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome.
qualified genomic feature set
The location of a sequence feature as defined by its start and end position on some reference coordinate system.
1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.
sequence feature location
An generically dependent continuant that carries biological sequence that is part of or derived from a genome.
An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities.
genomic entity
The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.
In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).
1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.
genomic feature location
A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).
useful organizational term to collect entities that have genomes/genotypes.
organismal entity
A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.
GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes.
qualified sequence feature
'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'.
qualified sequence feature set
A biolocical sequence, or set of such sequences.
biological sequence or set
A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).
A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.
genomic sequence
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
This is the same as GO molecular function
gene product or complex activity
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular response to DNA damage stimulus
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
A biological process is an evolved process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
transferase activity, transferring phosphorus-containing groups
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
The chemical reactions and pathways involving macromolecules, any 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.
multicellular organismal macromolecule metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
Any cellular metabolic process involving nucleic acids.
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
10 feet. 3 ml.
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
source code module
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
OBI branch derived
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
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.
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
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Clint Dowland
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
denotator type
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
A categorical value specification that is used to record the destruction of an organism cells or tissues by the organisms' own enzymes or processes with nominal categories ranging from none to severe.
Add instances 0-non, 1-slight, 2-moderate, 3-severe
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A data item that contains the outcome of a survey.
Alice Nzinga
survey data
A plan specification that is realized by process of gathering information (e.g. by asking questions).
survey plan specification
A planned process that realizes the concretization of a survey to generate an output(survey data.)
survey execution
A specimen that is normal.
normal specimen
A Homo sapiens who contributes specimen.
sample donor
specimen donor
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO.
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
responsible party role
a responsible party role played by a person responsible for the overall conduct of a study
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
principal investigator role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
GROUP: Role Branch
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
A clustered data set is the output of a K means clustering data transformation
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
James Malone
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
A person or organization that has a manufacturer role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
A device which has a function to emit light.
A device that is used to generate X-rays.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
A length measurement datum between a point at sea or ground level and some point above it.
Adapted from https://www.merriam-webster.com/dictionary/altitude
A person or organization that provides material supplies to other people or organizations.
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
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
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
leave one out cross validation method
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
PERSON: Elisabetta Manduchi
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
A planned process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays, X-rays, charged particles or neutrons) or non-ionizing radiation (such as UV light or microwaves)
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
planned irradiation
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
An object aggregate all of whose components are human beings.
collection of humans
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
material entity role
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A physical quality of the thermal energy of a system.
A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
A quality in which events occur in sequence.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
A hardness quality of being rigid and resistant to pressure.
A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature.
A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow.
A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
A structural quality inhering in a bearer by virtue of the bearer's having distinct structure.
A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base.
An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions.
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together.
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
A mass which is higher than normal or average.
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution.
A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface.
An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process.
A quality inhering in a plant by virtue of the bearer's disposition to shed foliage.
A quality inhering in a plant by virtue of the bearer's disposition to retain foliage.
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid.
A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions).
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
A quality that inheres in an entire organism or part of an organism.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
A quality inhering in a bearer by virtue of its constitution.
A quality inhering in a bearer by virtue of the bearer's being roundish, flattish shape, possibly with a slightly angled edge.
A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A temporal distribution pattern of process occurrences within a regulation/reference process.
A quality inhering in a bearer by virtue of the bearer's upper parts die back to the rootstock at the end of the growing season.
A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content.
The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids.
A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
quality of interaction of a substance with electromagnetic radiation
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
May be of the same or different species.
collection of organisms
This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed.
A collection of organisms, all of the same species, that live in the same place.
It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used.
population of organisms
A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members.
multispecies community
Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community.
ecological community
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
collection of organisms of the same species
single-species collection of organisms
A collection of organisms that consists of two or more organisms from at least two species.
Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))".
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
A plant structure (PO:0005679) which is a whole organism.
Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).
A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
&#225pice del epiblasto (epiblastema) (Spanish, exact)
A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
c&#233lula meristem&#225tica (Spanish, exact)
A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
portion of root primordium tissue (exact)
A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).
A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
meristema del epiblasto (epiblastema) (Spanish, exact)
A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state.
A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
Solanaceae whole plant growth stages (SGN:0000001) (related)
cereal plant growth stage ontology (GRO:0007199) (related)
maize growth stage (GRO:0007002) (related)
plant growth stages in Arabidopsis (TAIR:0000021) (related)
rice growth stage (GRO:0007040) (related)
sorghum growth stage (GRO:0007124) (related)
wheat, barley and oat growth stage (GRO:0007156) (related)
A cell which is a plant structure (PO:0009011).
Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.
A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).
A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
sistema de epiblasto (epiblastema) (Spanish, exact)
The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system.
A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
porci&#243n de un tejido vegetal (Spanish, exact)
A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.
A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).
A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
etapa de desarrollo de estructura vegetal (Spanish, exact)
plant growth and development stage (exact)
Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'.
A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
meristema apical del epiblasto (epiblastema) (Spanish, exact)
A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva de &#243rgano (Spanish, exact)
Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure.
A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
Generally the below ground portion of a vascular plant.
A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
eje del epiblasto (epiblastema) (Spanish, exact)
Often bears leaves and branches. In vascular plants, has at least one node and one internode.
A phyllome (PO:0006001) that is not associated with a reproductive structure.
A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.
A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
portion of phyllome primordium tissue (exact)
The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
A maximal whole plant development stage.
vida de la planta entera (Spanish, exact)
There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
The phyllome anlagen is only detectable by gene expression, not morphology.
A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).
A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types.
A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
estructura vegetal colectiva (Spanish, exact)
This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006).
A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).
A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis.
Ionizing radiation classified by the material entity which generates or emits it.
ionizing radiation categorized by source
Radiation originating outside the Earth's atmosphere.
One of the principal sources of ground radiation is radon gas.
Radiation produced on Earth or on another planetary body by natural or artificial means.
Material presenting, when irradiated, interaction properties similar to those of soft tissue.
ICRP glossary (http://icrpaedia.org/Tissue_equivalent_material)
Atomic nuclei, each with 26 protons and 30 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 6 protons and 6 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 14 protons and 14 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 10 protons and 10 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
An atomic nucleus, fully stripped of its orbital electrons, and containing 2, 3, 4, 5, or 6 protons.
Ionization chambers and silicon solid state detectors can be used as active dosimeters.
A radiation measuring device which records dose at the time of detection, with data available in real time
Thermoluminescent dosimeters and plastic nuclear track detectors are passive detectors.
A radiation measuring device which integrates the amount of radiation to which it is exposed. Passive detectors are interrogated at a later time to determine the dose.
The amount of ionizing radiation to which a member of the population on Earth is exposed from natural sources, such as terrestrial radiation from naturally-occurring radionuclides in the soil, cosmic radiation originating in outer space, and naturally-occurring ra
The effective dose was calculated to be 300 mSv.
The sum of the equivalent doses to all organs in the body, each adjusted to account for the sensitivity of the organ to radiation. Effective dose is calculated for the whole body. Effective dose is expressed in millisieverts (mSv).
The samples were exposed to a mixed radiation field consisting of several ions at different energies.
The process of exposing the same sample to more than one type and/or energy of radiation, in sequence or simultaneously.
Radiation classified by where the exposure to the radiation is occurring.
That part of the Earth exposed to the Earth atmosphere.
The region between the Earth's surface and an altitude of approximately 100 km
The region of outer space between the Earth's atmosphere and the innermost Earth radiation belt
That part of outer space beyond the Earth's radiation belts.
A radiation dose administered in two or more exposures at specified time intervals
A unit of absorbed dose equal to 1/1000 of a rad
The equivalent dose was calculated to be 300 mSv.
The product of the mean absorbed dose in an organ or tissue and the radiation weighting factor (w_R )of the radiation type of interest
The total dose was administered in five dose fractions.
The absorbed radiation dose administered in a single one of a series comprising a fractionated radiation exposure
Penetrating ionizing radiation, both particulate and electromagnetic, that originates in outer space
Galactic cosmic radiation is one of the principal sources of radiation dose outside low-earth orbit
Galactic cosmic radiation consists of high-energy charged particles originating from outside the solar system
Solar cosmic radiation contributes to the radiation dose to humans in space.
Solar cosmic radiation is high-energy charged particles that originate from the sun.
The measurement datum representing a dose to an organism or object per unit time.
The Apollo spacecraft took 24 astronauts to the Moon between 1968 and 1972.
Vehicles, crewed or uncrewed, which are designed to orbit about the Earth or another celestial body or be placed into a trajectory to another celestial body or location in space.
The experiment was conducted in the International Space Station module Columbus
The experiment was conducted on the Russian module of the ISS.
A self-contained unit of the International Space Station.
Mir was a space station that operated in low Earth orbit from 1986 to 2001, operated by the Soviet Union and later by Russia.
A spacecraft capable of supporting a human crew in orbit for an extended period of time. It lacks major propulsion or landing systems. Stations must have docking ports to allow other spacecraft to dock to transfer crew and supplies.
The HIMAC accelerator has a beamline dedicated for radiation biology experiments.
The path leading from a particle accelerator to an experimental station used in experiments in particle physics, materials science, chemistry, and molecular biology, or in irradiation tests or to produce isotopes.
Radiation produced by a particle accelerator.
Radiation produced by a nuclear reactor.
High energy photons emitted during nuclear decay of the Cesium-137 isotope.
High energy photons emitted during nuclear decay of the Cobalt-60 isotope.
High energy photons emitted during nuclear decay of the Cobalt-57 isotope.
Isotopes that exhibit radioactivity and undergo radioactive decay. (From Grant & Hackh's Chemical Dictionary, 5th ed & McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A series of radioactive elements from ACTINIUM, atomic number 89, to and including LAWRENCIUM, atomic number 103
A trivalent radioactive element and the prototypical member of the actinide family. It has the atomic symbol Ac, and atomic number 89. Its principal isotope is 227 and it decays primarily by beta-emission.
A completely man-made radioactive actinide with atomic symbol Am, and atomic number 95. Its valence can range from +3 to +6. Because of its nonmagnetic ground state, it is an excellent superconductor. It is also used in bone mineral analysis and as a radiation source for radiotherapy
A man-made radioactive actinide with atomic symbol Cf, atomic number 98, and atomic weight 251. Its valence can be +2 or +3. Californium has medical use as a radiation source for radiotherapy
A radioactive element of the actinide metals family. It has the atomic symbol Np, and atomic number 93.
A naturally radioactive element of the actinide metals series. It has the atomic symbol Pu, and atomic number 94. Plutonium is used as a nuclear fuel, to produce radioisotopes for research, in radionuclide batteries for pacemakers, and as the agent of fission in nuclear weapons.
A radioactive element of the actinide series of metals. It has an atomic symbol Th, atomic number 90, and atomic weight 232.04. It is used as fuel in nuclear reactors to produce fissionable uranium isotopes. Because of its radioopacity, various thorium compounds are used to facilitate visualization in roentgenography.
A radioactive element of the actinide series of metals. It has an atomic symbol U, atomic number 92, and atomic weight 238.03. U-235 is used as the fissionable fuel in nuclear weapons and as fuel in nuclear power reactors.
Electromagnetic radiation with photon energies approximately 3-120 eV. High energy UV radiation can be ioinizing.
A substance present at the time of irradiation that mitigates or prevents the biological effects of irradiation.
Richard T. Hoppe, Theodore Locke Phillips, Mack Roach, Leibel and Phillips Textbook of Radiation Oncology (Third Edition), W.B. Saunders, (2010), ISBN 9781416058977, https://doi.org/10.1016/B978-1-4160-5897-7.00093-7.
Radionuclide chelators are small organic molecules or in some cases larger peptides that chemically sequester the radionuclide ion by forming a complex that determines the thermodynamic stability and kinetic inertness of the radionuclide.
A co-carcinogen is generally a chemical that promotes the effects of a carcinogen in the production of cancer. In some circumstances exposure to radiation or physical trauma is considered to be co-carcinogenic.
Radiation response modifiers are agents that alter tumor or normal tissue response to radiation, such as radiation sensitizers and radiation protectors.
Citrin DE, Mitchell JB. Altering the response to radiation: sensitizers and protectors. Semin Oncol. 2014 Dec;41(6):848-59. doi: 10.1053/j.seminoncol.2014.09.013. Epub 2014 Oct 7. PMID: 25499642; PMCID: PMC4270009.
Radiation response modifiers that are peptides.
Shaghaghi, Zahra et al. “Potential utility of peptides against damage induced by ionizing radiation.” Future oncology (2021): doi/10.2217/fon-2020-0577
Radiation response modifiers that are small molecules.
small molecule radiation response modifier
A person employed or otherwise working in commercial activities where nuclear materials are created, handled or disposed and at risk of occupational radiation exposure. Excludes health workers.
Nezahat Hunter, Richard G.E. Haylock, Michael Gillies, Wei Zhang; Extended analysis of solid cancer incidence among the Nuclear Industry Workers in the UK: 1955–2011. Radiat Res 2022; doi: https://doi.org/10.1667/RADE-20-00269.1
The theme or modality of an experimental, theoretical, critical or summative study involving radiation, radioactive materials including their impacts on orgnisms and society.
An epidemiological study is the study (scientific, systematic, and data-driven) of the distribution (frequency, pattern) and determinants (causes, risk factors) of health-related states and events (not just diseases) in specified populations (neighborhood, school, city, state, country, global)
A study of the impact of radiation on the composition of or processes within the natural or anthropogenic environment.
A study who endpoint is the lifespan of the organism under investifgation.
A study of the effect of agents including radiation, seperately or together, on the incidence or type of neoplasia or pre-neoplasia.
A study in which the structural or processual damage to normal tissue caused by radiation is assessed. Often by histopathology or molecular profiling.
A study of the mechanism or effects of radiation on dna damage and its repair.
A study of the effects of internal or external radiation on cellular or organismal physiology.
A study of the effects of radiation on the integrity, composition and quality of adult, fetal or embryonic anatomical structures.
A study of the effects of external irradiation on an organism.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application.
A study of the effects of external irradiation on an organism where the most of the dose is given in a single or small number of fractions closely in time.
A study of the effects of external irradiation on an organism where the dose is given over a protracted time period either continuously or in many fractions. Often these are lose dose studies.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. The dose is delivered over a long period of time, often continuously and generlly at low dose. For example long term Radon exposure by inhalation.
A study of the effects of internal irradiation on an organism where the radiation source is internalised within the body tissues ( eg. by injection), gastrointestinal ( eg gavage), urogenital, auditory or respiratory ( eg instillation or inhalation) systems. Most of the dose is given over a short period of time and is generally unfractionated, such as in brachytherapy.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Acute exposure involves usually a single exposure over a short period of time with no fractionation.
A study of the effects of radiation exposure where the exposoure has an internal and external mode of application. Chronic exposure involves usually a continuous or highly fractionated exposure over a long period of time.
A study of the effects of radiation on gene expression.
A study of the effects of radiation on the proteome or individual proteins.
A study that aims at the discovery of protein, RNA or other molecular entities or modifcations that can act as reliable surrogates for the prediction or measurement of the effects of radiation or the response of the organism to radiation.
A study that aims at the discovery, development or assessment of efficacy of therapeutic agents or processes designed to mitigate or cure the effects of radiation exposure.
A study that uses survival as an endpoint. Generally applicable to animal studies rather than human studies which would use the "lifespan" measure (RBO:00000085)
A study of the effects of radiation on the metabolome or individual metabolites.
A study of the contributing factors consequences and prevention of nuclear accidents
A study of the toxicity of chemical or biological agents on cells or whole organisms.
A study of the effects of radiation on the endocrine system or of endocrine hormones on the effects of radiation.
A study of the effects of radiation on the offspring of an irradiated animal or plant.
A study of the distribution and metabolism orf drugs or biologicals used for therapeutic purposes.
A set of behaviours that have some socially agreed upon function and for which there is an accepted code of norms. This may refer to a role within an organisation or within society as a whole. For example a Profession” can be defined as a cluster of occupational roles, or roles in which the incumbents perform certain functions valued in the organisation or society.
Neutrons or charged particles, such as protons or alpha particles that produce ionizing events densely spaced on a molecular scale (e.g., >10 keV-micron^[-1].
NCRP https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf
X and gamma rays or light charged particles such as electrons that produce sparse ionizing events far apart on a molecular scale.
Electromagnetic radiation having sufficient energy to remove one or more electrons from an atom
A device that is used to measure the amount of ionizing radiation exposure or absorption.
Particle or electromagnetic radiation with sufficient energy to liberate one or more electrons from an atom.
Charged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)
electromagnetic radiation with photon energies greater than approximately 100 keV
A device used to impart kinetic energy to subatomic particles by means of electric and magnetic fields
A device in which nuclear fission may be initiated and controlled in a self-sustaining chain reaction to generate energy or produce useful radiation.
Atomic nuclei, each with 8 protons and 8 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 18 protons and 22 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 22 protons and 26 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 36 protons and 48 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 41 protons and 52 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 47 protons and 60 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 54 protons and 75 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 73 protons and 108 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 79 protons and 118 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
Atomic nuclei, each with 7 protons and 7 neutrons with kinetic energy imparted by natural or artificial means such as by a particle accelerator
The process by which an entity is exposed to electromagnetic or acoustic radiation radiation energy internally or externally.
Unplanned exposure to radiation of any type in any environment or otherwise planned process.
Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally or externally.
Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a diagnosis of disease.
Exposure to naturally occurring radiation (NORM) of any type in any environment .
exposure to naturally ocurring radioactive material
Planned exposure of an organism to radiation of any type, internally or externally, with the intention to effect a cure or mitigation of disease.
Unplanned exposure to anthropogenic radiation of any type in any environment ; for example radiation from nuclear waste, nuclear industry discharge or weapons.
accidental non-medical anthropogenic radiation exposure
Exposure to ionising radiation created by a man-made machine or exposure to a fixed source. For example a cobalt source, an X ray machine, an acceleratororf a nucler weapon.
Planned exposure to radiation generated through a device or exposure to a source emitting ionising radiation
planned anthropogenic radiation exposure
Accidental or incidental exposure to radiation from a man made process or machine. Covers both radiation accidents and routine occupational exposure.
accidental anthropogenic radiation exposure
Accidental exposure occurring during medical therapy or diagnostics, for example medical radiation accidents or overdoses.
accidental medical anthropogenic radiation exposure
Incidental exposure to naturally occurring radiation in a natural or anthropogenic environment, such as geographical areas with high background levels of radiation or specific locations such as Uranium mines.
unplanned naturally occurring radiation exposure
Deliberate or knowing exposure to naturally occurring radiation in a natural or anthropogenic environment, such as a radon spa.
planned naturally occurring radiation exposure
Studies relating to human society and the interrelation of social and educational factors with individual thought and behaviour including mental illness.
Studies on the distribution of information or opinion by technological means of communication that reach large numbers of people.
Studies on the civil, legal, and political preparedness for accidental or deliberate release of radioactive materials or radiation into the environment.
Studies in which research is conducted with human subjects or on material of human origin in which the investigator directly interacts with human subjects, including the dveelopment of new technologies, understanding of the mechanisms of disease, therapy, clinical trials, epidemiology behaviousrand health services research.
Study of the laws, statutes, ordinances, government or international treaty regulations or authoritative guidelines, as well as for legal controversy and court decisions, relating to the regulation of radiation safety, movement and containment of radioactive materials and the consequences for human health or the natural environment of radioactive contamination.
Studies relating to organisations and processes concerned with freedom from or resilience towards potential harm caused by hostile intent or circumstances (for example terrorism and illegal release of radioactive substances or radiation) towards the natural environment or human population, and the enforcement of relevant laws and international treaties.
A study whose intention is to discover knowledge concerning the origins, nature diagnosis or therapy for neoplastic disease and cancer. This includes studies in humans, model organisms, the laboratory and in silico. This class includes experimental and epidemiological studies specifically aimed at cancer.
The specific manner, characteristic, pattern of application, or the employment of any technology, approach or formal procedure to implement the study plan to generate a study type.
Studies of the presence of radiation of any type in the natural or anthropogenic environment and its impact on animals, plants, and microorganisms. This includes studies measuring nuclide transfer in the environment, and interaction with meteorological phenomena. This excludes occupational exposure and the human working environment.
Studies concerned with the regulation, monitoring and operation of the nuclear industry. For example nuclear power station and reprocessing plants, isotope purification and manufactore, weapons manufacture and testing. This includes occupation health studies, impact of accidental or deliberate release on the natural or man made environment and impact on organisms specifically affected directly or indirectly by contamination.
Research done in a laboratory. A laboratory study may use special equipment and cells or animals to investigate the effects of an experimental perturbation, discover fundamental molecular mechanisms, assay biological substances, or find out if a drug, procedure, or treatment is likely to be useful in humans. A laboratory investigation is often characterised by a hypothesis and is carried out with controls.
Study of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ethicolegal constructs surrounding radiation and radiation safety and regulation.
Study concerning exchange or transmission of thoughts, messages, or information between people or between authorities and the general public (for example educational information, risk communication, safety communication) concerning exposure to and use of radiation.
A study focussed on a set of people with some shared characteristic. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. For example communities collectively exposed to radioactive environmental contamination.
The study of political involvement in radiation and nuclear regulation, military use, and safety as shown by inclusion in political manifestos and messaging by established or informal groups and its impact on voting patterns and democracy.
A study measuring "psychological" aspects of a person such as knowledge, skills, abilities, attitudes, or personality using defined scales.
A study of human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology.
A study dealing with group relationships, patterns of collective behavior, and social organization.
Studies involving fields of inquiry into human constructs and concerns as opposed to natural processes . These are traditionally the study of literature, philosophy, and religion. Included in this definition are sociological studies, especially those concerned with the social impact of the humanities.
Specifically an attitudinal study looking at how perception, for example of risk, and expectations affect behaviour.
perceptions, expectations and behaviours study
Sociological, attitudinal, ethocolegal and regulatory approaches to governance of radiation and radioactive substance use.
Studies on policy concerning socially and ethically responsible research and innovation
responsible research and innovation study
Studies of the engagement between an organisational entity and those groups or individuals potentially or actually impacted by the actions of that entity over a range of activities and approaches.
Study concerning the modes, efficacy and response to communication of risk and health impacts of radiation in all aspects.
Studies concenring the attitudes to and practices of radiological protection in defined groups of people. For example the nuclear industry of a country or within a specific laboratory.
Genetic study done at the population level or among population groups, generally to find the cause, incidence or spread of a disease or to see the response to a treatment, nutrition or environment.
A type of study in which participants are enrolled into the study before they develop the disease or outcome in question.
Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ) An observational study that is also considered to be a Patient Registry.
A study looking backwards in time using observations collected predominantly prior to subject selection and enrolment
A study of the number of new cases of a given disease during a given period in a specified population. It also is used for the rate at which new events occur in a defined population. this class also includes PREVALENCE, which refers to all cases in the population at a given time.
Studies concerning the optimisation of situation awareness through gathering and analysing information, and methodologies for making decisions on that awareness, such as estimating the path of a radioactive fallout with respect to weather and population density and making a decision to evacuate a population.
situation awareness and decision support study
A study concerning the protection of the population from unexpected radioactive discharge or contamination, such as a dirty bomb, and civil safetyy coningency plans, such as deployment of emergency services and evacuation.
Studies on planning for unexpected natural or man-made radiological catastrophe of substantial extent causing significant property damage or destruction, loss of life or sometimes permanent changes to the natural environment. Broader scope than civil protection as may relate to livestock, food and water shortage, disease outbreak and extensive traumas caused by precipitating or consequential damage.
Studies on plannig for or analysing a nuclear accident with release of airborn or waterborn contamination into the environment. Narrower than Disaster planning study but may be used to qualify an annotation to Disaster planning study if the source of contamination is a nuclear accident. A nuclear accident is not necessarily a disaster.
A controlled study designed to assess the safety and efficacy of new drugs, devices, treatments, or preventive measures in humans by comparing two or more interventions or regimens
Study of the effects of radiation used in a medical therapeutic or diagnostic context. Inlcudes radiation accidents in this context, excludes occupational exposure for health professionals.
A study concerned with health and safety policy development, implementation and practice in the workplace including investigating accidents at work, and chronic occupational exposure. Includes monitoring compliance with health and safety legislation and study of the promotion and maintenance of physical and mental health in the work environment.
Study on the efficacy, outcomes and adverse consequences of exposure to medical diagnostic procedures using internal or external irradiation.
Study of the efficacy, outcomes and adverse consequences of exposure to therapeutic use of ionizing and nonionizing radiation including RADIONUCLIDE THERAPY, therapeutic radiation with visible, laser, or ultraviolet light. Includes technical development of protocols and equipment.
A study involvingdevelopment of agents or procedures intended to produce an effect that is intended to mitigate or stop a pathologic process.
A study of the macroscopic and microscopic anatomical changes in diseased tissue.
Study of legal and statutory instruments and legislation designed to regulate the safety, use and transport of radioactive materials, release of such materials into the environment, or external radiation.
Study of the policy approaches and their implementation concerned with harmonising regulatory guidelines and legislation dealing with radiation and radioactive substances between legislatures, generally internationally.
Study of the development, implementation and monitoring of nuclear non proliferation treaties between states.
Studies concerning intentional release of organisms (germs), toxic chemicals, or radioactive substances with intent to harm or kill people or the environment, or to inflict panic within a population.
Study of strategies and their implementation towards defence against radiation used as a weapon conducted by military powers and institutions. May also include civil defence where the military has a significant operational role, but not disaster preparedness.
Study of biological processes that involve adding/removing chemical moieties to/from DNA, including methylation, phosphorylation, dephosphorylation, etc. Includes interventional DNA modification.
Study of biological processes that involve adding/removing chemical moieties to/from histones, including methylation, acetylation,phosphorylation, dephosphorylation, etc.
Study conducted by means of structured or unstructured interviews of persons of interest.
A study of genetic variation and the inheritance of a trait or traits within a population or an individual including examination of genetic material for the presence or absence of cytogenetic or molecular genetic abnormalities.
A radiographic study used to evaluate a specific anatomic location for a specific purpose. This may include the assessment of imaging modalities and the development of new techniques. Includes PET, MRI, CT and related techniques.
Study concerned with the construction, analysis, evaluation, refinement etc. of mathematical or statistical models of the properties or behaviour of a set of entities, such as molecules, physiological processes, environmental processes such as nuclide transfer, such that functions are developed to reliably predict the behaviour of those entities.
A study usually conducted in a laboratory where non human animals are used to model aspects of a disease process or its therapy to provide insights into human biology or pathobiology.
Study concerning the development, use, calibration or standardisation of technologies for the qualitative or quantitative measurement of radiation and radionuclides.
monitoring technologies and metrology study
Study of the chemistry of radioactive materials including radioactive tracer studies of metabolic processes
Study of the development and implementation of public policy towards issues involving radiation
Study of the effects of acoustic radiation on cellular and organismal physiology and the effects of acoustic radiation emitted in response to exposure to ionising radiation.
Study of radiation levels and effects in the human built environment.
environmental study_ abiotic_anthropogenic
Study of radiation levels and effects in the natural environment.
The development and use of mathematical models and systems analysis for the description of naturally occurring non-human populations, and applications to measuring the effects of radiological contamination.
The study of environmental contamination with radiation and radioactive substances and the toxic effects on the ecosystem either through chemical toxicity or radiation exposure.
The study of environmental contamination with radon and the toxic effects on biota including humans. Both natural and anthropogenic environments. Includes radiometrics, safety policies and mitigation technologies.
Mathematical modelling of radionuclide transfer and dispersal processes in water, earth or air, either directly or through the mediation of biota.
Study of the ocurrence, levels and effects of naturally occurring radioactive materials such as Radon.
naturally occurring radioactive materials study
Study involving the measurement of radiation levels, or concentration of radionuclides, in the natural or man made environment. Usually in a time series.
environmental radiation monitoring study
Study concerned with the measurement of transfer of radionuclides to biota from the environment.
environmental radionuclide transfer study
Any study concenrd with the prevalence or effects on non-ionising radiations such as UV, acoustic, or RF.
non ionising electromagnetic radiation study
Study concerning the safety, regulation, activities and engineering of nuclear installations including power stations, waste processing plant, radionuclide generation and purification plant, and military nuclear establishments. May include occupational health studies if broader than just occupationaal health in scope.
Study of the process of generation of nuclear waste, its monitoring, regulation, disposal and inadvertent discharge.
Study of the engineering of nuclear installations such as power plants.
Study of the process, regulation and monitoring of mines where exposure to naturally occurring radiation presents an occupational hazard for workers or the process itself, for example run off water or spoil, constitutes an environmental hazard.
A study using cells derived from an organism grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent.
A study using an organ, part of an organ or an organoid culture, derived from an organism and grown in artificial culture medium in a laboratory with the aim of understanding some aspect(s) of cell physiology, genetics or behaviour, generally as part of the testing of an hypothesis but also for diagnostic intent. The system differs from cell culture in the generation or maintenance of multiple cell types with the spatial and functional relationship between them derived from or reflecting the normal organisation in vivo.
Any study involving the manipulation, measurement, or characterisation of DNA or RNA in a cell or organism.
Elucidation of the physical structure of a macromolecule, protein, carbohydrate, DNA or RNA, its analysis and manipulation based on structure/function considerations.
A study using an intact organism, plant, animal, or microorganism
Study of the cellular phenomenon which radiation energy is not been directly deposited in cells by transfer of medium, proximity/justaposition, or other means, but results in their behaving as if they had been irradiated.
A study of heritable phenotype changes that do not involve alterations in the DNA sequence. This may be in intact organisms or in cells and includes population analysis of epigenetic phenomena and molecular analysis of gene expression and epigenetic modifications of chromatin such as DNA methylation and histone acetylation.
Study of the frequency of induction , nature and consequences of the production of genetic or epigenetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods.
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or regulation of the nuclear industries.
attitudinal study of nuclear industry risk perception
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic ionising radiation in the environment.
attitudinal study towards ionising radiation in the environment
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety or ecological integrity towards natural or anthropogenic non-ionising radiation in the natural environment.
attitudinal study towards non-ionising radiation in the environment
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety and efficacy in a clinical context where radiation is used for diagnostic or therapeutic procedures..
attitudinal study towards medical radiation procedures
Studies of the status or origins of a mental position, feeling or emotion toward a fact or state with respect to information or experience concerning radiation, radiation safety towards natural or anthropogenic non-ionising radiation in the occupational environment.
attitudinal study towards radiation in the occupational environment
Study of social and individual trust in the position and activities of legal or other competent advisory or regulatory authorities.
Study on the modality, efficacy and responses to communcation of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context.
Study on the modality, efficacy and responses to communication of information or advice to populations or individuals, on the safety and risks of exposure to ionising radiation in any context.
Study on the modality, efficacy and responses to communication of information or advice to populations on any aspect of radiation, conceived of as an educational programme, and including a wider scope than just safety and risk. For example basic nuclear physics, emergency action advice.
Study involving attitudes, health status, social organisation of defined communities identified by common characteristics such as occupation type, geography, gender identity, with respect to radiation.
social affairs and community health study
Studies involving creation and assessment of plans for the future physical arrangement, well being, efficiency and condition of a community. It may have the goals of improving health, promoting efficiency in the provision of services and resources on a comprehensive basis for a whole community. In the context of radiation this may be concerned with community planning for dealing with mitigation measures for local NORM, or organised community-wide continegency measures for nuclear accident or recovery from such.
Study concerned with eliciting information in a structured way concerning issues of interest from members of a community defined by common characteristics, for example occupation, geographical location, personal history or gender.
A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology at the level of slected individuals. May be carried out by observation or as individual responses to a questioannaire or interview in the case of humans where the person records their own assessment of their behaviour.
A study concerned with human or animal activity, in terms of motivation, direction, result, emotion, perception, or etiology within substantial populations of individuals. Likely to be carried out by mass observation or indirect inference.
Mathematical modelling for theraputic regime optimisation and for optimal tumor response, for example modelling spatiotemporal dynamics of tumor and blood volume fraction, and predicting response to radiation therapy. Also studies for beam modelling and multiimaging techniques.
Study of the radiolonuclide components and emissions from building materials
building materials radiological safety study
Studies on radiological safety within buildings. Primary purpose os for buildings not specifially designed to hold radioactive materials but anaylyis and mitigation of risks from radioactive exposure from the local environment or materials.
Study of the weather and atmospheric dynamics mainly with respect to dissemination of radionuclides.
Study of non-living objects in the environment, such as soils or rocks.
Study of non-human biota in the natural environment.
Study which may include human and non-human biota in the environment.
Study of the measurement, effects and regulation of wireless communication signals, for example mobile phone radiation and microwave communication.
The sample was irradiated with Cs-137 gamma ray photons.
Photons having energies that are greater than tens of thousands of electron volts (eV).
The sample was irradiated with x-ray photons.
A photon with energies from about 100 eV (electron volts) to 1 MeV (million electron volts).
Irradiation of the sample was with x-ray photons.
An energy transfer process in which energy in the form of particles or waves is transferred from one entity to another
A process involving the emission of energy from an atomic nucleus resulting in change in the character of the nucleus
Irradiation that is not the result of a planned process
Unplanned irradiation that is of anthropogenic origin
Unplanned irradiation that is non-anthropogenic in origin
Environmental monitoring that includes continual assay for radiation dose or quality.
Monitoring within an environment which was not man-made.
Monitoring within a man-made or constructed environment
Monitoring for radiation dose or quality within a man-made or constructed environment such as a building or a vehicle.
anthropogenic environment radiation monitoring
Monitoring for radiation dose or quality within a natural environment.
natural environment radiation monitoring
Atomic nuclei, with atomic number 2 or greater and kinetic energy imparted by natural or artificial means
Atomic nuclei, variously defined as having atomic number 2, 3, 4, 5 or 6 and kinetic energy imparted by natural or artificial means
A particle with a positive or negative electric charge
An atomic nucleus with 26 protons and 30 neutrons
An atomic nucleus with 14 protons and 14 neutrons
An atomic nucleus with 6 protons and 6 neutrons
An atomic nucleus with 2 protons and 2 neutrons
An atomic nucleus with 10 protons and 10 neutrons
Activity carried out by crewed or robotic vehicles outside the Earth's atmmosphere.
The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium.
The amount of energy from any type of ionizing radiation deposited in a specified mass of any medium per unit time.
The kinetic energy carried by a particle or photon of ionizing radiation.
Electromagnetic radiation with photon energies approximately between 0.1 and 120 keV. The upper end of the x-ray spectrum overlaps with the lower end of the gamma ray spectrum.
Sham irradiation refers to a procedure in which participants or subjects in an experiment are exposed to simulated radiation, mimicking precisely the conditions of actual irradiation. The purpose of using sham irradiation is to create a control group that experiences the non-specific effects of the experimental setup, while excluding the specific effects associated with radiation exposure.
A protocol for administering a total radiation dose in two or more increments separated by a specified time interval
The region of space between the Earth and the Moon
A region of space defined by a regular, repeating path of a specified object about Earth's moon
The area of the lunar landmass exposed to space
The region of space between the Earth and Mars
A region of space defined by a regular, repeating path of a specified object about Mars
The area of the Mars landmass exposed to the Martian atmosphere
The region of space in the Solar System between planets
The outermost solid or liquid area of a planet
An organism or material entity kept unexposed to radiation, for purposes of comparison to a similar organism or material entity that has been exposed to radiation
A study at a ground facility designed so as to replicate one or more conditions in space (e.g. radiation, microgravity, isolation)
An study at a ground facility designed so as to replicate conditions in space (e.g. radiation, microgravity, isolation) with the exception of one condition, so as to ascertain the effects of that condition on an organism or instrument
A protocol for administering radiation to a sample
One of the series of individual doses administered to a sample in a fractionated irradiation.
Time between fractions in a fractionated irradiation.
The region of the atmosphere above 8000 feet above sea level. Altitudes above 12000 feet are sometimes referred to as very high altitude, and above 18000 feet as extremely high altitude.
The class should be used in cases where it is clear that the control sample was treated in precisely the same way as the experimental samples or sham irradiation is specified. It is therefore a more restricted quality definition than "non-irradiated". It is likely to be used more often with external radiation exposure or exposure to a beam, and with a biological rather than abiotic sample.
A quality of a biotic or abiotic sample or individual which is part of an experiment that tests the effects of radiation on organisms or materials by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. In sham irradiation the precise treatment of the sample must be identical to that of the experimental samples and should be made explicit in the description of the method.
An aircraft which flies a series of parabolic arcs to simulate micrgravity.
An aircraft which flies at altitudes greater than commercial aircraft altitudes for research purposes.
An research aircraft designed to operate without crew members, either autonomously or under control from a ground station
Fully ionized atomic nucleus with 2 or more protons and energies in excess of tens of MeV per nucleon
A study of a response to radiation conditioned by prior administration of radiation of a different type and/or at a different dose or dose rate
The total dose administered in a series of radiation fractions divided by the elapsed time between the beginning of the first exposure fraction and the end of the last exposure fraction
A device which exposes samples to gamma radiation.
The electric charge of a particle used in an irradiation
The measurement of the amount of radiation taken up by a sample.
A microbeam is a narrow beam of radiation, of micrometer or sub-micrometer dimensions. Together with integrated imaging techniques, microbeams allow precisely defined quantities of damage to be introduced at precisely defined locations.
An atomic nucleus with 41 protons and 52 neutrons
An atomic nucleus with 47 protons and 60 neutrons
An atomic nucleus with 54 protons and 75 neutrons
An atomic nucleus with 73 protons and 108 neutrons
An atomic nucleus with 79 protons and 118 neutrons
An atomic nucleus with 7 protons and 7 neutrons
An atomic nucleus with 8 protons and 8 neutrons
An atomic nucleus with 18 protons and 22 neutrons
An atomic nucleus with 22 protons and 26 neutrons
An atomic nucleus with 36 protons and 48 neutrons
A derived absorbed dose unit which is equal to one milligray absorbed per second
This could be used to describe a tissue response to immune stimulation, so for example an IL2 response of endothelial cells in response to lymphocytes stimulated by pathogen.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus which acts on another cell and not on the responding cell. The process begins with detection of the stimulus by a cell and ends with a change in state or activity of a different cell
The most obvious example is the bystander effect ( Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) where a naive cell behaves as if it has been irradiated because of its communication with an irradiated cell. It may also be used to describe the abscopal effect. Note that abscopal effects have been noted for ionising and non-ionising ( RF) radiation, eg. L?ffler MW. et al. . A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol. 2019 Nov 19;10:2526. doi: 10.3389/fimmu.2019.02526. PMID: 31803175; PMCID: PMC6877671
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of radiation acting on another cell and not on the responding cell. The process begins with detection of radiation by a cell or cells and ends with a change in state or activity of a different cell or cells.
Directly describes the bystander effect (Carmel Mothersill, Andrej Rusin, Cristian Fernandez-Palomo & Colin Seymour (2018) History of bystander effects research 1905-present; what is in a name?, International Journal of Radiation Biology, 94:8, 696-707, DOI: 10.1080/09553002.2017.1398436) but can alo sbe used to describe phenomena related to the abscopal effect, manifest in whole organisms where irradiation of one part of the organism causes changes in another un-irradiated component.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to ionising radiation which acts on another cell and not on the responding cell. The process begins with detection of the ionising radiation by one cell or cells and ends with a change in state or activity of a different cell or cells.
indirect cellular response to ionising radiation
A device for exposing materials or biological organisms to ionizing radiation for research or therapeutic purposes.
High-altitude balloons are crewed or uncrewed balloons, usually filled with helium or hydrogen, that are released into the stratosphere, generally attaining between 18 and 37 km (11 and 23 mi; 59,000 and 121,000 ft) above sea level.
non-targeted effects of ionising radiation
Non-targeted effects of ionising radiation are characterised by cellular responses that occur in cells in which energy from ionizing radiation has not been deposited. The distinct classes of non-targeted effects include Genomic Instability, and Bystander effect which latter includes Abscopal effects and Bystander-mediated adaptive response. These can also arise non-clonally in the progeny of irradiated somatic or germ cells, resulting in radiation-induced genomic instability and transgenerational genomic instability respectively. (Kadhim M, Salomaa S, Wright E, et al. Non-targeted effects of ionising radiation--implications for low dose risk. Mutat Res. 2013;752(2):84-98. doi:10.1016/j.mrrev.2012.12.001)
That energy which is transferred in space and time as part of the process of radiation (ENVO:01001023).
Uncharged particles with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)
An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers
See H.H. Rossi, Microdosimetry and Radiobiology, Radiation Protection Dosimetry, Volume 13, Issue 1-4, 1 December 1985, Pages 259�265, https://doi.org/10.1093/rpd/13.1-4.259 and Gustavo A. Santa Cruz,Microdosimetry: Principles and applications,Reports of Practical Oncology & Radiotherapy,Volume 21, Issue 2,2016,Pages 135-139,ISSN 1507-1367,https://doi.org/10.1016/j.rpor.2014.10.006.
Usually a track structure assay at nm scale
An assay of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers
Usually a track structure assay at micrometre scale
Nuclear decay in which an alpha particle is emitted.
Radioactive decay in which a beta particle is emitted or in which orbital electron capture occurs.
Processes in which electrons or components of the atomic nucleus are participants.
Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers
In microdosimetry the specific energy, z, is the energy deposited by radiation ( in one or more deposition events) in a specified micrometric (or smaller) site divided my the mass of the site. Measured in Gy.
The path of a particle in matter, delineated by sites where the particle deposits energy.
A pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 nanometers.
The complete set of spatial coordinates of energy deposition events along a particle track in matter
A group of ionization events closely related in time and space, occurring in a specified target volume and originating from a single primary ionizing particle.
Measurement of the pattern (frequency and spatial distribution) of ionization events produced by energy deposition in time and space in a substance characterized by linear dimensions of the order of 1-100 micrometers.
A volume of matter characterised by linear dimensions of the order of 0.5- 10's of microns, referred to as the "site" in microdosimetry.
A control specimen role of a biotic or abiotic sample or individual describes a specimen by its purpose, and therefore treatment, within a planned experimental process that tests hypotheses by isolating variables as dictated by the scientific method in order to make a conclusion about the effect of such variables. The quality of control inhering in the sample role exists as a result of the historical treatment of the sample. In a controlled experiment, two or more virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena. A control may have been subject to treatments during the experiment that might alter its state or behaviour and is therefore distinguishable from the sample as initial input into the experiment. However such treatments should in all cases but that of the variable under scrutiny, be the same as the experimental sample.
Sham irradiation in which an identical irradiation protocol (with the exception of the administration of the radiation exposure) is not followed in every respect.
Use approximate sham irradiation when at least one aspect of the irradiation (with the exception of the administration of the radiation exposure) is not followed precisely. For example, Not placing an organism or sample in a beam line for the same length of time as the irradiated organism(s) or sample(s) were left in the beam.
Experimental internal radiation exposure of rodents to radon gas through inhalation.
Exposure to an inhaled, ingested, injected or implanted source of radiation of any origin as part of a planned or accidental process.
Mice exposed to external radiation from a Sr source.
Exposure to an external source of radiation of any origin or type.
Sham irradiation in which an identical irradiation protocol is followed in every respect, with the exception of the administration of the radiation exposure.
Use complete sham irradiation when all steps of an irradiation protocol are followed for sham control group (with the exception of administration of the radiation exposure).
Planned exposure of an entity to radiation of any type, for example as part of a medical or experimental procedure with the intention of exposing the entity to radiation energy internally by the ingestion, inhalation or implantation of a source of radiation.
Research subjects participating in a clinical trial using an internally implanted radiation source have an internal experimental radiation exposure
internal experimental radiation exposure
The direct or indirect transfer of energy from radiation to a medium through ionisation or excitation of the atoms of the medium.
A mixed irradiation study typically involves exposing a sample or system to a combination of different types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A mixed ion and photon irradiation study typically involves exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A mixed ion and photon simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
mixed ion and photon simultaneous irradiation study
A mixed ion and photon sequential irradiation study typically involves sequentially exposing a sample or system to a combination of these types of radiation. This could include exposure to various forms of ionizing radiation, such as gamma rays, X-rays, and particle radiation. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
mixed ion and photon sequential irradiation study
A multiple ion irradiation study typically involves exposing a sample or system to a combination of different types of charged particle radiation. Exposure might be simultaneous or sequential and from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
A multiple ion simultaneous irradiation study typically involves simultaneously exposing a sample or system to a combination of ions. This could include exposure to various forms of particle radiation, for example ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
multiple ion simultaneous irradiation study
A multiple ion sequential irradiation study involves exposing a sample or system to a combination of different ions. This could include exposure to various forms of particle radiation such as ion beams. Exposure might be from anthropogenic or natural sources of radiation. The goal is to understand how the different types of radiation interact with each other and their combined effects on the material or biological system under investigation.
multiple ion sequential irradiation study
One of the measures to ensure ALARA is to minimize the time spent working around radioactive materials.
A principle of radiation protection philosophy that requires that exposures to ionizing radiation be kept as low as reasonably achievable, economic and social factors being taken into account. The protection from radiation exposure is ALARA when the expen
NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)
Attenuation in concrete or leadshielding is a common method of radiation protection on Earth, but is impractical in space due to mass constraints.
The reduction of radiation intensity upon passage of radiation through matter
Biodosimetry was used to measure the exposure of some victims of the Chernobyl nuclear accident.
Use of a biological response as an indicator of a dose of an effective agent (e.g., the extent of decline in peripheral blood lymphocytes of humans exposed to ionizing radiation can be used as an indicator of the absorbed dose to the whole body from that
The bystander effect can be studied by identifying cells that were traversed by a charged particle.
The term used to describe the effects on cells in proximity to irradiated cells, but through which radiation has not passed. In experimental radiation biology, the bystander effect can be investigated by targeting individual cells, or by using doses low enough that the probability for a given cell to be hit by a particle is less than one.
Delta ray energies increase with the velocity of the incident particle.
Highly energetic electrons produced during inelastic collisions between ionizing radiation and atomic electrons. In a small proportion of collisions, the ejected electron receives a considerable amount of energy (i.e., >1,000 eV), allowing it to travel a
The average annual dose equivalent for crew members on the ISS is approximately 300 mSv.
The product of the absorbed dose (D) at a point and the quality factor (Q) at that point for the radiation type (i.e., H = DQ). The unit of H is J-kg^[-1] with the special name sievert (Sv)
The increased risk from induced cancer due to exposure when the effects over an entire lifetime are accounted for. Individuals who would have died of cancer anyway but die early because of exposure are not included
The sample was irradiated with fast neutrons.
Neutrons of energies above a few hundred kiloelectron volts (keV)
The value of the fluence was approximately 1 particle per cm2.
The number of particles or photons per unit of cross-sectional area perpendicular to the direction of the particle (units of m^2 or cm^2) (i.e., particles-m^[-2] or particles-cm^[-2]).
The flux of cosmic ray muons per cm2 at the surface of the Earth is approximately 1.0.
The quotient of dN by dt, where dN is the increment of the particle number in the time interval dt. The unit for flux is reciprocal second (s^[-1].)
An atomic nucleus, fully stripped of its orbital electrons, containing 2 or more protons. Nuclei containing between 2 protons (helium) and 6 protons (carbon) are sometimes referred to as light ions.
In RBO--needs def from NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf)
Biological effects are a function of LET.
The energy deposited by an ionizing charged particle or photon in any medium per unit path length.
Radiation protection standards take into account organ dose as well as whole body dose.
The mean absorbed radiation dose in a specified tissue or organ of the human body.
Neutrons have a high quality factor compared to photons.
Dimensionless factor developed for purposes of radiation protection and assessing health risks in general terms that accounts for the relative biological effectiveness of different radiations in producing stochastic effects and is used to relate absorbed
The samples received a dose of 1 Gy. (The use of the gray unit implies that "dose" refers to a measured quantity, typically absorbed dose or organ dose.)
The samples received a dose of 1 Sv. (The use of the sievert unit implies that "dose" refers to a der
A measurement datum of the quantity of radiation absorbed by a substance or organism. The term "radiation dose" may for example refer to absorbed dose, organ dose, dose equivalent or equivalent dose, depending upon context and weighting factor(s).
Radiation quality is often expressed in terms of the linear energy transfer of the ionising particles that deliver the absorbed dose. Rossi, Harald H. Specification of Radiation Quality. Radiation Research, vol. 10, no. 5, Radiation Research Society, 1959, pp. 522 31, https://doi.org/10.2307/3570787. But this is an over simplification.
Is a quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited.
NCRP Glossary (https://ncrponline.org/wp-content/themes/ncrp/PDFs/NCRP-Composite-Glossary.pdf) and see https://melodi-online.eu/wp-content/uploads/2021/04/02-What-is-radiation-quality-Goodhead.pdf
Radiation weighting factors may change as more data on biological effects are obtained.
A factor used to allow for differences in the biological effectiveness between different radiations when calculating equivalent dose (H_T) (see equivalent dose). These factors are independent of the tissue or organ irradiated.
Neutrons have been found to have a higher RBE than electrons.
Factor used to compare the biological effectiveness of absorbed doses from different types of ionizing radiation, determined experimentally. RBE is the ratio of the absorbed dose of a reference radiation to the absorbed dose of the radiation in question r
Tissue equivalent materials can be used to study radiation effects at depth in the human body.
Denotes a substance with absorbing and scattering properties for a given radiation that sufficiently match those of a particular biological tissue.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
A PDS data product from the PDS 3 data model.
PDS data is tricky as while PDS3 has the concept of a data set; PDS4 doesn't really. You have to find Collections that have a collection_type of data.
pds_Data_Set_PDS3
Examples are line plots and spectrograms.
A graphical representation of data wherein the underlying numeric values are not (readily) accessible for analysis.
Catalogs include lists of events, files in a product, and data availability.
A tabular listing of events or observational notes, especially those that have utility in aiding a user in locating data.
Data stored as numerical values in one or more specified formats.
PDS data product
A PDS data product from the PDS 4 data model.
In the PDS 4 data model, only the collections that have a type of data point directly to data. Most other types point to other kinds of information products.
pds_Collection_with_Type_Data
An interface that 1) presents users with discovery criteria and may 2) lead to an access interface.
discovery interface
A campaign that is coordinated among one or more individuals and/or one or more organizations.
Field campaigns are often characterized by in situ terrestrial field work.
field campaign
A set of experiments and/or observations.
For example, the International Halley Watch mobilized observatories around the world for collection of data during the most recent apparition of Comet Halley. The Shoemaker-Levy-9 (SL9) campaign used both Earth-based and spacecraft instruments to monitor the SL9 impact on Jupiter.
A campaign that 1) uses primarily but not exclusively existing facilities and 2) after and possibly during which other investigations are carried out using the same facilities.
observing campaign
A coronal mass ejection, supernova, earthquake, spacecraft launch, etc.
Something observable that happened at a given time and place
Adapted from http://purl.obolibrary.org/obo/NCIT_C25499
event
A single science campaign may require all or part of several missions.
There may be several science campaigns occurring over the course of a single mission.
A systematic set of activities undertaken to meet a particular science objective.
Morris, Robert, Jennifer Dungan, Lina Khatib, A. Bachman, John Gasch, Paul Hempel, Jenny Williams, Terri Wood, and Christopher Bruno. "Coordinated science campaign planning for earth observing missions." In Proc. of ESTC’04. 2004.
campaign
An assay is an investigative (analytic) procedure for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of a target entity.
assay
A product containing science data from some investigation.
It is generally agreed that data is in the eye of the beholder; but, for the purposes of this project the terms data and data product are limited to traditional mostly numeric science data products that NASA holds and actually calls data or data products. Thus a DataProductService is any product or service that returns science data, normally compiled into a set according to shared characteristics.
data product
NASA (2012) NASA Thesaurus: Hierarchical Listing with Definitions. Vol 1, NASA.
The mechanical, magnetic, electronic, and electrical equipment necessary for conducting an activity.
Hardware is usually distinguished from the theory and design that make the activity possible.
hardware
author
A government agency engaged in activities related to outer space and space exploration.
space agency
A spacecraft, a person, a ship, a piece of laboratory equipment
The physical object upon or within which an instrument is mounted.
instrument host
"mouse", "Mus musculus", "rodent", "mammal", "microorganism", "fungi"
The quality of a living subject that indicates the taxonomical grouping of the subject. This grouping can be at any level in a hierachy of organism classification, or a collection of levels, and can be using scientific language or colloquial language.
MOD10A1 data files; structured metadata files; data landing page; scientific report; an API that provides search and access to a particular satellite's data; an application for displaying or analyzing data; a movie of a solar flare, images of the MODIS instrument, the Terra satellite, an astronaut, etc.
product
A data product from the GeneLab repository
study
Gender is known to be a factor in the study of high blood pressure.
The role played by an entity as part of a scientific investigation such that levels of the measurement or observation of the entity are thought to bear upon the hypotheses being investigated.
factor
A software interface that 1) presents users with selection criteria and 2) presents products or services that meet the criteria the user then selects.
access interface
For example, a series of related laboratory experiments/observations conducted by a small university team and funded through a single proposal could be an Individual Investigation. Library research by one person on previously published results to distill common conclusions could also be an Individual Investigation.
An investigation that 1) uses existing facilities and 2) is under the direction of a single individual.
research investigation
A part of a feature, taken to demonstrate or to determine the character of the whole.
A preparation of tissue or bodily fluid taken for examination or diagnosis.
Adapted from http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C19157
information product
Hardware used in conducting an experiment.
experiment Apparatus
The realisation of an application, or execution of a plan, idea, model, design, specification, standard, algorithm, or policy.
deployment
An information content entity that 1) contains a set of machine-readable instructions (most often in the form of a computer program) that 2) conform to a given syntax (sometimes referred to as a language) that 3) is interpretable by a given processor and that 4) directs a computer's processor to perform specific operations.
A role in which the bearer delivers financial support to enable some activity.
funder
An identified configuration for an instrument.
Instrument operating modes may include both hardware configurations (e.g., for instruments with multiple filters) as well as software configurations (e.g., to control how long an exposure should last). Some instruments have many such modes, others may only have one.
instrument operating mode
For example: (1) the NASA Voyager mission launched two spacecraft to Jupiter and Saturn; (2) the Deep Impact (DI) mission launched a spacecraft, part of which impacted the comet Tempel 2; and (3) the EPOXI mission redefined the objectives of the surviving DI hardware for further exploration of the solar system.
Coordinated tasks and operations undertaken to meet a set of specific objectives, within clearly delineated time and location constraints.
mission
Any procedure that involves testing or manipulating a sample or subject in a laboratory setting
A broadened version of http://purl.obolibrary.org/obo/NCIT_C25294
laboratoryProcedure
person
Per the NASA SMD glossary at https://science.nasa.gov/glossary/ a mission is a "NASA Science-funded activity with the purpose of meeting goals laid out by presidential directive, and detailed in Science Mission Directorate's strategic plan." This would mean the ontology would need to include the concepts of a presidential directive and a strategic plan - wait for a use case before implementing this change.
NASAMission
A camera, MODIS, a survey instrument (e.g., google form)
An instrument is a physical object that can be used to collect data.
instrument
A plan for a coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.
Added the phrase "plan for a" to the front of the definition per Dan's request
adapted from http://purl.obolibrary.org/obo/NCIT_C42790
experiment
An information product that contains structured metadata.
While agreed that metadata is just data about data and so is really an unneeded term, we recognize that the term metadata is often applied to information about data no matter its form. In many cases, a metadata product is available for access, even if the data is not.
metadata product
A material entity that has characteristics that can be qualified or quantified through observation or experiment.
Depending on the context, individual entities such as a human or star, may be either features or specimens - depending on whether you are interested in studying the entire class of humans or stars, or a particular star or human.
feature
Mars, a hurricane, the aurora, a molecular cloud, a sunspot, a mouse, its liver, etc.
A construction, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken.
facility
A fact or situation that is observed to exist.
phenomenon
Act of carrying out an procedure to estimate or calculate a value of a property of a feature.
observation
A graphical user interface that provides access to photographs/images.
photoGallery
An entity that can bear roles, has members, and has a set of organization rules.
A role which inheres in a person or organization and which is realized during an investigation.
investigator
A broad framework of goals to be achieved.
program
A written or printed paper that bears the original, official, or legal form of something and can be used to furnish decisive evidence or information.
Journal articles, technical or other reports, books, etc.
The American Heritage® Dictionary of the English Language, 5th Edition.
data element
The meaning of a column within a spreadsheet (e.g., identifier or height); the meaning of each pixel in an image (e.g., surface temperature)|another test example
A data element is any characteristic that can help in understanding data content. That is, a data element is any parameter or variable that is useful, or critical, when identifying or describing the content of a data object.
Software that provides the low-level control for a device's specific hardware.
firmware
A type of document, physical or digital, comprised of data and/or analytical assessment related to a scientific protocol.
Scientific documents can be referenced or included in publicationDocuments.
Any document (electronic or written record) that is about an experiment process (limited to the conduct of the experiment)
Modified from definition of http://purl.obolibrary.org/obo/NCIT_C142425
A data product that is an aggregate of data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Derived from http://purl.obolibrary.org/obo/IAO_0000100
A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.
A document that is about an item of hardware. For LSDA, hardware documents include hardware design, manufacturing, and operations documents
An individual who conducts scientific research. The investigator collects and analyses data and study documents, and provides reports in compliance with applicable requirements
Modified from http://purl.obolibrary.org/obo/NCIT_C25936
A document that is about a project. For LSDA, project documents include project operations, schedules, and other related documents.
A federally funded facility where NASA activities are undertaken.
This would include JPL and other federally funded Centers. Is that in line with NGLSDA usage?
Modified from http://purl.obolibrary.org/obo/ENVO_00000469
Semantic Type: Conceptual Entity NCIt Definition: A broad framework of goals to be achieved. Semantic Type: Organization: NCIt Definition: The principal administrative organization responsible for the research conducted.
https://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C52647 https://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C63409
NCIt Definition: A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.
"By this definition no binary files are documents (we assume they become dataset files in NGLSDA)"
for NCit: https://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C19498https://ncimetathesaurus.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20Metathesaurus&code=CL414404
A document that is an affine projection to a two dimensional surface, of EM spectrum radiation or 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 surface.)
Modified from IAO image definition and its stated relationship to the concept of document. Another source that was used to develop this definition is http://vocab.getty.edu/page/aat/300264387 which defines image as (quoting) Depictions and representations on a surface in two dimensions or low relief, or digital, whether the optical counterpart exists in reality or only in imagination. For example, the term may refer to a depiction as distinguished from its support, as when referring to a drawing as distinct from the paper upon which it is drawn.
The International Standard Payload Rack (ISPR) is a steel framework container that is designed and been adopted by the International Space Station (ISS) program to support efficient integration and interchangeability of space payload hardware, such as machines and experiment
https://home.iss.nasa.gov/home/ (under Research/Payloads) https://iss-science.jsc.nasa.gov/home
Devices, manned and unmanned, which are designed to be placed into an orbit about the Earth or into a trajectory to another celestial body.
Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products
Note that any whole entity cannot be a biospecimen
Modified from NCIT: http://purl.obolibrary.org/obo/NCIT_C70699
An entity of interest, either biological or otherwise. EXAMPLE(S): A human being who might be of interest because they are on a study, a sheep who might have experienced an adverse event, or a pacemaker that failed. An entity, either biologic or otherwise, of interest in an investigation. [Definition Source: NCI]
From investigative subject: http://purl.obolibrary.org/obo/NCIT_C79916
A set of related data (either written or electronic) and is a part of a dataset
Derived from http://purl.obolibrary.org/obo/NCIT_C42883
An item of hardware that is a part of another item of hardware.
A physical, manufactured or otherwise processed object that is used in a scientific investigation or clinical activity.
Coordinated tasks and operations undertaken to meet a set of specific scientific or technical objectives, within clearly delineated time and location constraints.
Modified from SMD Catalog definition of Mission
NCIt Definition: A printed or electronic work offered for distribution. MSH Definition: Copies of a work or document distributed to the public by sale, rental, lease, or lending. (From ALA Glossary of Library and Information Science, 1983, p181) CSP Definition: copy or copies of a document offered for distribution; includes the preparation of the documented material.
A bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate a particular subject, art, craft, technique, applied science and/or industrial service.
https://semanticscience.org/resource/SIO_000148.rdf NPD 2200.1C - https://www.nasa.gov/sites/default/files/atoms/files/n_pd_2200_001c_main.pdf Technical Publications and Reports - https://nasa.sharepoint.com/sites/NASASTIProgram/SitePages/Glossary.aspx#t
The name applied to a plant, animal, or other organism, according to the Codes of Nomenclature, consisting of a Genus and species.
Currently not in NGLSDA. (Dan to review with John)
NCIt Definition: A regularly issued printed or electronic report describing a main topic of interest to its subscribers.
NCIt Definition: An established society, corporation, foundation or other organization founded and united for a specific purpose, e.g. for health-related research; also used to refer to a building or buildings occupied or used by such organization. CDISC Definition: An established society, corporation, foundation or other organization founded and united for a specific purpose, e.g. for health-related research; also used to refer to a building or buildings occupied or used by such organization. MGED Definition: A contacts affiliation, e.g. university, research institute or business.
A document that is about a mission. For LSDA, mission documents include mission personnel, operations, schedules, and other related documents.
A person responsible for the overall conduct of a study
How long something or someone has existed; measured at launch/start
Indicates the scientific area addressed by the study. This clas is maintained by NASA Life Sciences Data Archive.
Any extent of continuous biological sequence.
A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.
Formalizes the first identity criteria for a sequence feature of its sequence.
Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property).
A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)
Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence.
A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.
Any organized collection of data in a computational format, defined by a theme or category that reflects what is being measured/observed/monitored. The presentation of the data in the application is enabled through metadata.REFERENCE. Research Data Alliance http://smw-rda.esc.rzg.mpg.de/index.php/Main_Page ; Mapping the Data Landscape 2011 Summit; TBS Standard on Geospatial Data (ISO 19115:2003); Environment Canada data stewardship … <a href=CASRAI. https://casrai.org/term/dataset/ class=more-link
Peter McQuilton
CASRAI. https://casrai.org/term/dataset/
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
Anatomical structure that is an individual member of a species and consists of more than one cell.
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Anatomical group whose component anatomical structures lie in close proximity to each other.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Functional system which consists of structures involved in respiration.
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
Anatomical structure that is part of an embryo.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].
Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
An anatomical structure that develops (entirely or partially) from the ectoderm.
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
A portion of tissue that is part of an embryo.
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
A rigid covering that envelops an object.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
Outermost layer of cells surrounding the embryo.
An anatomical structure that has more than one cell as a part.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
A basement membrane of epithelium that is part of a respiratory system.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
"A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia]
A unit which is a standard measure of the distance between two points.
"A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia]
A unit which is a standard measure of the amount of matter/energy of a physical object.
"A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia]
A unit which is a standard measure of the dimension in which events occur in sequence.
"A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the flow of electric charge." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia]
"A unit which is a standardised quantity of an element or compound with uniform composition." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the wavelength-weighted power emitted by a light source in a particular direction." [Wikipedia:Wikipedia]
"A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST]
"A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG]
"A unit which is a standard measure of the rate of change of velocity in either speed or direction." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of angular movement about an axis; the angle rotated in a given time." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of change of angular velocity." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [UOC:GVG]
"A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG]
"A unit which is a standard measure of the luminous intensity impinging on a given area." [Wikipedia:Wikipedia]
"A density unit which is a standard measure of the mass exerting an influence on a given area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the volume of a homogeneous substance containing 6.02 x 1023 atoms or molecules." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the quantity of motion measured by the product of mass and velocity." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the number of rotations in a given time." [NIST:NIST]
"A unit which is a standard measure of the volume of a given mass of substance (the reciprocal of density)." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the rate of movement. Speed is measured in the same physical units of measurement as velocity, but does not contain the element of direction that velocity has. Speed is thus the magnitude component of velocity." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution." [UOC:GVG]
"A concentration unit which is a standard measure of the number of moles of a given substance per kilogram of solvent." [UOC:GVG]
"A unit of concentration which highlights the chemical nature of salts." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST]
"A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST]
"A unit which is a standard measure of the force is applied when a mass is accelerated." [NIST:NIST]
"A unit which is a standard measure of the force applied to a given area." [NIST:NIST]
"A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST]
"A unit which is a standard measure power or the rate of doing work." [NIST:NIST]
"A unit which is a standard measure of the luminous flux incident on a unit area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the flow of radiant energy." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of the action of a catalyst." [NIST:NIST]
"A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the angle formed by three or more planes intersecting at a common point." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the amount of radiation emitted by a given radiation source as well as the amount of radiation absorbed or deposited in a specific material by a radiation source." [OCRBS:OCRBS]
"A unit which is a standard measure of the transformation (disintegration) rate of a radioactive substance." [DEFRA:DEFRA]
"A unit which is a standard measure of the energy imparted by ionizing radiation to unit mass of matter such as tissue." [DEFRA:DEFRA]
"A unit which is a standard measure of the expression of dose in terms of its biological effect." [ORCBS:ORCBS]
"A unit which is a standard measure of the quantity that expresses the ability of radiation to ionize air and thereby create electric charges which can be collected and measured." [ORCBS:ORCBS]
"A unit which is a standard measure of the power of electromagnetic radiation at a surface, per unit area." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the intensity of light." [NIST:NIST]
"A unit which is a standard measure of the intensity of electromagnetic radiation." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the power of electromagnetic radiation through space or through a material medium in the form of electromagnetic waves." [Wikipedia:Wikipedia]
"A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia]
"A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution." [Webmd:Webmd]
"A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia]
"A density unit which is a standard measure of the mass exerting an influence on a one-dimensional object." [Wikipedia:Wikipedia]
"A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia]
"A dimensionless unit which denotes a simple count of things." [MGED:MGED]
"A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia]
"A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia]
"A concentration unit which denotes the average cell number in a given volume." [Bioedonline:Bioedonline]
"A concentration unit which is a standard measure of the amount of the action of a catalyst in a given volume." [UOC:GVG]
"A dimensionless concentration unit which denotes the given volume of the solute in the total volume of the resulting solution." [NIST:NIST]
"A concentration unit which a measure of plaque forming units in a given volume." [UOC:GVG]
"A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the quantity of unbalanced electricity in a body (either positive or negative) and construed as an excess or deficiency of electrons." [WordNet:WordNet]
"A unit which is a standard measure of quantity of magnetism, taking account of the strength and the extent of a magnetic field." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet]
"A unit which is a standard measure of the amount of information." [Wikipedia:Wikipedia]
"An information unit which is a standard measure of the detail an image holds." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the way luminance and chrominance may be sampled at different levels." [Wikipedia:Wikipedia]
"A unit which is a standard measure of the ability of a liguid to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces." [NIST:NIST]
"A unit which is a standard measure of the internal resistance of fluids to flow." [UOC:GVG]
"A unit which represents a standard measurement of the transmission of an entity through a medium." [UOC:GVG]
"A unit which represents a standard measurement of the movement of electrically charged particles through a transmission medium (electrical conductor)." [UOC:GVG]
"A unit which represents a standard measurement of the spontaneous transfer of thermal energy through matter, from a region of higher temperature to a region of lower temperature." [Wikipedia:Wikipedia]
"The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
"A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia]
"A unit which represents a standard measurement occurrence of a process per unit time." [UOC:GVG]
"A prefix in the metric system denoting a factor of ten to the power of 9." [UO:GVG]
"A prefix in the metric system denoting a factor of million." [UO:GVG]
"A prefix in the metric system denoting a factor of one thousand." [UO:GVG]
"A prefix in the metric system denoting a factor of one tenth." [UO:GVG]
"A prefix in the metric system denoting a factor of one hundred." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -6." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -9." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -12." [GVG:UO]
"A prefix in the metric system denoting a factor of 10 to the power of -15." [UO:GVG]
"A prefix in the metric system denoting a factor of 10 to the power of -18." [UO:GVG]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
einstein per square meter per second based unit
watt per steradian per square meter based unit
colony forming unit per milliliter based unit
plaque forming unit per milliliter based unit
The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource.
A list of types used to categorize the nature or genre of the content of the resource.
DCMI Type Vocabulary
A set of date encoding schemes and/or formats
Date Encoding Schemes
A set of format encoding schemes.
Format Encoding Schemes
A set of resource identifier encoding schemes and/or formats
Resource Identifier Encoding Schemes
A set of language encoding schemes and/or formats.
Language Encoding Schemes
A set of resource relation encoding schemes and/or formats
Resource Relation Encoding Schemes
A set of source encoding schemes and/or formats
Source Encoding Schemes
A set of geographic place encoding schemes and/or formats
Place Encoding Schemes
A set of subject encoding schemes and/or formats
Subject Encoding Schemes
A set of encoding schemes for the coverage qualifier "temporal"
Encoding Schemes for temporal characteristics
A set of resource type encoding schemes and/or formats
Resource Type Encoding Schemes
Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.
Modified in parts from https://en.wikipedia.org/wiki/Software
AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship.
A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
Modified from http://en.wikipedia.org/wiki/Software_license
licence
The mode of interaction with a piece of software.
A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services.
Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013.
A Graphical user interface is a type of software interface that allows users to interact with electronic devices using images rather than text commands. A GUI represents the information and actions available to a user through graphical icons and visual indicators such as secondary notation, as opposed to text-based interfaces, typed command labels or text navigation.
https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013.
An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact.
http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014.
Acquaintance
Address
Agent
This class is deprecated
BBS
Car
Also called mobile telephone
Cell
Child
Colleague
Contact
Coresident
Coworker
Crush
Dom
To specify the electronic mail address for communication with the object the vCard represents. Use the hasEmail object property.
Email
Emergency
Fax
Female
Friend
Used for gender codes. The URI of the gender code must be used as the value for Gender.
Gender
Object representing a group of persons or entities. A group object will usually contain hasMember properties to specify the members of the group.
Group
This implies that the property is related to an individual's personal life
Home
ISDN
An object representing a single person or entity
Individual
Internet
Intl
Kin
The parent class for all objects
Kind
Label
An object representing a named geographical place
Location
Male
Met
Modem
Msg
Muse
Name
Neighbor
None
An object representing an organization. An organization is a single entity, and might represent a business or government, a department or division within a business or government, a club, an association, or the like.
Organization
Other
PCS
Pager
Parcel
Parent
Postal
Pref
Used for relation type codes. The URI of the relation type code must be used as the value for the Relation Type.
Relation Type
Sibling
Spouse
Sweetheart
This class is deprecated. Use the hasTelephone object property.
Tel
Used for telephone type codes. The URI of the telephone type code must be used as the value for the Telephone Type.
Phone
Also called sms telephone
Text
Text phone
Used for type codes. The URI of the type code must be used as the value for Type.
Type
Unknown
The vCard class is equivalent to the new Kind class, which is the parent for the four explicit types of vCards (Individual, Organization, Location, Group)
VCard
Video
Voice
This implies that the property is related to an individual's work place
Work
A curated collection of metadata about resources (e.g., datasets and data services in the context of a data catalog).
En udvalgt og arrangeret samling af metadata om ressourcer (fx datasæt og datatjenester i kontekst af et datakatalog).
Una colección curada de metadatos sobre recursos (por ejemplo, conjuntos de datos y servicios de datos en el contexto de un catálogo de datos).
Una raccolta curata di metadati sulle risorse (ad es. sui dataset e relativi servizi nel contesto di cataloghi di dati).
Une collection élaborée de métadonnées sur les jeux de données
Řízená kolekce metadat o datových sadách a datových službách
Μια επιμελημένη συλλογή μεταδεδομένων περί συνόλων δεδομένων
مجموعة من توصيفات قوائم البيانات
データ・カタログは、データセットに関するキュレートされたメタデータの集合です。
Catalog
Catalogo
Catalogue
Catálogo
Katalog
Κατάλογος
فهرس قوائم البيانات
カタログ
En samling af metadata om ressourcer (fx datasæt og datatjenester i kontekst af et datakatalog).
English, Italian, Spanish definitions updated in this revision. Multilingual text not yet updated.
A web-based data catalog is typically represented as a single instance of this class.
Et webbaseret datakatalog repræsenteres typisk ved en enkelt instans af denne klasse.
Normalmente, un catalogo di dati nel web viene rappresentato come una singola istanza di questa classe.
Normalmente, un catálogo de datos disponible en la web se representa como una única instancia de esta clase.
Webový datový katalog je typicky reprezentován jako jedna instance této třídy.
Συνήθως, ένας κατάλογος δεδομένων στον Παγκόσμιο Ιστό αναπαρίσταται ως ένα στιγμιότυπο αυτής της κλάσης.
通常、ウェブ・ベースのデータ・カタログは、このクラスの1つのインスタンスとして表わされます。
1つのデータセットを記述したデータ・カタログ内のレコード。
A record in a data catalog, describing the registration of a single dataset or data service.
En post i et datakatalog der beskriver registreringen af et enkelt datasæt eller en datatjeneste.
Un record in un catalogo di dati che descrive un singolo dataset o servizio di dati.
Un registre du catalogue ou une entrée du catalogue, décrivant un seul jeu de données.
Un registro en un catálogo de datos que describe un solo conjunto de datos o un servicio de datos.
Záznam v datovém katalogu popisující jednu datovou sadu či datovou službu.
Μία καταγραφή ενός καταλόγου, η οποία περιγράφει ένα συγκεκριμένο σύνολο δεδομένων.
Catalog Record
Katalogizační záznam
Katalogpost
Record di catalogo
Registre du catalogue
Registro del catálogo
Καταγραφή καταλόγου
English definition updated in this revision. Multilingual text not yet updated except the Spanish one and the Czech one and Italian one.
C'est une classe facultative et tous les catalogues ne l'utiliseront pas. Cette classe existe pour les catalogues ayant une distinction entre les métadonnées sur le jeu de données et les métadonnées sur une entrée du jeu de données dans le catalogue.
Denne klasse er valgfri og ikke alle kataloger vil anvende denne klasse. Den kan anvendes i de kataloger hvor der skelnes mellem metadata om datasættet eller datatjenesten og metadata om selve posten til registreringen af datasættet eller datatjenesten i kataloget. Udgivelsesdatoen for datasættet afspejler for eksempel den dato hvor informationerne oprindeligt blev gjort tilgængelige af udgiveren, hvorimod udgivelsesdatoen for katalogposten er den dato hvor datasættet blev føjet til kataloget. I de tilfælde hvor de to datoer er forskellige eller hvor blot sidstnævnte er kendt, bør udgivelsesdatoen kun angives for katalogposten. Bemærk at W3Cs PROV ontologi gør til muligt at tilføje yderligere proveniensoplysninger eksempelvis om processen eller aktøren involveret i en given ændring af datasættet.
Esta clase es opcional y no todos los catálogos la utilizarán. Esta clase existe para catálogos que hacen una distinción entre los metadatos acerca de un conjunto de datos o un servicio de datos y los metadatos acerca de una entrada en ese conjunto de datos en el catálogo. Por ejemplo, la propiedad sobre la fecha de la publicación de los datos refleja la fecha en que la información fue originalmente publicada, mientras que la fecha de publicación del registro del catálogo es la fecha en que los datos se agregaron al mismo. En caso en que ambas fechas fueran diferentes, o en que sólo la fecha de publicación del registro del catálogo estuviera disponible, sólo debe especificarse en el registro del catálogo. Tengan en cuenta que la ontología PROV de W3C permite describir otra información sobre la proveniencia de los datos, como por ejemplo detalles del proceso y de los agentes involucrados en algún cambio específico a los datos.
Questa classe è opzionale e non tutti i cataloghi la utilizzeranno. Esiste per cataloghi in cui si opera una distinzione tra i metadati relativi al dataset ed i metadati relativi alla gestione del dataset nel catalogo. Ad esempio, la proprietà per indicare la data di pubblicazione del dataset rifletterà la data in cui l'informazione è stata originariamente messa a disposizione dalla casa editrice, mentre la data di pubblicazione per il record nel catalogo rifletterà la data in cui il dataset è stato aggiunto al catalogo. Nei casi dove solo quest'ultima sia nota, si utilizzerà esclusivamente la data di pubblicazione relativa al record del catalogo. Si noti che l'Ontologia W3C PROV permette di descrivere ulteriori informazioni sulla provenienza, quali i dettagli del processo, la procedura e l'agente coinvolto in una particolare modifica di un dataset.
Tato třída je volitelná a ne všechny katalogy ji využijí. Existuje pro katalogy, ve kterých se rozlišují metadata datové sady či datové služby a metadata o záznamu o datové sadě či datové službě v katalogu. Například datum publikace datové sady odráží datum, kdy byla datová sada původně zveřejněna poskytovatelem dat, zatímco datum publikace katalogizačního záznamu je datum zanesení datové sady do katalogu. V případech kdy se obě data liší, nebo je známo jen to druhé, by mělo být specifikováno jen datum publikace katalogizačního záznamu. Všimněte si, že ontologie W3C PROV umožňuje popsat další informace o původu jako například podrobnosti o procesu konkrétní změny datové sady a jeho účastnících.
This class is optional and not all catalogs will use it. It exists for catalogs where a distinction is made between metadata about a dataset or data service and metadata about the entry for the dataset or data service in the catalog. For example, the publication date property of the dataset reflects the date when the information was originally made available by the publishing agency, while the publication date of the catalog record is the date when the dataset was added to the catalog. In cases where both dates differ, or where only the latter is known, the publication date should only be specified for the catalog record. Notice that the W3C PROV Ontology allows describing further provenance information such as the details of the process and the agent involved in a particular change to a dataset.
Αυτή η κλάση είναι προαιρετική και δεν χρησιμοποιείται από όλους τους καταλόγους. Υπάρχει για τις περιπτώσεις καταλόγων όπου γίνεται διαχωρισμός μεταξύ των μεταδεδομένων για το σύνολο των δεδομένων και των μεταδεδομένων για την καταγραφή του συνόλου δεδομένων εντός του καταλόγου. Για παράδειγμα, η ιδιότητα της ημερομηνίας δημοσίευσης του συνόλου δεδομένων δείχνει την ημερομηνία κατά την οποία οι πληροφορίες έγιναν διαθέσιμες από τον φορέα δημοσίευσης, ενώ η ημερομηνία δημοσίευσης της καταγραφής του καταλόγου δείχνει την ημερομηνία που το σύνολο δεδομένων προστέθηκε στον κατάλογο. Σε περιπτώσεις που οι δύο ημερομηνίες διαφέρουν, ή που μόνο η τελευταία είναι γνωστή, η ημερομηνία δημοσίευσης θα πρέπει να δίνεται για την καταγραφή του καταλόγου. Να σημειωθεί πως η οντολογία W3C PROV επιτρέπει την περιγραφή επιπλέον πληροφοριών ιστορικού όπως λεπτομέρειες για τη διαδικασία και τον δράστη που εμπλέκονται σε μία συγκεκριμένη αλλαγή εντός του συνόλου δεδομένων.
このクラスはオプションで、すべてのカタログがそれを用いるとは限りません。これは、データセットに関するメタデータとカタログ内のデータセットのエントリーに関するメタデータとで区別が行われるカタログのために存在しています。例えば、データセットの公開日プロパティーは、公開機関が情報を最初に利用可能とした日付を示しますが、カタログ・レコードの公開日は、データセットがカタログに追加された日付です。両方の日付が異っていたり、後者だけが分かっている場合は、カタログ・レコードに対してのみ公開日を指定すべきです。W3CのPROVオントロジー[prov-o]を用いれば、データセットに対する特定の変更に関連するプロセスやエージェントの詳細などの、さらに詳しい来歴情報の記述が可能となることに注意してください。
A site or end-point providing operations related to the discovery of, access to, or processing functions on, data or related resources.
Et websted eller endpoint der udstiller operationer relateret til opdagelse af, adgang til eller behandlende funktioner på data eller relaterede ressourcer.
Umístění či přístupový bod poskytující operace související s hledáním, přistupem k, či výkonem funkcí na datech či souvisejících zdrojích.
Un sitio o end-point que provee operaciones relacionadas a funciones de descubrimiento, acceso, o procesamiento de datos o recursos relacionados.
Un sito o end-point che fornisce operazioni relative alla scoperta, all'accesso o all'elaborazione di funzioni su dati o risorse correlate.
Data service
Datatjeneste
Servicio de datos
Servizio di dati
Dataservice
New class added in DCAT 2.0.
Nová třída přidaná ve verzi DCAT 2.0.
Nueva clase añadida en DCAT 2.0.
Nuova classe aggiunta in DCAT 2.0.
Ny klasse tilføjet i DCAT 2.0.
Et site eller endpoint der udstiller operationer relateret til opdagelse af, adgang til eller behandlende funktioner på data eller relaterede ressourcer.
Datatjenestetypen kan indikeres ved hjælp af egenskaben dct:type. Værdien kan tages fra kontrollerede udfaldsrum såsom INSPIRE spatial data service vocabulary.
Druh služby může být indikován vlastností dct:type. Její hodnota může být z řízeného slovníku, kterým je například slovník typů prostorových datových služeb INSPIRE.
El tipo de servicio puede indicarse usando la propiedad dct:type. Su valor puede provenir de un vocabulario controlado, como por ejemplo el vocabulario de servicios de datos espaciales de INSPIRE.
Hvis en dcat:DataService er bundet til en eller flere specifikke datasæt kan dette indikeres ved hjælp af egenskaben dcat:servesDataset.
If a dcat:DataService is bound to one or more specified Datasets, they are indicated by the dcat:servesDataset property.
Il tipo di servizio può essere indicato usando la proprietà dct:type. Il suo valore può essere preso da un vocabolario controllato come il vocabolario dei tipi di servizi per dati spaziali di INSPIRE.
Pokud je dcat:DataService navázána na jednu či více Datových sad, jsou tyto indikovány vlstností dcat:servesDataset.
Se un dcat:DataService è associato a uno o più Dataset specificati, questi sono indicati dalla proprietà dcat:serveDataset.
Si un dcat:DataService está asociado con uno o más conjuntos de datos especificados, dichos conjuntos de datos pueden indicarse con la propiedad dcat:servesDataset.
The kind of service can be indicated using the dct:type property. Its value may be taken from a controlled vocabulary such as the INSPIRE spatial data service type vocabulary.
1つのエージェントによって公開またはキュレートされ、1つ以上の形式でアクセスまたはダウンロードできるデータの集合。
A collection of data, published or curated by a single source, and available for access or download in one or more representations.
En samling af data, udgivet eller udvalgt og arrangeret af en enkelt kilde og som er til råde for adgang til eller download af i en eller flere repræsentationer.
Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech.
Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati.
Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos.
Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats.
Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές.
قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها
Conjunto de datos
Dataset
Datasæt
Datová sada
Jeu de données
Σύνολο Δεδομένων
Datasamling
2018-02 - odstraněno tvrzení o podtřídě dctype:Dataset, jelikož rozsah dcat:Dataset zahrnuje několik dalších typů ze slovníku dctype.
2018-02 - se eliminó el axioma de subclase con dctype:Dataset porque el alcance de dcat:Dataset incluye muchos otros tipos del vocabulario dctype.
2018-02 - sottoclasse di dctype:Dataset rimosso perché l'ambito di dcat:Dataset include diversi altri tipi dal vocabolario dctype.
2018-02 - subclass of dctype:Dataset removed because scope of dcat:Dataset includes several other types from the dctype vocabulary.
2018-02 - subklasse af dctype:Dataset fjernet da scope af dcat:Dataset omfatter flere forskellige typer fra dctype-vokabularet.
A collection of data, published or curated by a single source, and available for access or download in one or more represenations.
En samling a data, udgivet eller udvalgt og arrangeret af en enkelt kilde og som der er adgang til i en eller flere repræsentationer.
2020-03-16 A new scopenote added and need to be translated
Cette classe représente le jeu de données publié par le fournisseur de données. Dans les cas où une distinction est nécessaire entre le jeu de donénes et son entrée dans le catalogue, la classe registre de données peut être utilisée pour ce dernier.
Denne klasse beskriver det konceptuelle datasæt. En eller flere repræsentationer kan være tilgængelige med forskellige skematiske opsætninger, formater eller serialiseringer.
Denne klasse repræsenterer det konkrete datasæt som det udgives af datasætleverandøren. I de tilfælde hvor det er nødvendigt at skelne mellem det konkrete datasæt og dets registrering i kataloget (fordi metadata såsom ændringsdato og vedligeholder er forskellige), så kan klassen katalogpost anvendes.
Esta clase representa el conjunto de datos publicados. En los casos donde es necesario distinguir entre el conjunto de datos y su entrada en el catálogo de datos, se debe utilizar la clase 'registro del catálogo'.
Questa classe descrive il dataset dal punto di vista concettuale. Possono essere disponibili una o più rappresentazioni, con diversi layout e formati schematici o serializzazioni.
Questa classe rappresenta il dataset come pubblicato dall’editore. Nel caso in cui sia necessario operare una distinzione fra i metadati originali del dataset e il record dei metadati ad esso associato nel catalogo (ad esempio, per distinguere la data di modifica del dataset da quella del dataset nel catalogo) si può impiegare la classe catalog record.
Tato třída reprezentuje datovou sadu tak, jak je publikována poskytovatelem dat. V případě potřeby rozlišení datové sady a jejího katalogizačního záznamu (jelikož metadata jako datum modifikace se mohou lišit) pro něj může být použita třída "katalogizační záznam".
The notion of dataset in DCAT is broad and inclusive, with the intention of accommodating resource types arising from all communities. Data comes in many forms including numbers, text, pixels, imagery, sound and other multi-media, and potentially other types, any of which might be collected into a dataset.
This class describes the conceptual dataset. One or more representations might be available, with differing schematic layouts and formats or serializations.
This class represents the actual dataset as published by the dataset provider. In cases where a distinction between the actual dataset and its entry in the catalog is necessary (because metadata such as modification date and maintainer might differ), the catalog record class can be used for the latter.
Η κλάση αυτή αναπαριστά το σύνολο δεδομένων αυτό καθ'εαυτό, όπως έχει δημοσιευθεί από τον εκδότη. Σε περιπτώσεις όπου είναι απαραίτητος ο διαχωρισμός μεταξύ του συνόλου δεδομένων και της καταγραφής αυτού στον κατάλογο (γιατί μεταδεδομένα όπως η ημερομηνία αλλαγής και ο συντηρητής μπορεί να διαφέρουν) η κλάση της καταγραφής καταλόγου μπορεί να χρησιμοποιηθεί για το τελευταίο.
このクラスは、データセットの公開者が公開する実際のデータセットを表わします。カタログ内の実際のデータセットとそのエントリーとの区別が必要な場合（修正日と維持者などのメタデータが異なるかもしれないので）は、後者にcatalog recordというクラスを使用できます。
A specific representation of a dataset. A dataset might be available in multiple serializations that may differ in various ways, including natural language, media-type or format, schematic organization, temporal and spatial resolution, level of detail or profiles (which might specify any or all of the above).
En specifik repræsentation af et datasæt. Et datasæt kan være tilgængelig i mange serialiseringer der kan variere på forskellige vis, herunder sprog, medietype eller format, systemorganisering, tidslig- og geografisk opløsning, detaljeringsniveau eller profiler (der kan specificere en eller flere af ovenstående).
Konkrétní reprezentace datové sady. Datová sada může být dostupná v různých serializacích, které se mohou navzájem lišit různými způsoby, mimo jiné přirozeným jazykem, media-typem či formátem, schematickou organizací, časovým a prostorovým rozlišením, úrovní detailu či profily (které mohou specifikovat některé či všechny tyto rozdíly).
Rappresenta una forma disponibile e specifica del dataset. Ciascun dataset può essere disponibile in forme differenti, che possono rappresentare formati diversi o diversi punti di accesso per un dataset. Esempi di distribuzioni sono un file CSV scaricabile, una API o un RSS feed.
Représente une forme spécifique d'un jeu de données. Caque jeu de données peut être disponible sous différentes formes, celles-ci pouvant représenter différents formats du jeu de données ou différents endpoint. Des exemples de distribution sont des fichirs CSV, des API ou des flux RSS.
Una representación específica de los datos. Cada conjunto de datos puede estar disponible en formas diferentes, las cuáles pueden variar en distintas formas, incluyendo el idioma, 'media-type' o formato, organización esquemática, resolución temporal y espacial, nivel de detalle o perfiles (que pueden especificar cualquiera o todas las diferencias anteriores).
Αναπαριστά μία συγκεκριμένη διαθέσιμη μορφή ενός συνόλου δεδομένων. Κάθε σύνολο δεδομενων μπορεί να είναι διαθέσιμο σε διαφορετικές μορφές, οι μορφές αυτές μπορεί να αναπαριστούν διαφορετικές μορφές αρχείων ή διαφορετικά σημεία διάθεσης. Παραδείγματα διανομών συμπεριλαμβάνουν ένα μεταφορτώσιμο αρχείο μορφής CSV, ένα API ή ένα RSS feed.
شكل محدد لقائمة البيانات يمكن الوصول إليه. قائمة بيانات ما يمكن أن تكون متاحه باشكال و أنواع متعددة. ملف يمكن تحميله أو واجهة برمجية يمكن من خلالها الوصول إلى البيانات هي أمثلة على ذلك.
データセットの特定の利用可能な形式を表わします。各データセットは、異なる形式で利用できることがあり、これらの形式は、データセットの異なる形式や、異なるエンドポイントを表わす可能性があります。配信の例には、ダウンロード可能なCSVファイル、API、RSSフィードが含まれます。
Distribuce
Distribución
Distribution
Distribuzione
Διανομή
التوزيع
配信
Datadistribution
Datamanifestation
Datarepræsentation
Dataudstilling
Ceci représente une disponibilité générale du jeu de données, et implique qu'il n'existe pas d'information sur la méthode d'accès réelle des données, par exple, si c'est un lien de téléchargement direct ou à travers une page Web.
Denne klasse repræsenterer datasættets overordnede tilgængelighed og giver ikke oplysninger om hvilken metode der kan anvendes til at få adgang til data, dvs. om adgang til datasættet realiseres ved direkte download, API eller via et websted. Anvendelsen af egenskaben dcat:downloadURL indikerer at distributionen kan downloades direkte.
Esta clase representa una disponibilidad general de un conjunto de datos, e implica que no existe información acerca del método de acceso real a los datos, i.e., si es un enlace de descarga directa o a través de una página Web.
Questa classe rappresenta una disponibilità generale di un dataset e non implica alcuna informazione sul metodo di accesso effettivo ai dati, ad esempio se si tratta di un accesso a download diretto, API, o attraverso una pagina Web. L'utilizzo della proprietà dcat:downloadURL indica distribuzioni direttamente scaricabili.
This represents a general availability of a dataset it implies no information about the actual access method of the data, i.e. whether by direct download, API, or through a Web page. The use of dcat:downloadURL property indicates directly downloadable distributions.
Toto popisuje obecnou dostupnost datové sady. Neimplikuje žádnou informaci o skutečné metodě přístupu k datům, tj. zda jsou přímo ke stažení, skrze API či přes webovou stránku. Použití vlastnosti dcat:downloadURL indikuje přímo stažitelné distribuce.
Αυτό αναπαριστά μία γενική διαθεσιμότητα ενός συνόλου δεδομένων και δεν υπονοεί τίποτα περί του πραγματικού τρόπου πρόσβασης στα δεδομένα, αν είναι άμεσα μεταφορτώσιμα, μέσω API ή μέσω μίας ιστοσελίδας. Η χρήση της ιδιότητας dcat:downloadURL δείχνει μόνο άμεσα μεταφορτώσιμες διανομές.
これは、データセットの一般的な利用可能性を表わし、データの実際のアクセス方式に関する情報（つまり、直接ダウンロードなのか、APIなのか、ウェブページを介したものなのか）を意味しません。dcat:downloadURLプロパティーの使用は、直接ダウンロード可能な配信を意味します。
An association class for attaching additional information to a relationship between DCAT Resources.
Asociační třída pro připojení dodatečných informací ke vztahu mezi zdroji DCAT.
En associationsklasse til brug for tilknytning af yderligere information til en relation mellem DCAT-ressourcer.
Una clase de asociación para adjuntar información adicional a una relación entre recursos DCAT.
Una classe di associazione per il collegamento di informazioni aggiuntive a una relazione tra le risorse DCAT.
Relación
Relationship
Relazione
Vztah
Ny klasse i DCAT 2.0.
Anvendes til at karakterisere en relation mellem datasæt, og potentielt andre ressourcer, hvor relationen er kendt men ikke tilstrækkeligt beskrevet af de standardiserede egenskaber i Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) eller PROV-O-egenskaber (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Používá se pro charakterizaci vztahu mezi datovými sadami a případně i jinými zdroji, kde druh vztahu je sice znám, ale není přiměřeně charakterizován standardními vlastnostmi slovníku Dublin Core (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) či vlastnostmi slovníku PROV-O (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Se usa para caracterizar la relación entre conjuntos de datos, y potencialmente otros recursos, donde la naturaleza de la relación se conoce pero no está caracterizada adecuadamente con propiedades del estándar 'Dublin Core' (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) or PROV-O properties (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Use to characterize a relationship between datasets, and potentially other resources, where the nature of the relationship is known but is not adequately characterized by the standard Dublin Core properties (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:requires, dct:isRequiredBy) or PROV-O properties (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov:hadPrimarySource, prov:alternateOf, prov:specializationOf).
Viene utilizzato per caratterizzare la relazione tra insiemi di dati, e potenzialmente altri tipi di risorse, nei casi in cui la natura della relazione è nota ma non adeguatamente caratterizzata dalle proprietà dello standard 'Dublin Core' (dct:hasPart, dct:isPartOf, dct:conformsTo, dct:isFormatOf, dct:hasFormat, dct:isVersionOf, dct:hasVersion, dct:replaces, dct:isReplacedBy, dct:references, dct:isReferencedBy, dct:require, dct:isRequiredBy) o dalle propietà fornite da PROV-O (prov:wasDerivedFrom, prov:wasInfluencedBy, prov:wasQuotedFrom, prov:wasRevisionOf, prov: hadPrimarySource, prov:alternateOf, prov:specializationOf).
Recurso publicado o curado por un agente único.
Resource published or curated by a single agent.
Ressource udgivet eller udvalgt og arrangeret af en enkelt aktør.
Risorsa pubblicata o curata da un singolo agente.
Zdroj publikovaný či řízený jediným činitelem.
Catalogued resource
Katalogiseret ressource
Katalogizovaný zdroj
Recurso catalogado
Risorsa catalogata
Nueva clase agregada en DCAT 2.0.
Klassen for alle katalogiserede ressourcer, den overordnede klasse for dcat:Dataset, dcat:DataService, dcat:Catalog og enhvert medlem af et dcat:Catalog. Denne klasse bærer egenskaber der gælder alle katalogiserede ressourcer, herunder dataset og datatjenester. Det anbefales kraftigt at mere specifikke subklasser oprettes. Når der beskrives ressourcer der ikke er dcat:Dataset eller dcat:DataService, anbefales det at oprette passende subklasser af dcat:Resource eller at dcat:Resource anvendes sammen med egenskaben dct:type til opmærkning med en specifik typeangivelse.
La clase de todos los recursos catalogados, la superclase de dcat:Dataset, dcat:DataService, dcat:Catalog y cualquier otro miembro de un dcat:Catalog. Esta clase tiene propiedades comunes a todos los recursos catalogados, incluyendo conjuntos de datos y servicios de datos. Se recomienda fuertemente que se use una clase más específica. Cuando se describe un recurso que no es un dcat:Dataset o dcat:DataService, se recomienda crear una sub-clase apropiada de dcat:Resource, o usar dcat:Resource con la propiedad dct:type to indicar el tipo específico.
La classe di tutte le risorse catalogate, la Superclasse di dcat:Dataset, dcat:DataService, dcat:Catalog e qualsiasi altro membro di dcat:Catalog. Questa classe porta proprietà comuni a tutte le risorse catalogate, inclusi set di dati e servizi dati. Si raccomanda vivamente di utilizzare una sottoclasse più specifica. Quando si descrive una risorsa che non è un dcat:Dataset o dcat:DataService, si raccomanda di creare una sottoclasse di dcat:Resource appropriata, o utilizzare dcat:Resource con la proprietà dct:type per indicare il tipo specifico.
The class of all catalogued resources, the Superclass of dcat:Dataset, dcat:DataService, dcat:Catalog and any other member of a dcat:Catalog. This class carries properties common to all catalogued resources, including datasets and data services. It is strongly recommended to use a more specific sub-class. When describing a resource which is not a dcat:Dataset or dcat:DataService, it is recommended to create a suitable sub-class of dcat:Resource, or use dcat:Resource with the dct:type property to indicate the specific type.
Třída všech katalogizovaných zdrojů, nadtřída dcat:Dataset, dcat:DataService, dcat:Catalog a všech ostatních členů dcat:Catalog. Tato třída nese vlastnosti společné všem katalogizovaným zdrojům včetně datových sad a datových služeb. Je silně doporučeno používat specifičtější podtřídy, pokud je to možné. Při popisu zdroje, který není ani dcat:Dataset, ani dcat:DataService se doporučuje vytvořit odpovídající podtřídu dcat:Resrouce a nebo použít dcat:Resource s vlastností dct:type pro určení konkrétního typu.
dcat:Resource er et udvidelsespunkt der tillader oprettelsen af enhver type af kataloger. Yderligere subklasser kan defineres i en DCAT-profil eller i en applikation til kataloger med andre typer af ressourcer.
dcat:Resource es un punto de extensión que permite la definición de cualquier tipo de catálogo. Se pueden definir subclases adicionales en perfil de DCAT o una aplicación para catálogos de otro tipo de recursos.
dcat:Resource is an extension point that enables the definition of any kind of catalog. Additional subclasses may be defined in a DCAT profile or application for catalogs of other kinds of resources.
dcat:Resource je bod pro rozšíření umožňující definici různých druhů katalogů. Další podtřídy lze definovat v profilech DCAT či aplikacích pro katalogy zdrojů jiných druhů.
dcat:Resource è un punto di estensione che consente la definizione di qualsiasi tipo di catalogo. Sottoclassi aggiuntive possono essere definite in un profilo DCAT o in un'applicazione per cataloghi di altri tipi di risorse.
A role is the function of a resource or agent with respect to another resource, in the context of resource attribution or resource relationships.
En rolle er den funktion en ressource eller aktør har i forhold til en anden ressource, i forbindelse med ressourcekreditering eller ressourcerelationer.
Role je funkce zdroje či agenta ve vztahu k jinému zdroji, v kontextu přiřazení zdrojů či vztahů mezi zdroji.
Un rol es la función de un recurso o agente con respecto a otro recuros, en el contexto de atribución del recurso o de las relaciones entre recursos.
Un ruolo è la funzione di una risorsa o di un agente rispetto ad un'altra risorsa, nel contesto dell'attribuzione delle risorse o delle relazioni tra risorse.
Rol
Role
Rolle
Ruolo
Incluída en DCAT para complementar prov:Role (cuyo uso está limitado a roles en el contexto de una actividad, ya que es el rango es prov:hadRole).
Introdotta in DCAT per completare prov:Role (il cui uso è limitato ai ruoli nel contesto di un'attività, in conseguenza alla definizione del codominio di prov:hadRole).
Introduced into DCAT to complement prov:Role (whose use is limited to roles in the context of an activity, as the range of prov:hadRole).
Introduceret i DCAT for at supplere prov:Role (hvis anvendelse er begrænset til roller i forbindelse med en aktivitet, som er rækkevidde for prov:hadRole).
Přidáno do DCAT pro doplnění třídy prov:Role (jejíž užití je omezeno na role v kontextu aktivit, jakožto obor hodnot vlastnosti prov:hadRole).
Anvendes i forbindelse med kvalificerede krediteringer til at angive aktørens rolle i forhold til en entitet. Det anbefales at værdierne styres som et kontrolleret udfaldsrum med aktørroller, såsom http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Anvendes i forbindelse med kvalificerede relationer til at specificere en entitets rolle i forhold til en anden entitet. Det anbefales at værdierne styres med et kontrolleret udfaldsrum for for entitetsroller såsom: ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode; IANA Registry of Link Relations https://www.iana.org/assignments/link-relation; DataCite metadata schema; MARC relators https://id.loc.gov/vocabulary/relators.
Použito v kvalifikovaném přiřazení pro specifikaci role Agenta ve vztahu k Entitě. Je doporučeno množinu hodnot spravovat jako řízený slovník rolí agentů, jako například http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Použito v kvalifikovaném vztahu pro specifikaci role Entity ve vztahu k jiné Entitě. Je doporučeno množinu hodnot spravovat jako řízený slovník rolí entit, jako například ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode, IANA Registry of Link Relations https://www.iana.org/assignments/link-relation, DataCite metadata schema, či MARC relators https://id.loc.gov/vocabulary/relators.
Se usa en una atribución cualificada para especificar el rol de un Agente con respecto a una Entidad. Se recomienda que los valores se administren como un vocabulario controlado de roles de agente, como por ejemplo http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Se usa en una relación cualificada para especificar el rol de una Entidad con respecto a otra Entidad. Se recomienda que los valores se administren como los valores de un vocabulario controlado de roles de entidad como por ejemplo: ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode; IANA Registry of Link Relations https://www.iana.org/assignments/link-relation; el esquema de metadatos de DataCite; MARC relators https://id.loc.gov/vocabulary/relators.
Used in a qualified-attribution to specify the role of an Agent with respect to an Entity. It is recommended that the values be managed as a controlled vocabulary of agent roles, such as http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Used in a qualified-relation to specify the role of an Entity with respect to another Entity. It is recommended that the values be managed as a controlled vocabulary of entity roles such as: ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode; IANA Registry of Link Relations https://www.iana.org/assignments/link-relation; DataCite metadata schema; MARC relators https://id.loc.gov/vocabulary/relators.
Utilizzato in un'attribuzione qualificata per specificare il ruolo di un agente rispetto a un'entità. Si consiglia di attribuire i valori considerando un vocabolario controllato dei ruoli dell'agente, ad esempio http://registry.it.csiro.au/def/isotc211/CI_RoleCode.
Utilizzato in una relazione qualificata per specificare il ruolo di un'entità rispetto a un'altra entità. Si raccomanda che il valore sia preso da un vocabolario controllato di ruoli di entità come ISO 19115 DS_AssociationTypeCode http://registry.it.csiro.au/def/isotc211/DS_AssociationTypeCode, IANA Registry of Link Relations https://www.iana.org/assignments/link-relation, DataCite metadata schema, o MARC relators https://id.loc.gov/vocabulary/relators.
Act of carrying out an (Observation) Procedure to estimate or calculate a value of a property of a FeatureOfInterest. Links to a Sensor to describe what made the Observation and how; links to an ObservableProperty to describe what the result is an estimate of, and to a FeatureOfInterest to detail what that property was associated with.
Observation
The activity of estimating the intensity of an Earthquake using the Mercalli intensity scale is an Observation as is measuring the moment magnitude, i.e., the energy released by said earthquake.
A Platform is an entity that hosts other entities, particularly Sensors, Actuators, Samplers, and other Platforms.
Platform
A post, buoy, vehicle, ship, aircraft, satellite, cell-phone, human or animal may act as platforms for (technical or biological) sensors or actuators.
Device, agent (including humans), or software (simulation) involved in, or implementing, a Procedure. Sensors respond to a stimulus, e.g., a change in the environment, or input data composed from the results of prior Observations, and generate a Result. Sensors can be hosted by Platforms.
Sensor
Accelerometers, gyroscopes, barometers, magnetometers, and so forth are Sensors that are typically mounted on a modern smart phone (which acts as Platform). Other examples of sensors include the human eyes.
A bus (also omnibus or autobus) is a road vehicle designed to carry passengers. Coaches are luxury busses, usually in service for long distance travel.
BusOrCoach
A car is a wheeled, self-powered motor vehicle used for transportation.
A CompleteDataFeed is a DataFeed whose standard representation includes content for every item currently in the feed. This is the equivalent of Atom's element as defined in Feed Paging and Archiving RFC 5005, for example (and as defined for Atom), when using data from a feed that represents a collection of items that varies over time (e.g. "Top Twenty Records") there is no need to have newer entries mixed in alongside older, obsolete entries. By marking this feed as a CompleteDataFeed, old entries can be safely discarded when the feed is refreshed, since we can assume the feed has provided descriptions for all current items.
CompleteDataFeed
A single feed providing structured information about one or more entities or topics.
DataFeed
A body of structured information describing some topic(s) of interest.
A chemical or biologic substance, used as a medical therapy, that has a physiological effect on an organism. Here the term drug is used interchangeably with the term medicine although clinical knowledge makes a clear difference between them.
Drug
A subclass of OrganizationRole used to describe employee relationships.
EmployeeRole
Fitness-related activity designed for a specific health-related purpose, including defined exercise routines as well as activity prescribed by a clinician.
ExercisePlan
A Role that represents a Web link, e.g. as expressed via the 'url' property. Its linkRelationship property can indicate URL-based and plain textual link types, e.g. those in IANA link registry or others such as 'amphtml'. This structure provides a placeholder where details from HTML's link element can be represented outside of HTML, e.g. in JSON-LD feeds.
LinkRole
A type of blood vessel that specifically carries lymph fluid unidirectionally toward the heart.
LymphaticVessel
A guideline recommendation that is regarded as efficacious and where quality of the data supporting the recommendation is sound.
MedicalGuidelineRecommendation
An observational study is a type of medical study that attempts to infer the possible effect of a treatment through observation of a cohort of subjects over a period of time. In an observational study, the assignment of subjects into treatment groups versus control groups is outside the control of the investigator. This is in contrast with controlled studies, such as the randomized controlled trials represented by MedicalTrial, where each subject is randomly assigned to a treatment group or a control group before the start of the treatment.
MedicalObservationalStudy
A simple system that adds up the number of risk factors to yield a score that is associated with prognosis, e.g. CHAD score, TIMI risk score.
MedicalRiskScore
A motorcycle or motorbike is a single-track, two-wheeled motor vehicle.
Motorcycle
A motorized bicycle is a bicycle with an attached motor used to power the vehicle, or to assist with pedaling.
MotorizedBicycle
A subclass of Role used to describe roles within organizations.
OrganizationRole
A medical test performed by a laboratory that typically involves examination of a tissue sample by a pathologist.
PathologyTest
A PerformanceRole is a Role that some entity places with regard to a theatrical performance, e.g. in a Movie, TVSeries etc.
PerformanceRole
A photograph.
Photograph
A doctor's office.
Physician
A process of care using radiation aimed at improving a health condition.
RadiationTherapy
A patient-reported or observed dosing schedule for a drug or supplement.
ReportedDoseSchedule
A Research project.
ResearchProject
Represents additional information about a relationship or property. For example a Role can be used to say that a 'member' role linking some SportsTeam to a player occurred during a particular time period. Or that a Person's 'actor' role in a Movie was for some particular characterName. Such properties can be attached to a Role entity, which is then associated with the main entities using ordinary properties like 'member' or 'actor'. See also blog post.
An indication for treating an underlying condition, symptom, etc.
TreatmentIndication
A vehicle is a device that is designed or used to transport people or cargo over land, water, air, or through space.
Vehicle
Vital signs are measures of various physiological functions in order to assess the most basic body functions.
VitalSign
Western Australian Mulga Shrublands Ecoregion
Australasia Ecoregion
Southern central Australia Ecoregion
Simpson Desert Region
Pilbara Shrublands Ecoregion
Carnarvon Xeric Shrublands Ecoregion
Central Ranges Xeric Shrub Ecoregion
Gibson Desert Ecoregion
The Great Sandy-Tanami Desert Ecoregion
Great Victoria Desert Ecoregion
Nullarbor Plains Xeric Shrubland Ecoregion
Afrotropical Ecoregion
Southern Africa: Southern Namibia into South Africa
Succulent Karoo Ecoregion
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
Islands east of the Horn of Africa and south of Yemen Ecoregion
Socotran Archipelago Ecoregion
Red Sea Coastal Desert Ecoregion
Namibian Savanna Woodland Ecoregion
Namib Desert Ecoregion
Nama Karoo Ecoregion
Masai Xeric Grasslands and Shrublands Ecoregion
Madagascar Succulent Woodlands Ecoregion
Madagascar Spiny Thickets Ecoregion
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
Kalahari Xeric Savanna Ecoregion
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
Hobyo Grassland and Shrubland Ecoregion
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
Ethiopian Xeric Grasslands and Shrublands Ecoregion
Eritrean Coastal Desert Ecoregion
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
Aldabra Island Xeric Scrub Ecoregion
Indo-Malay Ecoregion
Southern Asia: Western India into Pakistan
Thar Desert
Southern Asia: Eastern India and western Pakistan
Northwestern Thorn Scrub Forests
A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth.
Arctic front
A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth.
Antarctic front
Solar radiation
exploratory term
exemplar term
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term split
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
universal
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
person:Jennifer Fostel
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
An organization which supplies technology, tools and protocols for use in high throughput applications
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An autolysis value specification that indicates no apparent autolytic destruction of an organism cells or tissues.
0-non autolyis
An autolysis value specification that indicates slight autolytic destruction of an organism cells or tissues.
1-slight autolysis
An autolysis value specification that indicates moderate autolytic destruction of an organism cells or tissues.
2-moderate autolysis
An autolysis value specification that indicates severe autolytic destruction of an organism cells or tissues.
3-severe autolysis
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
An organization that is developing and selling nanopore sequencing products and is based in the UK.
An organization that manufactures mosquito traps and other mosquito control products.
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A collection is an aggregation of items. The term collection means that the resource is described as a group; its parts may be separately described and navigated.
Collection
A dataset is information encoded in a defined structure (for example, lists, tables, and databases), intended to be useful for direct machine processing.
An event is a non-persistent, time-based occurrence. Metadata for an event provides descriptive information that is the basis for discovery of the purpose, location, duration, responsible agents, and links to related events and resources. The resource of type event may not be retrievable if the described instantiation has expired or is yet to occur. Examples - exhibition, web-cast, conference, workshop, open-day, performance, battle, trial, wedding, tea-party, conflagration.
Event
An image is a primarily symbolic visual representation other than text. For example - images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that image may include both electronic and physical representations.
Image
An interactive resource is a resource which requires interaction from the user to be understood, executed, or experienced. For example - forms on web pages, applets, multimedia learning objects, chat services, virtual reality.
Interactive Resource
An inanimate, three-dimensional object or substance. For example -- a computer, the great pyramid, a sculpture. Note that digital representations of, or surrogates for, these things should use Image, Text or one of the other types.
Physical Object
Software is a computer program in source or compiled form which may be available for installation non-transiently on another machine. For software which exists only to create an interactive environment, use interactive instead.
Software
A sound is a resource whose content is primarily intended to be rendered as audio. For example - a music playback file format, an audio compact disc, and recorded speech or sounds.
Sound
A text is a resource whose content is primarily words for reading. For example - books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre text.
The DCMI Box identifies a region of space using its geographic limits.
DCMI Box
Dewey Decimal Classification
DDC
The Internet media type of the resource.
IMT
ISO 3166 Codes for the representation of names of countries
ISO 3166
ISO 639-2: Codes for the representation of names of languages.
ISO 639-2
Library of Congress Classification
LCC
Library of Congress Subject Headings
LCSH
Medical Subject Headings
MeSH
A specification of the limits of a time interval.
DCMI Period
The DCMI Point identifies a point in space using its geographic coordinates.
DCMI Point
Internet RFC 1766 'Tags for the identification of Language' specifies a two letter code taken from ISO 639, followed optionally by a two letter country code taken from ISO 3166.
RFC 1766
Internet RFC 3066 'Tags for the Identification of Languages' specifies a primary subtag which is a two-letter code taken from ISO 639 part 1 or a three-letter code taken from ISO 639 part 2, followed optionally by a two-letter country code taken from ISO 3166. When a language in ISO 639 has both a two-letter and three-letter code, use the two-letter code; when it has only a three-letter code, use the three-letter code. This RFC replaces RFC 1766.
RFC 3066
The Getty Thesaurus of Geographic Names
TGN
Universal Decimal Classification
UDC
A URI Uniform Resource Identifier
URI
W3C Encoding rules for dates and times - a profile based on ISO 8601
W3C-DTF
third planet from the Sun in the Solar System
Earth
Sol
World Ocean
A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.
As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above.
Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO.
1. Scope of 'Genetic State': 'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. 2. Genotype Subtypes: In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. 3. The Genotype Partonomy: 'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) - Genomic Background: AB (the reference against which the GVC is variant) - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.
genotype
The samples were irradiated using the NSRL Galactic Cosmic Ray Simulation.
The NSRL Galactic Cosmic Ray Simulation is comprised of seven different species of ion, and fourteen different energies of H and He for 33 separate beams in a single GCRSim exposure. (https://www.bnl.gov/nsrl/userguide/GCRSim.php)
The experiment was conducted at the NSRL
A particle accelerator beamline located at Brookhaven National Laboratory
A particle accelerator at the National Institute of Radiological Sciences in Chiba, Japan
The experiment was conducted aboard the International Space Station
An instance of an Earth-orbiting space station that went operational in the year 2000.
The experiment was conducted on the Mir space station
An instance of an Earth-orbiting space station, operational from1986 to 2001, operated by the Soviet Union and later by Russia.
The biological payload was carried into orbit by the Space Shuttle
An instance of a reusable spacecraft designed to carry passengers and equipment into low Earth orbit and return to Earth. Operated by the United States and operational from 1981 to 2011.
The experiment was conducted aboard the Bion-MI satellite.
An instance of a Russian-operated Earth satellite carrying biological samples. Launched April 19, 2013 and returned to Earth May 19, 2013
The samples were flown on the Foton-M4 satellite
An instance of a Russian-operated Earth satellite carrying biological samples. Launched July 19, 2014 and returned to Earth September 1, 2014
The experiment was conducted on the Shenzhou-8 space station
An instance of a Chinese-operated Earth satellite carrying biological samples. Launched October 31, 2011 and returned to Earth November 17, 2011.
The experiment was conducted in the US Laboratory on the ISS
An instance of a module on the International Space Station, operated by the United States
The experiment was conducted on the Japanese Experiment Module
A Japanese science module for the International Space Station developed by JAXA. It is the largest single ISS module, and is attached to the Harmony module. The first two pieces of the module were launched on Space Shuttle missions STS-123 and STS-124.
The experiment was conducted on the Columbus module on the ISS
An instance of a module on the International Space Station, operated by the European Space Agency.
The experiment was conducted in the Zvezda module of the ISS.
An instance of a module on the International Space Station, operated by the Russian Space Agency.
The experiment was carried out at the SIS-18 accelerator.
An particle accelerator located at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germay.
The samples were irradiated using the NSRL Solar Particle Event Simulation.
The NSRL SPE simulatoris based on the fluence of the August 1972 event, with an energy spectrum similar to the March 1989 event. The majority of the protons are at very low energies, below 1 MeV, and pose little to no risk to astronauts in a space craft or space suit. The SPESim begins with 50 MeV protons, which amounts to 91.66% of the total dose. Then the beam energy increments in steps of 10 MeV up to 150 MeV where 0.14% of the total dose is delivered.
The samples were irradiated using the NSRL Simplified Galactic Cosmic Ray Simulation.
The NSRL Simplified Galactic Cosmic Ray Simulation uses 6 beams and 5 different ions including protons at two different energies. https://www.bnl.gov/nsrl/userguide/SimGCRSim.php
NSRL Simplified Galactic Cosmic Ray Simulation
The samples were irradiated with thermal neutrons at the KUR-HWNIF
A heavy water tank of approximately 2 m3 adjacent to the core of the Kyoto University Research Reactor (KUR), a light-water moderated tank-type reactor.
Kyoto University Research Reactor-Heavy Water Neutron Irradiation Facility
The samples were irradiated with fast neutrons at the HIRRAC.
A neutron generator at the Research Institute for Radiation Biology and Medicine, Hiroshima University (RIRBM). Monoenergetic neutrons of which energy is less than 1.3 MeV are generated by the 7Li(p,n)7 Be reaction at proton energies up to 3 MeV.
Hiroshima University Radiobiological Research Accelerator
The Gamma Radiation Facility known as GRSF houses a cesium-137 gamma ray source which can provide gamma rays at a variety of dose rates. The gamma source is an industry standar dJ.L. Shepherd Mark I Model 68A 137Cs ? Irradiator. The photon energy from the source is 662 keV, with a Lineal Energy Transfer (LET) in water of approximately 0.8 keV/um. (https://www.bnl.gov/nsrl/grsf/)
Brookhaven National Laboratory Gamma Radiation Source Facility
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
"A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST]
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
"A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." [BIPM:BIPM, NIST:NIST]
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
"A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST]
"An electric current unit which is equal to the constant current which, if maintained in two straight parallel conductors of infinite length, of negligible circular cross-section, and placed 1 m apart in vacuum, would produce between these conductors a force equal to 2 x 10^[-7] newton per meter of length." [BIPM:BIPM, NIST:NIST]
"A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST]
"A substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12." [BIPM:BIPM, NIST:NIST]
"A luminous intensity unit which equal to the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 1012 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian." [BIPM:BIPM, NIST:NIST]
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
"A length unit which is equal to one hundredth of a meter or 10^[-2] m." [NIST:NIST]
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
"A length unit which is equal to one thousandth of a meter or 10^[-3] m." [NIST:NIST]
A length unit which is equal to one millionth of a meter or 10^[-6] m.
"A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST]
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
"A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST]
A length unit which is equal to 10 [-10] m.
"A length unit which is equal to 10 [-10] m." [NIST:NIST]
"A length unit which is equal to 10^[-12] m." [NIST:NIST]
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
"A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST]
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
"A mass unit which is equal to one thousandth of a gram or 10^[-3] g." [UOC:GVG]
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
"A mass unit which is equal to one millionth of a gram or 10^[-6] g." [UOC:GVG]
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
"A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." [UOC:GVG]
A mass unit which is equal to 10^[-12] g.
"A mass unit which is equal to 10^[-12] g." [UOC:GVG]
"A mass unit which is equal to 10^[-15] g." [NIST:NIST]
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
"A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST]
"A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST]
"A time unit which is equal to one millionth of a second or 10^[-6] s." [NIST:NIST]
"A time unit which is equal to 10^[-12] s." [NIST:NIST]
A time unit which is equal to 60 seconds.
"A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia]
A time unit which is equal to 3600 seconds or 60 minutes.
"A time unit which is equal to 3600 seconds or 60 minutes." [Wikipedia:Wikipedia]
"A time unit which is equal to 24 hours." [Wikipedia:Wikipedia]
"A time unit which is equal to 7 days." [Wikipedia:Wikipedia]
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
"A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." [Wikipedia:Wikipedia]
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
"A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days." [Wikipedia:Wikipedia]
"An electric current unit current which is equal to one thousandth of an ampere or 10^[-3] A." [UOC:GVG]
"An electric current unit current which is equal to one millionth of an ampere or 10^[-6] A." [UOC:GVG]
A substance unit equal to a millionth of a mol or 10^[-6] mol.
"A substance unit equal to a millionth of a mol or 10^[-6] mol." [NIST:NIST]
"A substance unit equal to a thousandth of a mol or 10^[-3] mol." [NIST:NIST]
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
"A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." [NIST:NIST]
"A substance unit equal to 10^[-12] mol." [NIST:NIST]
"A substance unit equal to 10^[-15] mol." [NIST:NIST]
"A substance unit equal to 10^[-18] mol." [NIST:NIST]
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
"A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." [UOC:GVG]
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
"A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." [UOC:GVG]
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
"A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." [UOC:GVG]
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
"A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." [UOC:GVG]
A unit of molarity which is equal to 10^[-12] M.
"A unit of molarity which is equal to 10^[-12] M." [UOC:GVG]
"A unit of concentration which expresses a concentration of a solution of 1 mole per kilogram of solvent (mol/kg)." [UOC:GVG]
"A molality unit which is equal to one thousandth of a molal or 10^[-3] m." [UOC:GVG]
"A molality unit which is equal to one millionth of a molal or 10^[-6] m." [UOC:GVG]
"A molality unit which is equal to one thousandth of one millionth of a molal or 10^[-9] m." [UOC:GVG]
"A molality unit which is equal to 10^[-12] m." [UOC:GVG]
"A unit of molarity which is equal to 10^[-15] M." [UOC:GVG]
"A unit of concentration which is one gram equivalent of a solute per liter of solution. A gram equivalent weight or equivalent is a measure of the reactive capacity of a given molecule." [Wikipedia:Wikipedia]
"A concentration unit which denotes the number of moles of solute as a proportion of the total number of moles in a solution." [Wikipedia:Wikipedia]
"An acceleration unit which is equal to the acceleration an object changing its velocity by 1meter/s over a time period that equals one second." [NIST:NIST]
"An angular unit acceleration which is equal to the angular acceleration of an object changing its angular velocity by 1rad/s over a time period that equals one second." [NIST:NIST]
"An angular unit velocity which is equal to about 9.54930 rpm (revolutions per minute)." [NIST:NIST]
"An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST]
"An area unit which is equal to one ten thousandth of a square meter or 10^[-4] m^[2]." [NIST:NIST]
"An area unit which is equal to one millionth of a square meter or 10^[-6] m^[2]." [NIST:NIST]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters." [UOC:GVG]
"A luminance unit which is equal to a luminous intensity of one candela radiating from a surface whose area is one square meter." [NIST:NIST]
"An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared." [NIST:NIST]
"A molar mass unit which is equal to one kilogram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A molar mass unit which is equal to one gram of mass of one mole of chemical element or chemical compound." [NIST:NIST]
"A molar volume unit which is equal to 1 cubic meter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A molar volume unit which is equal to 1 cubic centimeter occupied by one mole of a substance in the form of a solid, liquid, or gas." [NIST:NIST]
"A momentum unit which is equal to the momentum of a one kilogram mass object with a speed of one meter per second." [NIST:NIST]
"A rotational frequency unit which is equal to the number complete turn in a period of time that equals to 1 second." [NIST:NIST]
"A specific volume unit which is equal to one cubic meter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A speed/velocity unit which is equal to the speed of an object traveling 1 meter distance in one second." [NIST:NIST]
"A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liters." [NIST:NIST]
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
"A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." [NIST:NIST]
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
"A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST]
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
"A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." [NIST:NIST]
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
"A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." [NIST:NIST]
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
"A volume unit which is equal to one millionth of a liter or 10^[-6] L." [NIST:NIST]
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
"A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." [NIST:NIST]
A volume unit which is equal to 10^[-12] L.
"A volume unit which is equal to 10^[-12] L." [NIST:NIST]
"A volume unit which is equal to 10^[-15] L." [NIST:NIST]
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
"A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST]
"A force unit which is equal to the force required to cause an acceleration of 1m/s2 of a mass of 1 Kg in the direction of the force." [NIST:NIST]
"A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST]
"An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST]
"A power unit which is equal to the power used when work is done at the rate of 1 joule per second." [NIST:NIST]
"An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 m^[2]." [NIST:NIST]
"A luminous flux unit which is equal to the luminous flux emitted into 1 steradian by a point source of 1 candela." [NIST:NIST]
"A catalytic unit activity which is equal to the activity of a catalyst in moles per second, such as the amount of an enzyme needed to transform one mole of substrate per second." [NIST:NIST]
"A plane angle unit which is equal to the angle subtended at the center of a circle by an arc equal in length to the radius of the circle, approximately 57 degrees 17 minutes and 44.6 seconds." [NIST:NIST]
"A solid angle unit which is equal to the solid angle subtended at the center of a sphere by an area on the surface of the sphere that is equal to the radius squared." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second (dps)." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which there are 3.7 x 10^[10] atom disintegration per second (dps)." [ORCBS:ORCBS]
"An absorbed dose unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST]
"An absorbed dose unit which is equal to 0.01 gray (Gy)." [Wikipedia:Wikipedia]
"An exposure unit which is equal to the amount of radiation required to liberate positive and negative charges of one electrostatic unit of charge in 1 cm^[3] of air at standard temperature and pressure (STP). This corresponds to the generation of approximately 2.0810^[9] ion pairs." [Wikipedia:Wikipedia]
"A dose equivalent unit which is equal to the absorption of one joule of radiation energy by one kilogram of matter." [NIST:NIST]
"A dose equivalent unit which is equal to one thousandth of a sievert or 10^[-3] Sv." [NIST:NIST]
"A dose equivalent unit which is equal to one millionth of a sievert or 10^[-6] Sv." [NIST:NIST]
"A dose equivalent unit which when multiplied by hundred is equal to one sievert or 1 Sv. 1 Sv is equal to 100 rem." [Wikipedia:Wikipedia]
"An absorbed dose unit which is equal to one millionth of a gray or 10^[-6] Gy." [NIST:NIST]
"An absorbed dose unit which is equal to one thousandth of a gray or 10^[-3] Gy." [NIST:NIST]
"An absorbed dose unit which is equal to one thousandth of a millionth of a gray or 10^[-9] Gy." [NIST:NIST]
"A dose equivalent unit which is equal to one thousandth of a millionth of a sievert or 10^[-9] Sv." [NIST:NIST]
"An activity (of a radionuclide) unit which is equal to one thousandth of a curie or 10^[-3] Ci." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to one millionth of a curie or 10^[-6] Ci." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per minute or there is one atom disintegration per minute." [ORCBS:ORCBS]
"An activity (of a radionuclide) unit which is equal to the number of light emissions produced by ionizing radiation in one minute." [ORCBS:ORCBS]
"A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST]
"A time unit which is equal to 100 years." [Wikipedia:Wikipedia]
"A time unit which represents the period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration." [MGED:MGED]
"An illuminance unit which is equal to the illuminance produced by 1 lumen evenly spread over an area 1 foot^[2]. One footcandle is equal to 10.76 lux." [Wikipedia:Wikipedia]
"An irradiance unit which is equal to 1 watt of radiant power incident per one square meter surface area." [NIST:NIST]
mole per second and square meter mol/sm^2
"An irradiance unit which is equal to one einstein per square meter per second. One einstein is one mole of photons, regardless of their frequency. Therefore, the number of photons in an einstein is Avogadro's number." [Wikipedia:Wikipedia]
"A radiance unit which is equal to one watt of radiant power incident per steradian solid angle per one square meter projected area of the source, as viewed from the given direction." [NIST:NIST]
microeinstein per square metre per second
micromole per second and square meter mmol/sm^2
"An irradiance unit which is equal to one microeinstein per square meter per second or 10^[-6] microeinstein/sm^[2]." [Wikipedia:Wikipedia]
microeinstein per square meter per second
"A radiant intensity unit which is equal to one kilogram meter squared per second cubed per steradian." [NIST:NIST]
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
"A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." [Wikipedia:Wikipedia]
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
"A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." [UOC:GVG]
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
"A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 100 regardless of the units of measure as long as they are the same." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure as long as they are the same or 1 part in 10^[9]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[12]." [UOC:GVG]
"A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[15]." [UOC:GVG]
"A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter." [UOC:GVG]
"A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters." [UOC:GVG]
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
"A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one milliliter." [Webmd:Webmd]
"A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter." [UOC:GVG]
"A concentration unit which is a standard measure of the mass of a substance in a given volume (density)." [Wikipedia:Wikipedia]
"A catalytic unit activity which is equal to the amount of the enzyme that catalyzes the conversion of 1 micro mole of substrate per minute." [Wikipedia:Wikipedia]
"An area density unit which is equal to the mass of an object in kilograms divided by one meter." [NIST:NIST]
"A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia]
"A dimensionless unit which denoted an irrational real number, approximately equal to 3.14159 which is the ratio of a circle's circumference to its diameter in Euclidean geometry." [Wikipedia:Wikipedia]
"A dimensionless count unit which denotes the number of molecules." [MGED:MGED]
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]
"A dimensionless percent unit which denotes the density of an attached or monolayer culture (e.g., cell culture)." [MGED:MGED]
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
"A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." [Wikipedia:Wikipedia]
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
"A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." [Wikipedia:Wikipedia]
"A specific volume unit which is equal to one liter volume occupied by one kilogram of a particular substance." [NIST:NIST]
"A specific volume unit which is equal to a thousandth of a liter per kilogram or 10^[-3] l/kg." [NIST:NIST]
"A specific volume unit which is equal to one millionth of a liter per kilogram or 10^[-6] l/kg." [NIST:NIST]
"A unit of cell concentration which is equal to one cell in a volume of 1 milliliter." [Bioedonline:Bioedonline]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one cubic meter." [NIST:NIST]
"A catalytic (activity) concentration unit which is equal to 1 katal activity of a catalyst in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one cubic meter of solution." [NIST:NIST]
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
"A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." [NIST:NIST]
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
"A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." [UOC:GVG]
"A volume unit which is equal to one tenth of a liter or 10^[-1] L." [NIST:NIST]
"A dimensionless count unit which a measure of viable bacterial numbers." [Wikipedia:Wikipedia]
"A dimensionless count unit which a measure of plaque forming units in a given volume." [Wikipedia:Wikipedia]
A concentration unit which a measure of viable bacterial numbers in a given volume.
"A concentration unit which a measure of viable bacterial numbers in a given volume." [Wikipedia:Wikipedia]
"A colony forming unit which a measure of viable bacterial numbers in one milliliter." [Wikipedia:Wikipedia]
"A concentration unit which a measure of plaque forming units in one milliliter." [UOC:GVG]
"An activity (of a radionuclide) unit which is equal to the activity of a quantity of radioactive material in which one nucleus decays per second or there is one atom disintegration per second." [ORCBS:ORCBS]
"An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia]
"An electrical charge unit which is equal to the amount of charge transferred by a current of 1 ampere in 1 second." [WordNet:WordNet]
"An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia]
"A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia]
"An energy unit which is equal to the amount of electrical energy equivalent to a one-watt load drawing power for one hour." [Wikipedia:Wikipedia]
"An energy unit which is equal to 1,000 watt-hours." [Wikipedia:Wikipedia]
"A magnetic flux unit which is equal to the amount of flux that when linked with a single turn of wire for an interval of one second will induce an electromotive force of one volt." [ScienceLobby:ScienceLobby]
"A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet]
"A magnetic flux unit which is equal to 3600 Wb." [UOC:GVG]
"A magnetic flux unit which is equal to one thousand volt-hours." [UOC:GVG]
"An information unit which refers to a digit in the binary numeral system, which consists of base 2 digits (ie there are only 2 possible values: 0 or 1)." [Wikipedia:Wikipedia]
"An information unit which is equal to 8 bits." [Wikipedia:Wikipedia]
"An information unit which is equal to 1000 bytes." [Wikipedia:Wikipedia]
"An information unit which is equal to 1000 kB." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the amount of spatial detail in an image." [Wikipedia:Wikipedia]
"An image resolution unit which is a standard measure of the amount of contrast available in a pixel." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the printing resolution, in particular the number of individual dots of ink a printer or toner can produce within a linear one-inch space." [Wikipedia:Wikipedia]
"A spatial resolution unit which is equal to a pixel size of one micrometer." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the resolution of a computer display, related to the size of the display in inches and the total number of pixels in the horizontal and vertical directions." [Wikipedia:Wikipedia]
"A spatial resolution unit which is a standard measure of the number of pixels in one millimeter length or width of a digital image divided by the physical length or width of a printed image." [Wikipedia:Wikipedia]
"A count unit which contains one nucleotide." [UO:GVG]
"An information unit which is equal to 1024 B." [NIST:NIST]
"An information unit which is equal to 1024 KiB." [NIST:NIST]
"An electric potential difference unit which is equal to one thousandth of a volt or 10^[-3] V." [UOC:GVG]
"An electric potential difference unit which is equal to one thousand volts or 10^[3] V." [UOC:GVG]
"An electric potential difference unit which is equal to one millionth of a volt or 10^[-6] V." [UOC:GVG]
"An electric potential difference unit which is equal to one billionth of a volt or 10^[-12] V." [UOC:GVG]
"An electric potential difference unit which is equal to one trillionth of a volt or 10^[-12] V." [UOC:GVG]
"An electric potential difference unit which is equal to one million volts or 10^[6] V." [UOC:GVG]
"A surface tension unit which is equal to one newton per meter." [NIST:NIST]
"A surface tension unit which is equal to one dyne per centimeter." [Wikipedia:Wikipedia]
"A viscosity unit which is equal to one pascale per second." [NIST:NIST]
"A viscosity unit which is equal to one dyne second per square centimeter." [Wikipedia:Wikipedia]
"A ratio unit which is an indicator of sound power per unit area." [techtarget:techtarget]
"A unit which is a standard measure of the estimate of the stochastic effect that a non-uniform radiation dose has on a human." [Wikipedia:Wikipedia]
"An electrical conduction unit which is equal to A/V." [NIST:NIST]
"An heat conduction unit which is equal to one watt divided by meter kelvin." [NIST:NIST]
"A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia]
"The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field]
"A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance]
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
"A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG]
"A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth." [url:en.wiktionary.org/wiki/mmHg]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters." [UOC:GVG]
mcg/mL
µg/mL
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters." [UOC:GVG]
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters." [UOC:GVG]
"A unit per milliliter unit which is equal to one thousandth of a unit of an agreed arbitrary amount per one milliliter." [UOC:GVG]
A rate unit which is equal to one over one nanomolar second.
"A rate unit which is equal to one over one nanomolar second." [UOC:GVG]
A rate unit which is equal to one over one molar second.
"A rate unit which is equal to one over one molar second." [UOC:GVG]
"An area density unit which is equal to the mass of an object in kilograms divided by the surface area in hectares." [UO:GVG]
A rate unit which is equal to one over one nanomolar.
"A rate unit which is equal to one over one nanomolar." [UO:GVG]
A rate unit which is equal to one over one molar.
"A rate unit which is equal to one over one molar." [UO:GVG]
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." [UOC:GVG]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A dose unit which is equal to 1 milligram of a toxic or pharmaceutical substance per square meter of surface area of the recipient subject." [UO:PC]
"A concentration unit which is a standard measure of the amount of a toxic or pharmaceutical substance administered over time to a recipient subject, expressed in terms of the size of the subject." [UO:PC]
"A dosage unit which is equal to 1 milligram per day of a toxic or pharmaceutical substance per kilogram body weight of the recipient subject." [UO:PC]
"A derived unit which is a measure of relative light intensity, as typically measured by a luminometer, spectrophotometer, or fluorimeter in biological research applications." [UO:PC]
"A relative light unit which is a measure of relative luminescence intensity." [UO:PC]
"A relative light unit which is a measure of relative fluorescence intensity." [UO:PC]
"A frequency unit which is equal to one million hertz or 10^[6] V." [UOC:GVG]
"A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability." [NCBI:http\://www.ncbi.nlm.nih.gov/SCIENCE96/Glossary.html]
"A unit equal to one million base pairs" [UOC:GVG]
"A unit equal to one billion base pairs." [UOC:GVG]
"An area unit which is equal to an area enclosed by a square with sides each 1 micrometer long." [NIST:NIST]
"An electrical conduction unit which is equal to one thousandth of a siemen or 10^[-3] siemens." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole in a given volume of one thousandth of a cubic meter." [NIST:NIST]
"A specific concentration unit which is equal to 1 micromole of a given substance per kilogram of solvent." [UOB:LKSR]
"A speed/velocity unit which is equal to the speed of an object traveling 1 millimeter distance in one day." [UOB:LKSR]
"A speed/velocity unit which is equal to the speed of an object traveling 1 kilometer distance in one hour." [NIST:NIST]
"A mass unit which is equal to 1/12 the mass of 12C" [Wikipedia:Wikipedia]
"An area unit which is equal to an area of 10,000 square meters. Equivalent to 2.471 acres." [Wikipedia:Wikipedia]
"A length unit which is equal to 0.0254 metres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.0254 millimetres." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.3048 metres, or 12 inches." [Wikipedia:Wikpiedia]
"A length unit which is equal to 0.9144 metres, or 3 feet." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards." [Wikipedia:Wikpiedia]
"A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains." [Wikipedia:Wikpiedia]
"A length unit which is equal to 1,609.344 metres, or 8 furlongs." [Wikipedia:Wikpiedia]
"A length unit which is equal to 3 miles, or 4,828.032 metres" [Wikipedia:Wikpiedia]
"A maritime length unit is one used primarily at sea." [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6.08 feet, or 1.853184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 608 feet, 100 fathoms, or 185.3184 metres" [Wikipedia:Wikpiedia]
"A maritime length unit which is equal to 6,080 feet, 10 cables, or 1,853.184 metres" [Wikipedia:Wikpiedia]
"An area unit which is equal to an area of 25.292,852,64 square meters, or 1 square rod." [Wikipedia:Wikipedia]
"An area unit which is equivalent to 1 furlong x 1 rod. This is equal to an area of 1,011.714,1056 square meters, or 40 square rods." [Wikipedia:Wikipedia]
"An area unit which is equivalent to 1 furlong x 1 chain. This is equal to an area of 4,046.856,4224 square meters, or 43,500 square feet." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 28.413,0625 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 142.065,3125 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 568.261,25 millilitres." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 1,136.5225 millilitres, or two pints." [Wikipedia:Wikipedia]
"An imperial volume unit which is equivalent to 4,546.09 millilitres, or 8 pints." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 64.798,91 milligrams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 453.592,37 grams." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone." [Wikipedia:Wikipedia]
"An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds." [Wikipedia:Wikipedia]
"An imperial gravitational unit which is equivalent to a mass that accelerates by 1ft/s² when a force of one pound (lbf) is exerted on it." [Wikipedia:Wikipedia]
"A metric teaspoon is a unit of measurement of volume widely used in cooking recipes and pharmaceutic prescriptions. It equals a 5mL volume." [Wikipedia:https://en.wikipedia.org/wiki/Teaspoon]
"An area density unit which is equal to the mass of an object in grams divided by the surface area in meters squared." [NIST:NIST]
"A mass unit density which is equal to mass of an object in nanograms divided by the volume in microliters." [UOB:LTS]
"A unit of energy widely used in nutrition, equivalent to the amount of heat needed to cause one kilogram of water to rise in temperature by one degree Celsius." [Wikipedia:Wikipedia]
"A unit of mass concentration defined as the number of micrograms of a substance per 250 ml Wheaton bottle." [UOB:LTS]
"An electric current unit current which is equal to one trillionth of an ampere or 10^[-12] A." [UOB:LTS]
"An absorbed dose unit which is equal to 0.01 gray (Gy)" [NIST:NIST]
"A unit of energy that is equal to one thousand million electronvolts." []
"Derived unit which is equal to the total kinetic energy of an atomic nucleus in GeV divided by the number of nucleons in the nucleus" []
"Derived unit which is equal to the total kinetic energy of an atomic nucleus in MeV divided by the number of nucleons in the nucleus" []
"A derived unit equal to the energy deposited by ionizing radiation per micron of path length in matter" []
"A derived absorbed dose unit which is equal to one gray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one centigray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per minute." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per day." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per hour." [NIST:NIST]
"A derived absorbed dose unit which is equal to one milligray absorbed per second." [NIST:NIST]
"A length unit which is equal to one thousand meters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in milligrams divided by the volume in deciliters." [UOB:LKSR]
"A mass unit density which is equal to mass of an object in micrograms divided by the volume in deciliters." [UOB:LKSR]
A service is a system that provides one or more functions of value to the end-user. Examples include: a photocopying service, a banking service, an authentication service, interlibrary loans, a Z39.50 or Web server.
Service
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).